Starting phenix.real_space_refine on Mon Aug 25 04:55:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h3h_34468/08_2025/8h3h_34468_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h3h_34468/08_2025/8h3h_34468.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8h3h_34468/08_2025/8h3h_34468_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h3h_34468/08_2025/8h3h_34468_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8h3h_34468/08_2025/8h3h_34468.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h3h_34468/08_2025/8h3h_34468.map" } resolution = 3.15 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= 0.000 sd= 0.004 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 P 17 5.49 5 S 110 5.16 5 C 16215 2.51 5 N 4381 2.21 5 O 4685 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 77 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25408 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4268 Classifications: {'peptide': 539} Link IDs: {'CIS': 3, 'PCIS': 2, 'PTRANS': 33, 'TRANS': 500} Chain breaks: 3 Chain: "B" Number of atoms: 4210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4210 Classifications: {'peptide': 529} Link IDs: {'CIS': 3, 'PCIS': 2, 'PTRANS': 32, 'TRANS': 491} Chain breaks: 2 Chain: "C" Number of atoms: 4199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4199 Classifications: {'peptide': 528} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 493} Chain breaks: 2 Chain: "D" Number of atoms: 4213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4213 Classifications: {'peptide': 530} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 495} Chain breaks: 2 Chain: "E" Number of atoms: 4202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4202 Classifications: {'peptide': 528} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 32, 'TRANS': 491} Chain breaks: 2 Chain: "F" Number of atoms: 4134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 4134 Classifications: {'peptide': 520} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 31, 'TRANS': 484} Chain breaks: 3 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.75, per 1000 atoms: 0.27 Number of scatterers: 25408 At special positions: 0 Unit cell: (152.15, 156.4, 98.6, 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 110 16.00 P 17 15.00 O 4685 8.00 N 4381 7.00 C 16215 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=9, symmetry=0 Number of additional bonds: simple=9, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.37 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 476.8 nanoseconds 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6058 Finding SS restraints... Secondary structure from input PDB file: 155 helices and 13 sheets defined 49.8% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 434 through 439 Processing helix chain 'A' and resid 443 through 448 Processing helix chain 'A' and resid 450 through 455 removed outlier: 3.838A pdb=" N PHE A 455 " --> pdb=" O VAL A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 485 removed outlier: 3.788A pdb=" N ALA A 477 " --> pdb=" O LYS A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 524 removed outlier: 3.770A pdb=" N ARG A 511 " --> pdb=" O GLY A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 536 removed outlier: 3.502A pdb=" N GLY A 535 " --> pdb=" O GLN A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 560 removed outlier: 3.571A pdb=" N THR A 554 " --> pdb=" O SER A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 580 removed outlier: 3.942A pdb=" N ILE A 580 " --> pdb=" O LEU A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 612 removed outlier: 3.600A pdb=" N GLU A 606 " --> pdb=" O GLU A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 631 removed outlier: 3.763A pdb=" N GLU A 629 " --> pdb=" O GLU A 625 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN A 630 " --> pdb=" O GLU A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 655 removed outlier: 3.750A pdb=" N ALA A 647 " --> pdb=" O CYS A 643 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU A 648 " --> pdb=" O ALA A 644 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA A 650 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 651 " --> pdb=" O ALA A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 685 removed outlier: 3.927A pdb=" N LYS A 685 " --> pdb=" O VAL A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 717 removed outlier: 6.234A pdb=" N ASN A 711 " --> pdb=" O PRO A 707 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N THR A 712 " --> pdb=" O LEU A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 729 removed outlier: 3.976A pdb=" N GLU A 728 " --> pdb=" O PRO A 725 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE A 729 " --> pdb=" O HIS A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 817 Processing helix chain 'A' and resid 826 through 831 Processing helix chain 'A' and resid 837 through 852 removed outlier: 3.736A pdb=" N THR A 841 " --> pdb=" O SER A 837 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N CYS A 842 " --> pdb=" O PRO A 838 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA A 843 " --> pdb=" O GLU A 839 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR A 852 " --> pdb=" O GLU A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 866 Processing helix chain 'A' and resid 870 through 881 removed outlier: 3.685A pdb=" N ALA A 875 " --> pdb=" O PRO A 871 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR A 879 " --> pdb=" O ALA A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 899 through 903 removed outlier: 3.537A pdb=" N LEU A 903 " --> pdb=" O HIS A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 909 Processing helix chain 'A' and resid 910 through 911 No H-bonds generated for 'chain 'A' and resid 910 through 911' Processing helix chain 'A' and resid 912 through 916 Processing helix chain 'A' and resid 925 through 938 removed outlier: 4.242A pdb=" N ASP A 935 " --> pdb=" O LYS A 931 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N LEU A 936 " --> pdb=" O PHE A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 943 removed outlier: 4.091A pdb=" N LYS A 943 " --> pdb=" O GLN A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1344 Processing helix chain 'A' and resid 1348 through 1353 Processing helix chain 'A' and resid 1359 through 1366 removed outlier: 4.100A pdb=" N ILE A1363 " --> pdb=" O ILE A1359 " (cutoff:3.500A) Processing helix chain 'A' and resid 1375 through 1384 Processing helix chain 'B' and resid 432 through 443 removed outlier: 3.596A pdb=" N GLU B 440 " --> pdb=" O ALA B 436 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N MET B 441 " --> pdb=" O ALA B 437 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL B 442 " --> pdb=" O LEU B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 455 removed outlier: 3.939A pdb=" N PHE B 455 " --> pdb=" O VAL B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 485 removed outlier: 3.616A pdb=" N ALA B 477 " --> pdb=" O LYS B 473 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N CYS B 484 " --> pdb=" O LEU B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 523 removed outlier: 3.869A pdb=" N ARG B 514 " --> pdb=" O GLU B 510 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN B 522 " --> pdb=" O ASP B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 556 removed outlier: 3.682A pdb=" N SER B 549 " --> pdb=" O ASP B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 580 removed outlier: 3.626A pdb=" N SER B 579 " --> pdb=" O ARG B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 612 removed outlier: 3.642A pdb=" N LYS B 605 " --> pdb=" O LYS B 601 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU B 606 " --> pdb=" O GLU B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 631 removed outlier: 3.593A pdb=" N LEU B 624 " --> pdb=" O LEU B 620 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN B 630 " --> pdb=" O GLU B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 643 removed outlier: 3.517A pdb=" N ILE B 642 " --> pdb=" O ASP B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 655 removed outlier: 3.865A pdb=" N LEU B 651 " --> pdb=" O ALA B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 676 through 686 removed outlier: 3.736A pdb=" N GLU B 680 " --> pdb=" O ALA B 676 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL B 681 " --> pdb=" O LYS B 677 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA B 682 " --> pdb=" O ASP B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 724 removed outlier: 6.731A pdb=" N ASN B 711 " --> pdb=" O PRO B 707 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N THR B 712 " --> pdb=" O LEU B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 808 through 817 Processing helix chain 'B' and resid 826 through 831 Processing helix chain 'B' and resid 837 through 852 removed outlier: 3.650A pdb=" N CYS B 842 " --> pdb=" O PRO B 838 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 866 Processing helix chain 'B' and resid 870 through 881 removed outlier: 3.708A pdb=" N ALA B 875 " --> pdb=" O PRO B 871 " (cutoff:3.500A) Processing helix chain 'B' and resid 899 through 903 Processing helix chain 'B' and resid 904 through 909 Processing helix chain 'B' and resid 910 through 911 No H-bonds generated for 'chain 'B' and resid 910 through 911' Processing helix chain 'B' and resid 912 through 916 Processing helix chain 'B' and resid 925 through 934 removed outlier: 3.542A pdb=" N PHE B 933 " --> pdb=" O ARG B 929 " (cutoff:3.500A) Processing helix chain 'B' and resid 1331 through 1344 removed outlier: 4.010A pdb=" N ASN B1335 " --> pdb=" O GLU B1331 " (cutoff:3.500A) Processing helix chain 'B' and resid 1348 through 1353 Processing helix chain 'B' and resid 1356 through 1365 removed outlier: 4.056A pdb=" N CYS B1362 " --> pdb=" O VAL B1358 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE B1363 " --> pdb=" O ILE B1359 " (cutoff:3.500A) Processing helix chain 'B' and resid 1375 through 1384 Processing helix chain 'C' and resid 432 through 439 Processing helix chain 'C' and resid 443 through 448 Processing helix chain 'C' and resid 450 through 455 removed outlier: 3.633A pdb=" N LYS C 454 " --> pdb=" O GLU C 450 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N PHE C 455 " --> pdb=" O VAL C 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 450 through 455' Processing helix chain 'C' and resid 472 through 486 removed outlier: 3.654A pdb=" N VAL C 476 " --> pdb=" O GLY C 472 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA C 477 " --> pdb=" O LYS C 473 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN C 486 " --> pdb=" O ASN C 482 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 520 removed outlier: 3.742A pdb=" N LEU C 513 " --> pdb=" O SER C 509 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG C 514 " --> pdb=" O GLU C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 536 Processing helix chain 'C' and resid 545 through 560 removed outlier: 4.077A pdb=" N SER C 549 " --> pdb=" O ASP C 545 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP C 560 " --> pdb=" O LEU C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 576 through 580 removed outlier: 3.706A pdb=" N SER C 579 " --> pdb=" O ARG C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 600 through 612 removed outlier: 3.741A pdb=" N LYS C 605 " --> pdb=" O LYS C 601 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU C 606 " --> pdb=" O GLU C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 629 removed outlier: 3.566A pdb=" N GLU C 626 " --> pdb=" O THR C 622 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU C 629 " --> pdb=" O GLU C 625 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 655 removed outlier: 3.701A pdb=" N ALA C 644 " --> pdb=" O LYS C 640 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ALA C 647 " --> pdb=" O CYS C 643 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 659 removed outlier: 4.088A pdb=" N TYR C 659 " --> pdb=" O PRO C 656 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 656 through 659' Processing helix chain 'C' and resid 675 through 686 removed outlier: 3.522A pdb=" N PHE C 679 " --> pdb=" O SER C 675 " (cutoff:3.500A) Processing helix chain 'C' and resid 705 through 724 removed outlier: 3.553A pdb=" N LEU C 709 " --> pdb=" O VAL C 705 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN C 710 " --> pdb=" O LYS C 706 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N ASN C 711 " --> pdb=" O PRO C 707 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N THR C 712 " --> pdb=" O LEU C 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 809 through 817 Processing helix chain 'C' and resid 826 through 831 Processing helix chain 'C' and resid 837 through 852 removed outlier: 3.528A pdb=" N GLN C 844 " --> pdb=" O GLU C 840 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE C 846 " --> pdb=" O CYS C 842 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG C 847 " --> pdb=" O ALA C 843 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA C 849 " --> pdb=" O VAL C 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 861 through 866 Processing helix chain 'C' and resid 870 through 881 removed outlier: 3.580A pdb=" N THR C 879 " --> pdb=" O ALA C 875 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 916 Processing helix chain 'C' and resid 925 through 939 removed outlier: 3.681A pdb=" N PHE C 933 " --> pdb=" O ARG C 929 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ASP C 935 " --> pdb=" O LYS C 931 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N LEU C 936 " --> pdb=" O PHE C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 1332 through 1344 Processing helix chain 'C' and resid 1348 through 1365 removed outlier: 4.203A pdb=" N CYS C1362 " --> pdb=" O VAL C1358 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ILE C1363 " --> pdb=" O ILE C1359 " (cutoff:3.500A) Processing helix chain 'C' and resid 1375 through 1385 Processing helix chain 'D' and resid 434 through 439 Processing helix chain 'D' and resid 443 through 448 Processing helix chain 'D' and resid 472 through 486 removed outlier: 3.612A pdb=" N ALA D 477 " --> pdb=" O LYS D 473 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN D 482 " --> pdb=" O ARG D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 507 through 522 removed outlier: 3.512A pdb=" N ARG D 511 " --> pdb=" O GLY D 507 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU D 513 " --> pdb=" O SER D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 536 Processing helix chain 'D' and resid 545 through 556 removed outlier: 3.774A pdb=" N SER D 549 " --> pdb=" O ASP D 545 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER D 553 " --> pdb=" O SER D 549 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR D 554 " --> pdb=" O SER D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 612 removed outlier: 3.978A pdb=" N GLU D 606 " --> pdb=" O GLU D 602 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE D 607 " --> pdb=" O ALA D 603 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N LYS D 609 " --> pdb=" O LYS D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 620 through 631 removed outlier: 3.696A pdb=" N ASN D 630 " --> pdb=" O GLU D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 655 removed outlier: 3.823A pdb=" N CYS D 643 " --> pdb=" O ILE D 639 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA D 644 " --> pdb=" O LYS D 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 678 through 683 Processing helix chain 'D' and resid 689 through 693 removed outlier: 3.614A pdb=" N ARG D 692 " --> pdb=" O ALA D 689 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ALA D 693 " --> pdb=" O SER D 690 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 689 through 693' Processing helix chain 'D' and resid 705 through 724 removed outlier: 6.554A pdb=" N ASN D 711 " --> pdb=" O PRO D 707 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N THR D 712 " --> pdb=" O LEU D 708 " (cutoff:3.500A) Processing helix chain 'D' and resid 809 through 817 Processing helix chain 'D' and resid 826 through 831 Processing helix chain 'D' and resid 837 through 852 removed outlier: 3.579A pdb=" N CYS D 842 " --> pdb=" O PRO D 838 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA D 843 " --> pdb=" O GLU D 839 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE D 846 " --> pdb=" O CYS D 842 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG D 847 " --> pdb=" O ALA D 843 " (cutoff:3.500A) Processing helix chain 'D' and resid 861 through 866 Processing helix chain 'D' and resid 870 through 881 removed outlier: 3.638A pdb=" N THR D 879 " --> pdb=" O ALA D 875 " (cutoff:3.500A) Processing helix chain 'D' and resid 899 through 903 Processing helix chain 'D' and resid 904 through 909 Processing helix chain 'D' and resid 910 through 911 No H-bonds generated for 'chain 'D' and resid 910 through 911' Processing helix chain 'D' and resid 912 through 916 Processing helix chain 'D' and resid 925 through 938 removed outlier: 4.684A pdb=" N ASP D 935 " --> pdb=" O LYS D 931 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N LEU D 936 " --> pdb=" O PHE D 932 " (cutoff:3.500A) Processing helix chain 'D' and resid 1332 through 1344 Processing helix chain 'D' and resid 1348 through 1366 removed outlier: 3.578A pdb=" N ALA D1357 " --> pdb=" O GLU D1353 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N CYS D1362 " --> pdb=" O VAL D1358 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE D1363 " --> pdb=" O ILE D1359 " (cutoff:3.500A) Processing helix chain 'D' and resid 1374 through 1386 removed outlier: 3.733A pdb=" N LYS D1378 " --> pdb=" O SER D1374 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 443 removed outlier: 3.539A pdb=" N LYS E 439 " --> pdb=" O ILE E 435 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU E 440 " --> pdb=" O ALA E 436 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N MET E 441 " --> pdb=" O ALA E 437 " (cutoff:3.500A) Processing helix chain 'E' and resid 443 through 448 Processing helix chain 'E' and resid 450 through 455 removed outlier: 3.867A pdb=" N PHE E 455 " --> pdb=" O VAL E 451 " (cutoff:3.500A) Processing helix chain 'E' and resid 473 through 487 Processing helix chain 'E' and resid 509 through 523 removed outlier: 3.714A pdb=" N LEU E 513 " --> pdb=" O SER E 509 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG E 514 " --> pdb=" O GLU E 510 " (cutoff:3.500A) Processing helix chain 'E' and resid 533 through 536 Processing helix chain 'E' and resid 545 through 559 removed outlier: 3.902A pdb=" N SER E 549 " --> pdb=" O ASP E 545 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU E 558 " --> pdb=" O THR E 554 " (cutoff:3.500A) Processing helix chain 'E' and resid 560 through 563 removed outlier: 4.591A pdb=" N ASP E 563 " --> pdb=" O ASP E 560 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 560 through 563' Processing helix chain 'E' and resid 576 through 580 removed outlier: 3.694A pdb=" N ILE E 580 " --> pdb=" O LEU E 577 " (cutoff:3.500A) Processing helix chain 'E' and resid 600 through 612 removed outlier: 3.827A pdb=" N LYS E 605 " --> pdb=" O LYS E 601 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLU E 606 " --> pdb=" O GLU E 602 " (cutoff:3.500A) Processing helix chain 'E' and resid 620 through 631 removed outlier: 4.170A pdb=" N GLU E 629 " --> pdb=" O GLU E 625 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ASN E 630 " --> pdb=" O GLU E 626 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N CYS E 631 " --> pdb=" O LEU E 627 " (cutoff:3.500A) Processing helix chain 'E' and resid 635 through 655 removed outlier: 3.548A pdb=" N SER E 641 " --> pdb=" O ALA E 637 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE E 642 " --> pdb=" O ASP E 638 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N CYS E 643 " --> pdb=" O ILE E 639 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA E 644 " --> pdb=" O LYS E 640 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA E 647 " --> pdb=" O CYS E 643 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG E 652 " --> pdb=" O LEU E 648 " (cutoff:3.500A) Processing helix chain 'E' and resid 675 through 686 removed outlier: 3.661A pdb=" N LYS E 685 " --> pdb=" O VAL E 681 " (cutoff:3.500A) Processing helix chain 'E' and resid 705 through 724 removed outlier: 6.482A pdb=" N ASN E 711 " --> pdb=" O PRO E 707 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N THR E 712 " --> pdb=" O LEU E 708 " (cutoff:3.500A) Processing helix chain 'E' and resid 808 through 817 removed outlier: 3.557A pdb=" N ALA E 812 " --> pdb=" O HIS E 808 " (cutoff:3.500A) Processing helix chain 'E' and resid 826 through 831 Processing helix chain 'E' and resid 837 through 852 removed outlier: 3.768A pdb=" N THR E 841 " --> pdb=" O SER E 837 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE E 846 " --> pdb=" O CYS E 842 " (cutoff:3.500A) Processing helix chain 'E' and resid 861 through 866 Processing helix chain 'E' and resid 870 through 881 removed outlier: 3.621A pdb=" N LYS E 874 " --> pdb=" O GLY E 870 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA E 875 " --> pdb=" O PRO E 871 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU E 881 " --> pdb=" O PHE E 877 " (cutoff:3.500A) Processing helix chain 'E' and resid 904 through 909 Processing helix chain 'E' and resid 925 through 934 removed outlier: 3.587A pdb=" N PHE E 933 " --> pdb=" O ARG E 929 " (cutoff:3.500A) Processing helix chain 'E' and resid 939 through 943 removed outlier: 3.759A pdb=" N ALA E 942 " --> pdb=" O LYS E 939 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS E 943 " --> pdb=" O GLN E 940 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 939 through 943' Processing helix chain 'E' and resid 1331 through 1344 removed outlier: 3.612A pdb=" N LEU E1336 " --> pdb=" O ARG E1332 " (cutoff:3.500A) Processing helix chain 'E' and resid 1348 through 1365 removed outlier: 3.769A pdb=" N ASN E1354 " --> pdb=" O PHE E1350 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA E1357 " --> pdb=" O GLU E1353 " (cutoff:3.500A) Processing helix chain 'E' and resid 1375 through 1386 Processing helix chain 'F' and resid 431 through 440 removed outlier: 4.091A pdb=" N ALA F 436 " --> pdb=" O SER F 432 " (cutoff:3.500A) Processing helix chain 'F' and resid 443 through 448 Processing helix chain 'F' and resid 448 through 453 removed outlier: 3.623A pdb=" N PHE F 452 " --> pdb=" O TYR F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 472 through 486 removed outlier: 3.845A pdb=" N VAL F 476 " --> pdb=" O GLY F 472 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA F 477 " --> pdb=" O LYS F 473 " (cutoff:3.500A) Processing helix chain 'F' and resid 508 through 517 removed outlier: 3.610A pdb=" N LEU F 513 " --> pdb=" O SER F 509 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG F 514 " --> pdb=" O GLU F 510 " (cutoff:3.500A) Processing helix chain 'F' and resid 532 through 536 Processing helix chain 'F' and resid 545 through 559 removed outlier: 3.947A pdb=" N SER F 549 " --> pdb=" O ASP F 545 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA F 557 " --> pdb=" O SER F 553 " (cutoff:3.500A) Processing helix chain 'F' and resid 581 through 585 removed outlier: 3.517A pdb=" N ARG F 585 " --> pdb=" O PRO F 582 " (cutoff:3.500A) Processing helix chain 'F' and resid 602 through 612 removed outlier: 3.652A pdb=" N GLU F 606 " --> pdb=" O GLU F 602 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU F 608 " --> pdb=" O ARG F 604 " (cutoff:3.500A) Processing helix chain 'F' and resid 620 through 631 removed outlier: 3.539A pdb=" N LEU F 624 " --> pdb=" O LEU F 620 " (cutoff:3.500A) Processing helix chain 'F' and resid 636 through 655 removed outlier: 3.828A pdb=" N CYS F 643 " --> pdb=" O ILE F 639 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA F 644 " --> pdb=" O LYS F 640 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA F 647 " --> pdb=" O CYS F 643 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU F 651 " --> pdb=" O ALA F 647 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG F 652 " --> pdb=" O LEU F 648 " (cutoff:3.500A) Processing helix chain 'F' and resid 675 through 683 removed outlier: 3.928A pdb=" N PHE F 679 " --> pdb=" O SER F 675 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU F 680 " --> pdb=" O ALA F 676 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL F 681 " --> pdb=" O LYS F 677 " (cutoff:3.500A) Processing helix chain 'F' and resid 705 through 724 removed outlier: 6.695A pdb=" N ASN F 711 " --> pdb=" O PRO F 707 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N THR F 712 " --> pdb=" O LEU F 708 " (cutoff:3.500A) Processing helix chain 'F' and resid 808 through 817 Processing helix chain 'F' and resid 826 through 831 Processing helix chain 'F' and resid 842 through 852 removed outlier: 3.601A pdb=" N ILE F 846 " --> pdb=" O CYS F 842 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR F 852 " --> pdb=" O GLU F 848 " (cutoff:3.500A) Processing helix chain 'F' and resid 861 through 866 Processing helix chain 'F' and resid 870 through 884 removed outlier: 3.872A pdb=" N ALA F 875 " --> pdb=" O PRO F 871 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR F 879 " --> pdb=" O ALA F 875 " (cutoff:3.500A) Processing helix chain 'F' and resid 899 through 903 removed outlier: 3.844A pdb=" N LEU F 903 " --> pdb=" O HIS F 900 " (cutoff:3.500A) Processing helix chain 'F' and resid 904 through 909 Processing helix chain 'F' and resid 925 through 933 removed outlier: 3.815A pdb=" N PHE F 933 " --> pdb=" O ARG F 929 " (cutoff:3.500A) Processing helix chain 'F' and resid 935 through 940 removed outlier: 3.651A pdb=" N GLN F 940 " --> pdb=" O LEU F 936 " (cutoff:3.500A) Processing helix chain 'F' and resid 1332 through 1344 Processing helix chain 'F' and resid 1345 through 1347 No H-bonds generated for 'chain 'F' and resid 1345 through 1347' Processing helix chain 'F' and resid 1348 through 1366 removed outlier: 4.190A pdb=" N CYS F1362 " --> pdb=" O VAL F1358 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ILE F1363 " --> pdb=" O ILE F1359 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR F1364 " --> pdb=" O SER F1360 " (cutoff:3.500A) Processing helix chain 'F' and resid 1374 through 1384 removed outlier: 3.583A pdb=" N LYS F1378 " --> pdb=" O SER F1374 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 492 through 497 removed outlier: 6.577A pdb=" N ALA A 492 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N PHE A 529 " --> pdb=" O ALA A 492 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N PHE A 494 " --> pdb=" O PHE A 529 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ASP A 531 " --> pdb=" O PHE A 494 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ARG A 496 " --> pdb=" O ASP A 531 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N PHE A 594 " --> pdb=" O GLY A 462 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU A 464 " --> pdb=" O PHE A 594 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 821 through 824 removed outlier: 6.588A pdb=" N SER A 855 " --> pdb=" O LEU A 891 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N LEU A 893 " --> pdb=" O SER A 855 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL A 857 " --> pdb=" O LEU A 893 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N THR A 895 " --> pdb=" O VAL A 857 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N VAL A 859 " --> pdb=" O THR A 895 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 494 through 496 removed outlier: 8.256A pdb=" N PHE B 594 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU B 464 " --> pdb=" O PHE B 594 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 822 through 824 removed outlier: 6.701A pdb=" N TYR B 823 " --> pdb=" O TYR B 858 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR B 895 " --> pdb=" O VAL B 859 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 494 through 496 removed outlier: 3.582A pdb=" N GLY C 572 " --> pdb=" O CYS C 463 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLY C 462 " --> pdb=" O ARG C 592 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N PHE C 594 " --> pdb=" O GLY C 462 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU C 464 " --> pdb=" O PHE C 594 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 821 through 824 removed outlier: 6.534A pdb=" N THR C 821 " --> pdb=" O ILE C 856 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N TYR C 858 " --> pdb=" O THR C 821 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N TYR C 823 " --> pdb=" O TYR C 858 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR C 895 " --> pdb=" O VAL C 859 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 464 through 466 removed outlier: 6.268A pdb=" N LEU D 464 " --> pdb=" O PHE D 594 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 492 through 496 removed outlier: 6.437A pdb=" N ALA D 492 " --> pdb=" O ILE D 527 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N PHE D 529 " --> pdb=" O ALA D 492 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N PHE D 494 " --> pdb=" O PHE D 529 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ASP D 531 " --> pdb=" O PHE D 494 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ARG D 496 " --> pdb=" O ASP D 531 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 821 through 824 removed outlier: 6.312A pdb=" N THR D 821 " --> pdb=" O ILE D 856 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N TYR D 858 " --> pdb=" O THR D 821 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N TYR D 823 " --> pdb=" O TYR D 858 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR D 895 " --> pdb=" O VAL D 859 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 492 through 497 removed outlier: 6.495A pdb=" N ALA E 492 " --> pdb=" O ILE E 527 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N PHE E 529 " --> pdb=" O ALA E 492 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N PHE E 494 " --> pdb=" O PHE E 529 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ASP E 531 " --> pdb=" O PHE E 494 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ARG E 496 " --> pdb=" O ASP E 531 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N SER E 526 " --> pdb=" O VAL E 569 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N ILE E 571 " --> pdb=" O SER E 526 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ILE E 528 " --> pdb=" O ILE E 571 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ALA E 573 " --> pdb=" O ILE E 528 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N PHE E 530 " --> pdb=" O ALA E 573 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY E 572 " --> pdb=" O CYS E 463 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 822 through 824 removed outlier: 6.593A pdb=" N TYR E 823 " --> pdb=" O TYR E 858 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR E 895 " --> pdb=" O VAL E 859 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 492 through 497 removed outlier: 6.752A pdb=" N ALA F 492 " --> pdb=" O ILE F 527 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N PHE F 529 " --> pdb=" O ALA F 492 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N PHE F 494 " --> pdb=" O PHE F 529 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N ASP F 531 " --> pdb=" O PHE F 494 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ARG F 496 " --> pdb=" O ASP F 531 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N SER F 526 " --> pdb=" O VAL F 569 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ILE F 571 " --> pdb=" O SER F 526 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE F 528 " --> pdb=" O ILE F 571 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N ALA F 573 " --> pdb=" O ILE F 528 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N PHE F 530 " --> pdb=" O ALA F 573 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY F 572 " --> pdb=" O CYS F 463 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N PHE F 594 " --> pdb=" O GLY F 462 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU F 464 " --> pdb=" O PHE F 594 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 821 through 824 removed outlier: 6.486A pdb=" N THR F 821 " --> pdb=" O ILE F 856 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N TYR F 858 " --> pdb=" O THR F 821 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N TYR F 823 " --> pdb=" O TYR F 858 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR F 895 " --> pdb=" O VAL F 859 " (cutoff:3.500A) 912 hydrogen bonds defined for protein. 2643 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: 4.22 Time building geometry restraints manager: 3.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8225 1.34 - 1.46: 4908 1.46 - 1.58: 12650 1.58 - 1.70: 28 1.70 - 1.82: 159 Bond restraints: 25970 Sorted by residual: bond pdb=" C4 ATP E1402 " pdb=" C5 ATP E1402 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.58e+01 bond pdb=" O1A ATP C1401 " pdb=" PA ATP C1401 " ideal model delta sigma weight residual 1.477 1.557 -0.080 1.10e-02 8.26e+03 5.31e+01 bond pdb=" C4 ATP B1401 " pdb=" C5 ATP B1401 " ideal model delta sigma weight residual 1.388 1.460 -0.072 1.00e-02 1.00e+04 5.24e+01 bond pdb=" C4 ATP C1401 " pdb=" C5 ATP C1401 " ideal model delta sigma weight residual 1.388 1.460 -0.072 1.00e-02 1.00e+04 5.17e+01 bond pdb=" C4 ATP C1402 " pdb=" C5 ATP C1402 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.05e+01 ... (remaining 25965 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.28: 35110 5.28 - 10.56: 93 10.56 - 15.85: 4 15.85 - 21.13: 6 21.13 - 26.41: 2 Bond angle restraints: 35215 Sorted by residual: angle pdb=" PB ATP C1402 " pdb=" O3B ATP C1402 " pdb=" PG ATP C1402 " ideal model delta sigma weight residual 139.87 113.46 26.41 1.00e+00 1.00e+00 6.98e+02 angle pdb=" PB ATP C1401 " pdb=" O3B ATP C1401 " pdb=" PG ATP C1401 " ideal model delta sigma weight residual 139.87 117.90 21.97 1.00e+00 1.00e+00 4.83e+02 angle pdb=" PB ATP E1402 " pdb=" O3B ATP E1402 " pdb=" PG ATP E1402 " ideal model delta sigma weight residual 139.87 118.76 21.11 1.00e+00 1.00e+00 4.45e+02 angle pdb=" PB ATP B1401 " pdb=" O3B ATP B1401 " pdb=" PG ATP B1401 " ideal model delta sigma weight residual 139.87 119.17 20.70 1.00e+00 1.00e+00 4.29e+02 angle pdb=" PA ATP C1401 " pdb=" O3A ATP C1401 " pdb=" PB ATP C1401 " ideal model delta sigma weight residual 136.83 117.40 19.43 1.00e+00 1.00e+00 3.78e+02 ... (remaining 35210 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 13975 17.85 - 35.71: 1510 35.71 - 53.56: 393 53.56 - 71.41: 95 71.41 - 89.27: 26 Dihedral angle restraints: 15999 sinusoidal: 6710 harmonic: 9289 Sorted by residual: dihedral pdb=" CA ALA A 693 " pdb=" C ALA A 693 " pdb=" N VAL A 694 " pdb=" CA VAL A 694 " ideal model delta harmonic sigma weight residual -180.00 -154.25 -25.75 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA TRP C 505 " pdb=" C TRP C 505 " pdb=" N VAL C 506 " pdb=" CA VAL C 506 " ideal model delta harmonic sigma weight residual -180.00 -155.55 -24.45 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA TRP B 505 " pdb=" C TRP B 505 " pdb=" N VAL B 506 " pdb=" CA VAL B 506 " ideal model delta harmonic sigma weight residual -180.00 -155.56 -24.44 0 5.00e+00 4.00e-02 2.39e+01 ... (remaining 15996 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 3675 0.094 - 0.188: 286 0.188 - 0.282: 9 0.282 - 0.376: 0 0.376 - 0.471: 2 Chirality restraints: 3972 Sorted by residual: chirality pdb=" CA PHE E 425 " pdb=" N PHE E 425 " pdb=" C PHE E 425 " pdb=" CB PHE E 425 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.54e+00 chirality pdb=" CA PHE F 425 " pdb=" N PHE F 425 " pdb=" C PHE F 425 " pdb=" CB PHE F 425 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.77e+00 chirality pdb=" CA ARG D 490 " pdb=" N ARG D 490 " pdb=" C ARG D 490 " pdb=" CB ARG D 490 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 3969 not shown) Planarity restraints: 4517 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS E 473 " -0.019 2.00e-02 2.50e+03 3.71e-02 1.38e+01 pdb=" C LYS E 473 " 0.064 2.00e-02 2.50e+03 pdb=" O LYS E 473 " -0.024 2.00e-02 2.50e+03 pdb=" N THR E 474 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 554 " 0.014 2.00e-02 2.50e+03 2.87e-02 8.25e+00 pdb=" C THR C 554 " -0.050 2.00e-02 2.50e+03 pdb=" O THR C 554 " 0.018 2.00e-02 2.50e+03 pdb=" N LEU C 555 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO D 468 " -0.044 5.00e-02 4.00e+02 6.68e-02 7.14e+00 pdb=" N PRO D 469 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO D 469 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 469 " -0.037 5.00e-02 4.00e+02 ... (remaining 4514 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 112 2.46 - 3.07: 16606 3.07 - 3.68: 35369 3.68 - 4.29: 54258 4.29 - 4.90: 91916 Nonbonded interactions: 198261 Sorted by model distance: nonbonded pdb=" NZ LYS A 454 " pdb=" ND2 ASN B 616 " model vdw 1.854 3.200 nonbonded pdb=" OD1 ASP C 534 " pdb=" OG1 THR C 574 " model vdw 2.032 3.040 nonbonded pdb=" OD1 ASN A 616 " pdb=" CD PRO A 617 " model vdw 2.045 3.440 nonbonded pdb=" OG SER E 837 " pdb=" OE1 GLU E 840 " model vdw 2.053 3.040 nonbonded pdb=" OH TYR D 786 " pdb=" OE1 GLN E 940 " model vdw 2.101 3.040 ... (remaining 198256 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 422 through 688 or resid 696 through 727 or resid 787 thro \ ugh 944 or resid 1331 through 1388)) selection = (chain 'B' and (resid 422 through 539 or resid 546 through 688 or resid 696 thro \ ugh 727 or resid 787 through 944 or resid 1331 through 1388)) selection = (chain 'C' and (resid 422 through 539 or resid 546 through 688 or resid 696 thro \ ugh 727 or resid 787 through 944 or resid 1331 through 1388)) selection = (chain 'D' and (resid 422 through 539 or resid 546 through 688 or resid 696 thro \ ugh 727 or resid 787 through 944 or resid 1331 through 1388)) selection = (chain 'E' and (resid 422 through 539 or resid 546 through 688 or resid 696 thro \ ugh 727 or resid 787 through 944 or resid 1331 through 1388)) selection = (chain 'F' and (resid 422 through 539 or resid 546 through 727 or resid 787 thro \ ugh 1388)) } 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 individual isotropic 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: 1.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 23.840 Find NCS groups from input model: 0.670 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 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 : 0.007 0.080 25979 Z= 0.342 Angle : 0.924 26.412 35215 Z= 0.615 Chirality : 0.051 0.471 3972 Planarity : 0.005 0.067 4517 Dihedral : 16.367 89.267 9941 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.45 % Allowed : 9.22 % Favored : 90.33 % Rotamer: Outliers : 3.65 % Allowed : 8.77 % Favored : 87.58 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.34 % 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: -4.15 (0.13), residues: 3134 helix: -2.72 (0.11), residues: 1431 sheet: -1.35 (0.25), residues: 391 loop : -3.13 (0.15), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 576 TYR 0.008 0.001 TYR A 466 PHE 0.013 0.002 PHE B 724 TRP 0.017 0.001 TRP E 505 HIS 0.006 0.001 HIS F 861 Details of bonding type rmsd covalent geometry : bond 0.00686 (25970) covalent geometry : angle 0.92415 (35215) hydrogen bonds : bond 0.20343 ( 912) hydrogen bonds : angle 6.85135 ( 2643) Misc. bond : bond 0.00593 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 348 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 586 ARG cc_start: 0.7043 (mpt90) cc_final: 0.6219 (tmm160) REVERT: A 666 GLN cc_start: 0.5817 (OUTLIER) cc_final: 0.5481 (mt0) REVERT: A 792 ARG cc_start: 0.8907 (OUTLIER) cc_final: 0.8061 (mtt90) REVERT: B 867 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7508 (mt-10) REVERT: B 1384 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.7190 (pp20) REVERT: C 658 ILE cc_start: 0.8314 (OUTLIER) cc_final: 0.8114 (tt) REVERT: C 1332 ARG cc_start: 0.7184 (ptm160) cc_final: 0.6968 (ptm160) REVERT: D 495 MET cc_start: 0.7655 (tmm) cc_final: 0.7416 (tmm) REVERT: D 677 LYS cc_start: 0.8085 (tppt) cc_final: 0.7844 (tppt) REVERT: D 867 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7381 (mm-30) REVERT: D 1338 LYS cc_start: 0.8439 (tttt) cc_final: 0.8226 (tmtt) REVERT: E 559 MET cc_start: 0.8953 (ttm) cc_final: 0.8722 (ttp) REVERT: E 683 MET cc_start: 0.8658 (mtp) cc_final: 0.8341 (mtt) REVERT: F 489 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7796 (mttt) REVERT: F 576 ARG cc_start: 0.7713 (mtt90) cc_final: 0.7025 (mtm-85) REVERT: F 789 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.8141 (ttt) REVERT: F 867 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7630 (mm-30) outliers start: 102 outliers final: 44 residues processed: 427 average time/residue: 0.2089 time to fit residues: 129.6497 Evaluate side-chains 310 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 257 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 GLN Chi-restraints excluded: chain A residue 489 LYS Chi-restraints excluded: chain A residue 618 LYS Chi-restraints excluded: chain A residue 658 ILE Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 666 GLN Chi-restraints excluded: chain A residue 792 ARG Chi-restraints excluded: chain A residue 926 LYS Chi-restraints excluded: chain A residue 943 LYS Chi-restraints excluded: chain A residue 1358 VAL Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 618 LYS Chi-restraints excluded: chain B residue 659 TYR Chi-restraints excluded: chain B residue 786 TYR Chi-restraints excluded: chain B residue 789 MET Chi-restraints excluded: chain B residue 867 GLU Chi-restraints excluded: chain B residue 928 GLU Chi-restraints excluded: chain B residue 943 LYS Chi-restraints excluded: chain B residue 1358 VAL Chi-restraints excluded: chain B residue 1384 GLU Chi-restraints excluded: chain B residue 1385 ASN Chi-restraints excluded: chain C residue 427 SER Chi-restraints excluded: chain C residue 658 ILE Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 943 LYS Chi-restraints excluded: chain C residue 1361 GLN Chi-restraints excluded: chain D residue 427 SER Chi-restraints excluded: chain D residue 618 LYS Chi-restraints excluded: chain D residue 658 ILE Chi-restraints excluded: chain D residue 667 LEU Chi-restraints excluded: chain D residue 789 MET Chi-restraints excluded: chain D residue 867 GLU Chi-restraints excluded: chain D residue 1358 VAL Chi-restraints excluded: chain E residue 618 LYS Chi-restraints excluded: chain E residue 666 GLN Chi-restraints excluded: chain E residue 786 TYR Chi-restraints excluded: chain E residue 789 MET Chi-restraints excluded: chain E residue 867 GLU Chi-restraints excluded: chain E residue 1358 VAL Chi-restraints excluded: chain E residue 1388 CYS Chi-restraints excluded: chain F residue 426 ASP Chi-restraints excluded: chain F residue 488 ASP Chi-restraints excluded: chain F residue 489 LYS Chi-restraints excluded: chain F residue 661 THR Chi-restraints excluded: chain F residue 789 MET Chi-restraints excluded: chain F residue 867 GLU Chi-restraints excluded: chain F residue 928 GLU Chi-restraints excluded: chain F residue 1358 VAL Chi-restraints excluded: chain F residue 1361 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 GLN A 691 GLN A 808 HIS A 844 GLN A1377 GLN B 512 GLN B 611 HIS B 808 HIS B 844 GLN B1385 ASN C 673 ASN C 711 ASN C1346 ASN D 611 HIS D 657 GLN E 575 ASN E 710 GLN E1335 ASN F 710 GLN F 920 ASN F 922 GLN F1345 GLN F1377 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.137443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.112400 restraints weight = 34254.093| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.80 r_work: 0.3092 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25979 Z= 0.134 Angle : 0.668 13.212 35215 Z= 0.332 Chirality : 0.045 0.442 3972 Planarity : 0.005 0.060 4517 Dihedral : 10.578 91.982 3736 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.72 % Favored : 92.12 % Rotamer: Outliers : 2.40 % Allowed : 12.31 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.34 % 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: -2.65 (0.14), residues: 3134 helix: -1.31 (0.13), residues: 1455 sheet: -0.78 (0.25), residues: 387 loop : -2.52 (0.16), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 424 TYR 0.016 0.001 TYR A 448 PHE 0.019 0.001 PHE E 791 TRP 0.013 0.001 TRP E 505 HIS 0.004 0.001 HIS C 863 Details of bonding type rmsd covalent geometry : bond 0.00299 (25970) covalent geometry : angle 0.66781 (35215) hydrogen bonds : bond 0.04712 ( 912) hydrogen bonds : angle 4.91480 ( 2643) Misc. bond : bond 0.00505 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 288 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 586 ARG cc_start: 0.7465 (mpt90) cc_final: 0.6238 (tmm160) REVERT: A 666 GLN cc_start: 0.5941 (OUTLIER) cc_final: 0.5170 (mt0) REVERT: A 681 VAL cc_start: 0.8501 (p) cc_final: 0.8204 (t) REVERT: B 519 GLN cc_start: 0.8558 (tt0) cc_final: 0.8339 (mt0) REVERT: B 683 MET cc_start: 0.9113 (mtp) cc_final: 0.8908 (mtt) REVERT: B 786 TYR cc_start: 0.6457 (OUTLIER) cc_final: 0.5617 (t80) REVERT: B 1384 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7279 (pp20) REVERT: C 490 ARG cc_start: 0.7735 (ttm110) cc_final: 0.7301 (tpt170) REVERT: C 562 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8753 (tt) REVERT: C 1332 ARG cc_start: 0.7553 (ptm160) cc_final: 0.7341 (ptm160) REVERT: C 1346 ASN cc_start: 0.8525 (OUTLIER) cc_final: 0.8246 (t0) REVERT: D 683 MET cc_start: 0.9314 (mtm) cc_final: 0.9038 (mtt) REVERT: D 847 ARG cc_start: 0.8154 (ttm110) cc_final: 0.7949 (ttp-110) REVERT: D 1338 LYS cc_start: 0.8446 (tttt) cc_final: 0.8227 (tmtt) REVERT: E 558 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8913 (pt) REVERT: E 683 MET cc_start: 0.8970 (mtp) cc_final: 0.8612 (mtt) REVERT: E 1372 LYS cc_start: 0.6565 (mmtt) cc_final: 0.4709 (pttp) REVERT: F 576 ARG cc_start: 0.7824 (mtt90) cc_final: 0.7115 (mtm-85) REVERT: F 867 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8166 (mm-30) REVERT: F 1332 ARG cc_start: 0.7622 (ttp-170) cc_final: 0.6957 (mpp-170) outliers start: 67 outliers final: 24 residues processed: 337 average time/residue: 0.1838 time to fit residues: 93.8890 Evaluate side-chains 269 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 238 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 455 PHE Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 666 GLN Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 821 THR Chi-restraints excluded: chain A residue 943 LYS Chi-restraints excluded: chain A residue 1358 VAL Chi-restraints excluded: chain A residue 1388 CYS Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 695 THR Chi-restraints excluded: chain B residue 786 TYR Chi-restraints excluded: chain B residue 867 GLU Chi-restraints excluded: chain B residue 937 ILE Chi-restraints excluded: chain B residue 1384 GLU Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 886 SER Chi-restraints excluded: chain C residue 1346 ASN Chi-restraints excluded: chain C residue 1379 MET Chi-restraints excluded: chain D residue 471 THR Chi-restraints excluded: chain D residue 618 LYS Chi-restraints excluded: chain D residue 657 GLN Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain E residue 662 SER Chi-restraints excluded: chain E residue 867 GLU Chi-restraints excluded: chain F residue 502 LEU Chi-restraints excluded: chain F residue 661 THR Chi-restraints excluded: chain F residue 867 GLU Chi-restraints excluded: chain F residue 938 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 1 optimal weight: 8.9990 chunk 176 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 166 optimal weight: 5.9990 chunk 170 optimal weight: 4.9990 chunk 105 optimal weight: 0.1980 chunk 135 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 161 optimal weight: 0.0970 chunk 308 optimal weight: 9.9990 chunk 276 optimal weight: 9.9990 overall best weight: 2.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 657 GLN E 575 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.135946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.110746 restraints weight = 34527.364| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.80 r_work: 0.3063 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 25979 Z= 0.164 Angle : 0.666 11.909 35215 Z= 0.326 Chirality : 0.045 0.313 3972 Planarity : 0.005 0.061 4517 Dihedral : 9.129 86.589 3634 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.43 % Favored : 92.41 % Rotamer: Outliers : 2.68 % Allowed : 13.71 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.34 % 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: -2.06 (0.15), residues: 3134 helix: -0.77 (0.13), residues: 1454 sheet: -0.52 (0.25), residues: 388 loop : -2.27 (0.17), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 847 TYR 0.012 0.001 TYR A 448 PHE 0.015 0.001 PHE E 791 TRP 0.012 0.001 TRP E 865 HIS 0.004 0.001 HIS F 861 Details of bonding type rmsd covalent geometry : bond 0.00401 (25970) covalent geometry : angle 0.66566 (35215) hydrogen bonds : bond 0.04536 ( 912) hydrogen bonds : angle 4.65469 ( 2643) Misc. bond : bond 0.00565 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 250 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 586 ARG cc_start: 0.7518 (mpt90) cc_final: 0.6278 (tmm160) REVERT: A 681 VAL cc_start: 0.8501 (p) cc_final: 0.8227 (t) REVERT: B 683 MET cc_start: 0.9162 (mtp) cc_final: 0.8921 (mtt) REVERT: B 720 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8591 (tt) REVERT: B 786 TYR cc_start: 0.6629 (OUTLIER) cc_final: 0.5705 (t80) REVERT: B 1384 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7286 (pp20) REVERT: C 490 ARG cc_start: 0.7882 (ttm110) cc_final: 0.7449 (tpt170) REVERT: C 562 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8686 (tt) REVERT: C 701 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8965 (mm) REVERT: C 1332 ARG cc_start: 0.7504 (ptm160) cc_final: 0.7296 (ptm160) REVERT: C 1346 ASN cc_start: 0.8420 (t0) cc_final: 0.7880 (t0) REVERT: C 1390 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.7038 (mmm160) REVERT: D 683 MET cc_start: 0.9300 (mtm) cc_final: 0.9051 (mtt) REVERT: D 847 ARG cc_start: 0.8275 (ttm110) cc_final: 0.8061 (ttp-110) REVERT: E 463 CYS cc_start: 0.8546 (m) cc_final: 0.8223 (m) REVERT: E 558 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.8882 (pt) REVERT: E 559 MET cc_start: 0.8696 (ttm) cc_final: 0.8084 (ttp) REVERT: E 1372 LYS cc_start: 0.6529 (mmtt) cc_final: 0.4703 (pttp) REVERT: F 576 ARG cc_start: 0.7788 (mtt90) cc_final: 0.7112 (mtm-85) REVERT: F 616 ASN cc_start: 0.7383 (OUTLIER) cc_final: 0.6941 (p0) REVERT: F 1332 ARG cc_start: 0.7510 (ttp-170) cc_final: 0.6864 (mpp-170) outliers start: 75 outliers final: 41 residues processed: 307 average time/residue: 0.1868 time to fit residues: 86.8369 Evaluate side-chains 280 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 231 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 455 PHE Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 821 THR Chi-restraints excluded: chain A residue 1358 VAL Chi-restraints excluded: chain A residue 1360 SER Chi-restraints excluded: chain A residue 1375 LEU Chi-restraints excluded: chain A residue 1388 CYS Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 695 THR Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 786 TYR Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 821 THR Chi-restraints excluded: chain B residue 837 SER Chi-restraints excluded: chain B residue 867 GLU Chi-restraints excluded: chain B residue 937 ILE Chi-restraints excluded: chain B residue 1375 LEU Chi-restraints excluded: chain B residue 1380 GLU Chi-restraints excluded: chain B residue 1384 GLU Chi-restraints excluded: chain C residue 486 GLN Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 821 THR Chi-restraints excluded: chain C residue 886 SER Chi-restraints excluded: chain C residue 1379 MET Chi-restraints excluded: chain C residue 1390 ARG Chi-restraints excluded: chain D residue 618 LYS Chi-restraints excluded: chain E residue 518 ASP Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain E residue 642 ILE Chi-restraints excluded: chain E residue 662 SER Chi-restraints excluded: chain E residue 867 GLU Chi-restraints excluded: chain E residue 938 LEU Chi-restraints excluded: chain F residue 502 LEU Chi-restraints excluded: chain F residue 534 ASP Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 661 THR Chi-restraints excluded: chain F residue 821 THR Chi-restraints excluded: chain F residue 938 LEU Chi-restraints excluded: chain F residue 1375 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 166 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 238 optimal weight: 0.0000 chunk 148 optimal weight: 4.9990 chunk 78 optimal weight: 8.9990 chunk 94 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 159 optimal weight: 4.9990 chunk 195 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 630 ASN C1346 ASN E 575 ASN E1351 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.137324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.111937 restraints weight = 34307.254| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.78 r_work: 0.3082 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25979 Z= 0.129 Angle : 0.621 10.877 35215 Z= 0.305 Chirality : 0.044 0.279 3972 Planarity : 0.005 0.060 4517 Dihedral : 8.611 80.684 3622 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.18 % Favored : 92.66 % Rotamer: Outliers : 2.79 % Allowed : 14.92 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.34 % 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: -1.61 (0.15), residues: 3134 helix: -0.37 (0.14), residues: 1458 sheet: -0.36 (0.25), residues: 384 loop : -2.05 (0.17), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 424 TYR 0.011 0.001 TYR A 448 PHE 0.014 0.001 PHE F 877 TRP 0.014 0.001 TRP B 615 HIS 0.004 0.001 HIS F 861 Details of bonding type rmsd covalent geometry : bond 0.00306 (25970) covalent geometry : angle 0.62061 (35215) hydrogen bonds : bond 0.03833 ( 912) hydrogen bonds : angle 4.44204 ( 2643) Misc. bond : bond 0.00536 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 259 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 586 ARG cc_start: 0.7478 (mpt90) cc_final: 0.6234 (tmm160) REVERT: A 681 VAL cc_start: 0.8492 (p) cc_final: 0.8243 (t) REVERT: B 614 ASP cc_start: 0.8393 (OUTLIER) cc_final: 0.8011 (p0) REVERT: B 672 ILE cc_start: 0.7813 (OUTLIER) cc_final: 0.7610 (mt) REVERT: B 683 MET cc_start: 0.9157 (mtp) cc_final: 0.8906 (mtt) REVERT: B 720 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8500 (tt) REVERT: B 1384 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7239 (pp20) REVERT: C 562 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8654 (tt) REVERT: C 1332 ARG cc_start: 0.7510 (ptm160) cc_final: 0.7275 (ptm160) REVERT: C 1346 ASN cc_start: 0.8482 (OUTLIER) cc_final: 0.8102 (t0) REVERT: C 1390 ARG cc_start: 0.7658 (OUTLIER) cc_final: 0.7208 (mmm160) REVERT: D 683 MET cc_start: 0.9272 (mtm) cc_final: 0.9045 (mtt) REVERT: D 1338 LYS cc_start: 0.8534 (tmtt) cc_final: 0.8249 (tttt) REVERT: E 463 CYS cc_start: 0.8465 (m) cc_final: 0.8123 (m) REVERT: E 473 LYS cc_start: 0.7621 (OUTLIER) cc_final: 0.7097 (pttm) REVERT: E 558 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8845 (pt) REVERT: E 559 MET cc_start: 0.8621 (ttm) cc_final: 0.7988 (ttp) REVERT: E 1372 LYS cc_start: 0.6674 (mmtt) cc_final: 0.4792 (pttp) REVERT: F 576 ARG cc_start: 0.7759 (mtt90) cc_final: 0.7109 (mtm-85) REVERT: F 1332 ARG cc_start: 0.7444 (ttp-170) cc_final: 0.6845 (mpp-170) outliers start: 78 outliers final: 43 residues processed: 315 average time/residue: 0.1851 time to fit residues: 89.3898 Evaluate side-chains 286 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 234 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 455 PHE Chi-restraints excluded: chain A residue 668 ASP Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 821 THR Chi-restraints excluded: chain A residue 937 ILE Chi-restraints excluded: chain A residue 1358 VAL Chi-restraints excluded: chain A residue 1375 LEU Chi-restraints excluded: chain A residue 1388 CYS Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain B residue 695 THR Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 867 GLU Chi-restraints excluded: chain B residue 937 ILE Chi-restraints excluded: chain B residue 1375 LEU Chi-restraints excluded: chain B residue 1380 GLU Chi-restraints excluded: chain B residue 1384 GLU Chi-restraints excluded: chain C residue 486 GLN Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 686 MET Chi-restraints excluded: chain C residue 886 SER Chi-restraints excluded: chain C residue 1346 ASN Chi-restraints excluded: chain C residue 1390 ARG Chi-restraints excluded: chain D residue 471 THR Chi-restraints excluded: chain D residue 618 LYS Chi-restraints excluded: chain E residue 473 LYS Chi-restraints excluded: chain E residue 518 ASP Chi-restraints excluded: chain E residue 533 ILE Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain E residue 642 ILE Chi-restraints excluded: chain E residue 662 SER Chi-restraints excluded: chain E residue 703 THR Chi-restraints excluded: chain E residue 841 THR Chi-restraints excluded: chain E residue 867 GLU Chi-restraints excluded: chain E residue 925 ASP Chi-restraints excluded: chain E residue 938 LEU Chi-restraints excluded: chain F residue 502 LEU Chi-restraints excluded: chain F residue 661 THR Chi-restraints excluded: chain F residue 928 GLU Chi-restraints excluded: chain F residue 938 LEU Chi-restraints excluded: chain F residue 1375 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 263 optimal weight: 8.9990 chunk 78 optimal weight: 8.9990 chunk 135 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 255 optimal weight: 0.1980 chunk 87 optimal weight: 0.7980 chunk 137 optimal weight: 0.0040 chunk 203 optimal weight: 9.9990 chunk 228 optimal weight: 5.9990 chunk 170 optimal weight: 5.9990 overall best weight: 1.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1346 ASN E 575 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.137069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.111571 restraints weight = 34178.009| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.79 r_work: 0.3077 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25979 Z= 0.138 Angle : 0.626 10.851 35215 Z= 0.306 Chirality : 0.044 0.291 3972 Planarity : 0.005 0.063 4517 Dihedral : 8.429 83.898 3620 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.12 % Favored : 92.72 % Rotamer: Outliers : 2.93 % Allowed : 15.50 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.34 % 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: -1.37 (0.15), residues: 3134 helix: -0.19 (0.14), residues: 1468 sheet: -0.24 (0.26), residues: 385 loop : -1.93 (0.18), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 847 TYR 0.010 0.001 TYR A 448 PHE 0.012 0.001 PHE F 877 TRP 0.011 0.001 TRP E 865 HIS 0.004 0.001 HIS E 611 Details of bonding type rmsd covalent geometry : bond 0.00335 (25970) covalent geometry : angle 0.62584 (35215) hydrogen bonds : bond 0.03811 ( 912) hydrogen bonds : angle 4.35875 ( 2643) Misc. bond : bond 0.00459 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 250 time to evaluate : 0.960 Fit side-chains revert: symmetry clash REVERT: A 486 GLN cc_start: 0.7030 (OUTLIER) cc_final: 0.6467 (tp40) REVERT: A 586 ARG cc_start: 0.7468 (mpt90) cc_final: 0.6219 (tmm160) REVERT: A 681 VAL cc_start: 0.8490 (p) cc_final: 0.8246 (t) REVERT: B 614 ASP cc_start: 0.8291 (OUTLIER) cc_final: 0.7970 (p0) REVERT: B 672 ILE cc_start: 0.7814 (OUTLIER) cc_final: 0.7611 (mt) REVERT: B 683 MET cc_start: 0.9112 (mtp) cc_final: 0.8847 (mtt) REVERT: B 720 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8572 (tt) REVERT: B 786 TYR cc_start: 0.6716 (OUTLIER) cc_final: 0.5588 (t80) REVERT: B 839 GLU cc_start: 0.8954 (OUTLIER) cc_final: 0.8724 (mp0) REVERT: B 1384 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7268 (pp20) REVERT: C 562 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8684 (tt) REVERT: C 701 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8937 (mt) REVERT: C 833 VAL cc_start: 0.8907 (t) cc_final: 0.8626 (m) REVERT: C 1332 ARG cc_start: 0.7480 (ptm160) cc_final: 0.7253 (ptm160) REVERT: C 1346 ASN cc_start: 0.8463 (OUTLIER) cc_final: 0.7866 (t0) REVERT: C 1390 ARG cc_start: 0.7601 (OUTLIER) cc_final: 0.7035 (mmm160) REVERT: D 683 MET cc_start: 0.9276 (mtm) cc_final: 0.9051 (mtt) REVERT: E 463 CYS cc_start: 0.8493 (m) cc_final: 0.8179 (m) REVERT: E 473 LYS cc_start: 0.7668 (OUTLIER) cc_final: 0.7158 (pttm) REVERT: E 558 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8831 (pt) REVERT: E 867 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8208 (mm-30) REVERT: E 1372 LYS cc_start: 0.6534 (mmtt) cc_final: 0.4664 (pttp) REVERT: F 576 ARG cc_start: 0.7780 (mtt90) cc_final: 0.7152 (mtm-85) REVERT: F 1332 ARG cc_start: 0.7412 (ttp-170) cc_final: 0.6824 (mpp-170) outliers start: 82 outliers final: 48 residues processed: 312 average time/residue: 0.1734 time to fit residues: 82.1862 Evaluate side-chains 293 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 231 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 455 PHE Chi-restraints excluded: chain A residue 486 GLN Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 668 ASP Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 821 THR Chi-restraints excluded: chain A residue 934 GLU Chi-restraints excluded: chain A residue 937 ILE Chi-restraints excluded: chain A residue 1375 LEU Chi-restraints excluded: chain A residue 1388 CYS Chi-restraints excluded: chain B residue 457 ILE Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain B residue 694 VAL Chi-restraints excluded: chain B residue 695 THR Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 786 TYR Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 821 THR Chi-restraints excluded: chain B residue 837 SER Chi-restraints excluded: chain B residue 839 GLU Chi-restraints excluded: chain B residue 867 GLU Chi-restraints excluded: chain B residue 937 ILE Chi-restraints excluded: chain B residue 1375 LEU Chi-restraints excluded: chain B residue 1380 GLU Chi-restraints excluded: chain B residue 1384 GLU Chi-restraints excluded: chain C residue 486 GLN Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 686 MET Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 821 THR Chi-restraints excluded: chain C residue 886 SER Chi-restraints excluded: chain C residue 1346 ASN Chi-restraints excluded: chain C residue 1390 ARG Chi-restraints excluded: chain D residue 471 THR Chi-restraints excluded: chain D residue 618 LYS Chi-restraints excluded: chain E residue 473 LYS Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain E residue 642 ILE Chi-restraints excluded: chain E residue 669 LEU Chi-restraints excluded: chain E residue 680 GLU Chi-restraints excluded: chain E residue 703 THR Chi-restraints excluded: chain E residue 841 THR Chi-restraints excluded: chain E residue 867 GLU Chi-restraints excluded: chain E residue 938 LEU Chi-restraints excluded: chain F residue 502 LEU Chi-restraints excluded: chain F residue 534 ASP Chi-restraints excluded: chain F residue 661 THR Chi-restraints excluded: chain F residue 821 THR Chi-restraints excluded: chain F residue 928 GLU Chi-restraints excluded: chain F residue 938 LEU Chi-restraints excluded: chain F residue 1375 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 12 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 228 optimal weight: 4.9990 chunk 191 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 chunk 120 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 157 optimal weight: 8.9990 chunk 79 optimal weight: 4.9990 chunk 238 optimal weight: 2.9990 chunk 128 optimal weight: 9.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1381 GLN C1346 ASN E 575 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.135855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.110395 restraints weight = 34164.022| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.78 r_work: 0.3060 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 25979 Z= 0.167 Angle : 0.648 10.085 35215 Z= 0.317 Chirality : 0.046 0.284 3972 Planarity : 0.005 0.064 4517 Dihedral : 8.439 85.672 3619 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.37 % Favored : 92.47 % Rotamer: Outliers : 3.26 % Allowed : 15.50 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.34 % 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: -1.24 (0.15), residues: 3134 helix: -0.07 (0.14), residues: 1456 sheet: -0.13 (0.26), residues: 382 loop : -1.88 (0.17), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 847 TYR 0.013 0.001 TYR B 655 PHE 0.012 0.001 PHE C 530 TRP 0.011 0.001 TRP E 865 HIS 0.004 0.001 HIS F 861 Details of bonding type rmsd covalent geometry : bond 0.00415 (25970) covalent geometry : angle 0.64786 (35215) hydrogen bonds : bond 0.04059 ( 912) hydrogen bonds : angle 4.37816 ( 2643) Misc. bond : bond 0.00521 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 244 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 586 ARG cc_start: 0.7450 (mpt90) cc_final: 0.6224 (tmm160) REVERT: A 681 VAL cc_start: 0.8498 (p) cc_final: 0.8270 (t) REVERT: B 453 GLU cc_start: 0.8482 (pp20) cc_final: 0.8273 (pp20) REVERT: B 683 MET cc_start: 0.9092 (mtp) cc_final: 0.8834 (mtt) REVERT: B 720 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8670 (tt) REVERT: B 786 TYR cc_start: 0.6648 (OUTLIER) cc_final: 0.5574 (t80) REVERT: B 1384 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.7293 (pp20) REVERT: C 424 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7606 (mtp-110) REVERT: C 562 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8715 (tt) REVERT: C 701 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.9020 (mm) REVERT: C 833 VAL cc_start: 0.8935 (t) cc_final: 0.8652 (m) REVERT: C 1332 ARG cc_start: 0.7477 (ptm160) cc_final: 0.7249 (ptm160) REVERT: C 1346 ASN cc_start: 0.8465 (OUTLIER) cc_final: 0.7923 (t0) REVERT: C 1390 ARG cc_start: 0.7635 (OUTLIER) cc_final: 0.7103 (mmm160) REVERT: D 683 MET cc_start: 0.9286 (mtm) cc_final: 0.9046 (mtt) REVERT: E 463 CYS cc_start: 0.8551 (m) cc_final: 0.8241 (m) REVERT: E 473 LYS cc_start: 0.7720 (OUTLIER) cc_final: 0.7261 (pttm) REVERT: E 558 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.8841 (pt) REVERT: E 867 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8432 (mm-30) REVERT: E 1372 LYS cc_start: 0.6583 (mmtt) cc_final: 0.4708 (pttp) REVERT: F 559 MET cc_start: 0.8721 (ttm) cc_final: 0.8438 (mmm) REVERT: F 576 ARG cc_start: 0.7782 (mtt90) cc_final: 0.7113 (mtm-85) REVERT: F 1332 ARG cc_start: 0.7407 (ttp-170) cc_final: 0.6809 (mpp-170) outliers start: 91 outliers final: 57 residues processed: 316 average time/residue: 0.1954 time to fit residues: 93.3917 Evaluate side-chains 302 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 234 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 455 PHE Chi-restraints excluded: chain A residue 618 LYS Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 668 ASP Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 821 THR Chi-restraints excluded: chain A residue 934 GLU Chi-restraints excluded: chain A residue 937 ILE Chi-restraints excluded: chain A residue 943 LYS Chi-restraints excluded: chain A residue 1358 VAL Chi-restraints excluded: chain A residue 1375 LEU Chi-restraints excluded: chain A residue 1381 GLN Chi-restraints excluded: chain A residue 1388 CYS Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 457 ILE Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 694 VAL Chi-restraints excluded: chain B residue 695 THR Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 786 TYR Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 821 THR Chi-restraints excluded: chain B residue 837 SER Chi-restraints excluded: chain B residue 867 GLU Chi-restraints excluded: chain B residue 937 ILE Chi-restraints excluded: chain B residue 1375 LEU Chi-restraints excluded: chain B residue 1380 GLU Chi-restraints excluded: chain B residue 1384 GLU Chi-restraints excluded: chain C residue 424 ARG Chi-restraints excluded: chain C residue 486 GLN Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 686 MET Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 821 THR Chi-restraints excluded: chain C residue 886 SER Chi-restraints excluded: chain C residue 1346 ASN Chi-restraints excluded: chain C residue 1390 ARG Chi-restraints excluded: chain D residue 427 SER Chi-restraints excluded: chain D residue 618 LYS Chi-restraints excluded: chain E residue 473 LYS Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 518 ASP Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain E residue 642 ILE Chi-restraints excluded: chain E residue 662 SER Chi-restraints excluded: chain E residue 669 LEU Chi-restraints excluded: chain E residue 680 GLU Chi-restraints excluded: chain E residue 683 MET Chi-restraints excluded: chain E residue 703 THR Chi-restraints excluded: chain E residue 841 THR Chi-restraints excluded: chain E residue 867 GLU Chi-restraints excluded: chain E residue 938 LEU Chi-restraints excluded: chain F residue 502 LEU Chi-restraints excluded: chain F residue 534 ASP Chi-restraints excluded: chain F residue 661 THR Chi-restraints excluded: chain F residue 821 THR Chi-restraints excluded: chain F residue 928 GLU Chi-restraints excluded: chain F residue 938 LEU Chi-restraints excluded: chain F residue 1358 VAL Chi-restraints excluded: chain F residue 1375 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 129 optimal weight: 0.0060 chunk 144 optimal weight: 1.9990 chunk 190 optimal weight: 2.9990 chunk 202 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 172 optimal weight: 3.9990 chunk 266 optimal weight: 6.9990 chunk 158 optimal weight: 6.9990 chunk 196 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 255 optimal weight: 0.0370 overall best weight: 1.4080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1381 GLN C1346 ASN E 575 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.137141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.111594 restraints weight = 34127.424| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.79 r_work: 0.3085 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25979 Z= 0.129 Angle : 0.615 10.153 35215 Z= 0.301 Chirality : 0.044 0.303 3972 Planarity : 0.005 0.067 4517 Dihedral : 8.243 86.800 3619 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.08 % Favored : 92.76 % Rotamer: Outliers : 2.65 % Allowed : 16.32 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.34 % 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: -1.04 (0.15), residues: 3134 helix: 0.10 (0.14), residues: 1457 sheet: -0.06 (0.26), residues: 382 loop : -1.78 (0.18), residues: 1295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 543 TYR 0.011 0.001 TYR B 655 PHE 0.012 0.001 PHE F 877 TRP 0.012 0.001 TRP E 865 HIS 0.003 0.001 HIS C 863 Details of bonding type rmsd covalent geometry : bond 0.00311 (25970) covalent geometry : angle 0.61521 (35215) hydrogen bonds : bond 0.03671 ( 912) hydrogen bonds : angle 4.29612 ( 2643) Misc. bond : bond 0.00522 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 246 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 486 GLN cc_start: 0.7147 (OUTLIER) cc_final: 0.6494 (tp40) REVERT: A 586 ARG cc_start: 0.7433 (mpt90) cc_final: 0.6196 (tmm160) REVERT: A 681 VAL cc_start: 0.8451 (p) cc_final: 0.8228 (t) REVERT: B 1384 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7247 (pp20) REVERT: C 424 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7480 (mtp-110) REVERT: C 562 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8705 (tt) REVERT: C 701 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8919 (mt) REVERT: C 833 VAL cc_start: 0.8906 (t) cc_final: 0.8639 (m) REVERT: C 1332 ARG cc_start: 0.7462 (ptm160) cc_final: 0.7201 (ptm160) REVERT: C 1346 ASN cc_start: 0.8321 (OUTLIER) cc_final: 0.7732 (t0) REVERT: C 1390 ARG cc_start: 0.7516 (OUTLIER) cc_final: 0.6941 (mmm160) REVERT: D 683 MET cc_start: 0.9275 (mtm) cc_final: 0.9036 (mtt) REVERT: E 463 CYS cc_start: 0.8453 (m) cc_final: 0.8041 (m) REVERT: E 473 LYS cc_start: 0.7635 (OUTLIER) cc_final: 0.7121 (pttm) REVERT: E 558 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8818 (pt) REVERT: E 867 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8360 (mm-30) REVERT: E 935 ASP cc_start: 0.8124 (t0) cc_final: 0.7338 (p0) REVERT: E 1372 LYS cc_start: 0.6508 (mmtt) cc_final: 0.4696 (pttp) REVERT: F 559 MET cc_start: 0.8691 (ttm) cc_final: 0.8417 (mmm) REVERT: F 576 ARG cc_start: 0.7765 (mtt90) cc_final: 0.7079 (mtm-85) REVERT: F 1332 ARG cc_start: 0.7496 (ttp-170) cc_final: 0.6863 (mpp-170) outliers start: 74 outliers final: 50 residues processed: 305 average time/residue: 0.1885 time to fit residues: 86.4880 Evaluate side-chains 292 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 232 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 455 PHE Chi-restraints excluded: chain A residue 486 GLN Chi-restraints excluded: chain A residue 618 LYS Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 668 ASP Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 821 THR Chi-restraints excluded: chain A residue 937 ILE Chi-restraints excluded: chain A residue 943 LYS Chi-restraints excluded: chain A residue 1375 LEU Chi-restraints excluded: chain A residue 1388 CYS Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 694 VAL Chi-restraints excluded: chain B residue 695 THR Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 821 THR Chi-restraints excluded: chain B residue 867 GLU Chi-restraints excluded: chain B residue 937 ILE Chi-restraints excluded: chain B residue 1375 LEU Chi-restraints excluded: chain B residue 1380 GLU Chi-restraints excluded: chain B residue 1384 GLU Chi-restraints excluded: chain C residue 424 ARG Chi-restraints excluded: chain C residue 486 GLN Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 686 MET Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 821 THR Chi-restraints excluded: chain C residue 886 SER Chi-restraints excluded: chain C residue 1346 ASN Chi-restraints excluded: chain C residue 1390 ARG Chi-restraints excluded: chain D residue 427 SER Chi-restraints excluded: chain D residue 618 LYS Chi-restraints excluded: chain E residue 473 LYS Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 518 ASP Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain E residue 642 ILE Chi-restraints excluded: chain E residue 662 SER Chi-restraints excluded: chain E residue 669 LEU Chi-restraints excluded: chain E residue 701 LEU Chi-restraints excluded: chain E residue 703 THR Chi-restraints excluded: chain E residue 867 GLU Chi-restraints excluded: chain E residue 938 LEU Chi-restraints excluded: chain F residue 502 LEU Chi-restraints excluded: chain F residue 661 THR Chi-restraints excluded: chain F residue 821 THR Chi-restraints excluded: chain F residue 938 LEU Chi-restraints excluded: chain F residue 1358 VAL Chi-restraints excluded: chain F residue 1375 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 129 optimal weight: 9.9990 chunk 213 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 184 optimal weight: 1.9990 chunk 271 optimal weight: 8.9990 chunk 151 optimal weight: 0.9990 chunk 261 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 chunk 205 optimal weight: 1.9990 chunk 177 optimal weight: 5.9990 chunk 198 optimal weight: 4.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 844 GLN C1346 ASN E 575 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.136368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.110754 restraints weight = 34201.079| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.80 r_work: 0.3071 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25979 Z= 0.156 Angle : 0.643 10.710 35215 Z= 0.313 Chirality : 0.045 0.318 3972 Planarity : 0.005 0.076 4517 Dihedral : 8.298 87.886 3619 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.28 % Favored : 92.57 % Rotamer: Outliers : 2.68 % Allowed : 16.71 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.34 % 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: -1.00 (0.15), residues: 3134 helix: 0.13 (0.14), residues: 1459 sheet: -0.02 (0.26), residues: 384 loop : -1.76 (0.18), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 586 TYR 0.028 0.001 TYR B 655 PHE 0.011 0.001 PHE C 530 TRP 0.011 0.001 TRP E 865 HIS 0.004 0.001 HIS E 611 Details of bonding type rmsd covalent geometry : bond 0.00387 (25970) covalent geometry : angle 0.64291 (35215) hydrogen bonds : bond 0.03882 ( 912) hydrogen bonds : angle 4.30814 ( 2643) Misc. bond : bond 0.00549 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 235 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 486 GLN cc_start: 0.7166 (OUTLIER) cc_final: 0.6464 (tp40) REVERT: A 586 ARG cc_start: 0.7467 (mpt90) cc_final: 0.6226 (tmm160) REVERT: A 681 VAL cc_start: 0.8472 (p) cc_final: 0.8246 (t) REVERT: A 729 PHE cc_start: 0.7487 (m-10) cc_final: 0.7248 (m-10) REVERT: B 1384 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7251 (pp20) REVERT: C 424 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7486 (mtp-110) REVERT: C 562 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8716 (tt) REVERT: C 683 MET cc_start: 0.8821 (mtm) cc_final: 0.8600 (mtt) REVERT: C 701 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8998 (mm) REVERT: C 833 VAL cc_start: 0.8922 (t) cc_final: 0.8654 (m) REVERT: C 1332 ARG cc_start: 0.7443 (ptm160) cc_final: 0.7185 (ptm160) REVERT: C 1346 ASN cc_start: 0.8224 (OUTLIER) cc_final: 0.7856 (t0) REVERT: C 1390 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.7080 (mmm160) REVERT: D 683 MET cc_start: 0.9266 (mtm) cc_final: 0.9029 (mtt) REVERT: E 473 LYS cc_start: 0.7696 (OUTLIER) cc_final: 0.7218 (pttm) REVERT: E 558 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8833 (pt) REVERT: E 867 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8378 (mm-30) REVERT: E 935 ASP cc_start: 0.8141 (t0) cc_final: 0.7358 (p0) REVERT: E 1372 LYS cc_start: 0.6448 (mmtt) cc_final: 0.4617 (pttp) REVERT: F 559 MET cc_start: 0.8718 (ttm) cc_final: 0.8464 (mmm) REVERT: F 576 ARG cc_start: 0.7764 (mtt90) cc_final: 0.7074 (mtm-85) REVERT: F 820 PHE cc_start: 0.8176 (m-80) cc_final: 0.7880 (m-80) REVERT: F 1332 ARG cc_start: 0.7506 (ttp-170) cc_final: 0.6853 (mpp-170) outliers start: 75 outliers final: 57 residues processed: 294 average time/residue: 0.1915 time to fit residues: 85.3968 Evaluate side-chains 294 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 227 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 455 PHE Chi-restraints excluded: chain A residue 486 GLN Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 618 LYS Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 668 ASP Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 821 THR Chi-restraints excluded: chain A residue 934 GLU Chi-restraints excluded: chain A residue 937 ILE Chi-restraints excluded: chain A residue 943 LYS Chi-restraints excluded: chain A residue 1358 VAL Chi-restraints excluded: chain A residue 1375 LEU Chi-restraints excluded: chain A residue 1388 CYS Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 457 ILE Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 694 VAL Chi-restraints excluded: chain B residue 695 THR Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 821 THR Chi-restraints excluded: chain B residue 867 GLU Chi-restraints excluded: chain B residue 937 ILE Chi-restraints excluded: chain B residue 1375 LEU Chi-restraints excluded: chain B residue 1380 GLU Chi-restraints excluded: chain B residue 1384 GLU Chi-restraints excluded: chain C residue 424 ARG Chi-restraints excluded: chain C residue 486 GLN Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 686 MET Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 821 THR Chi-restraints excluded: chain C residue 886 SER Chi-restraints excluded: chain C residue 1346 ASN Chi-restraints excluded: chain C residue 1390 ARG Chi-restraints excluded: chain D residue 427 SER Chi-restraints excluded: chain E residue 473 LYS Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 518 ASP Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 642 ILE Chi-restraints excluded: chain E residue 662 SER Chi-restraints excluded: chain E residue 669 LEU Chi-restraints excluded: chain E residue 680 GLU Chi-restraints excluded: chain E residue 701 LEU Chi-restraints excluded: chain E residue 703 THR Chi-restraints excluded: chain E residue 841 THR Chi-restraints excluded: chain E residue 867 GLU Chi-restraints excluded: chain E residue 938 LEU Chi-restraints excluded: chain F residue 502 LEU Chi-restraints excluded: chain F residue 534 ASP Chi-restraints excluded: chain F residue 661 THR Chi-restraints excluded: chain F residue 821 THR Chi-restraints excluded: chain F residue 938 LEU Chi-restraints excluded: chain F residue 1358 VAL Chi-restraints excluded: chain F residue 1375 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 22 optimal weight: 0.9980 chunk 190 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 161 optimal weight: 1.9990 chunk 204 optimal weight: 9.9990 chunk 238 optimal weight: 2.9990 chunk 201 optimal weight: 4.9990 chunk 45 optimal weight: 0.4980 chunk 259 optimal weight: 0.7980 chunk 232 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 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 844 GLN E 575 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.137217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.111745 restraints weight = 34084.412| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.77 r_work: 0.3082 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25979 Z= 0.131 Angle : 0.631 14.133 35215 Z= 0.307 Chirality : 0.044 0.350 3972 Planarity : 0.005 0.065 4517 Dihedral : 8.143 88.904 3615 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.02 % Favored : 92.82 % Rotamer: Outliers : 2.51 % Allowed : 17.00 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.34 % 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: -0.88 (0.15), residues: 3134 helix: 0.21 (0.14), residues: 1472 sheet: 0.03 (0.26), residues: 382 loop : -1.69 (0.18), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 543 TYR 0.017 0.001 TYR C1347 PHE 0.012 0.001 PHE F 877 TRP 0.012 0.001 TRP E 865 HIS 0.003 0.001 HIS E 611 Details of bonding type rmsd covalent geometry : bond 0.00316 (25970) covalent geometry : angle 0.63059 (35215) hydrogen bonds : bond 0.03617 ( 912) hydrogen bonds : angle 4.26564 ( 2643) Misc. bond : bond 0.00530 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 235 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 486 GLN cc_start: 0.7255 (OUTLIER) cc_final: 0.6588 (tp40) REVERT: A 586 ARG cc_start: 0.7467 (mpt90) cc_final: 0.6243 (tmm160) REVERT: A 681 VAL cc_start: 0.8482 (p) cc_final: 0.8244 (t) REVERT: A 729 PHE cc_start: 0.7439 (m-10) cc_final: 0.7216 (m-10) REVERT: A 931 LYS cc_start: 0.8802 (tttt) cc_final: 0.8502 (mmmm) REVERT: B 622 THR cc_start: 0.8196 (OUTLIER) cc_final: 0.7995 (p) REVERT: B 683 MET cc_start: 0.9080 (mtp) cc_final: 0.8829 (mtt) REVERT: B 1384 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7242 (pp20) REVERT: C 424 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7459 (mtp-110) REVERT: C 510 GLU cc_start: 0.9223 (OUTLIER) cc_final: 0.8961 (mp0) REVERT: C 562 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8702 (tt) REVERT: C 683 MET cc_start: 0.8792 (mtm) cc_final: 0.8573 (mtt) REVERT: C 701 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8901 (mt) REVERT: C 833 VAL cc_start: 0.8901 (t) cc_final: 0.8654 (m) REVERT: C 1332 ARG cc_start: 0.7423 (ptm160) cc_final: 0.7175 (ptm160) REVERT: C 1390 ARG cc_start: 0.7419 (OUTLIER) cc_final: 0.6967 (mmm160) REVERT: D 683 MET cc_start: 0.9270 (mtm) cc_final: 0.9045 (mtt) REVERT: E 473 LYS cc_start: 0.7622 (OUTLIER) cc_final: 0.7114 (pttm) REVERT: E 558 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8831 (pt) REVERT: E 935 ASP cc_start: 0.8150 (t0) cc_final: 0.7381 (p0) REVERT: E 1372 LYS cc_start: 0.6430 (mmtt) cc_final: 0.4610 (pttp) REVERT: F 559 MET cc_start: 0.8696 (ttm) cc_final: 0.8451 (mmm) REVERT: F 576 ARG cc_start: 0.7764 (mtt90) cc_final: 0.7096 (mtm-85) REVERT: F 820 PHE cc_start: 0.8173 (m-80) cc_final: 0.7969 (m-80) REVERT: F 1332 ARG cc_start: 0.7463 (ttp-170) cc_final: 0.6832 (mpp-170) outliers start: 70 outliers final: 55 residues processed: 289 average time/residue: 0.2039 time to fit residues: 88.5189 Evaluate side-chains 292 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 227 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 455 PHE Chi-restraints excluded: chain A residue 486 GLN Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 668 ASP Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 821 THR Chi-restraints excluded: chain A residue 934 GLU Chi-restraints excluded: chain A residue 937 ILE Chi-restraints excluded: chain A residue 943 LYS Chi-restraints excluded: chain A residue 1358 VAL Chi-restraints excluded: chain A residue 1375 LEU Chi-restraints excluded: chain A residue 1388 CYS Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 457 ILE Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 622 THR Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 694 VAL Chi-restraints excluded: chain B residue 695 THR Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 821 THR Chi-restraints excluded: chain B residue 867 GLU Chi-restraints excluded: chain B residue 937 ILE Chi-restraints excluded: chain B residue 1370 HIS Chi-restraints excluded: chain B residue 1375 LEU Chi-restraints excluded: chain B residue 1380 GLU Chi-restraints excluded: chain B residue 1384 GLU Chi-restraints excluded: chain C residue 424 ARG Chi-restraints excluded: chain C residue 486 GLN Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 686 MET Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 821 THR Chi-restraints excluded: chain C residue 886 SER Chi-restraints excluded: chain C residue 1390 ARG Chi-restraints excluded: chain D residue 427 SER Chi-restraints excluded: chain E residue 473 LYS Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 642 ILE Chi-restraints excluded: chain E residue 662 SER Chi-restraints excluded: chain E residue 669 LEU Chi-restraints excluded: chain E residue 680 GLU Chi-restraints excluded: chain E residue 701 LEU Chi-restraints excluded: chain E residue 703 THR Chi-restraints excluded: chain E residue 938 LEU Chi-restraints excluded: chain F residue 502 LEU Chi-restraints excluded: chain F residue 661 THR Chi-restraints excluded: chain F residue 821 THR Chi-restraints excluded: chain F residue 938 LEU Chi-restraints excluded: chain F residue 1358 VAL Chi-restraints excluded: chain F residue 1375 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 290 optimal weight: 6.9990 chunk 285 optimal weight: 0.9990 chunk 194 optimal weight: 5.9990 chunk 254 optimal weight: 0.9990 chunk 190 optimal weight: 0.9990 chunk 196 optimal weight: 0.0010 chunk 149 optimal weight: 2.9990 chunk 176 optimal weight: 0.7980 chunk 215 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 171 optimal weight: 4.9990 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1345 GLN C1346 ASN D 900 HIS E 434 HIS E 575 ASN F 519 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.139848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.114357 restraints weight = 34024.118| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.75 r_work: 0.3127 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 25979 Z= 0.105 Angle : 0.591 12.225 35215 Z= 0.289 Chirality : 0.043 0.287 3972 Planarity : 0.004 0.061 4517 Dihedral : 7.626 87.166 3612 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.99 % Favored : 92.85 % Rotamer: Outliers : 1.90 % Allowed : 17.57 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.34 % 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: -0.62 (0.16), residues: 3134 helix: 0.42 (0.14), residues: 1481 sheet: 0.11 (0.26), residues: 384 loop : -1.55 (0.18), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 543 TYR 0.023 0.001 TYR B 655 PHE 0.014 0.001 PHE F 877 TRP 0.011 0.001 TRP E 865 HIS 0.003 0.001 HIS C 863 Details of bonding type rmsd covalent geometry : bond 0.00243 (25970) covalent geometry : angle 0.59074 (35215) hydrogen bonds : bond 0.03040 ( 912) hydrogen bonds : angle 4.14679 ( 2643) Misc. bond : bond 0.00387 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 271 time to evaluate : 1.099 Fit side-chains REVERT: A 486 GLN cc_start: 0.7134 (OUTLIER) cc_final: 0.6693 (tp40) REVERT: A 586 ARG cc_start: 0.7422 (mpt90) cc_final: 0.7068 (mmt180) REVERT: A 681 VAL cc_start: 0.8399 (p) cc_final: 0.8173 (t) REVERT: A 931 LYS cc_start: 0.8786 (tttt) cc_final: 0.8414 (mmmm) REVERT: B 819 LYS cc_start: 0.8035 (pttm) cc_final: 0.7766 (ptmt) REVERT: B 1384 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7188 (pp20) REVERT: C 510 GLU cc_start: 0.9225 (OUTLIER) cc_final: 0.8998 (mp0) REVERT: C 562 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8655 (tt) REVERT: C 683 MET cc_start: 0.8740 (mtm) cc_final: 0.8523 (mtt) REVERT: C 701 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8885 (mt) REVERT: C 833 VAL cc_start: 0.8849 (t) cc_final: 0.8626 (m) REVERT: C 939 LYS cc_start: 0.8404 (tttm) cc_final: 0.7947 (mppt) REVERT: C 1332 ARG cc_start: 0.7390 (ptm160) cc_final: 0.7183 (ptm160) REVERT: C 1345 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7742 (pt0) REVERT: C 1390 ARG cc_start: 0.7342 (OUTLIER) cc_final: 0.6975 (mmm160) REVERT: D 683 MET cc_start: 0.9255 (mtm) cc_final: 0.9027 (mtt) REVERT: D 826 ASP cc_start: 0.7841 (p0) cc_final: 0.7239 (t0) REVERT: D 1338 LYS cc_start: 0.8503 (tmtt) cc_final: 0.8209 (tttt) REVERT: E 473 LYS cc_start: 0.7350 (OUTLIER) cc_final: 0.6915 (ptpp) REVERT: E 558 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8806 (pt) REVERT: E 559 MET cc_start: 0.8797 (tpp) cc_final: 0.8470 (tpt) REVERT: E 844 GLN cc_start: 0.7704 (mm-40) cc_final: 0.7426 (mm-40) REVERT: E 935 ASP cc_start: 0.8116 (t0) cc_final: 0.7378 (p0) REVERT: E 1372 LYS cc_start: 0.6415 (mmtt) cc_final: 0.4663 (pttp) REVERT: F 576 ARG cc_start: 0.7760 (mtt90) cc_final: 0.7102 (mtm-85) REVERT: F 1332 ARG cc_start: 0.7415 (ttp-170) cc_final: 0.6813 (mpp-170) outliers start: 53 outliers final: 32 residues processed: 313 average time/residue: 0.1821 time to fit residues: 85.4917 Evaluate side-chains 286 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 245 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 455 PHE Chi-restraints excluded: chain A residue 486 GLN Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 668 ASP Chi-restraints excluded: chain A residue 821 THR Chi-restraints excluded: chain A residue 1375 LEU Chi-restraints excluded: chain A residue 1388 CYS Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 694 VAL Chi-restraints excluded: chain B residue 695 THR Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 821 THR Chi-restraints excluded: chain B residue 937 ILE Chi-restraints excluded: chain B residue 1370 HIS Chi-restraints excluded: chain B residue 1384 GLU Chi-restraints excluded: chain C residue 486 GLN Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 686 MET Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 886 SER Chi-restraints excluded: chain C residue 1345 GLN Chi-restraints excluded: chain C residue 1390 ARG Chi-restraints excluded: chain D residue 427 SER Chi-restraints excluded: chain E residue 473 LYS Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain E residue 642 ILE Chi-restraints excluded: chain E residue 669 LEU Chi-restraints excluded: chain E residue 938 LEU Chi-restraints excluded: chain F residue 502 LEU Chi-restraints excluded: chain F residue 661 THR Chi-restraints excluded: chain F residue 821 THR Chi-restraints excluded: chain F residue 938 LEU Chi-restraints excluded: chain F residue 1375 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 148 optimal weight: 0.0040 chunk 255 optimal weight: 4.9990 chunk 33 optimal weight: 0.0060 chunk 118 optimal weight: 2.9990 chunk 231 optimal weight: 0.9990 chunk 164 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 chunk 85 optimal weight: 3.9990 chunk 163 optimal weight: 6.9990 chunk 201 optimal weight: 1.9990 overall best weight: 1.2014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 611 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1346 ASN E 575 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.138817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.113527 restraints weight = 33879.155| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.76 r_work: 0.3108 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 25979 Z= 0.121 Angle : 0.626 16.590 35215 Z= 0.304 Chirality : 0.044 0.289 3972 Planarity : 0.004 0.060 4517 Dihedral : 7.646 85.799 3609 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.86 % Favored : 92.98 % Rotamer: Outliers : 1.61 % Allowed : 18.32 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.34 % 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: -0.56 (0.16), residues: 3134 helix: 0.47 (0.14), residues: 1478 sheet: 0.14 (0.26), residues: 384 loop : -1.52 (0.18), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 543 TYR 0.021 0.001 TYR B 655 PHE 0.017 0.001 PHE F 820 TRP 0.013 0.001 TRP F 505 HIS 0.008 0.001 HIS A 611 Details of bonding type rmsd covalent geometry : bond 0.00288 (25970) covalent geometry : angle 0.62613 (35215) hydrogen bonds : bond 0.03259 ( 912) hydrogen bonds : angle 4.15323 ( 2643) Misc. bond : bond 0.00551 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6263.70 seconds wall clock time: 107 minutes 47.22 seconds (6467.22 seconds total)