Starting phenix.real_space_refine on Sun Jun 22 00:54:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h3h_34468/06_2025/8h3h_34468_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h3h_34468/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8h3h_34468/06_2025/8h3h_34468.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h3h_34468/06_2025/8h3h_34468.map" model { file = "/net/cci-nas-00/data/ceres_data/8h3h_34468/06_2025/8h3h_34468_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h3h_34468/06_2025/8h3h_34468_neut.cif" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 16.41, per 1000 atoms: 0.65 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: 6.24 Conformation dependent library (CDL) restraints added in 3.5 seconds 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: 2.63 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: 7.97 Time building geometry restraints manager: 7.29 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: 1.570 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: 1.060 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 57.040 Find NCS groups from input model: 1.730 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.600 ------------------------------------------------------------------------------- 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 : 12.44 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.017 0.001 TRP E 505 HIS 0.006 0.001 HIS F 861 PHE 0.013 0.002 PHE B 724 TYR 0.008 0.001 TYR A 466 ARG 0.010 0.000 ARG C 576 Details of bonding type rmsd hydrogen bonds : bond 0.20343 ( 912) hydrogen bonds : angle 6.85135 ( 2643) covalent geometry : bond 0.00686 (25970) covalent geometry : angle 0.92415 (35215) 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 : 2.884 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: 0.4514 time to fit residues: 279.7610 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 : 2.914 ------------------------------------------------------------------------------- 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 265 optimal weight: 5.9990 chunk 237 optimal weight: 7.9990 chunk 132 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 160 optimal weight: 6.9990 chunk 127 optimal weight: 0.3980 chunk 246 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 149 optimal weight: 4.9990 chunk 183 optimal weight: 0.9990 chunk 285 optimal weight: 0.3980 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 C 673 ASN C 711 ASN C1346 ASN D 611 HIS D 657 GLN E 575 ASN E 710 GLN E1335 ASN F 922 GLN F1345 GLN F1377 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.136162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.110888 restraints weight = 34167.806| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.82 r_work: 0.3066 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.1273 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= 0.151 Angle : 0.685 14.028 35215 Z= 0.339 Chirality : 0.045 0.271 3972 Planarity : 0.005 0.061 4517 Dihedral : 10.678 92.673 3736 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.75 % Favored : 92.09 % Rotamer: Outliers : 2.54 % Allowed : 12.67 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.14), residues: 3134 helix: -1.35 (0.13), residues: 1458 sheet: -0.74 (0.25), residues: 385 loop : -2.52 (0.16), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 505 HIS 0.004 0.001 HIS E 815 PHE 0.019 0.001 PHE E 791 TYR 0.016 0.001 TYR A 448 ARG 0.006 0.000 ARG F 424 Details of bonding type rmsd hydrogen bonds : bond 0.04907 ( 912) hydrogen bonds : angle 4.92194 ( 2643) covalent geometry : bond 0.00361 (25970) covalent geometry : angle 0.68520 (35215) Misc. bond : bond 0.00521 ( 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 353 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 282 time to evaluate : 3.003 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 586 ARG cc_start: 0.7474 (mpt90) cc_final: 0.6245 (tmm160) REVERT: A 666 GLN cc_start: 0.5839 (OUTLIER) cc_final: 0.5111 (mt0) REVERT: A 681 VAL cc_start: 0.8521 (p) cc_final: 0.8212 (t) REVERT: B 519 GLN cc_start: 0.8554 (tt0) cc_final: 0.8322 (mt0) REVERT: B 683 MET cc_start: 0.9157 (mtp) cc_final: 0.8952 (mtt) REVERT: B 786 TYR cc_start: 0.6522 (OUTLIER) cc_final: 0.5656 (t80) REVERT: B 1384 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7344 (pp20) REVERT: C 490 ARG cc_start: 0.7862 (ttm110) cc_final: 0.7336 (tpt170) REVERT: C 562 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8714 (tt) REVERT: C 1332 ARG cc_start: 0.7573 (ptm160) cc_final: 0.7364 (ptm160) REVERT: C 1346 ASN cc_start: 0.8448 (OUTLIER) cc_final: 0.7975 (t0) REVERT: C 1390 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.7190 (mmm160) REVERT: D 683 MET cc_start: 0.9336 (mtm) cc_final: 0.8934 (mtt) REVERT: D 847 ARG cc_start: 0.8125 (ttm110) cc_final: 0.7899 (ttp-110) REVERT: D 1338 LYS cc_start: 0.8530 (tttt) cc_final: 0.8237 (tmtt) REVERT: E 558 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.8912 (pt) REVERT: E 683 MET cc_start: 0.8967 (mtp) cc_final: 0.8594 (mtt) REVERT: E 1372 LYS cc_start: 0.6593 (mmtt) cc_final: 0.4740 (pttp) REVERT: F 576 ARG cc_start: 0.7763 (mtt90) cc_final: 0.7052 (mtm-85) REVERT: F 867 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8227 (mm-30) REVERT: F 1332 ARG cc_start: 0.7598 (ttp-170) cc_final: 0.6923 (mpp-170) outliers start: 71 outliers final: 29 residues processed: 336 average time/residue: 0.4455 time to fit residues: 225.0317 Evaluate side-chains 274 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 237 time to evaluate : 3.478 ------------------------------------------------------------------------------- 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 665 LEU Chi-restraints excluded: chain A residue 666 GLN Chi-restraints excluded: chain A residue 694 VAL 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 1360 SER 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 1380 GLU 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 669 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 C residue 1390 ARG 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 630 ASN 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 122 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 270 optimal weight: 0.0060 chunk 130 optimal weight: 2.9990 chunk 301 optimal weight: 1.9990 chunk 188 optimal weight: 5.9990 chunk 133 optimal weight: 6.9990 chunk 290 optimal weight: 0.7980 chunk 246 optimal weight: 6.9990 chunk 92 optimal weight: 6.9990 overall best weight: 1.3600 ------------------------------------------------------------------------------- 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 F 710 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.137181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.112173 restraints weight = 34252.177| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.82 r_work: 0.3085 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.1563 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= 0.132 Angle : 0.634 11.738 35215 Z= 0.312 Chirality : 0.044 0.255 3972 Planarity : 0.005 0.059 4517 Dihedral : 9.011 85.608 3636 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.28 % Favored : 92.57 % Rotamer: Outliers : 2.58 % Allowed : 13.78 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.15), residues: 3134 helix: -0.71 (0.13), residues: 1454 sheet: -0.49 (0.25), residues: 390 loop : -2.24 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 865 HIS 0.004 0.001 HIS F 861 PHE 0.015 0.001 PHE E 791 TYR 0.013 0.001 TYR A 448 ARG 0.004 0.000 ARG B 424 Details of bonding type rmsd hydrogen bonds : bond 0.04170 ( 912) hydrogen bonds : angle 4.59733 ( 2643) covalent geometry : bond 0.00311 (25970) covalent geometry : angle 0.63354 (35215) Misc. bond : bond 0.00453 ( 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 329 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 257 time to evaluate : 4.752 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 461 ARG cc_start: 0.8004 (mmp-170) cc_final: 0.7462 (mmp-170) REVERT: A 586 ARG cc_start: 0.7516 (mpt90) cc_final: 0.6260 (tmm160) REVERT: A 681 VAL cc_start: 0.8486 (p) cc_final: 0.8223 (t) REVERT: B 683 MET cc_start: 0.9149 (mtp) cc_final: 0.8901 (mtt) REVERT: B 720 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8506 (tt) REVERT: B 786 TYR cc_start: 0.6612 (OUTLIER) cc_final: 0.5716 (t80) REVERT: B 1384 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7258 (pp20) REVERT: C 701 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8934 (mt) REVERT: C 1332 ARG cc_start: 0.7527 (ptm160) cc_final: 0.7318 (ptm160) REVERT: C 1346 ASN cc_start: 0.8345 (t0) cc_final: 0.8090 (t0) REVERT: D 683 MET cc_start: 0.9291 (mtm) cc_final: 0.9056 (mtt) REVERT: D 847 ARG cc_start: 0.8267 (ttm110) cc_final: 0.8040 (ttp-110) REVERT: E 463 CYS cc_start: 0.8496 (m) cc_final: 0.8145 (m) REVERT: E 558 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.8863 (pt) REVERT: E 559 MET cc_start: 0.8644 (ttm) cc_final: 0.8096 (ttp) REVERT: E 1372 LYS cc_start: 0.6526 (mmtt) cc_final: 0.4744 (pttp) REVERT: F 576 ARG cc_start: 0.7781 (mtt90) cc_final: 0.7107 (mtm-85) REVERT: F 616 ASN cc_start: 0.7439 (OUTLIER) cc_final: 0.7048 (p0) REVERT: F 1332 ARG cc_start: 0.7484 (ttp-170) cc_final: 0.6880 (mpp-170) REVERT: F 1360 SER cc_start: 0.9044 (OUTLIER) cc_final: 0.8680 (p) outliers start: 72 outliers final: 42 residues processed: 311 average time/residue: 0.7481 time to fit residues: 379.0061 Evaluate side-chains 284 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 235 time to evaluate : 4.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 1384 GLU Chi-restraints excluded: chain C residue 486 GLN Chi-restraints excluded: chain C residue 515 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 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 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 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 1358 VAL Chi-restraints excluded: chain F residue 1360 SER 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 9 optimal weight: 8.9990 chunk 221 optimal weight: 7.9990 chunk 293 optimal weight: 6.9990 chunk 217 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 124 optimal weight: 6.9990 chunk 171 optimal weight: 7.9990 chunk 158 optimal weight: 6.9990 chunk 249 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 72 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 546 GLN E 575 ASN E1366 HIS F 808 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.131100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.105145 restraints weight = 34564.578| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.90 r_work: 0.2982 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.087 25979 Z= 0.305 Angle : 0.813 14.177 35215 Z= 0.397 Chirality : 0.052 0.360 3972 Planarity : 0.006 0.067 4517 Dihedral : 9.413 81.806 3622 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.74 % Favored : 91.10 % Rotamer: Outliers : 3.29 % Allowed : 15.68 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.15), residues: 3134 helix: -0.75 (0.13), residues: 1464 sheet: -0.32 (0.26), residues: 380 loop : -2.23 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 615 HIS 0.007 0.001 HIS F 861 PHE 0.016 0.002 PHE C 530 TYR 0.011 0.002 TYR F 448 ARG 0.005 0.001 ARG D 851 Details of bonding type rmsd hydrogen bonds : bond 0.05743 ( 912) hydrogen bonds : angle 4.81594 ( 2643) covalent geometry : bond 0.00769 (25970) covalent geometry : angle 0.81263 (35215) Misc. bond : bond 0.00860 ( 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 334 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 242 time to evaluate : 4.362 Fit side-chains revert: symmetry clash REVERT: A 447 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8341 (tp) REVERT: A 586 ARG cc_start: 0.7521 (mpt90) cc_final: 0.6326 (tmm160) REVERT: A 681 VAL cc_start: 0.8569 (p) cc_final: 0.8284 (t) REVERT: A 943 LYS cc_start: 0.6703 (OUTLIER) cc_final: 0.4846 (mptt) REVERT: B 453 GLU cc_start: 0.8559 (pp20) cc_final: 0.8268 (pp20) REVERT: B 614 ASP cc_start: 0.8436 (OUTLIER) cc_final: 0.8130 (p0) REVERT: B 683 MET cc_start: 0.9158 (mtp) cc_final: 0.8894 (mtt) REVERT: B 786 TYR cc_start: 0.6721 (OUTLIER) cc_final: 0.5681 (t80) REVERT: B 1384 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7332 (pp20) REVERT: C 1332 ARG cc_start: 0.7554 (ptm160) cc_final: 0.7316 (ptm160) REVERT: D 591 ASP cc_start: 0.8591 (p0) cc_final: 0.8126 (p0) REVERT: D 683 MET cc_start: 0.9354 (mtm) cc_final: 0.8965 (mtt) REVERT: E 463 CYS cc_start: 0.8638 (m) cc_final: 0.8376 (m) REVERT: E 558 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.8888 (pt) REVERT: E 559 MET cc_start: 0.8842 (ttm) cc_final: 0.8224 (ttp) REVERT: F 576 ARG cc_start: 0.7821 (mtt90) cc_final: 0.7031 (mtm-85) REVERT: F 820 PHE cc_start: 0.8385 (m-80) cc_final: 0.8084 (m-80) REVERT: F 1332 ARG cc_start: 0.7498 (ttp-170) cc_final: 0.6803 (mpp-170) outliers start: 92 outliers final: 59 residues processed: 319 average time/residue: 0.4473 time to fit residues: 219.1740 Evaluate side-chains 291 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 226 time to evaluate : 2.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 455 PHE 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 694 VAL 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 438 LEU 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 614 ASP 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 786 TYR Chi-restraints excluded: chain B residue 821 THR 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 1358 VAL 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 667 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 D residue 427 SER Chi-restraints excluded: chain D residue 618 LYS Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 527 ILE Chi-restraints excluded: chain E residue 533 ILE Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain E residue 575 ASN Chi-restraints excluded: chain E residue 642 ILE Chi-restraints excluded: chain E residue 662 SER 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 1358 VAL 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 194 optimal weight: 2.9990 chunk 309 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 chunk 305 optimal weight: 3.9990 chunk 197 optimal weight: 1.9990 chunk 286 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 575 ASN E1351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.135542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.110478 restraints weight = 34202.589| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.77 r_work: 0.3062 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.1741 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= 0.136 Angle : 0.647 11.073 35215 Z= 0.318 Chirality : 0.045 0.350 3972 Planarity : 0.005 0.064 4517 Dihedral : 8.792 81.471 3622 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.15 % Favored : 92.69 % Rotamer: Outliers : 2.79 % Allowed : 17.00 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.15), residues: 3134 helix: -0.35 (0.14), residues: 1460 sheet: -0.25 (0.26), residues: 382 loop : -2.01 (0.17), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 505 HIS 0.004 0.001 HIS C 863 PHE 0.013 0.001 PHE F 877 TYR 0.013 0.001 TYR A 448 ARG 0.009 0.000 ARG C 847 Details of bonding type rmsd hydrogen bonds : bond 0.04083 ( 912) hydrogen bonds : angle 4.52965 ( 2643) covalent geometry : bond 0.00322 (25970) covalent geometry : angle 0.64671 (35215) Misc. bond : bond 0.00514 ( 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 319 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 241 time to evaluate : 3.271 Fit side-chains revert: symmetry clash REVERT: A 586 ARG cc_start: 0.7450 (mpt90) cc_final: 0.6266 (tmm160) REVERT: A 666 GLN cc_start: 0.5929 (pt0) cc_final: 0.5532 (pt0) REVERT: A 681 VAL cc_start: 0.8495 (p) cc_final: 0.8244 (t) REVERT: B 614 ASP cc_start: 0.8384 (OUTLIER) cc_final: 0.8050 (p0) REVERT: B 1384 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7275 (pp20) REVERT: C 424 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.7989 (mtp-110) REVERT: C 562 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8734 (tt) REVERT: C 1332 ARG cc_start: 0.7524 (ptm160) cc_final: 0.7286 (ptm160) REVERT: C 1390 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.7411 (mmm160) REVERT: D 683 MET cc_start: 0.9280 (mtm) cc_final: 0.9022 (mtt) REVERT: E 463 CYS cc_start: 0.8514 (m) cc_final: 0.8203 (m) REVERT: E 473 LYS cc_start: 0.7696 (OUTLIER) cc_final: 0.7079 (pttt) REVERT: E 558 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8860 (pt) REVERT: E 559 MET cc_start: 0.8695 (ttm) cc_final: 0.8049 (ttp) REVERT: E 867 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8305 (mm-30) REVERT: E 1372 LYS cc_start: 0.6657 (mmtt) cc_final: 0.4795 (pttp) REVERT: F 559 MET cc_start: 0.8726 (ttm) cc_final: 0.8449 (mmm) REVERT: F 576 ARG cc_start: 0.7740 (mtt90) cc_final: 0.7061 (mtm-85) REVERT: F 1332 ARG cc_start: 0.7429 (ttp-170) cc_final: 0.6824 (mpp-170) outliers start: 78 outliers final: 42 residues processed: 300 average time/residue: 0.4738 time to fit residues: 216.8046 Evaluate side-chains 273 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 223 time to evaluate : 3.095 ------------------------------------------------------------------------------- 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 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 614 ASP Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 695 THR 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 686 MET 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 427 SER 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 683 MET 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 31 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 181 optimal weight: 5.9990 chunk 251 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 228 optimal weight: 4.9990 chunk 187 optimal weight: 4.9990 chunk 277 optimal weight: 0.0070 chunk 119 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 296 optimal weight: 3.9990 overall best weight: 1.9804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 630 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 = 0.3562 r_free = 0.3562 target = 0.135203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.109878 restraints weight = 34075.168| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.76 r_work: 0.3056 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 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 : 0.004 0.053 25979 Z= 0.157 Angle : 0.654 10.001 35215 Z= 0.320 Chirality : 0.046 0.280 3972 Planarity : 0.005 0.066 4517 Dihedral : 8.580 84.175 3620 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.31 % Favored : 92.53 % Rotamer: Outliers : 2.93 % Allowed : 17.04 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.15), residues: 3134 helix: -0.19 (0.14), residues: 1459 sheet: -0.14 (0.26), residues: 384 loop : -1.91 (0.17), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 865 HIS 0.004 0.001 HIS F 861 PHE 0.012 0.001 PHE F 877 TYR 0.010 0.001 TYR A 448 ARG 0.007 0.000 ARG C 586 Details of bonding type rmsd hydrogen bonds : bond 0.04103 ( 912) hydrogen bonds : angle 4.45649 ( 2643) covalent geometry : bond 0.00388 (25970) covalent geometry : angle 0.65401 (35215) Misc. bond : bond 0.00539 ( 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 325 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 243 time to evaluate : 2.858 Fit side-chains revert: symmetry clash REVERT: A 580 ILE cc_start: 0.8842 (OUTLIER) cc_final: 0.8470 (pt) REVERT: A 586 ARG cc_start: 0.7495 (mpt90) cc_final: 0.6283 (tmm160) REVERT: A 666 GLN cc_start: 0.5921 (pt0) cc_final: 0.5563 (pt0) REVERT: A 681 VAL cc_start: 0.8493 (p) cc_final: 0.8249 (t) REVERT: A 931 LYS cc_start: 0.8795 (tttt) cc_final: 0.8489 (mmmm) REVERT: A 943 LYS cc_start: 0.6672 (OUTLIER) cc_final: 0.4794 (mptt) REVERT: B 614 ASP cc_start: 0.8379 (OUTLIER) cc_final: 0.8090 (p0) REVERT: B 1384 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7368 (pp20) REVERT: C 424 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.7874 (mtp-110) REVERT: C 562 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8742 (tt) REVERT: C 833 VAL cc_start: 0.8937 (t) cc_final: 0.8667 (m) REVERT: C 1332 ARG cc_start: 0.7488 (ptm160) cc_final: 0.7229 (ptm160) REVERT: C 1390 ARG cc_start: 0.7696 (OUTLIER) cc_final: 0.7398 (mmm160) REVERT: D 683 MET cc_start: 0.9295 (mtm) cc_final: 0.9046 (mtt) REVERT: E 463 CYS cc_start: 0.8511 (m) cc_final: 0.8190 (m) REVERT: E 473 LYS cc_start: 0.7732 (OUTLIER) cc_final: 0.7096 (pttt) REVERT: E 558 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8865 (pt) REVERT: E 559 MET cc_start: 0.8698 (ttm) cc_final: 0.8063 (ttp) REVERT: E 867 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8410 (mm-30) REVERT: E 1372 LYS cc_start: 0.6549 (mmtt) cc_final: 0.4700 (pttp) REVERT: F 559 MET cc_start: 0.8724 (ttm) cc_final: 0.8458 (mmm) REVERT: F 576 ARG cc_start: 0.7739 (mtt90) cc_final: 0.7031 (mtm-85) REVERT: F 820 PHE cc_start: 0.8185 (m-80) cc_final: 0.7888 (m-80) REVERT: F 1332 ARG cc_start: 0.7434 (ttp-170) cc_final: 0.6808 (mpp-170) REVERT: F 1375 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7849 (tt) outliers start: 82 outliers final: 55 residues processed: 308 average time/residue: 0.4206 time to fit residues: 195.3886 Evaluate side-chains 290 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 224 time to evaluate : 2.796 ------------------------------------------------------------------------------- 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 533 ILE Chi-restraints excluded: chain A residue 580 ILE 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 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 614 ASP 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 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 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 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 427 SER Chi-restraints excluded: chain D residue 618 LYS Chi-restraints excluded: chain E residue 473 LYS Chi-restraints excluded: chain E residue 527 ILE 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 683 MET 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 125 optimal weight: 5.9990 chunk 224 optimal weight: 9.9990 chunk 194 optimal weight: 0.5980 chunk 114 optimal weight: 3.9990 chunk 201 optimal weight: 0.0070 chunk 150 optimal weight: 3.9990 chunk 153 optimal weight: 0.8980 chunk 309 optimal weight: 5.9990 chunk 289 optimal weight: 0.2980 chunk 151 optimal weight: 5.9990 chunk 253 optimal weight: 7.9990 overall best weight: 1.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 575 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.137470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.112368 restraints weight = 34105.639| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.73 r_work: 0.3090 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25979 Z= 0.119 Angle : 0.609 10.167 35215 Z= 0.298 Chirality : 0.044 0.303 3972 Planarity : 0.005 0.068 4517 Dihedral : 8.199 87.061 3620 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.86 % Favored : 92.98 % Rotamer: Outliers : 2.51 % Allowed : 17.93 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.15), residues: 3134 helix: 0.06 (0.14), residues: 1467 sheet: -0.04 (0.26), residues: 384 loop : -1.76 (0.18), residues: 1283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 865 HIS 0.003 0.001 HIS C 863 PHE 0.014 0.001 PHE F 877 TYR 0.019 0.001 TYR B 655 ARG 0.006 0.000 ARG E1367 Details of bonding type rmsd hydrogen bonds : bond 0.03499 ( 912) hydrogen bonds : angle 4.31876 ( 2643) covalent geometry : bond 0.00280 (25970) covalent geometry : angle 0.60863 (35215) Misc. bond : bond 0.00408 ( 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 319 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 249 time to evaluate : 2.923 Fit side-chains revert: symmetry clash REVERT: A 580 ILE cc_start: 0.8793 (OUTLIER) cc_final: 0.8442 (pt) REVERT: A 586 ARG cc_start: 0.7462 (mpt90) cc_final: 0.6268 (tmm160) REVERT: A 666 GLN cc_start: 0.5873 (pt0) cc_final: 0.5538 (pt0) REVERT: A 681 VAL cc_start: 0.8471 (p) cc_final: 0.8233 (t) REVERT: A 931 LYS cc_start: 0.8791 (tttt) cc_final: 0.8545 (mmmm) REVERT: B 614 ASP cc_start: 0.8342 (OUTLIER) cc_final: 0.7939 (p0) REVERT: B 683 MET cc_start: 0.9056 (mtp) cc_final: 0.8797 (mtt) REVERT: B 839 GLU cc_start: 0.8979 (OUTLIER) cc_final: 0.8715 (mp0) REVERT: B 1384 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7282 (pp20) REVERT: C 424 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7489 (mtp-110) REVERT: C 562 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8714 (tt) REVERT: C 833 VAL cc_start: 0.8899 (t) cc_final: 0.8655 (m) REVERT: C 1332 ARG cc_start: 0.7455 (ptm160) cc_final: 0.7202 (ptm160) REVERT: C 1390 ARG cc_start: 0.7541 (OUTLIER) cc_final: 0.7284 (mmm160) REVERT: D 683 MET cc_start: 0.9274 (mtm) cc_final: 0.9044 (mtt) REVERT: E 473 LYS cc_start: 0.7555 (OUTLIER) cc_final: 0.7128 (ptpp) REVERT: E 558 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8834 (pt) REVERT: E 867 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8401 (mm-30) REVERT: E 1372 LYS cc_start: 0.6526 (mmtt) cc_final: 0.4649 (pttp) REVERT: F 559 MET cc_start: 0.8691 (ttm) cc_final: 0.8446 (mmm) REVERT: F 576 ARG cc_start: 0.7776 (mtt90) cc_final: 0.7094 (mtm-85) REVERT: F 680 GLU cc_start: 0.7126 (mm-30) cc_final: 0.6923 (mm-30) REVERT: F 820 PHE cc_start: 0.8135 (m-80) cc_final: 0.7933 (m-80) REVERT: F 1332 ARG cc_start: 0.7456 (ttp-170) cc_final: 0.6855 (mpp-170) outliers start: 70 outliers final: 40 residues processed: 304 average time/residue: 0.4155 time to fit residues: 191.0586 Evaluate side-chains 279 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 229 time to evaluate : 2.909 ------------------------------------------------------------------------------- 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 580 ILE 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 1375 LEU Chi-restraints excluded: chain A residue 1388 CYS 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 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 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 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 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 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 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 661 THR Chi-restraints excluded: chain F residue 821 THR Chi-restraints excluded: chain F residue 938 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 167 optimal weight: 2.9990 chunk 214 optimal weight: 0.9990 chunk 150 optimal weight: 2.9990 chunk 161 optimal weight: 0.9990 chunk 217 optimal weight: 7.9990 chunk 286 optimal weight: 0.0870 chunk 48 optimal weight: 7.9990 chunk 190 optimal weight: 2.9990 chunk 309 optimal weight: 1.9990 chunk 293 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 overall best weight: 1.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 575 ASN F 519 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.137645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.112655 restraints weight = 34006.354| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.81 r_work: 0.3088 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25979 Z= 0.121 Angle : 0.618 13.066 35215 Z= 0.301 Chirality : 0.044 0.320 3972 Planarity : 0.005 0.072 4517 Dihedral : 8.037 89.990 3615 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.24 % Favored : 92.60 % Rotamer: Outliers : 2.51 % Allowed : 17.93 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.15), residues: 3134 helix: 0.21 (0.14), residues: 1471 sheet: 0.04 (0.26), residues: 385 loop : -1.66 (0.18), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 865 HIS 0.003 0.001 HIS F 861 PHE 0.015 0.001 PHE A 729 TYR 0.010 0.001 TYR A 448 ARG 0.006 0.000 ARG C 847 Details of bonding type rmsd hydrogen bonds : bond 0.03447 ( 912) hydrogen bonds : angle 4.24376 ( 2643) covalent geometry : bond 0.00288 (25970) covalent geometry : angle 0.61843 (35215) Misc. bond : bond 0.00427 ( 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 312 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 242 time to evaluate : 3.134 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 461 ARG cc_start: 0.7950 (mmp-170) cc_final: 0.7422 (mmp-170) REVERT: A 586 ARG cc_start: 0.7452 (mpt90) cc_final: 0.6263 (tmm160) REVERT: A 681 VAL cc_start: 0.8454 (p) cc_final: 0.8214 (t) REVERT: A 931 LYS cc_start: 0.8790 (tttt) cc_final: 0.8491 (mmmm) REVERT: B 614 ASP cc_start: 0.8365 (OUTLIER) cc_final: 0.8036 (p0) REVERT: B 683 MET cc_start: 0.9058 (mtp) cc_final: 0.8812 (mtt) REVERT: B 819 LYS cc_start: 0.8183 (pttm) cc_final: 0.7982 (ptmt) REVERT: B 839 GLU cc_start: 0.8994 (OUTLIER) cc_final: 0.8749 (mp0) REVERT: B 1384 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.7270 (pp20) REVERT: C 424 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7501 (mtp-110) REVERT: C 562 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8713 (tt) REVERT: C 833 VAL cc_start: 0.8899 (t) cc_final: 0.8662 (m) REVERT: C 939 LYS cc_start: 0.8419 (tttm) cc_final: 0.7967 (mppt) REVERT: C 1332 ARG cc_start: 0.7467 (ptm160) cc_final: 0.7230 (ptm160) REVERT: C 1346 ASN cc_start: 0.8408 (t0) cc_final: 0.8188 (t0) REVERT: C 1390 ARG cc_start: 0.7586 (OUTLIER) cc_final: 0.7380 (mmm160) REVERT: D 683 MET cc_start: 0.9271 (mtm) cc_final: 0.9042 (mtt) REVERT: E 473 LYS cc_start: 0.7569 (OUTLIER) cc_final: 0.7204 (pttm) REVERT: E 558 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8810 (pt) REVERT: E 935 ASP cc_start: 0.8144 (t0) cc_final: 0.7363 (p0) REVERT: E 1372 LYS cc_start: 0.6467 (mmtt) cc_final: 0.4618 (pttp) REVERT: E 1377 GLN cc_start: 0.7637 (mp10) cc_final: 0.7402 (mp10) REVERT: F 559 MET cc_start: 0.8693 (ttm) cc_final: 0.8458 (mmm) REVERT: F 576 ARG cc_start: 0.7807 (mtt90) cc_final: 0.7108 (mtm-85) REVERT: F 820 PHE cc_start: 0.8166 (m-80) cc_final: 0.7892 (m-80) REVERT: F 1332 ARG cc_start: 0.7455 (ttp-170) cc_final: 0.6835 (mpp-170) outliers start: 70 outliers final: 48 residues processed: 297 average time/residue: 0.4368 time to fit residues: 196.8062 Evaluate side-chains 287 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 231 time to evaluate : 3.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 455 PHE Chi-restraints excluded: chain A residue 533 ILE 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 943 LYS Chi-restraints excluded: chain A residue 1375 LEU Chi-restraints excluded: chain A residue 1388 CYS 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 614 ASP 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 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 1370 HIS Chi-restraints excluded: chain B residue 1375 LEU 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 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 D residue 559 MET Chi-restraints excluded: chain E residue 473 LYS 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 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 223 optimal weight: 3.9990 chunk 215 optimal weight: 2.9990 chunk 228 optimal weight: 4.9990 chunk 178 optimal weight: 7.9990 chunk 240 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 211 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 286 optimal weight: 0.0060 chunk 173 optimal weight: 1.9990 chunk 150 optimal weight: 4.9990 overall best weight: 2.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 575 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.136095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.110786 restraints weight = 34121.352| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.84 r_work: 0.3059 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 25979 Z= 0.160 Angle : 0.671 22.695 35215 Z= 0.323 Chirality : 0.046 0.287 3972 Planarity : 0.005 0.081 4517 Dihedral : 8.212 89.654 3612 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.18 % Favored : 92.66 % Rotamer: Outliers : 2.33 % Allowed : 18.15 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.15), residues: 3134 helix: 0.19 (0.14), residues: 1477 sheet: 0.08 (0.26), residues: 385 loop : -1.64 (0.18), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 865 HIS 0.004 0.001 HIS E 611 PHE 0.012 0.001 PHE B 724 TYR 0.026 0.001 TYR B 655 ARG 0.011 0.000 ARG B 543 Details of bonding type rmsd hydrogen bonds : bond 0.03860 ( 912) hydrogen bonds : angle 4.28753 ( 2643) covalent geometry : bond 0.00396 (25970) covalent geometry : angle 0.67118 (35215) Misc. bond : bond 0.00745 ( 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 302 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 237 time to evaluate : 3.054 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 486 GLN cc_start: 0.7205 (OUTLIER) cc_final: 0.6581 (tp40) REVERT: A 586 ARG cc_start: 0.7507 (mpt90) cc_final: 0.6266 (tmm160) REVERT: A 681 VAL cc_start: 0.8504 (p) cc_final: 0.8247 (t) REVERT: A 931 LYS cc_start: 0.8803 (tttt) cc_final: 0.8543 (mmmm) REVERT: B 614 ASP cc_start: 0.8349 (OUTLIER) cc_final: 0.8067 (p0) REVERT: B 683 MET cc_start: 0.9078 (mtp) cc_final: 0.8833 (mtt) REVERT: B 839 GLU cc_start: 0.9022 (OUTLIER) cc_final: 0.8784 (mp0) REVERT: B 1384 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7285 (pp20) REVERT: C 424 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.7647 (mtp-110) REVERT: C 562 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8735 (tt) REVERT: C 683 MET cc_start: 0.8828 (mtm) cc_final: 0.8606 (mtt) REVERT: C 833 VAL cc_start: 0.8927 (t) cc_final: 0.8681 (m) REVERT: C 939 LYS cc_start: 0.8410 (tttm) cc_final: 0.7958 (mppt) REVERT: C 1332 ARG cc_start: 0.7490 (ptm160) cc_final: 0.7252 (ptm160) REVERT: D 683 MET cc_start: 0.9287 (mtm) cc_final: 0.9057 (mtt) REVERT: E 463 CYS cc_start: 0.8505 (m) cc_final: 0.8188 (m) REVERT: E 473 LYS cc_start: 0.7730 (OUTLIER) cc_final: 0.7075 (pttt) REVERT: E 558 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8823 (pt) REVERT: E 935 ASP cc_start: 0.8160 (t0) cc_final: 0.7379 (p0) REVERT: E 1372 LYS cc_start: 0.6479 (mmtt) cc_final: 0.4608 (pttp) REVERT: F 559 MET cc_start: 0.8722 (ttm) cc_final: 0.8497 (mmm) REVERT: F 576 ARG cc_start: 0.7781 (mtt90) cc_final: 0.7106 (mtm-85) REVERT: F 820 PHE cc_start: 0.8203 (m-80) cc_final: 0.7933 (m-80) REVERT: F 1332 ARG cc_start: 0.7467 (ttp-170) cc_final: 0.6818 (mpp-170) outliers start: 65 outliers final: 50 residues processed: 289 average time/residue: 0.4195 time to fit residues: 183.0079 Evaluate side-chains 286 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 228 time to evaluate : 2.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 LEU 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 618 LYS Chi-restraints excluded: chain A residue 632 VAL 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 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 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 614 ASP 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 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 1370 HIS Chi-restraints excluded: chain B residue 1375 LEU 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 821 THR Chi-restraints excluded: chain C residue 886 SER 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 562 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 683 MET 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 195 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 108 optimal weight: 0.4980 chunk 237 optimal weight: 10.0000 chunk 274 optimal weight: 3.9990 chunk 192 optimal weight: 0.0970 chunk 230 optimal weight: 1.9990 chunk 37 optimal weight: 0.2980 chunk 149 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 179 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1385 ASN D 900 HIS E 434 HIS E 575 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.139515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.114304 restraints weight = 34085.010| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.79 r_work: 0.3108 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 25979 Z= 0.108 Angle : 0.609 20.455 35215 Z= 0.295 Chirality : 0.044 0.287 3972 Planarity : 0.004 0.077 4517 Dihedral : 7.736 87.269 3612 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.67 % Favored : 93.17 % Rotamer: Outliers : 2.04 % Allowed : 18.32 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.16), residues: 3134 helix: 0.43 (0.14), residues: 1475 sheet: 0.14 (0.26), residues: 386 loop : -1.49 (0.18), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 865 HIS 0.003 0.001 HIS C 863 PHE 0.015 0.001 PHE A 729 TYR 0.021 0.001 TYR B 655 ARG 0.010 0.000 ARG B 543 Details of bonding type rmsd hydrogen bonds : bond 0.03096 ( 912) hydrogen bonds : angle 4.16709 ( 2643) covalent geometry : bond 0.00251 (25970) covalent geometry : angle 0.60859 (35215) Misc. bond : bond 0.00595 ( 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 311 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 254 time to evaluate : 3.219 Fit side-chains REVERT: A 461 ARG cc_start: 0.7885 (mmp-170) cc_final: 0.7342 (mmp-170) REVERT: A 486 GLN cc_start: 0.7170 (OUTLIER) cc_final: 0.6716 (tp40) REVERT: A 586 ARG cc_start: 0.7458 (mpt90) cc_final: 0.7096 (mmt180) REVERT: A 681 VAL cc_start: 0.8519 (p) cc_final: 0.8270 (t) REVERT: A 931 LYS cc_start: 0.8805 (tttt) cc_final: 0.8542 (mmmm) REVERT: B 614 ASP cc_start: 0.8333 (OUTLIER) cc_final: 0.8075 (p0) REVERT: B 683 MET cc_start: 0.9063 (mtp) cc_final: 0.8824 (mtt) REVERT: B 839 GLU cc_start: 0.8960 (OUTLIER) cc_final: 0.8721 (mp0) REVERT: B 1384 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7241 (pp20) REVERT: C 424 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7343 (mtp-110) REVERT: C 562 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8702 (tt) REVERT: C 683 MET cc_start: 0.8766 (mtm) cc_final: 0.8543 (mtt) REVERT: C 833 VAL cc_start: 0.8884 (t) cc_final: 0.8673 (m) REVERT: C 939 LYS cc_start: 0.8420 (tttm) cc_final: 0.7970 (mppt) REVERT: C 1332 ARG cc_start: 0.7447 (ptm160) cc_final: 0.7242 (ptm160) REVERT: D 683 MET cc_start: 0.9269 (mtm) cc_final: 0.9039 (mtt) REVERT: D 1338 LYS cc_start: 0.8508 (tmtt) cc_final: 0.8207 (tttt) REVERT: E 473 LYS cc_start: 0.7400 (OUTLIER) cc_final: 0.6873 (pttm) REVERT: E 558 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8807 (pt) REVERT: E 559 MET cc_start: 0.8820 (tpp) cc_final: 0.8476 (tpt) REVERT: E 614 ASP cc_start: 0.8860 (p0) cc_final: 0.8651 (p0) REVERT: E 935 ASP cc_start: 0.8166 (t0) cc_final: 0.7400 (p0) REVERT: E 1372 LYS cc_start: 0.6424 (mmtt) cc_final: 0.4604 (pttp) REVERT: F 559 MET cc_start: 0.8673 (ttm) cc_final: 0.8429 (mmm) REVERT: F 576 ARG cc_start: 0.7773 (mtt90) cc_final: 0.7116 (mtm-85) REVERT: F 820 PHE cc_start: 0.8134 (m-80) cc_final: 0.7877 (m-80) REVERT: F 1332 ARG cc_start: 0.7468 (ttp-170) cc_final: 0.6832 (mpp-170) outliers start: 57 outliers final: 39 residues processed: 297 average time/residue: 0.4260 time to fit residues: 191.7321 Evaluate side-chains 283 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 236 time to evaluate : 3.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 LEU 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 1358 VAL Chi-restraints excluded: chain A residue 1375 LEU Chi-restraints excluded: chain A residue 1388 CYS 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 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 837 SER Chi-restraints excluded: chain B residue 839 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 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 821 THR Chi-restraints excluded: chain C residue 886 SER Chi-restraints excluded: chain D residue 427 SER Chi-restraints excluded: chain D residue 471 THR Chi-restraints excluded: chain D residue 515 LEU 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 701 LEU Chi-restraints excluded: chain E residue 938 LEU Chi-restraints excluded: chain F residue 495 MET Chi-restraints excluded: chain F residue 502 LEU Chi-restraints excluded: chain F residue 661 THR Chi-restraints excluded: chain F residue 938 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 83 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 95 optimal weight: 8.9990 chunk 30 optimal weight: 3.9990 chunk 24 optimal weight: 0.0170 chunk 107 optimal weight: 0.8980 chunk 267 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 254 optimal weight: 0.3980 chunk 78 optimal weight: 5.9990 overall best weight: 1.0622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1381 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 = 0.3607 r_free = 0.3607 target = 0.138882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.113725 restraints weight = 34062.966| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.81 r_work: 0.3104 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25979 Z= 0.116 Angle : 0.611 19.410 35215 Z= 0.297 Chirality : 0.044 0.289 3972 Planarity : 0.005 0.109 4517 Dihedral : 7.693 84.951 3609 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.76 % Favored : 93.08 % Rotamer: Outliers : 1.90 % Allowed : 18.68 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.16), residues: 3134 helix: 0.49 (0.14), residues: 1480 sheet: 0.19 (0.26), residues: 384 loop : -1.47 (0.18), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 505 HIS 0.003 0.001 HIS C 863 PHE 0.013 0.001 PHE A 729 TYR 0.022 0.001 TYR B 655 ARG 0.009 0.000 ARG B 543 Details of bonding type rmsd hydrogen bonds : bond 0.03228 ( 912) hydrogen bonds : angle 4.13702 ( 2643) covalent geometry : bond 0.00273 (25970) covalent geometry : angle 0.61079 (35215) Misc. bond : bond 0.00566 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14469.74 seconds wall clock time: 253 minutes 36.64 seconds (15216.64 seconds total)