Starting phenix.real_space_refine on Fri Aug 9 07:29:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h3h_34468/08_2024/8h3h_34468_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h3h_34468/08_2024/8h3h_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h3h_34468/08_2024/8h3h_34468.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h3h_34468/08_2024/8h3h_34468.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h3h_34468/08_2024/8h3h_34468_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h3h_34468/08_2024/8h3h_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 Residue "A ARG 461": "NH1" <-> "NH2" Residue "A ARG 511": "NH1" <-> "NH2" Residue "A ARG 514": "NH1" <-> "NH2" Residue "A ARG 585": "NH1" <-> "NH2" Residue "A ARG 586": "NH1" <-> "NH2" Residue "A GLU 602": "OE1" <-> "OE2" Residue "A GLU 626": "OE1" <-> "OE2" Residue "A GLU 629": "OE1" <-> "OE2" Residue "A GLU 645": "OE1" <-> "OE2" Residue "A ARG 654": "NH1" <-> "NH2" Residue "A GLU 800": "OE1" <-> "OE2" Residue "A GLU 1384": "OE1" <-> "OE2" Residue "B ARG 461": "NH1" <-> "NH2" Residue "B ARG 511": "NH1" <-> "NH2" Residue "B ARG 514": "NH1" <-> "NH2" Residue "B TYR 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 585": "NH1" <-> "NH2" Residue "B ARG 586": "NH1" <-> "NH2" Residue "B GLU 602": "OE1" <-> "OE2" Residue "B GLU 606": "OE1" <-> "OE2" Residue "B GLU 629": "OE1" <-> "OE2" Residue "B ARG 654": "NH1" <-> "NH2" Residue "B GLU 848": "OE1" <-> "OE2" Residue "B GLU 1331": "OE1" <-> "OE2" Residue "C GLU 453": "OE1" <-> "OE2" Residue "C ARG 461": "NH1" <-> "NH2" Residue "C ARG 511": "NH1" <-> "NH2" Residue "C ARG 514": "NH1" <-> "NH2" Residue "C ARG 585": "NH1" <-> "NH2" Residue "C GLU 602": "OE1" <-> "OE2" Residue "C GLU 606": "OE1" <-> "OE2" Residue "C ARG 654": "NH1" <-> "NH2" Residue "C GLU 680": "OE1" <-> "OE2" Residue "C GLU 1331": "OE1" <-> "OE2" Residue "C GLU 1380": "OE1" <-> "OE2" Residue "C GLU 1384": "OE1" <-> "OE2" Residue "D GLU 453": "OE1" <-> "OE2" Residue "D ARG 461": "NH1" <-> "NH2" Residue "D ARG 511": "NH1" <-> "NH2" Residue "D ARG 514": "NH1" <-> "NH2" Residue "D ARG 585": "NH1" <-> "NH2" Residue "D ARG 586": "NH1" <-> "NH2" Residue "D GLU 629": "OE1" <-> "OE2" Residue "D ARG 654": "NH1" <-> "NH2" Residue "D GLU 680": "OE1" <-> "OE2" Residue "D GLU 818": "OE1" <-> "OE2" Residue "D GLU 905": "OE1" <-> "OE2" Residue "D GLU 928": "OE1" <-> "OE2" Residue "D GLU 1380": "OE1" <-> "OE2" Residue "E ARG 461": "NH1" <-> "NH2" Residue "E ARG 511": "NH1" <-> "NH2" Residue "E ARG 514": "NH1" <-> "NH2" Residue "E TYR 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 585": "NH1" <-> "NH2" Residue "E ARG 586": "NH1" <-> "NH2" Residue "E GLU 593": "OE1" <-> "OE2" Residue "E GLU 602": "OE1" <-> "OE2" Residue "E GLU 626": "OE1" <-> "OE2" Residue "E GLU 629": "OE1" <-> "OE2" Residue "E ARG 654": "NH1" <-> "NH2" Residue "E GLU 663": "OE1" <-> "OE2" Residue "E GLU 728": "OE1" <-> "OE2" Residue "E GLU 818": "OE1" <-> "OE2" Residue "E GLU 906": "OE1" <-> "OE2" Residue "E GLU 928": "OE1" <-> "OE2" Residue "F GLU 453": "OE1" <-> "OE2" Residue "F ARG 461": "NH1" <-> "NH2" Residue "F ARG 490": "NH1" <-> "NH2" Residue "F GLU 510": "OE1" <-> "OE2" Residue "F ARG 511": "NH1" <-> "NH2" Residue "F ARG 514": "NH1" <-> "NH2" Residue "F ARG 585": "NH1" <-> "NH2" Residue "F ARG 586": "NH1" <-> "NH2" Residue "F ARG 654": "NH1" <-> "NH2" Residue "F GLU 905": "OE1" <-> "OE2" Residue "F GLU 928": "OE1" <-> "OE2" Residue "F GLU 1380": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 13.67, per 1000 atoms: 0.54 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 - 3.50 Amino acid : False - 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: 11.02 Conformation dependent library (CDL) restraints added in 5.1 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: 2.97 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: 8.08 Time building geometry restraints manager: 11.60 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: 98.35 - 105.98: 781 105.98 - 113.61: 14626 113.61 - 121.25: 13350 121.25 - 128.88: 6289 128.88 - 136.51: 169 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: 3.530 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: 1.050 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 67.980 Find NCS groups from input model: 1.660 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.0000 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: