Starting phenix.real_space_refine on Sun Sep 29 22:42:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vtq_32120/09_2024/7vtq_32120.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vtq_32120/09_2024/7vtq_32120.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vtq_32120/09_2024/7vtq_32120.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vtq_32120/09_2024/7vtq_32120.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vtq_32120/09_2024/7vtq_32120.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vtq_32120/09_2024/7vtq_32120.cif" } resolution = 3.55 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 24 5.49 5 S 636 5.16 5 C 48924 2.51 5 N 13056 2.21 5 O 13932 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 76572 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 6326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 789, 6326 Classifications: {'peptide': 789} Link IDs: {'PTRANS': 19, 'TRANS': 769} Chain breaks: 6 Chain: "B" Number of atoms: 6326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 789, 6326 Classifications: {'peptide': 789} Link IDs: {'PTRANS': 19, 'TRANS': 769} Chain breaks: 6 Chain: "C" Number of atoms: 6326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 789, 6326 Classifications: {'peptide': 789} Link IDs: {'PTRANS': 19, 'TRANS': 769} Chain breaks: 6 Chain: "D" Number of atoms: 6326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 789, 6326 Classifications: {'peptide': 789} Link IDs: {'PTRANS': 19, 'TRANS': 769} Chain breaks: 6 Chain: "E" Number of atoms: 6326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 789, 6326 Classifications: {'peptide': 789} Link IDs: {'PTRANS': 19, 'TRANS': 769} Chain breaks: 6 Chain: "F" Number of atoms: 6326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 789, 6326 Classifications: {'peptide': 789} Link IDs: {'PTRANS': 19, 'TRANS': 769} Chain breaks: 6 Chain: "G" Number of atoms: 6326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 789, 6326 Classifications: {'peptide': 789} Link IDs: {'PTRANS': 19, 'TRANS': 769} Chain breaks: 6 Chain: "H" Number of atoms: 6326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 789, 6326 Classifications: {'peptide': 789} Link IDs: {'PTRANS': 19, 'TRANS': 769} Chain breaks: 6 Chain: "I" Number of atoms: 6326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 789, 6326 Classifications: {'peptide': 789} Link IDs: {'PTRANS': 19, 'TRANS': 769} Chain breaks: 6 Chain: "J" Number of atoms: 6326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 789, 6326 Classifications: {'peptide': 789} Link IDs: {'PTRANS': 19, 'TRANS': 769} Chain breaks: 6 Chain: "K" Number of atoms: 6326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 789, 6326 Classifications: {'peptide': 789} Link IDs: {'PTRANS': 19, 'TRANS': 769} Chain breaks: 6 Chain: "L" Number of atoms: 6326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 789, 6326 Classifications: {'peptide': 789} Link IDs: {'PTRANS': 19, 'TRANS': 769} Chain breaks: 6 Chain: "A" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'7YN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'7YN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'7YN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'7YN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'7YN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'7YN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'7YN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'7YN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'7YN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'7YN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'7YN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'7YN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 32.18, per 1000 atoms: 0.42 Number of scatterers: 76572 At special positions: 0 Unit cell: (217.875, 220.365, 158.115, 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 636 16.00 P 24 15.00 O 13932 8.00 N 13056 7.00 C 48924 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 955 " - pdb=" SG CYS A 982 " distance=2.04 Simple disulfide: pdb=" SG CYS B 955 " - pdb=" SG CYS B 982 " distance=2.04 Simple disulfide: pdb=" SG CYS C 955 " - pdb=" SG CYS C 982 " distance=2.04 Simple disulfide: pdb=" SG CYS D 955 " - pdb=" SG CYS D 982 " distance=2.04 Simple disulfide: pdb=" SG CYS E 955 " - pdb=" SG CYS E 982 " distance=2.04 Simple disulfide: pdb=" SG CYS F 955 " - pdb=" SG CYS F 982 " distance=2.04 Simple disulfide: pdb=" SG CYS G 955 " - pdb=" SG CYS G 982 " distance=2.04 Simple disulfide: pdb=" SG CYS H 955 " - pdb=" SG CYS H 982 " distance=2.04 Simple disulfide: pdb=" SG CYS I 955 " - pdb=" SG CYS I 982 " distance=2.04 Simple disulfide: pdb=" SG CYS J 955 " - pdb=" SG CYS J 982 " distance=2.04 Simple disulfide: pdb=" SG CYS K 955 " - pdb=" SG CYS K 982 " distance=2.04 Simple disulfide: pdb=" SG CYS L 955 " - pdb=" SG CYS L 982 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.25 Conformation dependent library (CDL) restraints added in 7.0 seconds 18600 Ramachandran restraints generated. 9300 Oldfield, 0 Emsley, 9300 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17976 Finding SS restraints... Secondary structure from input PDB file: 470 helices and 40 sheets defined 56.2% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.81 Creating SS restraints... Processing helix chain 'A' and resid 131 through 144 Processing helix chain 'A' and resid 159 through 164 removed outlier: 3.717A pdb=" N ARG A 163 " --> pdb=" O ASP A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 204 removed outlier: 4.052A pdb=" N LEU A 204 " --> pdb=" O LEU A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 241 Processing helix chain 'A' and resid 267 through 276 Processing helix chain 'A' and resid 282 through 287 Processing helix chain 'A' and resid 289 through 291 No H-bonds generated for 'chain 'A' and resid 289 through 291' Processing helix chain 'A' and resid 300 through 303 Processing helix chain 'A' and resid 323 through 333 removed outlier: 3.617A pdb=" N ARG A 333 " --> pdb=" O SER A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 358 removed outlier: 3.721A pdb=" N LEU A 357 " --> pdb=" O LYS A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 382 Processing helix chain 'A' and resid 384 through 398 removed outlier: 3.558A pdb=" N ASN A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 405 Processing helix chain 'A' and resid 407 through 424 Processing helix chain 'A' and resid 428 through 434 removed outlier: 3.654A pdb=" N SER A 432 " --> pdb=" O LEU A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 447 Processing helix chain 'A' and resid 459 through 476 Processing helix chain 'A' and resid 481 through 489 removed outlier: 3.899A pdb=" N LEU A 485 " --> pdb=" O GLU A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 495 removed outlier: 3.946A pdb=" N VAL A 495 " --> pdb=" O LYS A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 530 removed outlier: 3.678A pdb=" N GLN A 522 " --> pdb=" O HIS A 518 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TYR A 530 " --> pdb=" O ALA A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 562 Processing helix chain 'A' and resid 569 through 582 removed outlier: 4.538A pdb=" N PHE A 573 " --> pdb=" O GLY A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 595 Processing helix chain 'A' and resid 600 through 616 removed outlier: 3.972A pdb=" N LEU A 604 " --> pdb=" O GLN A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 636 removed outlier: 3.834A pdb=" N LEU A 628 " --> pdb=" O SER A 624 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN A 636 " --> pdb=" O LEU A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 646 Processing helix chain 'A' and resid 657 through 671 Processing helix chain 'A' and resid 724 through 737 removed outlier: 4.659A pdb=" N SER A 733 " --> pdb=" O GLY A 729 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU A 734 " --> pdb=" O LEU A 730 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER A 735 " --> pdb=" O PHE A 731 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR A 736 " --> pdb=" O SER A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 763 removed outlier: 3.788A pdb=" N GLY A 754 " --> pdb=" O LEU A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 794 removed outlier: 4.049A pdb=" N PHE A 785 " --> pdb=" O HIS A 781 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASP A 786 " --> pdb=" O GLN A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 820 removed outlier: 3.901A pdb=" N VAL A 817 " --> pdb=" O ARG A 813 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLY A 818 " --> pdb=" O LEU A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 851 removed outlier: 4.151A pdb=" N CYS A 841 " --> pdb=" O THR A 837 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLN A 842 " --> pdb=" O SER A 838 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ASP A 843 " --> pdb=" O ALA A 839 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A 847 " --> pdb=" O ASP A 843 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER A 849 " --> pdb=" O ALA A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 877 removed outlier: 4.002A pdb=" N GLY A 868 " --> pdb=" O LEU A 864 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS A 875 " --> pdb=" O VAL A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 896 No H-bonds generated for 'chain 'A' and resid 894 through 896' Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 921 through 934 removed outlier: 3.765A pdb=" N GLY A 932 " --> pdb=" O LEU A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 965 Processing helix chain 'A' and resid 979 through 992 removed outlier: 4.216A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1008 through 1022 Processing helix chain 'B' and resid 132 through 145 Processing helix chain 'B' and resid 159 through 164 removed outlier: 3.719A pdb=" N ARG B 163 " --> pdb=" O ASP B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 204 Processing helix chain 'B' and resid 227 through 241 Processing helix chain 'B' and resid 267 through 276 Processing helix chain 'B' and resid 282 through 287 Processing helix chain 'B' and resid 289 through 291 No H-bonds generated for 'chain 'B' and resid 289 through 291' Processing helix chain 'B' and resid 299 through 303 removed outlier: 3.561A pdb=" N GLU B 302 " --> pdb=" O GLY B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 333 removed outlier: 3.616A pdb=" N ARG B 333 " --> pdb=" O SER B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 351 removed outlier: 4.287A pdb=" N ALA B 350 " --> pdb=" O ARG B 347 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU B 351 " --> pdb=" O PRO B 348 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 347 through 351' Processing helix chain 'B' and resid 353 through 358 removed outlier: 3.721A pdb=" N LEU B 357 " --> pdb=" O LYS B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 382 removed outlier: 3.626A pdb=" N PHE B 382 " --> pdb=" O PHE B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 398 removed outlier: 3.543A pdb=" N ASN B 398 " --> pdb=" O LEU B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 405 Processing helix chain 'B' and resid 407 through 424 Processing helix chain 'B' and resid 428 through 434 removed outlier: 3.676A pdb=" N SER B 432 " --> pdb=" O LEU B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 447 Processing helix chain 'B' and resid 459 through 476 Processing helix chain 'B' and resid 481 through 489 removed outlier: 3.946A pdb=" N LEU B 485 " --> pdb=" O GLU B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 530 removed outlier: 3.721A pdb=" N GLN B 522 " --> pdb=" O HIS B 518 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR B 530 " --> pdb=" O ALA B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 562 Processing helix chain 'B' and resid 569 through 582 removed outlier: 4.482A pdb=" N PHE B 573 " --> pdb=" O GLY B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 595 Processing helix chain 'B' and resid 600 through 616 removed outlier: 3.965A pdb=" N LEU B 604 " --> pdb=" O GLN B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 636 removed outlier: 3.767A pdb=" N LEU B 628 " --> pdb=" O SER B 624 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN B 636 " --> pdb=" O LEU B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 646 Processing helix chain 'B' and resid 657 through 671 Processing helix chain 'B' and resid 724 through 737 removed outlier: 4.656A pdb=" N SER B 733 " --> pdb=" O GLY B 729 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU B 734 " --> pdb=" O LEU B 730 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER B 735 " --> pdb=" O PHE B 731 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N THR B 736 " --> pdb=" O SER B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 763 removed outlier: 3.775A pdb=" N GLY B 754 " --> pdb=" O LEU B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 780 through 794 removed outlier: 3.919A pdb=" N CYS B 784 " --> pdb=" O SER B 780 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N PHE B 785 " --> pdb=" O HIS B 781 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASP B 786 " --> pdb=" O GLN B 782 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 820 removed outlier: 3.863A pdb=" N VAL B 817 " --> pdb=" O ARG B 813 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY B 818 " --> pdb=" O LEU B 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 837 through 851 removed outlier: 4.191A pdb=" N CYS B 841 " --> pdb=" O THR B 837 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLN B 842 " --> pdb=" O SER B 838 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ASP B 843 " --> pdb=" O ALA B 839 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 877 removed outlier: 4.111A pdb=" N GLY B 868 " --> pdb=" O LEU B 864 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS B 875 " --> pdb=" O VAL B 871 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 896 No H-bonds generated for 'chain 'B' and resid 894 through 896' Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 921 through 934 removed outlier: 3.507A pdb=" N GLY B 925 " --> pdb=" O LEU B 921 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY B 932 " --> pdb=" O LEU B 928 " (cutoff:3.500A) Processing helix chain 'B' and resid 954 through 965 Processing helix chain 'B' and resid 979 through 992 removed outlier: 4.223A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1008 through 1022 Processing helix chain 'C' and resid 132 through 144 Processing helix chain 'C' and resid 159 through 164 removed outlier: 3.743A pdb=" N ARG C 163 " --> pdb=" O ASP C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 204 removed outlier: 3.504A pdb=" N LEU C 204 " --> pdb=" O LEU C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 241 Processing helix chain 'C' and resid 267 through 276 Processing helix chain 'C' and resid 282 through 287 Processing helix chain 'C' and resid 289 through 291 No H-bonds generated for 'chain 'C' and resid 289 through 291' Processing helix chain 'C' and resid 300 through 303 Processing helix chain 'C' and resid 323 through 333 removed outlier: 3.665A pdb=" N ARG C 333 " --> pdb=" O SER C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 351 removed outlier: 4.273A pdb=" N ALA C 350 " --> pdb=" O ARG C 347 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LEU C 351 " --> pdb=" O PRO C 348 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 347 through 351' Processing helix chain 'C' and resid 353 through 358 removed outlier: 3.706A pdb=" N LEU C 357 " --> pdb=" O LYS C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 382 Processing helix chain 'C' and resid 384 through 398 Processing helix chain 'C' and resid 398 through 405 Processing helix chain 'C' and resid 407 through 424 Processing helix chain 'C' and resid 428 through 434 removed outlier: 3.635A pdb=" N SER C 432 " --> pdb=" O LEU C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 447 Processing helix chain 'C' and resid 459 through 476 Processing helix chain 'C' and resid 481 through 489 removed outlier: 3.948A pdb=" N LEU C 485 " --> pdb=" O GLU C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 530 removed outlier: 3.848A pdb=" N GLN C 522 " --> pdb=" O HIS C 518 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TYR C 530 " --> pdb=" O ALA C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 562 Processing helix chain 'C' and resid 569 through 582 removed outlier: 4.432A pdb=" N PHE C 573 " --> pdb=" O GLY C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 595 Processing helix chain 'C' and resid 600 through 616 removed outlier: 3.983A pdb=" N LEU C 604 " --> pdb=" O GLN C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 636 removed outlier: 3.784A pdb=" N LEU C 628 " --> pdb=" O SER C 624 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN C 636 " --> pdb=" O LEU C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 637 through 646 Processing helix chain 'C' and resid 657 through 671 Processing helix chain 'C' and resid 724 through 737 removed outlier: 4.700A pdb=" N SER C 733 " --> pdb=" O GLY C 729 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU C 734 " --> pdb=" O LEU C 730 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER C 735 " --> pdb=" O PHE C 731 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N THR C 736 " --> pdb=" O SER C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 750 through 763 removed outlier: 3.779A pdb=" N GLY C 754 " --> pdb=" O LEU C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 780 through 794 removed outlier: 3.900A pdb=" N CYS C 784 " --> pdb=" O SER C 780 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE C 785 " --> pdb=" O HIS C 781 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ASP C 786 " --> pdb=" O GLN C 782 " (cutoff:3.500A) Processing helix chain 'C' and resid 807 through 820 removed outlier: 3.844A pdb=" N VAL C 817 " --> pdb=" O ARG C 813 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLY C 818 " --> pdb=" O LEU C 814 " (cutoff:3.500A) Processing helix chain 'C' and resid 837 through 851 removed outlier: 4.187A pdb=" N CYS C 841 " --> pdb=" O THR C 837 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLN C 842 " --> pdb=" O SER C 838 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ASP C 843 " --> pdb=" O ALA C 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 864 through 877 removed outlier: 4.013A pdb=" N GLY C 868 " --> pdb=" O LEU C 864 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS C 875 " --> pdb=" O VAL C 871 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 896 No H-bonds generated for 'chain 'C' and resid 894 through 896' Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 921 through 934 removed outlier: 3.508A pdb=" N GLY C 925 " --> pdb=" O LEU C 921 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY C 932 " --> pdb=" O LEU C 928 " (cutoff:3.500A) Processing helix chain 'C' and resid 954 through 965 Processing helix chain 'C' and resid 978 through 992 removed outlier: 4.142A pdb=" N CYS C 982 " --> pdb=" O LEU C 978 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1008 through 1022 Processing helix chain 'D' and resid 132 through 144 Processing helix chain 'D' and resid 159 through 164 removed outlier: 3.717A pdb=" N ARG D 163 " --> pdb=" O ASP D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 204 removed outlier: 4.052A pdb=" N LEU D 204 " --> pdb=" O LEU D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 241 Processing helix chain 'D' and resid 267 through 276 Processing helix chain 'D' and resid 282 through 287 Processing helix chain 'D' and resid 289 through 291 No H-bonds generated for 'chain 'D' and resid 289 through 291' Processing helix chain 'D' and resid 300 through 303 Processing helix chain 'D' and resid 323 through 333 removed outlier: 3.617A pdb=" N ARG D 333 " --> pdb=" O SER D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 358 removed outlier: 3.721A pdb=" N LEU D 357 " --> pdb=" O LYS D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 382 Processing helix chain 'D' and resid 384 through 398 removed outlier: 3.558A pdb=" N ASN D 398 " --> pdb=" O LEU D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 405 Processing helix chain 'D' and resid 407 through 424 Processing helix chain 'D' and resid 428 through 434 removed outlier: 3.654A pdb=" N SER D 432 " --> pdb=" O LEU D 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 447 Processing helix chain 'D' and resid 459 through 476 Processing helix chain 'D' and resid 481 through 489 removed outlier: 3.899A pdb=" N LEU D 485 " --> pdb=" O GLU D 481 " (cutoff:3.500A) Processing helix chain 'D' and resid 491 through 495 removed outlier: 3.946A pdb=" N VAL D 495 " --> pdb=" O LYS D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 518 through 530 removed outlier: 3.678A pdb=" N GLN D 522 " --> pdb=" O HIS D 518 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TYR D 530 " --> pdb=" O ALA D 526 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 562 Processing helix chain 'D' and resid 569 through 582 removed outlier: 4.538A pdb=" N PHE D 573 " --> pdb=" O GLY D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 595 Processing helix chain 'D' and resid 600 through 616 removed outlier: 3.972A pdb=" N LEU D 604 " --> pdb=" O GLN D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 636 removed outlier: 3.835A pdb=" N LEU D 628 " --> pdb=" O SER D 624 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN D 636 " --> pdb=" O LEU D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 637 through 646 Processing helix chain 'D' and resid 657 through 671 Processing helix chain 'D' and resid 724 through 737 removed outlier: 4.659A pdb=" N SER D 733 " --> pdb=" O GLY D 729 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU D 734 " --> pdb=" O LEU D 730 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER D 735 " --> pdb=" O PHE D 731 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR D 736 " --> pdb=" O SER D 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 750 through 763 removed outlier: 3.788A pdb=" N GLY D 754 " --> pdb=" O LEU D 750 " (cutoff:3.500A) Processing helix chain 'D' and resid 781 through 794 removed outlier: 4.049A pdb=" N PHE D 785 " --> pdb=" O HIS D 781 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASP D 786 " --> pdb=" O GLN D 782 " (cutoff:3.500A) Processing helix chain 'D' and resid 807 through 820 removed outlier: 3.902A pdb=" N VAL D 817 " --> pdb=" O ARG D 813 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLY D 818 " --> pdb=" O LEU D 814 " (cutoff:3.500A) Processing helix chain 'D' and resid 837 through 851 removed outlier: 4.151A pdb=" N CYS D 841 " --> pdb=" O THR D 837 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLN D 842 " --> pdb=" O SER D 838 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ASP D 843 " --> pdb=" O ALA D 839 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL D 847 " --> pdb=" O ASP D 843 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER D 849 " --> pdb=" O ALA D 845 " (cutoff:3.500A) Processing helix chain 'D' and resid 864 through 877 removed outlier: 4.003A pdb=" N GLY D 868 " --> pdb=" O LEU D 864 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS D 875 " --> pdb=" O VAL D 871 " (cutoff:3.500A) Processing helix chain 'D' and resid 894 through 896 No H-bonds generated for 'chain 'D' and resid 894 through 896' Processing helix chain 'D' and resid 897 through 908 Processing helix chain 'D' and resid 921 through 934 removed outlier: 3.765A pdb=" N GLY D 932 " --> pdb=" O LEU D 928 " (cutoff:3.500A) Processing helix chain 'D' and resid 954 through 965 Processing helix chain 'D' and resid 979 through 992 removed outlier: 4.216A pdb=" N GLN D 992 " --> pdb=" O GLU D 988 " (cutoff:3.500A) Processing helix chain 'D' and resid 1008 through 1022 Processing helix chain 'E' and resid 132 through 145 Processing helix chain 'E' and resid 159 through 164 removed outlier: 3.719A pdb=" N ARG E 163 " --> pdb=" O ASP E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 200 through 204 Processing helix chain 'E' and resid 227 through 241 Processing helix chain 'E' and resid 267 through 276 Processing helix chain 'E' and resid 282 through 287 Processing helix chain 'E' and resid 289 through 291 No H-bonds generated for 'chain 'E' and resid 289 through 291' Processing helix chain 'E' and resid 299 through 307 removed outlier: 3.554A pdb=" N GLU E 302 " --> pdb=" O GLY E 299 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N GLN E 304 " --> pdb=" O ASP E 301 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N GLY E 305 " --> pdb=" O GLU E 302 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ALA E 306 " --> pdb=" O LEU E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 333 removed outlier: 3.615A pdb=" N ARG E 333 " --> pdb=" O SER E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 351 removed outlier: 4.281A pdb=" N ALA E 350 " --> pdb=" O ARG E 347 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU E 351 " --> pdb=" O PRO E 348 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 347 through 351' Processing helix chain 'E' and resid 353 through 358 removed outlier: 3.727A pdb=" N LEU E 357 " --> pdb=" O LYS E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 382 removed outlier: 3.626A pdb=" N PHE E 382 " --> pdb=" O PHE E 378 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 398 removed outlier: 3.543A pdb=" N ASN E 398 " --> pdb=" O LEU E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 398 through 405 Processing helix chain 'E' and resid 407 through 424 Processing helix chain 'E' and resid 428 through 434 removed outlier: 3.680A pdb=" N SER E 432 " --> pdb=" O LEU E 428 " (cutoff:3.500A) Processing helix chain 'E' and resid 437 through 447 Processing helix chain 'E' and resid 459 through 476 Processing helix chain 'E' and resid 481 through 489 removed outlier: 3.947A pdb=" N LEU E 485 " --> pdb=" O GLU E 481 " (cutoff:3.500A) Processing helix chain 'E' and resid 518 through 530 removed outlier: 3.725A pdb=" N GLN E 522 " --> pdb=" O HIS E 518 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR E 530 " --> pdb=" O ALA E 526 " (cutoff:3.500A) Processing helix chain 'E' and resid 556 through 562 Processing helix chain 'E' and resid 569 through 582 removed outlier: 4.485A pdb=" N PHE E 573 " --> pdb=" O GLY E 569 " (cutoff:3.500A) Processing helix chain 'E' and resid 583 through 595 Processing helix chain 'E' and resid 600 through 616 removed outlier: 3.965A pdb=" N LEU E 604 " --> pdb=" O GLN E 600 " (cutoff:3.500A) Processing helix chain 'E' and resid 624 through 636 removed outlier: 3.766A pdb=" N LEU E 628 " --> pdb=" O SER E 624 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN E 636 " --> pdb=" O LEU E 632 " (cutoff:3.500A) Processing helix chain 'E' and resid 637 through 646 Processing helix chain 'E' and resid 657 through 671 Processing helix chain 'E' and resid 724 through 737 removed outlier: 4.653A pdb=" N SER E 733 " --> pdb=" O GLY E 729 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU E 734 " --> pdb=" O LEU E 730 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER E 735 " --> pdb=" O PHE E 731 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N THR E 736 " --> pdb=" O SER E 732 " (cutoff:3.500A) Processing helix chain 'E' and resid 750 through 763 removed outlier: 3.775A pdb=" N GLY E 754 " --> pdb=" O LEU E 750 " (cutoff:3.500A) Processing helix chain 'E' and resid 780 through 794 removed outlier: 3.918A pdb=" N CYS E 784 " --> pdb=" O SER E 780 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N PHE E 785 " --> pdb=" O HIS E 781 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ASP E 786 " --> pdb=" O GLN E 782 " (cutoff:3.500A) Processing helix chain 'E' and resid 807 through 820 removed outlier: 3.873A pdb=" N VAL E 817 " --> pdb=" O ARG E 813 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY E 818 " --> pdb=" O LEU E 814 " (cutoff:3.500A) Processing helix chain 'E' and resid 837 through 851 removed outlier: 4.191A pdb=" N CYS E 841 " --> pdb=" O THR E 837 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLN E 842 " --> pdb=" O SER E 838 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ASP E 843 " --> pdb=" O ALA E 839 " (cutoff:3.500A) Processing helix chain 'E' and resid 864 through 877 removed outlier: 4.116A pdb=" N GLY E 868 " --> pdb=" O LEU E 864 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS E 875 " --> pdb=" O VAL E 871 " (cutoff:3.500A) Processing helix chain 'E' and resid 894 through 896 No H-bonds generated for 'chain 'E' and resid 894 through 896' Processing helix chain 'E' and resid 897 through 908 Processing helix chain 'E' and resid 921 through 934 removed outlier: 3.508A pdb=" N GLY E 925 " --> pdb=" O LEU E 921 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY E 932 " --> pdb=" O LEU E 928 " (cutoff:3.500A) Processing helix chain 'E' and resid 954 through 965 Processing helix chain 'E' and resid 979 through 992 removed outlier: 4.221A pdb=" N GLN E 992 " --> pdb=" O GLU E 988 " (cutoff:3.500A) Processing helix chain 'E' and resid 1008 through 1022 Processing helix chain 'F' and resid 132 through 144 Processing helix chain 'F' and resid 159 through 164 removed outlier: 3.742A pdb=" N ARG F 163 " --> pdb=" O ASP F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 200 through 204 Processing helix chain 'F' and resid 227 through 241 Processing helix chain 'F' and resid 267 through 276 Processing helix chain 'F' and resid 282 through 287 Processing helix chain 'F' and resid 289 through 291 No H-bonds generated for 'chain 'F' and resid 289 through 291' Processing helix chain 'F' and resid 300 through 303 Processing helix chain 'F' and resid 323 through 333 removed outlier: 3.669A pdb=" N ARG F 333 " --> pdb=" O SER F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 347 through 351 removed outlier: 4.279A pdb=" N ALA F 350 " --> pdb=" O ARG F 347 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LEU F 351 " --> pdb=" O PRO F 348 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 347 through 351' Processing helix chain 'F' and resid 353 through 358 removed outlier: 3.698A pdb=" N LEU F 357 " --> pdb=" O LYS F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 370 through 382 Processing helix chain 'F' and resid 384 through 398 Processing helix chain 'F' and resid 398 through 405 Processing helix chain 'F' and resid 407 through 424 Processing helix chain 'F' and resid 428 through 434 removed outlier: 3.631A pdb=" N SER F 432 " --> pdb=" O LEU F 428 " (cutoff:3.500A) Processing helix chain 'F' and resid 437 through 447 Processing helix chain 'F' and resid 459 through 476 Processing helix chain 'F' and resid 481 through 489 removed outlier: 3.948A pdb=" N LEU F 485 " --> pdb=" O GLU F 481 " (cutoff:3.500A) Processing helix chain 'F' and resid 491 through 495 removed outlier: 3.983A pdb=" N VAL F 495 " --> pdb=" O LYS F 492 " (cutoff:3.500A) Processing helix chain 'F' and resid 518 through 530 removed outlier: 3.845A pdb=" N GLN F 522 " --> pdb=" O HIS F 518 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TYR F 530 " --> pdb=" O ALA F 526 " (cutoff:3.500A) Processing helix chain 'F' and resid 556 through 562 removed outlier: 3.501A pdb=" N LEU F 560 " --> pdb=" O VAL F 556 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 582 removed outlier: 4.438A pdb=" N PHE F 573 " --> pdb=" O GLY F 569 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 595 Processing helix chain 'F' and resid 600 through 616 removed outlier: 3.972A pdb=" N LEU F 604 " --> pdb=" O GLN F 600 " (cutoff:3.500A) Processing helix chain 'F' and resid 624 through 636 removed outlier: 3.761A pdb=" N LEU F 628 " --> pdb=" O SER F 624 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN F 636 " --> pdb=" O LEU F 632 " (cutoff:3.500A) Processing helix chain 'F' and resid 637 through 646 Processing helix chain 'F' and resid 657 through 671 Processing helix chain 'F' and resid 724 through 737 removed outlier: 4.703A pdb=" N SER F 733 " --> pdb=" O GLY F 729 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU F 734 " --> pdb=" O LEU F 730 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER F 735 " --> pdb=" O PHE F 731 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N THR F 736 " --> pdb=" O SER F 732 " (cutoff:3.500A) Processing helix chain 'F' and resid 750 through 763 removed outlier: 3.778A pdb=" N GLY F 754 " --> pdb=" O LEU F 750 " (cutoff:3.500A) Processing helix chain 'F' and resid 780 through 794 removed outlier: 3.898A pdb=" N CYS F 784 " --> pdb=" O SER F 780 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N PHE F 785 " --> pdb=" O HIS F 781 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASP F 786 " --> pdb=" O GLN F 782 " (cutoff:3.500A) Processing helix chain 'F' and resid 807 through 820 removed outlier: 3.844A pdb=" N VAL F 817 " --> pdb=" O ARG F 813 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLY F 818 " --> pdb=" O LEU F 814 " (cutoff:3.500A) Processing helix chain 'F' and resid 837 through 851 removed outlier: 4.186A pdb=" N CYS F 841 " --> pdb=" O THR F 837 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLN F 842 " --> pdb=" O SER F 838 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ASP F 843 " --> pdb=" O ALA F 839 " (cutoff:3.500A) Processing helix chain 'F' and resid 864 through 877 removed outlier: 4.014A pdb=" N GLY F 868 " --> pdb=" O LEU F 864 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS F 875 " --> pdb=" O VAL F 871 " (cutoff:3.500A) Processing helix chain 'F' and resid 894 through 896 No H-bonds generated for 'chain 'F' and resid 894 through 896' Processing helix chain 'F' and resid 897 through 908 Processing helix chain 'F' and resid 921 through 934 removed outlier: 3.508A pdb=" N GLY F 925 " --> pdb=" O LEU F 921 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY F 932 " --> pdb=" O LEU F 928 " (cutoff:3.500A) Processing helix chain 'F' and resid 954 through 965 Processing helix chain 'F' and resid 978 through 992 removed outlier: 4.142A pdb=" N CYS F 982 " --> pdb=" O LEU F 978 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLN F 992 " --> pdb=" O GLU F 988 " (cutoff:3.500A) Processing helix chain 'F' and resid 1008 through 1022 Processing helix chain 'G' and resid 132 through 144 Processing helix chain 'G' and resid 159 through 164 removed outlier: 3.717A pdb=" N ARG G 163 " --> pdb=" O ASP G 159 " (cutoff:3.500A) Processing helix chain 'G' and resid 200 through 204 removed outlier: 4.052A pdb=" N LEU G 204 " --> pdb=" O LEU G 201 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 241 Processing helix chain 'G' and resid 267 through 276 Processing helix chain 'G' and resid 282 through 287 Processing helix chain 'G' and resid 289 through 291 No H-bonds generated for 'chain 'G' and resid 289 through 291' Processing helix chain 'G' and resid 300 through 303 Processing helix chain 'G' and resid 323 through 333 removed outlier: 3.617A pdb=" N ARG G 333 " --> pdb=" O SER G 329 " (cutoff:3.500A) Processing helix chain 'G' and resid 353 through 358 removed outlier: 3.721A pdb=" N LEU G 357 " --> pdb=" O LYS G 353 " (cutoff:3.500A) Processing helix chain 'G' and resid 370 through 382 Processing helix chain 'G' and resid 384 through 398 removed outlier: 3.558A pdb=" N ASN G 398 " --> pdb=" O LEU G 394 " (cutoff:3.500A) Processing helix chain 'G' and resid 398 through 405 Processing helix chain 'G' and resid 407 through 424 Processing helix chain 'G' and resid 428 through 434 removed outlier: 3.654A pdb=" N SER G 432 " --> pdb=" O LEU G 428 " (cutoff:3.500A) Processing helix chain 'G' and resid 437 through 447 Processing helix chain 'G' and resid 459 through 476 Processing helix chain 'G' and resid 481 through 489 removed outlier: 3.899A pdb=" N LEU G 485 " --> pdb=" O GLU G 481 " (cutoff:3.500A) Processing helix chain 'G' and resid 491 through 495 removed outlier: 3.946A pdb=" N VAL G 495 " --> pdb=" O LYS G 492 " (cutoff:3.500A) Processing helix chain 'G' and resid 518 through 530 removed outlier: 3.677A pdb=" N GLN G 522 " --> pdb=" O HIS G 518 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TYR G 530 " --> pdb=" O ALA G 526 " (cutoff:3.500A) Processing helix chain 'G' and resid 556 through 562 Processing helix chain 'G' and resid 569 through 582 removed outlier: 4.538A pdb=" N PHE G 573 " --> pdb=" O GLY G 569 " (cutoff:3.500A) Processing helix chain 'G' and resid 583 through 595 Processing helix chain 'G' and resid 600 through 616 removed outlier: 3.971A pdb=" N LEU G 604 " --> pdb=" O GLN G 600 " (cutoff:3.500A) Processing helix chain 'G' and resid 624 through 636 removed outlier: 3.835A pdb=" N LEU G 628 " --> pdb=" O SER G 624 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN G 636 " --> pdb=" O LEU G 632 " (cutoff:3.500A) Processing helix chain 'G' and resid 637 through 646 Processing helix chain 'G' and resid 657 through 671 Processing helix chain 'G' and resid 724 through 737 removed outlier: 4.659A pdb=" N SER G 733 " --> pdb=" O GLY G 729 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU G 734 " --> pdb=" O LEU G 730 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER G 735 " --> pdb=" O PHE G 731 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR G 736 " --> pdb=" O SER G 732 " (cutoff:3.500A) Processing helix chain 'G' and resid 750 through 763 removed outlier: 3.789A pdb=" N GLY G 754 " --> pdb=" O LEU G 750 " (cutoff:3.500A) Processing helix chain 'G' and resid 780 through 794 removed outlier: 3.912A pdb=" N CYS G 784 " --> pdb=" O SER G 780 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE G 785 " --> pdb=" O HIS G 781 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASP G 786 " --> pdb=" O GLN G 782 " (cutoff:3.500A) Processing helix chain 'G' and resid 807 through 820 removed outlier: 3.901A pdb=" N VAL G 817 " --> pdb=" O ARG G 813 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLY G 818 " --> pdb=" O LEU G 814 " (cutoff:3.500A) Processing helix chain 'G' and resid 837 through 851 removed outlier: 4.153A pdb=" N CYS G 841 " --> pdb=" O THR G 837 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLN G 842 " --> pdb=" O SER G 838 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ASP G 843 " --> pdb=" O ALA G 839 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL G 847 " --> pdb=" O ASP G 843 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER G 849 " --> pdb=" O ALA G 845 " (cutoff:3.500A) Processing helix chain 'G' and resid 864 through 877 removed outlier: 4.003A pdb=" N GLY G 868 " --> pdb=" O LEU G 864 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS G 875 " --> pdb=" O VAL G 871 " (cutoff:3.500A) Processing helix chain 'G' and resid 894 through 896 No H-bonds generated for 'chain 'G' and resid 894 through 896' Processing helix chain 'G' and resid 897 through 908 Processing helix chain 'G' and resid 921 through 934 removed outlier: 3.765A pdb=" N GLY G 932 " --> pdb=" O LEU G 928 " (cutoff:3.500A) Processing helix chain 'G' and resid 954 through 965 Processing helix chain 'G' and resid 979 through 992 removed outlier: 4.216A pdb=" N GLN G 992 " --> pdb=" O GLU G 988 " (cutoff:3.500A) Processing helix chain 'G' and resid 1008 through 1022 Processing helix chain 'H' and resid 132 through 145 Processing helix chain 'H' and resid 159 through 164 removed outlier: 3.721A pdb=" N ARG H 163 " --> pdb=" O ASP H 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 200 through 204 removed outlier: 4.013A pdb=" N LEU H 204 " --> pdb=" O LEU H 201 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 241 Processing helix chain 'H' and resid 267 through 276 Processing helix chain 'H' and resid 282 through 287 Processing helix chain 'H' and resid 289 through 291 No H-bonds generated for 'chain 'H' and resid 289 through 291' Processing helix chain 'H' and resid 299 through 307 removed outlier: 3.556A pdb=" N GLU H 302 " --> pdb=" O GLY H 299 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N GLN H 304 " --> pdb=" O ASP H 301 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N GLY H 305 " --> pdb=" O GLU H 302 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ALA H 306 " --> pdb=" O LEU H 303 " (cutoff:3.500A) Processing helix chain 'H' and resid 323 through 333 removed outlier: 3.689A pdb=" N ARG H 333 " --> pdb=" O SER H 329 " (cutoff:3.500A) Processing helix chain 'H' and resid 353 through 358 removed outlier: 3.730A pdb=" N LEU H 357 " --> pdb=" O LYS H 353 " (cutoff:3.500A) Processing helix chain 'H' and resid 370 through 382 removed outlier: 3.643A pdb=" N PHE H 382 " --> pdb=" O PHE H 378 " (cutoff:3.500A) Processing helix chain 'H' and resid 384 through 398 removed outlier: 3.543A pdb=" N ASN H 398 " --> pdb=" O LEU H 394 " (cutoff:3.500A) Processing helix chain 'H' and resid 398 through 405 Processing helix chain 'H' and resid 407 through 424 Processing helix chain 'H' and resid 428 through 434 removed outlier: 3.684A pdb=" N SER H 432 " --> pdb=" O LEU H 428 " (cutoff:3.500A) Processing helix chain 'H' and resid 437 through 447 Processing helix chain 'H' and resid 459 through 476 Processing helix chain 'H' and resid 481 through 489 removed outlier: 3.961A pdb=" N LEU H 485 " --> pdb=" O GLU H 481 " (cutoff:3.500A) Processing helix chain 'H' and resid 518 through 530 removed outlier: 3.890A pdb=" N GLN H 522 " --> pdb=" O HIS H 518 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TYR H 530 " --> pdb=" O ALA H 526 " (cutoff:3.500A) Processing helix chain 'H' and resid 556 through 562 Processing helix chain 'H' and resid 569 through 582 removed outlier: 4.495A pdb=" N PHE H 573 " --> pdb=" O GLY H 569 " (cutoff:3.500A) Processing helix chain 'H' and resid 583 through 595 Processing helix chain 'H' and resid 600 through 616 removed outlier: 3.968A pdb=" N LEU H 604 " --> pdb=" O GLN H 600 " (cutoff:3.500A) Processing helix chain 'H' and resid 624 through 636 removed outlier: 3.766A pdb=" N LEU H 628 " --> pdb=" O SER H 624 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN H 636 " --> pdb=" O LEU H 632 " (cutoff:3.500A) Processing helix chain 'H' and resid 637 through 646 Processing helix chain 'H' and resid 657 through 671 Processing helix chain 'H' and resid 724 through 737 removed outlier: 4.658A pdb=" N SER H 733 " --> pdb=" O GLY H 729 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU H 734 " --> pdb=" O LEU H 730 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER H 735 " --> pdb=" O PHE H 731 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N THR H 736 " --> pdb=" O SER H 732 " (cutoff:3.500A) Processing helix chain 'H' and resid 750 through 763 removed outlier: 3.775A pdb=" N GLY H 754 " --> pdb=" O LEU H 750 " (cutoff:3.500A) Processing helix chain 'H' and resid 780 through 794 removed outlier: 3.919A pdb=" N CYS H 784 " --> pdb=" O SER H 780 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N PHE H 785 " --> pdb=" O HIS H 781 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ASP H 786 " --> pdb=" O GLN H 782 " (cutoff:3.500A) Processing helix chain 'H' and resid 807 through 820 removed outlier: 3.874A pdb=" N VAL H 817 " --> pdb=" O ARG H 813 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLY H 818 " --> pdb=" O LEU H 814 " (cutoff:3.500A) Processing helix chain 'H' and resid 837 through 851 removed outlier: 4.191A pdb=" N CYS H 841 " --> pdb=" O THR H 837 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLN H 842 " --> pdb=" O SER H 838 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ASP H 843 " --> pdb=" O ALA H 839 " (cutoff:3.500A) Processing helix chain 'H' and resid 864 through 877 removed outlier: 4.113A pdb=" N GLY H 868 " --> pdb=" O LEU H 864 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS H 875 " --> pdb=" O VAL H 871 " (cutoff:3.500A) Processing helix chain 'H' and resid 894 through 896 No H-bonds generated for 'chain 'H' and resid 894 through 896' Processing helix chain 'H' and resid 897 through 908 Processing helix chain 'H' and resid 921 through 934 removed outlier: 3.508A pdb=" N GLY H 925 " --> pdb=" O LEU H 921 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY H 932 " --> pdb=" O LEU H 928 " (cutoff:3.500A) Processing helix chain 'H' and resid 954 through 965 Processing helix chain 'H' and resid 979 through 992 removed outlier: 4.221A pdb=" N GLN H 992 " --> pdb=" O GLU H 988 " (cutoff:3.500A) Processing helix chain 'H' and resid 1008 through 1022 Processing helix chain 'I' and resid 132 through 144 Processing helix chain 'I' and resid 159 through 164 removed outlier: 3.742A pdb=" N ARG I 163 " --> pdb=" O ASP I 159 " (cutoff:3.500A) Processing helix chain 'I' and resid 200 through 204 Processing helix chain 'I' and resid 227 through 241 Processing helix chain 'I' and resid 267 through 276 Processing helix chain 'I' and resid 282 through 287 Processing helix chain 'I' and resid 289 through 291 No H-bonds generated for 'chain 'I' and resid 289 through 291' Processing helix chain 'I' and resid 300 through 303 Processing helix chain 'I' and resid 323 through 333 removed outlier: 3.662A pdb=" N ARG I 333 " --> pdb=" O SER I 329 " (cutoff:3.500A) Processing helix chain 'I' and resid 347 through 351 removed outlier: 4.283A pdb=" N ALA I 350 " --> pdb=" O ARG I 347 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LEU I 351 " --> pdb=" O PRO I 348 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 347 through 351' Processing helix chain 'I' and resid 353 through 358 removed outlier: 3.715A pdb=" N LEU I 357 " --> pdb=" O LYS I 353 " (cutoff:3.500A) Processing helix chain 'I' and resid 370 through 382 Processing helix chain 'I' and resid 384 through 398 Processing helix chain 'I' and resid 398 through 405 Processing helix chain 'I' and resid 407 through 424 Processing helix chain 'I' and resid 428 through 434 removed outlier: 3.631A pdb=" N SER I 432 " --> pdb=" O LEU I 428 " (cutoff:3.500A) Processing helix chain 'I' and resid 437 through 447 Processing helix chain 'I' and resid 459 through 476 Processing helix chain 'I' and resid 481 through 489 removed outlier: 3.949A pdb=" N LEU I 485 " --> pdb=" O GLU I 481 " (cutoff:3.500A) Processing helix chain 'I' and resid 491 through 495 removed outlier: 3.982A pdb=" N VAL I 495 " --> pdb=" O LYS I 492 " (cutoff:3.500A) Processing helix chain 'I' and resid 518 through 530 removed outlier: 3.845A pdb=" N GLN I 522 " --> pdb=" O HIS I 518 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TYR I 530 " --> pdb=" O ALA I 526 " (cutoff:3.500A) Processing helix chain 'I' and resid 556 through 562 Processing helix chain 'I' and resid 569 through 582 removed outlier: 4.439A pdb=" N PHE I 573 " --> pdb=" O GLY I 569 " (cutoff:3.500A) Processing helix chain 'I' and resid 583 through 595 Processing helix chain 'I' and resid 600 through 616 removed outlier: 3.973A pdb=" N LEU I 604 " --> pdb=" O GLN I 600 " (cutoff:3.500A) Processing helix chain 'I' and resid 624 through 636 removed outlier: 3.767A pdb=" N LEU I 628 " --> pdb=" O SER I 624 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN I 636 " --> pdb=" O LEU I 632 " (cutoff:3.500A) Processing helix chain 'I' and resid 637 through 646 Processing helix chain 'I' and resid 657 through 671 Processing helix chain 'I' and resid 724 through 737 removed outlier: 4.700A pdb=" N SER I 733 " --> pdb=" O GLY I 729 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU I 734 " --> pdb=" O LEU I 730 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER I 735 " --> pdb=" O PHE I 731 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N THR I 736 " --> pdb=" O SER I 732 " (cutoff:3.500A) Processing helix chain 'I' and resid 750 through 763 removed outlier: 3.774A pdb=" N GLY I 754 " --> pdb=" O LEU I 750 " (cutoff:3.500A) Processing helix chain 'I' and resid 780 through 794 removed outlier: 3.898A pdb=" N CYS I 784 " --> pdb=" O SER I 780 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N PHE I 785 " --> pdb=" O HIS I 781 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASP I 786 " --> pdb=" O GLN I 782 " (cutoff:3.500A) Processing helix chain 'I' and resid 807 through 820 removed outlier: 3.842A pdb=" N VAL I 817 " --> pdb=" O ARG I 813 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLY I 818 " --> pdb=" O LEU I 814 " (cutoff:3.500A) Processing helix chain 'I' and resid 837 through 851 removed outlier: 4.186A pdb=" N CYS I 841 " --> pdb=" O THR I 837 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLN I 842 " --> pdb=" O SER I 838 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ASP I 843 " --> pdb=" O ALA I 839 " (cutoff:3.500A) Processing helix chain 'I' and resid 864 through 877 removed outlier: 4.014A pdb=" N GLY I 868 " --> pdb=" O LEU I 864 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS I 875 " --> pdb=" O VAL I 871 " (cutoff:3.500A) Processing helix chain 'I' and resid 894 through 896 No H-bonds generated for 'chain 'I' and resid 894 through 896' Processing helix chain 'I' and resid 897 through 908 Processing helix chain 'I' and resid 921 through 934 removed outlier: 3.508A pdb=" N GLY I 925 " --> pdb=" O LEU I 921 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY I 932 " --> pdb=" O LEU I 928 " (cutoff:3.500A) Processing helix chain 'I' and resid 954 through 965 Processing helix chain 'I' and resid 978 through 992 removed outlier: 4.146A pdb=" N CYS I 982 " --> pdb=" O LEU I 978 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLN I 992 " --> pdb=" O GLU I 988 " (cutoff:3.500A) Processing helix chain 'I' and resid 1008 through 1022 Processing helix chain 'J' and resid 132 through 144 Processing helix chain 'J' and resid 159 through 164 removed outlier: 3.717A pdb=" N ARG J 163 " --> pdb=" O ASP J 159 " (cutoff:3.500A) Processing helix chain 'J' and resid 200 through 204 removed outlier: 4.052A pdb=" N LEU J 204 " --> pdb=" O LEU J 201 " (cutoff:3.500A) Processing helix chain 'J' and resid 227 through 241 Processing helix chain 'J' and resid 267 through 276 Processing helix chain 'J' and resid 282 through 287 Processing helix chain 'J' and resid 289 through 291 No H-bonds generated for 'chain 'J' and resid 289 through 291' Processing helix chain 'J' and resid 300 through 303 Processing helix chain 'J' and resid 323 through 333 removed outlier: 3.617A pdb=" N ARG J 333 " --> pdb=" O SER J 329 " (cutoff:3.500A) Processing helix chain 'J' and resid 353 through 358 removed outlier: 3.721A pdb=" N LEU J 357 " --> pdb=" O LYS J 353 " (cutoff:3.500A) Processing helix chain 'J' and resid 370 through 382 Processing helix chain 'J' and resid 384 through 398 removed outlier: 3.558A pdb=" N ASN J 398 " --> pdb=" O LEU J 394 " (cutoff:3.500A) Processing helix chain 'J' and resid 398 through 405 Processing helix chain 'J' and resid 407 through 424 Processing helix chain 'J' and resid 428 through 434 removed outlier: 3.654A pdb=" N SER J 432 " --> pdb=" O LEU J 428 " (cutoff:3.500A) Processing helix chain 'J' and resid 437 through 447 Processing helix chain 'J' and resid 459 through 476 Processing helix chain 'J' and resid 481 through 489 removed outlier: 3.899A pdb=" N LEU J 485 " --> pdb=" O GLU J 481 " (cutoff:3.500A) Processing helix chain 'J' and resid 491 through 495 removed outlier: 3.946A pdb=" N VAL J 495 " --> pdb=" O LYS J 492 " (cutoff:3.500A) Processing helix chain 'J' and resid 518 through 530 removed outlier: 3.677A pdb=" N GLN J 522 " --> pdb=" O HIS J 518 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TYR J 530 " --> pdb=" O ALA J 526 " (cutoff:3.500A) Processing helix chain 'J' and resid 556 through 562 Processing helix chain 'J' and resid 569 through 582 removed outlier: 4.538A pdb=" N PHE J 573 " --> pdb=" O GLY J 569 " (cutoff:3.500A) Processing helix chain 'J' and resid 583 through 595 Processing helix chain 'J' and resid 600 through 616 removed outlier: 3.971A pdb=" N LEU J 604 " --> pdb=" O GLN J 600 " (cutoff:3.500A) Processing helix chain 'J' and resid 624 through 636 removed outlier: 3.835A pdb=" N LEU J 628 " --> pdb=" O SER J 624 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN J 636 " --> pdb=" O LEU J 632 " (cutoff:3.500A) Processing helix chain 'J' and resid 637 through 646 Processing helix chain 'J' and resid 657 through 671 Processing helix chain 'J' and resid 724 through 737 removed outlier: 4.659A pdb=" N SER J 733 " --> pdb=" O GLY J 729 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU J 734 " --> pdb=" O LEU J 730 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER J 735 " --> pdb=" O PHE J 731 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR J 736 " --> pdb=" O SER J 732 " (cutoff:3.500A) Processing helix chain 'J' and resid 750 through 763 removed outlier: 3.788A pdb=" N GLY J 754 " --> pdb=" O LEU J 750 " (cutoff:3.500A) Processing helix chain 'J' and resid 781 through 794 removed outlier: 4.049A pdb=" N PHE J 785 " --> pdb=" O HIS J 781 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASP J 786 " --> pdb=" O GLN J 782 " (cutoff:3.500A) Processing helix chain 'J' and resid 807 through 820 removed outlier: 3.902A pdb=" N VAL J 817 " --> pdb=" O ARG J 813 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLY J 818 " --> pdb=" O LEU J 814 " (cutoff:3.500A) Processing helix chain 'J' and resid 837 through 851 removed outlier: 4.151A pdb=" N CYS J 841 " --> pdb=" O THR J 837 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLN J 842 " --> pdb=" O SER J 838 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ASP J 843 " --> pdb=" O ALA J 839 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL J 847 " --> pdb=" O ASP J 843 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER J 849 " --> pdb=" O ALA J 845 " (cutoff:3.500A) Processing helix chain 'J' and resid 864 through 877 removed outlier: 4.003A pdb=" N GLY J 868 " --> pdb=" O LEU J 864 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS J 875 " --> pdb=" O VAL J 871 " (cutoff:3.500A) Processing helix chain 'J' and resid 894 through 896 No H-bonds generated for 'chain 'J' and resid 894 through 896' Processing helix chain 'J' and resid 897 through 908 Processing helix chain 'J' and resid 921 through 934 removed outlier: 3.765A pdb=" N GLY J 932 " --> pdb=" O LEU J 928 " (cutoff:3.500A) Processing helix chain 'J' and resid 954 through 965 Processing helix chain 'J' and resid 979 through 992 removed outlier: 4.216A pdb=" N GLN J 992 " --> pdb=" O GLU J 988 " (cutoff:3.500A) Processing helix chain 'J' and resid 1008 through 1022 Processing helix chain 'K' and resid 132 through 145 Processing helix chain 'K' and resid 159 through 164 removed outlier: 3.721A pdb=" N ARG K 163 " --> pdb=" O ASP K 159 " (cutoff:3.500A) Processing helix chain 'K' and resid 200 through 204 removed outlier: 4.014A pdb=" N LEU K 204 " --> pdb=" O LEU K 201 " (cutoff:3.500A) Processing helix chain 'K' and resid 227 through 241 Processing helix chain 'K' and resid 267 through 276 Processing helix chain 'K' and resid 282 through 287 Processing helix chain 'K' and resid 289 through 291 No H-bonds generated for 'chain 'K' and resid 289 through 291' Processing helix chain 'K' and resid 299 through 307 removed outlier: 3.553A pdb=" N GLU K 302 " --> pdb=" O GLY K 299 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N GLN K 304 " --> pdb=" O ASP K 301 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N GLY K 305 " --> pdb=" O GLU K 302 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ALA K 306 " --> pdb=" O LEU K 303 " (cutoff:3.500A) Processing helix chain 'K' and resid 323 through 333 removed outlier: 3.614A pdb=" N ARG K 333 " --> pdb=" O SER K 329 " (cutoff:3.500A) Processing helix chain 'K' and resid 347 through 351 removed outlier: 4.286A pdb=" N ALA K 350 " --> pdb=" O ARG K 347 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU K 351 " --> pdb=" O PRO K 348 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 347 through 351' Processing helix chain 'K' and resid 353 through 358 removed outlier: 3.724A pdb=" N LEU K 357 " --> pdb=" O LYS K 353 " (cutoff:3.500A) Processing helix chain 'K' and resid 370 through 382 removed outlier: 3.627A pdb=" N PHE K 382 " --> pdb=" O PHE K 378 " (cutoff:3.500A) Processing helix chain 'K' and resid 384 through 398 removed outlier: 3.544A pdb=" N ASN K 398 " --> pdb=" O LEU K 394 " (cutoff:3.500A) Processing helix chain 'K' and resid 398 through 405 Processing helix chain 'K' and resid 407 through 424 Processing helix chain 'K' and resid 428 through 434 removed outlier: 3.678A pdb=" N SER K 432 " --> pdb=" O LEU K 428 " (cutoff:3.500A) Processing helix chain 'K' and resid 437 through 447 Processing helix chain 'K' and resid 459 through 476 Processing helix chain 'K' and resid 481 through 489 removed outlier: 3.962A pdb=" N LEU K 485 " --> pdb=" O GLU K 481 " (cutoff:3.500A) Processing helix chain 'K' and resid 518 through 530 removed outlier: 3.719A pdb=" N GLN K 522 " --> pdb=" O HIS K 518 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TYR K 530 " --> pdb=" O ALA K 526 " (cutoff:3.500A) Processing helix chain 'K' and resid 556 through 562 Processing helix chain 'K' and resid 569 through 582 removed outlier: 4.482A pdb=" N PHE K 573 " --> pdb=" O GLY K 569 " (cutoff:3.500A) Processing helix chain 'K' and resid 583 through 595 Processing helix chain 'K' and resid 600 through 616 removed outlier: 3.965A pdb=" N LEU K 604 " --> pdb=" O GLN K 600 " (cutoff:3.500A) Processing helix chain 'K' and resid 624 through 636 removed outlier: 3.766A pdb=" N LEU K 628 " --> pdb=" O SER K 624 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN K 636 " --> pdb=" O LEU K 632 " (cutoff:3.500A) Processing helix chain 'K' and resid 637 through 646 Processing helix chain 'K' and resid 657 through 671 Processing helix chain 'K' and resid 724 through 737 removed outlier: 4.654A pdb=" N SER K 733 " --> pdb=" O GLY K 729 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU K 734 " --> pdb=" O LEU K 730 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER K 735 " --> pdb=" O PHE K 731 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N THR K 736 " --> pdb=" O SER K 732 " (cutoff:3.500A) Processing helix chain 'K' and resid 750 through 763 removed outlier: 3.774A pdb=" N GLY K 754 " --> pdb=" O LEU K 750 " (cutoff:3.500A) Processing helix chain 'K' and resid 780 through 794 removed outlier: 3.919A pdb=" N CYS K 784 " --> pdb=" O SER K 780 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N PHE K 785 " --> pdb=" O HIS K 781 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ASP K 786 " --> pdb=" O GLN K 782 " (cutoff:3.500A) Processing helix chain 'K' and resid 807 through 820 removed outlier: 3.875A pdb=" N VAL K 817 " --> pdb=" O ARG K 813 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY K 818 " --> pdb=" O LEU K 814 " (cutoff:3.500A) Processing helix chain 'K' and resid 837 through 851 removed outlier: 4.191A pdb=" N CYS K 841 " --> pdb=" O THR K 837 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLN K 842 " --> pdb=" O SER K 838 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ASP K 843 " --> pdb=" O ALA K 839 " (cutoff:3.500A) Processing helix chain 'K' and resid 864 through 877 removed outlier: 4.111A pdb=" N GLY K 868 " --> pdb=" O LEU K 864 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS K 875 " --> pdb=" O VAL K 871 " (cutoff:3.500A) Processing helix chain 'K' and resid 894 through 896 No H-bonds generated for 'chain 'K' and resid 894 through 896' Processing helix chain 'K' and resid 897 through 908 Processing helix chain 'K' and resid 921 through 934 removed outlier: 3.741A pdb=" N GLY K 932 " --> pdb=" O LEU K 928 " (cutoff:3.500A) Processing helix chain 'K' and resid 954 through 965 Processing helix chain 'K' and resid 979 through 992 removed outlier: 4.224A pdb=" N GLN K 992 " --> pdb=" O GLU K 988 " (cutoff:3.500A) Processing helix chain 'K' and resid 1008 through 1022 Processing helix chain 'L' and resid 132 through 144 Processing helix chain 'L' and resid 159 through 164 removed outlier: 3.741A pdb=" N ARG L 163 " --> pdb=" O ASP L 159 " (cutoff:3.500A) Processing helix chain 'L' and resid 200 through 204 removed outlier: 3.501A pdb=" N LEU L 204 " --> pdb=" O LEU L 201 " (cutoff:3.500A) Processing helix chain 'L' and resid 227 through 241 Processing helix chain 'L' and resid 267 through 276 Processing helix chain 'L' and resid 282 through 287 Processing helix chain 'L' and resid 289 through 291 No H-bonds generated for 'chain 'L' and resid 289 through 291' Processing helix chain 'L' and resid 300 through 303 Processing helix chain 'L' and resid 323 through 333 removed outlier: 3.665A pdb=" N ARG L 333 " --> pdb=" O SER L 329 " (cutoff:3.500A) Processing helix chain 'L' and resid 347 through 351 removed outlier: 4.281A pdb=" N ALA L 350 " --> pdb=" O ARG L 347 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU L 351 " --> pdb=" O PRO L 348 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 347 through 351' Processing helix chain 'L' and resid 353 through 358 removed outlier: 3.704A pdb=" N LEU L 357 " --> pdb=" O LYS L 353 " (cutoff:3.500A) Processing helix chain 'L' and resid 370 through 382 Processing helix chain 'L' and resid 384 through 398 Processing helix chain 'L' and resid 398 through 405 Processing helix chain 'L' and resid 407 through 424 Processing helix chain 'L' and resid 428 through 434 removed outlier: 3.631A pdb=" N SER L 432 " --> pdb=" O LEU L 428 " (cutoff:3.500A) Processing helix chain 'L' and resid 437 through 447 Processing helix chain 'L' and resid 459 through 476 Processing helix chain 'L' and resid 481 through 489 removed outlier: 3.947A pdb=" N LEU L 485 " --> pdb=" O GLU L 481 " (cutoff:3.500A) Processing helix chain 'L' and resid 491 through 495 removed outlier: 3.981A pdb=" N VAL L 495 " --> pdb=" O LYS L 492 " (cutoff:3.500A) Processing helix chain 'L' and resid 518 through 530 removed outlier: 3.851A pdb=" N GLN L 522 " --> pdb=" O HIS L 518 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TYR L 530 " --> pdb=" O ALA L 526 " (cutoff:3.500A) Processing helix chain 'L' and resid 556 through 562 Processing helix chain 'L' and resid 569 through 582 removed outlier: 4.430A pdb=" N PHE L 573 " --> pdb=" O GLY L 569 " (cutoff:3.500A) Processing helix chain 'L' and resid 583 through 595 Processing helix chain 'L' and resid 600 through 616 removed outlier: 3.978A pdb=" N LEU L 604 " --> pdb=" O GLN L 600 " (cutoff:3.500A) Processing helix chain 'L' and resid 624 through 636 removed outlier: 3.762A pdb=" N LEU L 628 " --> pdb=" O SER L 624 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN L 636 " --> pdb=" O LEU L 632 " (cutoff:3.500A) Processing helix chain 'L' and resid 637 through 646 Processing helix chain 'L' and resid 657 through 671 Processing helix chain 'L' and resid 724 through 737 removed outlier: 4.701A pdb=" N SER L 733 " --> pdb=" O GLY L 729 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU L 734 " --> pdb=" O LEU L 730 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER L 735 " --> pdb=" O PHE L 731 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N THR L 736 " --> pdb=" O SER L 732 " (cutoff:3.500A) Processing helix chain 'L' and resid 750 through 763 removed outlier: 3.778A pdb=" N GLY L 754 " --> pdb=" O LEU L 750 " (cutoff:3.500A) Processing helix chain 'L' and resid 780 through 794 removed outlier: 3.899A pdb=" N CYS L 784 " --> pdb=" O SER L 780 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N PHE L 785 " --> pdb=" O HIS L 781 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ASP L 786 " --> pdb=" O GLN L 782 " (cutoff:3.500A) Processing helix chain 'L' and resid 807 through 820 removed outlier: 3.843A pdb=" N VAL L 817 " --> pdb=" O ARG L 813 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLY L 818 " --> pdb=" O LEU L 814 " (cutoff:3.500A) Processing helix chain 'L' and resid 837 through 851 removed outlier: 4.191A pdb=" N CYS L 841 " --> pdb=" O THR L 837 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLN L 842 " --> pdb=" O SER L 838 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ASP L 843 " --> pdb=" O ALA L 839 " (cutoff:3.500A) Processing helix chain 'L' and resid 864 through 877 removed outlier: 4.015A pdb=" N GLY L 868 " --> pdb=" O LEU L 864 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS L 875 " --> pdb=" O VAL L 871 " (cutoff:3.500A) Processing helix chain 'L' and resid 894 through 896 No H-bonds generated for 'chain 'L' and resid 894 through 896' Processing helix chain 'L' and resid 897 through 908 Processing helix chain 'L' and resid 921 through 934 removed outlier: 3.518A pdb=" N GLY L 925 " --> pdb=" O LEU L 921 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY L 932 " --> pdb=" O LEU L 928 " (cutoff:3.500A) Processing helix chain 'L' and resid 954 through 965 Processing helix chain 'L' and resid 978 through 992 removed outlier: 4.147A pdb=" N CYS L 982 " --> pdb=" O LEU L 978 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLN L 992 " --> pdb=" O GLU L 988 " (cutoff:3.500A) Processing helix chain 'L' and resid 1008 through 1022 Processing sheet with id=AA1, first strand: chain 'A' and resid 168 through 171 removed outlier: 5.705A pdb=" N GLN A 168 " --> pdb=" O LEU A 367 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N THR A 217 " --> pdb=" O ARG A 362 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N VAL A 364 " --> pdb=" O THR A 217 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL A 219 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ILE A 366 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N GLN A 221 " --> pdb=" O ILE A 366 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N GLY A 368 " --> pdb=" O GLN A 221 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL A 218 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP A 298 " --> pdb=" O ILE A 255 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 650 through 652 removed outlier: 6.482A pdb=" N ILE A 651 " --> pdb=" O SER A 678 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU A 677 " --> pdb=" O ASP A 744 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LEU A 743 " --> pdb=" O TRP A 773 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LEU A 772 " --> pdb=" O ASP A 801 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LEU A 800 " --> pdb=" O TRP A 830 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N LEU A 829 " --> pdb=" O TYR A 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 999 through 1000 Processing sheet with id=AA4, first strand: chain 'B' and resid 168 through 171 removed outlier: 5.841A pdb=" N GLN B 168 " --> pdb=" O LEU B 367 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N THR B 217 " --> pdb=" O ARG B 362 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N VAL B 364 " --> pdb=" O THR B 217 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL B 219 " --> pdb=" O VAL B 364 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ILE B 366 " --> pdb=" O VAL B 219 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N GLN B 221 " --> pdb=" O ILE B 366 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N GLY B 368 " --> pdb=" O GLN B 221 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL B 218 " --> pdb=" O ILE B 344 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N THR B 346 " --> pdb=" O VAL B 218 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N PHE B 220 " --> pdb=" O THR B 346 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP B 298 " --> pdb=" O ILE B 255 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 499 through 501 Processing sheet with id=AA6, first strand: chain 'B' and resid 650 through 652 removed outlier: 6.439A pdb=" N ILE B 651 " --> pdb=" O SER B 678 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU B 677 " --> pdb=" O ASP B 744 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LEU B 743 " --> pdb=" O TRP B 773 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N LEU B 772 " --> pdb=" O ASP B 801 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N LEU B 800 " --> pdb=" O TRP B 830 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LEU B 829 " --> pdb=" O TYR B 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 999 through 1000 Processing sheet with id=AA8, first strand: chain 'C' and resid 168 through 171 removed outlier: 5.785A pdb=" N GLN C 168 " --> pdb=" O LEU C 367 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N THR C 217 " --> pdb=" O ARG C 362 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N VAL C 364 " --> pdb=" O THR C 217 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL C 219 " --> pdb=" O VAL C 364 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N ILE C 366 " --> pdb=" O VAL C 219 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N GLN C 221 " --> pdb=" O ILE C 366 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N GLY C 368 " --> pdb=" O GLN C 221 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL C 218 " --> pdb=" O LEU C 342 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP C 298 " --> pdb=" O ILE C 255 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 499 through 501 Processing sheet with id=AB1, first strand: chain 'C' and resid 650 through 655 removed outlier: 3.662A pdb=" N ILE C 653 " --> pdb=" O SER C 678 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEU C 677 " --> pdb=" O ASP C 744 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU C 743 " --> pdb=" O TRP C 773 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LEU C 772 " --> pdb=" O ASP C 801 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LEU C 800 " --> pdb=" O TRP C 830 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 168 through 171 removed outlier: 5.705A pdb=" N GLN D 168 " --> pdb=" O LEU D 367 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N THR D 217 " --> pdb=" O ARG D 362 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N VAL D 364 " --> pdb=" O THR D 217 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL D 219 " --> pdb=" O VAL D 364 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ILE D 366 " --> pdb=" O VAL D 219 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N GLN D 221 " --> pdb=" O ILE D 366 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N GLY D 368 " --> pdb=" O GLN D 221 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL D 218 " --> pdb=" O LEU D 342 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP D 298 " --> pdb=" O ILE D 255 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 650 through 652 removed outlier: 6.486A pdb=" N ILE D 651 " --> pdb=" O SER D 678 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU D 677 " --> pdb=" O ASP D 744 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LEU D 743 " --> pdb=" O TRP D 773 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N LEU D 772 " --> pdb=" O ASP D 801 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LEU D 800 " --> pdb=" O TRP D 830 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N LEU D 829 " --> pdb=" O TYR D 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'D' and resid 999 through 1000 Processing sheet with id=AB5, first strand: chain 'E' and resid 168 through 171 removed outlier: 5.809A pdb=" N GLN E 168 " --> pdb=" O LEU E 367 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N THR E 217 " --> pdb=" O ARG E 362 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N VAL E 364 " --> pdb=" O THR E 217 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL E 219 " --> pdb=" O VAL E 364 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N ILE E 366 " --> pdb=" O VAL E 219 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLN E 221 " --> pdb=" O ILE E 366 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N GLY E 368 " --> pdb=" O GLN E 221 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL E 218 " --> pdb=" O LEU E 342 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP E 298 " --> pdb=" O ILE E 255 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 499 through 501 Processing sheet with id=AB7, first strand: chain 'E' and resid 650 through 655 removed outlier: 3.677A pdb=" N ILE E 653 " --> pdb=" O SER E 678 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU E 677 " --> pdb=" O ASP E 744 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N LEU E 743 " --> pdb=" O TRP E 773 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N LEU E 772 " --> pdb=" O ASP E 801 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LEU E 800 " --> pdb=" O TRP E 830 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LEU E 829 " --> pdb=" O TYR E 858 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 999 through 1000 Processing sheet with id=AB9, first strand: chain 'F' and resid 168 through 171 removed outlier: 5.850A pdb=" N GLN F 168 " --> pdb=" O LEU F 367 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N THR F 217 " --> pdb=" O ARG F 362 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N VAL F 364 " --> pdb=" O THR F 217 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL F 219 " --> pdb=" O VAL F 364 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N ILE F 366 " --> pdb=" O VAL F 219 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N GLN F 221 " --> pdb=" O ILE F 366 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N GLY F 368 " --> pdb=" O GLN F 221 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL F 218 " --> pdb=" O ILE F 344 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP F 298 " --> pdb=" O ILE F 255 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 499 through 501 Processing sheet with id=AC2, first strand: chain 'F' and resid 650 through 655 removed outlier: 3.658A pdb=" N ILE F 653 " --> pdb=" O SER F 678 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU F 677 " --> pdb=" O ASP F 744 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LEU F 743 " --> pdb=" O TRP F 773 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LEU F 772 " --> pdb=" O ASP F 801 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LEU F 800 " --> pdb=" O TRP F 830 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N LEU F 829 " --> pdb=" O TYR F 858 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 168 through 171 removed outlier: 5.676A pdb=" N GLN G 168 " --> pdb=" O LEU G 367 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N THR G 217 " --> pdb=" O ARG G 362 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N VAL G 364 " --> pdb=" O THR G 217 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL G 219 " --> pdb=" O VAL G 364 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ILE G 366 " --> pdb=" O VAL G 219 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N GLN G 221 " --> pdb=" O ILE G 366 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N GLY G 368 " --> pdb=" O GLN G 221 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL G 218 " --> pdb=" O LEU G 342 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP G 298 " --> pdb=" O ILE G 255 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 650 through 652 removed outlier: 6.482A pdb=" N ILE G 651 " --> pdb=" O SER G 678 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU G 677 " --> pdb=" O ASP G 744 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LEU G 743 " --> pdb=" O TRP G 773 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N LEU G 772 " --> pdb=" O ASP G 801 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LEU G 800 " --> pdb=" O TRP G 830 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N LEU G 829 " --> pdb=" O TYR G 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'G' and resid 999 through 1000 Processing sheet with id=AC6, first strand: chain 'H' and resid 168 through 171 removed outlier: 5.826A pdb=" N GLN H 168 " --> pdb=" O LEU H 367 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N THR H 217 " --> pdb=" O ARG H 362 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N VAL H 364 " --> pdb=" O THR H 217 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL H 219 " --> pdb=" O VAL H 364 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N ILE H 366 " --> pdb=" O VAL H 219 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N GLN H 221 " --> pdb=" O ILE H 366 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N GLY H 368 " --> pdb=" O GLN H 221 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL H 218 " --> pdb=" O LEU H 342 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP H 298 " --> pdb=" O ILE H 255 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 499 through 501 Processing sheet with id=AC8, first strand: chain 'H' and resid 650 through 655 removed outlier: 3.674A pdb=" N ILE H 653 " --> pdb=" O SER H 678 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU H 677 " --> pdb=" O ASP H 744 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LEU H 743 " --> pdb=" O TRP H 773 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N LEU H 772 " --> pdb=" O ASP H 801 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N LEU H 800 " --> pdb=" O TRP H 830 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N LEU H 829 " --> pdb=" O TYR H 858 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 999 through 1000 Processing sheet with id=AD1, first strand: chain 'I' and resid 168 through 171 removed outlier: 5.831A pdb=" N GLN I 168 " --> pdb=" O LEU I 367 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N THR I 217 " --> pdb=" O ARG I 362 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N VAL I 364 " --> pdb=" O THR I 217 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N VAL I 219 " --> pdb=" O VAL I 364 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N ILE I 366 " --> pdb=" O VAL I 219 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N GLN I 221 " --> pdb=" O ILE I 366 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N GLY I 368 " --> pdb=" O GLN I 221 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL I 218 " --> pdb=" O ILE I 344 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP I 298 " --> pdb=" O ILE I 255 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 499 through 501 Processing sheet with id=AD3, first strand: chain 'I' and resid 650 through 655 removed outlier: 3.657A pdb=" N ILE I 653 " --> pdb=" O SER I 678 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU I 677 " --> pdb=" O ASP I 744 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N LEU I 743 " --> pdb=" O TRP I 773 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N LEU I 772 " --> pdb=" O ASP I 801 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N LEU I 800 " --> pdb=" O TRP I 830 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 168 through 171 removed outlier: 5.676A pdb=" N GLN J 168 " --> pdb=" O LEU J 367 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N THR J 217 " --> pdb=" O ARG J 362 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N VAL J 364 " --> pdb=" O THR J 217 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL J 219 " --> pdb=" O VAL J 364 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ILE J 366 " --> pdb=" O VAL J 219 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N GLN J 221 " --> pdb=" O ILE J 366 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N GLY J 368 " --> pdb=" O GLN J 221 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL J 218 " --> pdb=" O LEU J 342 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP J 298 " --> pdb=" O ILE J 255 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 650 through 652 removed outlier: 6.482A pdb=" N ILE J 651 " --> pdb=" O SER J 678 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU J 677 " --> pdb=" O ASP J 744 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LEU J 743 " --> pdb=" O TRP J 773 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LEU J 772 " --> pdb=" O ASP J 801 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LEU J 800 " --> pdb=" O TRP J 830 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N LEU J 829 " --> pdb=" O TYR J 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'J' and resid 999 through 1000 Processing sheet with id=AD7, first strand: chain 'K' and resid 168 through 171 removed outlier: 5.810A pdb=" N GLN K 168 " --> pdb=" O LEU K 367 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N THR K 217 " --> pdb=" O ARG K 362 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N VAL K 364 " --> pdb=" O THR K 217 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL K 219 " --> pdb=" O VAL K 364 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N ILE K 366 " --> pdb=" O VAL K 219 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N GLN K 221 " --> pdb=" O ILE K 366 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N GLY K 368 " --> pdb=" O GLN K 221 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL K 218 " --> pdb=" O LEU K 342 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASP K 298 " --> pdb=" O ILE K 255 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 499 through 501 Processing sheet with id=AD9, first strand: chain 'K' and resid 650 through 652 removed outlier: 6.437A pdb=" N ILE K 651 " --> pdb=" O SER K 678 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU K 677 " --> pdb=" O ASP K 744 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU K 743 " --> pdb=" O TRP K 773 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N LEU K 772 " --> pdb=" O ASP K 801 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N LEU K 800 " --> pdb=" O TRP K 830 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LEU K 829 " --> pdb=" O TYR K 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'K' and resid 999 through 1000 Processing sheet with id=AE2, first strand: chain 'L' and resid 168 through 171 removed outlier: 5.798A pdb=" N GLN L 168 " --> pdb=" O LEU L 367 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N THR L 217 " --> pdb=" O ARG L 362 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N VAL L 364 " --> pdb=" O THR L 217 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL L 219 " --> pdb=" O VAL L 364 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N ILE L 366 " --> pdb=" O VAL L 219 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N GLN L 221 " --> pdb=" O ILE L 366 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N GLY L 368 " --> pdb=" O GLN L 221 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL L 218 " --> pdb=" O LEU L 342 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP L 298 " --> pdb=" O ILE L 255 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 499 through 501 Processing sheet with id=AE4, first strand: chain 'L' and resid 650 through 655 removed outlier: 3.663A pdb=" N ILE L 653 " --> pdb=" O SER L 678 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LEU L 677 " --> pdb=" O ASP L 744 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LEU L 743 " --> pdb=" O TRP L 773 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N LEU L 772 " --> pdb=" O ASP L 801 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LEU L 800 " --> pdb=" O TRP L 830 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N LEU L 829 " --> pdb=" O TYR L 858 " (cutoff:3.500A) 3313 hydrogen bonds defined for protein. 9789 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: 29.58 Time building geometry restraints manager: 15.96 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: 24491 1.34 - 1.46: 16868 1.46 - 1.58: 35825 1.58 - 1.70: 36 1.70 - 1.82: 828 Bond restraints: 78048 Sorted by residual: bond pdb=" C08 7YN G1502 " pdb=" C09 7YN G1502 " ideal model delta sigma weight residual 1.340 1.530 -0.190 2.00e-02 2.50e+03 9.03e+01 bond pdb=" C08 7YN J1502 " pdb=" C09 7YN J1502 " ideal model delta sigma weight residual 1.340 1.530 -0.190 2.00e-02 2.50e+03 9.03e+01 bond pdb=" C08 7YN B1502 " pdb=" C09 7YN B1502 " ideal model delta sigma weight residual 1.340 1.530 -0.190 2.00e-02 2.50e+03 9.03e+01 bond pdb=" C08 7YN H1502 " pdb=" C09 7YN H1502 " ideal model delta sigma weight residual 1.340 1.530 -0.190 2.00e-02 2.50e+03 9.00e+01 bond pdb=" C08 7YN C1502 " pdb=" C09 7YN C1502 " ideal model delta sigma weight residual 1.340 1.530 -0.190 2.00e-02 2.50e+03 9.00e+01 ... (remaining 78043 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 102342 1.68 - 3.35: 2229 3.35 - 5.03: 527 5.03 - 6.70: 166 6.70 - 8.38: 72 Bond angle restraints: 105336 Sorted by residual: angle pdb=" CA CYS J 955 " pdb=" CB CYS J 955 " pdb=" SG CYS J 955 " ideal model delta sigma weight residual 114.40 121.71 -7.31 2.30e+00 1.89e-01 1.01e+01 angle pdb=" CA CYS D 955 " pdb=" CB CYS D 955 " pdb=" SG CYS D 955 " ideal model delta sigma weight residual 114.40 121.71 -7.31 2.30e+00 1.89e-01 1.01e+01 angle pdb=" CA CYS G 955 " pdb=" CB CYS G 955 " pdb=" SG CYS G 955 " ideal model delta sigma weight residual 114.40 121.68 -7.28 2.30e+00 1.89e-01 1.00e+01 angle pdb=" CA CYS A 955 " pdb=" CB CYS A 955 " pdb=" SG CYS A 955 " ideal model delta sigma weight residual 114.40 121.67 -7.27 2.30e+00 1.89e-01 1.00e+01 angle pdb=" CA CYS C 955 " pdb=" CB CYS C 955 " pdb=" SG CYS C 955 " ideal model delta sigma weight residual 114.40 121.67 -7.27 2.30e+00 1.89e-01 9.99e+00 ... (remaining 105331 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.29: 44500 26.29 - 52.58: 2286 52.58 - 78.87: 198 78.87 - 105.16: 44 105.16 - 131.45: 24 Dihedral angle restraints: 47052 sinusoidal: 19452 harmonic: 27600 Sorted by residual: dihedral pdb=" CB CYS F 955 " pdb=" SG CYS F 955 " pdb=" SG CYS F 982 " pdb=" CB CYS F 982 " ideal model delta sinusoidal sigma weight residual -86.00 -159.59 73.59 1 1.00e+01 1.00e-02 6.89e+01 dihedral pdb=" CB CYS C 955 " pdb=" SG CYS C 955 " pdb=" SG CYS C 982 " pdb=" CB CYS C 982 " ideal model delta sinusoidal sigma weight residual -86.00 -159.51 73.51 1 1.00e+01 1.00e-02 6.88e+01 dihedral pdb=" CB CYS I 955 " pdb=" SG CYS I 955 " pdb=" SG CYS I 982 " pdb=" CB CYS I 982 " ideal model delta sinusoidal sigma weight residual -86.00 -159.47 73.47 1 1.00e+01 1.00e-02 6.87e+01 ... (remaining 47049 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 8462 0.038 - 0.076: 2723 0.076 - 0.114: 672 0.114 - 0.152: 101 0.152 - 0.190: 18 Chirality restraints: 11976 Sorted by residual: chirality pdb=" CG LEU E 916 " pdb=" CB LEU E 916 " pdb=" CD1 LEU E 916 " pdb=" CD2 LEU E 916 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.01e-01 chirality pdb=" CG LEU D 916 " pdb=" CB LEU D 916 " pdb=" CD1 LEU D 916 " pdb=" CD2 LEU D 916 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.87e-01 chirality pdb=" CG LEU B 916 " pdb=" CB LEU B 916 " pdb=" CD1 LEU B 916 " pdb=" CD2 LEU B 916 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.84e-01 ... (remaining 11973 not shown) Planarity restraints: 13116 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C01 7YN E1502 " -0.029 2.00e-02 2.50e+03 5.25e-02 8.97e+01 pdb=" C02 7YN E1502 " -0.017 2.00e-02 2.50e+03 pdb=" C03 7YN E1502 " -0.035 2.00e-02 2.50e+03 pdb=" C04 7YN E1502 " -0.006 2.00e-02 2.50e+03 pdb=" C05 7YN E1502 " -0.026 2.00e-02 2.50e+03 pdb=" C06 7YN E1502 " -0.011 2.00e-02 2.50e+03 pdb=" C07 7YN E1502 " 0.011 2.00e-02 2.50e+03 pdb=" C08 7YN E1502 " 0.062 2.00e-02 2.50e+03 pdb=" C09 7YN E1502 " -0.000 2.00e-02 2.50e+03 pdb=" C10 7YN E1502 " -0.040 2.00e-02 2.50e+03 pdb=" C11 7YN E1502 " 0.155 2.00e-02 2.50e+03 pdb=" C12 7YN E1502 " -0.052 2.00e-02 2.50e+03 pdb=" N13 7YN E1502 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C01 7YN K1502 " -0.030 2.00e-02 2.50e+03 5.25e-02 8.96e+01 pdb=" C02 7YN K1502 " -0.018 2.00e-02 2.50e+03 pdb=" C03 7YN K1502 " -0.035 2.00e-02 2.50e+03 pdb=" C04 7YN K1502 " -0.006 2.00e-02 2.50e+03 pdb=" C05 7YN K1502 " -0.026 2.00e-02 2.50e+03 pdb=" C06 7YN K1502 " -0.011 2.00e-02 2.50e+03 pdb=" C07 7YN K1502 " 0.011 2.00e-02 2.50e+03 pdb=" C08 7YN K1502 " 0.063 2.00e-02 2.50e+03 pdb=" C09 7YN K1502 " -0.000 2.00e-02 2.50e+03 pdb=" C10 7YN K1502 " -0.040 2.00e-02 2.50e+03 pdb=" C11 7YN K1502 " 0.155 2.00e-02 2.50e+03 pdb=" C12 7YN K1502 " -0.052 2.00e-02 2.50e+03 pdb=" N13 7YN K1502 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C01 7YN B1502 " 0.029 2.00e-02 2.50e+03 5.18e-02 8.73e+01 pdb=" C02 7YN B1502 " 0.017 2.00e-02 2.50e+03 pdb=" C03 7YN B1502 " 0.035 2.00e-02 2.50e+03 pdb=" C04 7YN B1502 " 0.006 2.00e-02 2.50e+03 pdb=" C05 7YN B1502 " 0.026 2.00e-02 2.50e+03 pdb=" C06 7YN B1502 " 0.011 2.00e-02 2.50e+03 pdb=" C07 7YN B1502 " -0.011 2.00e-02 2.50e+03 pdb=" C08 7YN B1502 " -0.061 2.00e-02 2.50e+03 pdb=" C09 7YN B1502 " -0.000 2.00e-02 2.50e+03 pdb=" C10 7YN B1502 " 0.040 2.00e-02 2.50e+03 pdb=" C11 7YN B1502 " -0.153 2.00e-02 2.50e+03 pdb=" C12 7YN B1502 " 0.051 2.00e-02 2.50e+03 pdb=" N13 7YN B1502 " 0.010 2.00e-02 2.50e+03 ... (remaining 13113 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 1633 2.69 - 3.24: 77401 3.24 - 3.79: 120294 3.79 - 4.35: 163397 4.35 - 4.90: 261153 Nonbonded interactions: 623878 Sorted by model distance: nonbonded pdb=" O ASP A 301 " pdb=" OH TYR A 570 " model vdw 2.136 3.040 nonbonded pdb=" O ASP D 301 " pdb=" OH TYR D 570 " model vdw 2.136 3.040 nonbonded pdb=" O ASP G 301 " pdb=" OH TYR G 570 " model vdw 2.136 3.040 nonbonded pdb=" O ASP J 301 " pdb=" OH TYR J 570 " model vdw 2.136 3.040 nonbonded pdb=" O ASP H 301 " pdb=" OH TYR H 570 " model vdw 2.140 3.040 ... (remaining 623873 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.500 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: 0.050 Extract box with map and model: 2.040 Check model and map are aligned: 0.430 Set scattering table: 0.520 Process input model: 126.330 Find NCS groups from input model: 2.610 Set up NCS constraints: 0.360 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:2.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 134.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6290 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.190 78048 Z= 0.266 Angle : 0.684 8.376 105336 Z= 0.338 Chirality : 0.040 0.190 11976 Planarity : 0.003 0.053 13116 Dihedral : 15.119 131.446 29040 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 0.05 % Allowed : 0.22 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.09), residues: 9300 helix: 1.13 (0.08), residues: 4548 sheet: -1.43 (0.16), residues: 1188 loop : -0.99 (0.11), residues: 3564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP C 474 HIS 0.004 0.001 HIS C 518 PHE 0.040 0.002 PHE C 378 TYR 0.012 0.001 TYR H 630 ARG 0.009 0.000 ARG L1013 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18600 Ramachandran restraints generated. 9300 Oldfield, 0 Emsley, 9300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18600 Ramachandran restraints generated. 9300 Oldfield, 0 Emsley, 9300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 8616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 520 time to evaluate : 6.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 422 MET cc_start: 0.3095 (ptt) cc_final: 0.2848 (ptp) REVERT: F 422 MET cc_start: 0.3071 (ptt) cc_final: 0.2813 (ptp) REVERT: H 422 MET cc_start: 0.3263 (ptt) cc_final: 0.2969 (ptp) REVERT: I 422 MET cc_start: 0.3103 (ptt) cc_final: 0.2843 (ptp) REVERT: L 422 MET cc_start: 0.3078 (ptt) cc_final: 0.2829 (ptp) outliers start: 4 outliers final: 4 residues processed: 524 average time/residue: 0.6516 time to fit residues: 608.4271 Evaluate side-chains 310 residues out of total 8616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 306 time to evaluate : 6.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 396 GLN Chi-restraints excluded: chain E residue 396 GLN Chi-restraints excluded: chain H residue 396 GLN Chi-restraints excluded: chain K residue 396 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 936 random chunks: chunk 790 optimal weight: 5.9990 chunk 709 optimal weight: 5.9990 chunk 393 optimal weight: 4.9990 chunk 242 optimal weight: 20.0000 chunk 478 optimal weight: 50.0000 chunk 379 optimal weight: 20.0000 chunk 733 optimal weight: 7.9990 chunk 283 optimal weight: 20.0000 chunk 446 optimal weight: 9.9990 chunk 546 optimal weight: 50.0000 chunk 849 optimal weight: 20.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 ASN B 957 ASN C 957 ASN D 957 ASN E 957 ASN F 957 ASN G 957 ASN H 957 ASN I 957 ASN J 957 ASN L 957 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6383 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 78048 Z= 0.252 Angle : 0.665 12.421 105336 Z= 0.323 Chirality : 0.040 0.335 11976 Planarity : 0.003 0.029 13116 Dihedral : 8.980 140.635 10416 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.91 % Allowed : 6.72 % Favored : 92.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.09), residues: 9300 helix: 1.44 (0.08), residues: 4548 sheet: -1.62 (0.16), residues: 1212 loop : -0.80 (0.11), residues: 3540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 621 HIS 0.004 0.001 HIS E 781 PHE 0.024 0.002 PHE C 378 TYR 0.014 0.001 TYR C 514 ARG 0.005 0.000 ARG D1013 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18600 Ramachandran restraints generated. 9300 Oldfield, 0 Emsley, 9300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18600 Ramachandran restraints generated. 9300 Oldfield, 0 Emsley, 9300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 8616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 335 time to evaluate : 6.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 78 outliers final: 35 residues processed: 382 average time/residue: 0.6642 time to fit residues: 454.9589 Evaluate side-chains 326 residues out of total 8616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 291 time to evaluate : 6.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 570 TYR Chi-restraints excluded: chain A residue 621 TRP Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 1021 GLU Chi-restraints excluded: chain B residue 396 GLN Chi-restraints excluded: chain B residue 501 MET Chi-restraints excluded: chain B residue 1021 GLU Chi-restraints excluded: chain C residue 1021 GLU Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 570 TYR Chi-restraints excluded: chain D residue 621 TRP Chi-restraints excluded: chain D residue 787 ILE Chi-restraints excluded: chain D residue 1021 GLU Chi-restraints excluded: chain E residue 396 GLN Chi-restraints excluded: chain E residue 501 MET Chi-restraints excluded: chain E residue 1021 GLU Chi-restraints excluded: chain F residue 1021 GLU Chi-restraints excluded: chain G residue 343 LEU Chi-restraints excluded: chain G residue 570 TYR Chi-restraints excluded: chain G residue 621 TRP Chi-restraints excluded: chain G residue 1021 GLU Chi-restraints excluded: chain H residue 396 GLN Chi-restraints excluded: chain H residue 1021 GLU Chi-restraints excluded: chain I residue 231 LEU Chi-restraints excluded: chain I residue 1021 GLU Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 570 TYR Chi-restraints excluded: chain J residue 621 TRP Chi-restraints excluded: chain J residue 787 ILE Chi-restraints excluded: chain J residue 1021 GLU Chi-restraints excluded: chain K residue 396 GLN Chi-restraints excluded: chain K residue 1021 GLU Chi-restraints excluded: chain L residue 231 LEU Chi-restraints excluded: chain L residue 1021 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 936 random chunks: chunk 472 optimal weight: 7.9990 chunk 263 optimal weight: 7.9990 chunk 707 optimal weight: 50.0000 chunk 578 optimal weight: 7.9990 chunk 234 optimal weight: 50.0000 chunk 851 optimal weight: 9.9990 chunk 919 optimal weight: 8.9990 chunk 758 optimal weight: 9.9990 chunk 844 optimal weight: 7.9990 chunk 290 optimal weight: 10.0000 chunk 683 optimal weight: 7.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 600 GLN ** A 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 600 GLN C 600 GLN ** C 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 976 ASN D 600 GLN E 600 GLN F 600 GLN ** F 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 600 GLN ** G 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 600 GLN I 600 GLN ** I 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 976 ASN J 600 GLN K 600 GLN L 600 GLN ** L 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6435 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 78048 Z= 0.259 Angle : 0.646 10.702 105336 Z= 0.311 Chirality : 0.040 0.322 11976 Planarity : 0.003 0.028 13116 Dihedral : 8.480 140.952 10416 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.15 % Allowed : 9.39 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.09), residues: 9300 helix: 1.47 (0.08), residues: 4620 sheet: -1.83 (0.15), residues: 1224 loop : -0.80 (0.11), residues: 3456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 621 HIS 0.005 0.001 HIS A 672 PHE 0.019 0.002 PHE C 378 TYR 0.010 0.001 TYR I 570 ARG 0.005 0.000 ARG E 756 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18600 Ramachandran restraints generated. 9300 Oldfield, 0 Emsley, 9300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18600 Ramachandran restraints generated. 9300 Oldfield, 0 Emsley, 9300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 8616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 305 time to evaluate : 6.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 942 MET cc_start: 0.7176 (tmm) cc_final: 0.6712 (tmm) REVERT: E 942 MET cc_start: 0.7145 (tmm) cc_final: 0.6768 (tmm) REVERT: H 942 MET cc_start: 0.7149 (tmm) cc_final: 0.6767 (tmm) REVERT: K 942 MET cc_start: 0.7151 (tmm) cc_final: 0.6764 (tmm) outliers start: 99 outliers final: 35 residues processed: 385 average time/residue: 0.6953 time to fit residues: 488.1844 Evaluate side-chains 294 residues out of total 8616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 259 time to evaluate : 6.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 570 TYR Chi-restraints excluded: chain A residue 621 TRP Chi-restraints excluded: chain A residue 1021 GLU Chi-restraints excluded: chain B residue 396 GLN Chi-restraints excluded: chain B residue 501 MET Chi-restraints excluded: chain B residue 872 LEU Chi-restraints excluded: chain B residue 1021 GLU Chi-restraints excluded: chain C residue 876 MET Chi-restraints excluded: chain C residue 1021 GLU Chi-restraints excluded: chain D residue 570 TYR Chi-restraints excluded: chain D residue 621 TRP Chi-restraints excluded: chain D residue 1021 GLU Chi-restraints excluded: chain E residue 396 GLN Chi-restraints excluded: chain E residue 501 MET Chi-restraints excluded: chain E residue 872 LEU Chi-restraints excluded: chain E residue 1021 GLU Chi-restraints excluded: chain F residue 876 MET Chi-restraints excluded: chain F residue 1021 GLU Chi-restraints excluded: chain G residue 570 TYR Chi-restraints excluded: chain G residue 621 TRP Chi-restraints excluded: chain G residue 1021 GLU Chi-restraints excluded: chain H residue 396 GLN Chi-restraints excluded: chain H residue 570 TYR Chi-restraints excluded: chain H residue 872 LEU Chi-restraints excluded: chain H residue 1021 GLU Chi-restraints excluded: chain I residue 876 MET Chi-restraints excluded: chain I residue 1021 GLU Chi-restraints excluded: chain J residue 570 TYR Chi-restraints excluded: chain J residue 621 TRP Chi-restraints excluded: chain J residue 1021 GLU Chi-restraints excluded: chain K residue 396 GLN Chi-restraints excluded: chain K residue 872 LEU Chi-restraints excluded: chain K residue 1021 GLU Chi-restraints excluded: chain L residue 876 MET Chi-restraints excluded: chain L residue 1021 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 936 random chunks: chunk 841 optimal weight: 0.3980 chunk 640 optimal weight: 50.0000 chunk 441 optimal weight: 7.9990 chunk 94 optimal weight: 40.0000 chunk 406 optimal weight: 50.0000 chunk 571 optimal weight: 20.0000 chunk 854 optimal weight: 6.9990 chunk 904 optimal weight: 10.0000 chunk 446 optimal weight: 5.9990 chunk 809 optimal weight: 50.0000 chunk 243 optimal weight: 8.9990 overall best weight: 6.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6428 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 78048 Z= 0.215 Angle : 0.639 12.523 105336 Z= 0.299 Chirality : 0.040 0.408 11976 Planarity : 0.003 0.030 13116 Dihedral : 8.301 142.234 10416 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.17 % Allowed : 10.82 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.09), residues: 9300 helix: 1.43 (0.08), residues: 4716 sheet: -1.88 (0.15), residues: 1224 loop : -0.83 (0.11), residues: 3360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 621 HIS 0.004 0.001 HIS C 139 PHE 0.016 0.001 PHE I 640 TYR 0.011 0.001 TYR E 132 ARG 0.002 0.000 ARG E 673 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18600 Ramachandran restraints generated. 9300 Oldfield, 0 Emsley, 9300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18600 Ramachandran restraints generated. 9300 Oldfield, 0 Emsley, 9300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 8616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 297 time to evaluate : 6.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 942 MET cc_start: 0.7018 (tmm) cc_final: 0.6664 (tmm) REVERT: E 942 MET cc_start: 0.6969 (tmm) cc_final: 0.6646 (tmm) REVERT: H 942 MET cc_start: 0.6972 (tmm) cc_final: 0.6637 (tmm) REVERT: K 942 MET cc_start: 0.6984 (tmm) cc_final: 0.6651 (tmm) outliers start: 101 outliers final: 38 residues processed: 385 average time/residue: 0.6240 time to fit residues: 440.3780 Evaluate side-chains 297 residues out of total 8616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 259 time to evaluate : 6.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 621 TRP Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 1021 GLU Chi-restraints excluded: chain B residue 396 GLN Chi-restraints excluded: chain B residue 501 MET Chi-restraints excluded: chain B residue 570 TYR Chi-restraints excluded: chain B residue 872 LEU Chi-restraints excluded: chain B residue 1021 GLU Chi-restraints excluded: chain C residue 876 MET Chi-restraints excluded: chain C residue 1021 GLU Chi-restraints excluded: chain D residue 621 TRP Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain D residue 1021 GLU Chi-restraints excluded: chain E residue 396 GLN Chi-restraints excluded: chain E residue 501 MET Chi-restraints excluded: chain E residue 570 TYR Chi-restraints excluded: chain E residue 872 LEU Chi-restraints excluded: chain E residue 1021 GLU Chi-restraints excluded: chain F residue 876 MET Chi-restraints excluded: chain F residue 1021 GLU Chi-restraints excluded: chain G residue 621 TRP Chi-restraints excluded: chain G residue 762 LEU Chi-restraints excluded: chain G residue 1021 GLU Chi-restraints excluded: chain H residue 396 GLN Chi-restraints excluded: chain H residue 570 TYR Chi-restraints excluded: chain H residue 872 LEU Chi-restraints excluded: chain H residue 1021 GLU Chi-restraints excluded: chain I residue 876 MET Chi-restraints excluded: chain I residue 1021 GLU Chi-restraints excluded: chain J residue 621 TRP Chi-restraints excluded: chain J residue 762 LEU Chi-restraints excluded: chain J residue 1021 GLU Chi-restraints excluded: chain K residue 396 GLN Chi-restraints excluded: chain K residue 570 TYR Chi-restraints excluded: chain K residue 872 LEU Chi-restraints excluded: chain K residue 1021 GLU Chi-restraints excluded: chain L residue 876 MET Chi-restraints excluded: chain L residue 1021 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 936 random chunks: chunk 753 optimal weight: 9.9990 chunk 513 optimal weight: 2.9990 chunk 13 optimal weight: 50.0000 chunk 673 optimal weight: 20.0000 chunk 373 optimal weight: 0.4980 chunk 772 optimal weight: 20.0000 chunk 625 optimal weight: 2.9990 chunk 1 optimal weight: 50.0000 chunk 461 optimal weight: 10.0000 chunk 812 optimal weight: 30.0000 chunk 228 optimal weight: 0.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6391 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 78048 Z= 0.164 Angle : 0.646 13.919 105336 Z= 0.296 Chirality : 0.042 0.490 11976 Planarity : 0.002 0.030 13116 Dihedral : 8.140 143.354 10416 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.94 % Allowed : 11.93 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.09), residues: 9300 helix: 1.54 (0.08), residues: 4656 sheet: -1.78 (0.15), residues: 1200 loop : -0.54 (0.11), residues: 3444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 621 HIS 0.004 0.001 HIS A 139 PHE 0.015 0.001 PHE D 392 TYR 0.009 0.001 TYR A 132 ARG 0.002 0.000 ARG E 673 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18600 Ramachandran restraints generated. 9300 Oldfield, 0 Emsley, 9300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18600 Ramachandran restraints generated. 9300 Oldfield, 0 Emsley, 9300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 8616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 329 time to evaluate : 6.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.5060 (ppp) cc_final: 0.4747 (ppp) REVERT: B 942 MET cc_start: 0.7014 (tmm) cc_final: 0.6597 (tmm) REVERT: C 942 MET cc_start: 0.7718 (tmm) cc_final: 0.7294 (tmm) REVERT: E 942 MET cc_start: 0.7006 (tmm) cc_final: 0.6580 (tmm) REVERT: F 942 MET cc_start: 0.7687 (tmm) cc_final: 0.7231 (tmm) REVERT: H 942 MET cc_start: 0.7008 (tmm) cc_final: 0.6583 (tmm) REVERT: I 942 MET cc_start: 0.7709 (tmm) cc_final: 0.7286 (tmm) REVERT: K 942 MET cc_start: 0.6912 (tmm) cc_final: 0.6519 (tmm) REVERT: L 942 MET cc_start: 0.7708 (tmm) cc_final: 0.7292 (tmm) outliers start: 81 outliers final: 42 residues processed: 400 average time/residue: 0.6471 time to fit residues: 470.7758 Evaluate side-chains 320 residues out of total 8616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 278 time to evaluate : 6.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 570 TYR Chi-restraints excluded: chain A residue 621 TRP Chi-restraints excluded: chain A residue 1021 GLU Chi-restraints excluded: chain B residue 396 GLN Chi-restraints excluded: chain B residue 501 MET Chi-restraints excluded: chain B residue 570 TYR Chi-restraints excluded: chain B residue 611 GLU Chi-restraints excluded: chain B residue 872 LEU Chi-restraints excluded: chain B residue 1021 GLU Chi-restraints excluded: chain C residue 876 MET Chi-restraints excluded: chain C residue 1021 GLU Chi-restraints excluded: chain D residue 570 TYR Chi-restraints excluded: chain D residue 621 TRP Chi-restraints excluded: chain D residue 1021 GLU Chi-restraints excluded: chain E residue 396 GLN Chi-restraints excluded: chain E residue 501 MET Chi-restraints excluded: chain E residue 570 TYR Chi-restraints excluded: chain E residue 611 GLU Chi-restraints excluded: chain E residue 872 LEU Chi-restraints excluded: chain E residue 1021 GLU Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain F residue 876 MET Chi-restraints excluded: chain F residue 1021 GLU Chi-restraints excluded: chain G residue 570 TYR Chi-restraints excluded: chain G residue 621 TRP Chi-restraints excluded: chain G residue 1021 GLU Chi-restraints excluded: chain H residue 396 GLN Chi-restraints excluded: chain H residue 570 TYR Chi-restraints excluded: chain H residue 872 LEU Chi-restraints excluded: chain H residue 1021 GLU Chi-restraints excluded: chain I residue 876 MET Chi-restraints excluded: chain I residue 1021 GLU Chi-restraints excluded: chain J residue 570 TYR Chi-restraints excluded: chain J residue 621 TRP Chi-restraints excluded: chain J residue 1021 GLU Chi-restraints excluded: chain K residue 396 GLN Chi-restraints excluded: chain K residue 570 TYR Chi-restraints excluded: chain K residue 611 GLU Chi-restraints excluded: chain K residue 872 LEU Chi-restraints excluded: chain K residue 1021 GLU Chi-restraints excluded: chain L residue 876 MET Chi-restraints excluded: chain L residue 1021 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 936 random chunks: chunk 304 optimal weight: 20.0000 chunk 814 optimal weight: 40.0000 chunk 178 optimal weight: 5.9990 chunk 531 optimal weight: 10.0000 chunk 223 optimal weight: 8.9990 chunk 905 optimal weight: 20.0000 chunk 751 optimal weight: 0.9980 chunk 419 optimal weight: 50.0000 chunk 75 optimal weight: 10.0000 chunk 299 optimal weight: 7.9990 chunk 475 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6451 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 78048 Z= 0.227 Angle : 0.687 14.496 105336 Z= 0.321 Chirality : 0.042 0.512 11976 Planarity : 0.003 0.031 13116 Dihedral : 8.023 143.527 10416 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.88 % Allowed : 13.51 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.09), residues: 9300 helix: 1.37 (0.08), residues: 4728 sheet: -1.98 (0.15), residues: 1296 loop : -0.40 (0.11), residues: 3276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 773 HIS 0.004 0.001 HIS F 781 PHE 0.013 0.001 PHE D 392 TYR 0.016 0.001 TYR I 132 ARG 0.011 0.000 ARG F1013 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18600 Ramachandran restraints generated. 9300 Oldfield, 0 Emsley, 9300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18600 Ramachandran restraints generated. 9300 Oldfield, 0 Emsley, 9300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 8616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 295 time to evaluate : 6.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.5369 (ppp) cc_final: 0.5119 (ppp) REVERT: A 297 MET cc_start: 0.7412 (mpp) cc_final: 0.7187 (mpp) REVERT: A 501 MET cc_start: 0.5811 (mmp) cc_final: 0.5552 (mmp) REVERT: D 135 MET cc_start: 0.5368 (ppp) cc_final: 0.4800 (ppp) REVERT: D 297 MET cc_start: 0.7411 (mpp) cc_final: 0.7185 (mpp) REVERT: D 501 MET cc_start: 0.5834 (mmp) cc_final: 0.5573 (mmp) REVERT: G 135 MET cc_start: 0.5388 (ppp) cc_final: 0.4822 (ppp) REVERT: J 135 MET cc_start: 0.5374 (ppp) cc_final: 0.4809 (ppp) REVERT: J 501 MET cc_start: 0.5803 (mmp) cc_final: 0.5539 (mmp) outliers start: 76 outliers final: 38 residues processed: 361 average time/residue: 0.6411 time to fit residues: 423.2772 Evaluate side-chains 303 residues out of total 8616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 265 time to evaluate : 6.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 570 TYR Chi-restraints excluded: chain A residue 621 TRP Chi-restraints excluded: chain A residue 1021 GLU Chi-restraints excluded: chain B residue 396 GLN Chi-restraints excluded: chain B residue 501 MET Chi-restraints excluded: chain B residue 570 TYR Chi-restraints excluded: chain B residue 872 LEU Chi-restraints excluded: chain B residue 1021 GLU Chi-restraints excluded: chain C residue 876 MET Chi-restraints excluded: chain C residue 1021 GLU Chi-restraints excluded: chain D residue 570 TYR Chi-restraints excluded: chain D residue 621 TRP Chi-restraints excluded: chain D residue 1021 GLU Chi-restraints excluded: chain E residue 396 GLN Chi-restraints excluded: chain E residue 501 MET Chi-restraints excluded: chain E residue 570 TYR Chi-restraints excluded: chain E residue 872 LEU Chi-restraints excluded: chain E residue 1021 GLU Chi-restraints excluded: chain F residue 876 MET Chi-restraints excluded: chain F residue 1021 GLU Chi-restraints excluded: chain G residue 570 TYR Chi-restraints excluded: chain G residue 1021 GLU Chi-restraints excluded: chain H residue 396 GLN Chi-restraints excluded: chain H residue 570 TYR Chi-restraints excluded: chain H residue 611 GLU Chi-restraints excluded: chain H residue 872 LEU Chi-restraints excluded: chain H residue 1021 GLU Chi-restraints excluded: chain I residue 876 MET Chi-restraints excluded: chain I residue 1021 GLU Chi-restraints excluded: chain J residue 570 TYR Chi-restraints excluded: chain J residue 621 TRP Chi-restraints excluded: chain J residue 1021 GLU Chi-restraints excluded: chain K residue 396 GLN Chi-restraints excluded: chain K residue 570 TYR Chi-restraints excluded: chain K residue 872 LEU Chi-restraints excluded: chain K residue 1021 GLU Chi-restraints excluded: chain L residue 876 MET Chi-restraints excluded: chain L residue 1021 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 936 random chunks: chunk 873 optimal weight: 50.0000 chunk 102 optimal weight: 8.9990 chunk 515 optimal weight: 0.5980 chunk 661 optimal weight: 20.0000 chunk 512 optimal weight: 8.9990 chunk 762 optimal weight: 5.9990 chunk 505 optimal weight: 8.9990 chunk 902 optimal weight: 30.0000 chunk 564 optimal weight: 6.9990 chunk 550 optimal weight: 10.0000 chunk 416 optimal weight: 6.9990 overall best weight: 5.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6448 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 78048 Z= 0.207 Angle : 0.682 17.111 105336 Z= 0.316 Chirality : 0.042 0.509 11976 Planarity : 0.003 0.032 13116 Dihedral : 7.911 144.104 10416 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.85 % Allowed : 14.14 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.09), residues: 9300 helix: 1.40 (0.08), residues: 4740 sheet: -2.03 (0.15), residues: 1296 loop : -0.38 (0.11), residues: 3264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 773 HIS 0.005 0.001 HIS E 647 PHE 0.014 0.001 PHE E 648 TYR 0.011 0.001 TYR C 630 ARG 0.010 0.000 ARG C1013 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18600 Ramachandran restraints generated. 9300 Oldfield, 0 Emsley, 9300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18600 Ramachandran restraints generated. 9300 Oldfield, 0 Emsley, 9300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 8616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 292 time to evaluate : 6.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 MET cc_start: 0.7331 (mpp) cc_final: 0.7084 (mpp) REVERT: D 135 MET cc_start: 0.5123 (ppp) cc_final: 0.4575 (ppp) REVERT: D 297 MET cc_start: 0.7332 (mpp) cc_final: 0.7086 (mpp) REVERT: G 135 MET cc_start: 0.5156 (ppp) cc_final: 0.4602 (ppp) REVERT: J 135 MET cc_start: 0.5142 (ppp) cc_final: 0.4593 (ppp) outliers start: 73 outliers final: 45 residues processed: 354 average time/residue: 0.6399 time to fit residues: 413.0299 Evaluate side-chains 324 residues out of total 8616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 279 time to evaluate : 6.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 570 TYR Chi-restraints excluded: chain A residue 621 TRP Chi-restraints excluded: chain A residue 1021 GLU Chi-restraints excluded: chain B residue 396 GLN Chi-restraints excluded: chain B residue 501 MET Chi-restraints excluded: chain B residue 570 TYR Chi-restraints excluded: chain B residue 611 GLU Chi-restraints excluded: chain B residue 872 LEU Chi-restraints excluded: chain B residue 1021 GLU Chi-restraints excluded: chain C residue 876 MET Chi-restraints excluded: chain C residue 1021 GLU Chi-restraints excluded: chain D residue 570 TYR Chi-restraints excluded: chain D residue 621 TRP Chi-restraints excluded: chain D residue 1021 GLU Chi-restraints excluded: chain E residue 396 GLN Chi-restraints excluded: chain E residue 501 MET Chi-restraints excluded: chain E residue 570 TYR Chi-restraints excluded: chain E residue 611 GLU Chi-restraints excluded: chain E residue 872 LEU Chi-restraints excluded: chain E residue 1021 GLU Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain F residue 876 MET Chi-restraints excluded: chain F residue 1021 GLU Chi-restraints excluded: chain G residue 570 TYR Chi-restraints excluded: chain G residue 621 TRP Chi-restraints excluded: chain G residue 1021 GLU Chi-restraints excluded: chain H residue 396 GLN Chi-restraints excluded: chain H residue 570 TYR Chi-restraints excluded: chain H residue 611 GLU Chi-restraints excluded: chain H residue 630 TYR Chi-restraints excluded: chain H residue 872 LEU Chi-restraints excluded: chain H residue 1021 GLU Chi-restraints excluded: chain I residue 876 MET Chi-restraints excluded: chain I residue 1021 GLU Chi-restraints excluded: chain J residue 570 TYR Chi-restraints excluded: chain J residue 621 TRP Chi-restraints excluded: chain J residue 1021 GLU Chi-restraints excluded: chain K residue 396 GLN Chi-restraints excluded: chain K residue 570 TYR Chi-restraints excluded: chain K residue 611 GLU Chi-restraints excluded: chain K residue 872 LEU Chi-restraints excluded: chain K residue 1021 GLU Chi-restraints excluded: chain L residue 343 LEU Chi-restraints excluded: chain L residue 876 MET Chi-restraints excluded: chain L residue 1021 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 936 random chunks: chunk 558 optimal weight: 9.9990 chunk 360 optimal weight: 20.0000 chunk 538 optimal weight: 9.9990 chunk 271 optimal weight: 20.0000 chunk 177 optimal weight: 8.9990 chunk 174 optimal weight: 40.0000 chunk 573 optimal weight: 5.9990 chunk 614 optimal weight: 6.9990 chunk 446 optimal weight: 7.9990 chunk 84 optimal weight: 9.9990 chunk 709 optimal weight: 7.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6489 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 78048 Z= 0.246 Angle : 0.716 16.013 105336 Z= 0.334 Chirality : 0.043 0.491 11976 Planarity : 0.003 0.032 13116 Dihedral : 7.868 144.221 10416 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.79 % Allowed : 14.38 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.09), residues: 9300 helix: 1.35 (0.08), residues: 4740 sheet: -2.07 (0.15), residues: 1308 loop : -0.44 (0.11), residues: 3252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 773 HIS 0.004 0.001 HIS J 781 PHE 0.012 0.001 PHE J 640 TYR 0.015 0.001 TYR A 132 ARG 0.009 0.000 ARG F1013 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18600 Ramachandran restraints generated. 9300 Oldfield, 0 Emsley, 9300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18600 Ramachandran restraints generated. 9300 Oldfield, 0 Emsley, 9300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 8616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 287 time to evaluate : 6.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 MET cc_start: 0.7348 (mpp) cc_final: 0.7117 (mpp) REVERT: D 135 MET cc_start: 0.5155 (ppp) cc_final: 0.4529 (ppp) REVERT: D 297 MET cc_start: 0.7350 (mpp) cc_final: 0.7120 (mpp) REVERT: G 135 MET cc_start: 0.5187 (ppp) cc_final: 0.4551 (ppp) REVERT: J 135 MET cc_start: 0.5175 (ppp) cc_final: 0.4546 (ppp) REVERT: L 297 MET cc_start: 0.7337 (mpp) cc_final: 0.6987 (tmm) outliers start: 68 outliers final: 48 residues processed: 336 average time/residue: 0.7645 time to fit residues: 475.0413 Evaluate side-chains 328 residues out of total 8616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 280 time to evaluate : 6.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 570 TYR Chi-restraints excluded: chain A residue 621 TRP Chi-restraints excluded: chain A residue 1021 GLU Chi-restraints excluded: chain B residue 396 GLN Chi-restraints excluded: chain B residue 501 MET Chi-restraints excluded: chain B residue 570 TYR Chi-restraints excluded: chain B residue 611 GLU Chi-restraints excluded: chain B residue 872 LEU Chi-restraints excluded: chain B residue 915 TYR Chi-restraints excluded: chain B residue 1021 GLU Chi-restraints excluded: chain C residue 876 MET Chi-restraints excluded: chain C residue 1021 GLU Chi-restraints excluded: chain D residue 570 TYR Chi-restraints excluded: chain D residue 621 TRP Chi-restraints excluded: chain D residue 1021 GLU Chi-restraints excluded: chain E residue 396 GLN Chi-restraints excluded: chain E residue 501 MET Chi-restraints excluded: chain E residue 570 TYR Chi-restraints excluded: chain E residue 611 GLU Chi-restraints excluded: chain E residue 872 LEU Chi-restraints excluded: chain E residue 915 TYR Chi-restraints excluded: chain E residue 1021 GLU Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain F residue 876 MET Chi-restraints excluded: chain F residue 1021 GLU Chi-restraints excluded: chain G residue 570 TYR Chi-restraints excluded: chain G residue 621 TRP Chi-restraints excluded: chain G residue 1021 GLU Chi-restraints excluded: chain H residue 396 GLN Chi-restraints excluded: chain H residue 570 TYR Chi-restraints excluded: chain H residue 611 GLU Chi-restraints excluded: chain H residue 872 LEU Chi-restraints excluded: chain H residue 915 TYR Chi-restraints excluded: chain H residue 1021 GLU Chi-restraints excluded: chain I residue 876 MET Chi-restraints excluded: chain I residue 1021 GLU Chi-restraints excluded: chain J residue 570 TYR Chi-restraints excluded: chain J residue 621 TRP Chi-restraints excluded: chain J residue 1021 GLU Chi-restraints excluded: chain K residue 396 GLN Chi-restraints excluded: chain K residue 570 TYR Chi-restraints excluded: chain K residue 611 GLU Chi-restraints excluded: chain K residue 872 LEU Chi-restraints excluded: chain K residue 915 TYR Chi-restraints excluded: chain K residue 1021 GLU Chi-restraints excluded: chain L residue 343 LEU Chi-restraints excluded: chain L residue 876 MET Chi-restraints excluded: chain L residue 1021 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 936 random chunks: chunk 820 optimal weight: 10.0000 chunk 864 optimal weight: 40.0000 chunk 788 optimal weight: 5.9990 chunk 840 optimal weight: 6.9990 chunk 506 optimal weight: 2.9990 chunk 366 optimal weight: 9.9990 chunk 660 optimal weight: 6.9990 chunk 257 optimal weight: 4.9990 chunk 759 optimal weight: 7.9990 chunk 795 optimal weight: 40.0000 chunk 837 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6462 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 78048 Z= 0.201 Angle : 0.699 19.227 105336 Z= 0.324 Chirality : 0.043 0.461 11976 Planarity : 0.003 0.033 13116 Dihedral : 7.770 145.186 10416 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.66 % Allowed : 14.51 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.09), residues: 9300 helix: 1.41 (0.08), residues: 4740 sheet: -1.99 (0.16), residues: 1212 loop : -0.37 (0.11), residues: 3348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 773 HIS 0.004 0.001 HIS I 139 PHE 0.013 0.001 PHE D 640 TYR 0.023 0.001 TYR C 132 ARG 0.009 0.000 ARG F1013 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18600 Ramachandran restraints generated. 9300 Oldfield, 0 Emsley, 9300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18600 Ramachandran restraints generated. 9300 Oldfield, 0 Emsley, 9300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 8616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 297 time to evaluate : 6.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.5204 (ppp) cc_final: 0.4954 (ppp) REVERT: A 297 MET cc_start: 0.7321 (mpp) cc_final: 0.7096 (mpp) REVERT: D 135 MET cc_start: 0.5181 (ppp) cc_final: 0.4595 (ppp) REVERT: D 297 MET cc_start: 0.7324 (mpp) cc_final: 0.7093 (mpp) REVERT: E 135 MET cc_start: 0.5653 (tmm) cc_final: 0.5437 (ppp) REVERT: F 297 MET cc_start: 0.7276 (mpp) cc_final: 0.6922 (tmm) REVERT: G 135 MET cc_start: 0.5252 (ppp) cc_final: 0.4628 (ppp) REVERT: J 135 MET cc_start: 0.5242 (ppp) cc_final: 0.4621 (ppp) REVERT: K 135 MET cc_start: 0.5622 (tmm) cc_final: 0.5420 (ppp) REVERT: L 297 MET cc_start: 0.7309 (mpp) cc_final: 0.6978 (tmm) outliers start: 57 outliers final: 47 residues processed: 342 average time/residue: 0.6455 time to fit residues: 403.8770 Evaluate side-chains 330 residues out of total 8616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 283 time to evaluate : 6.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 570 TYR Chi-restraints excluded: chain A residue 621 TRP Chi-restraints excluded: chain A residue 1021 GLU Chi-restraints excluded: chain B residue 396 GLN Chi-restraints excluded: chain B residue 570 TYR Chi-restraints excluded: chain B residue 611 GLU Chi-restraints excluded: chain B residue 872 LEU Chi-restraints excluded: chain B residue 1021 GLU Chi-restraints excluded: chain C residue 876 MET Chi-restraints excluded: chain C residue 1021 GLU Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 570 TYR Chi-restraints excluded: chain D residue 621 TRP Chi-restraints excluded: chain D residue 1021 GLU Chi-restraints excluded: chain E residue 396 GLN Chi-restraints excluded: chain E residue 570 TYR Chi-restraints excluded: chain E residue 611 GLU Chi-restraints excluded: chain E residue 872 LEU Chi-restraints excluded: chain E residue 1021 GLU Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain F residue 876 MET Chi-restraints excluded: chain F residue 1021 GLU Chi-restraints excluded: chain G residue 322 VAL Chi-restraints excluded: chain G residue 570 TYR Chi-restraints excluded: chain G residue 621 TRP Chi-restraints excluded: chain G residue 1021 GLU Chi-restraints excluded: chain H residue 396 GLN Chi-restraints excluded: chain H residue 570 TYR Chi-restraints excluded: chain H residue 611 GLU Chi-restraints excluded: chain H residue 630 TYR Chi-restraints excluded: chain H residue 872 LEU Chi-restraints excluded: chain H residue 1021 GLU Chi-restraints excluded: chain I residue 876 MET Chi-restraints excluded: chain I residue 1021 GLU Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain J residue 570 TYR Chi-restraints excluded: chain J residue 621 TRP Chi-restraints excluded: chain J residue 1021 GLU Chi-restraints excluded: chain K residue 396 GLN Chi-restraints excluded: chain K residue 570 TYR Chi-restraints excluded: chain K residue 611 GLU Chi-restraints excluded: chain K residue 872 LEU Chi-restraints excluded: chain K residue 1021 GLU Chi-restraints excluded: chain L residue 343 LEU Chi-restraints excluded: chain L residue 876 MET Chi-restraints excluded: chain L residue 1021 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 936 random chunks: chunk 552 optimal weight: 7.9990 chunk 888 optimal weight: 50.0000 chunk 542 optimal weight: 8.9990 chunk 421 optimal weight: 7.9990 chunk 617 optimal weight: 5.9990 chunk 932 optimal weight: 1.9990 chunk 858 optimal weight: 70.0000 chunk 742 optimal weight: 7.9990 chunk 77 optimal weight: 8.9990 chunk 573 optimal weight: 40.0000 chunk 455 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6474 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 78048 Z= 0.212 Angle : 0.712 15.123 105336 Z= 0.328 Chirality : 0.043 0.467 11976 Planarity : 0.003 0.033 13116 Dihedral : 7.722 145.165 10416 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.58 % Allowed : 14.75 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.09), residues: 9300 helix: 1.39 (0.08), residues: 4740 sheet: -1.88 (0.16), residues: 1188 loop : -0.33 (0.11), residues: 3372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.001 TRP H 621 HIS 0.004 0.001 HIS F 139 PHE 0.012 0.001 PHE G 392 TYR 0.021 0.001 TYR B 132 ARG 0.009 0.000 ARG C1013 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18600 Ramachandran restraints generated. 9300 Oldfield, 0 Emsley, 9300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18600 Ramachandran restraints generated. 9300 Oldfield, 0 Emsley, 9300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 8616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 283 time to evaluate : 6.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.5222 (ppp) cc_final: 0.4930 (ppp) REVERT: A 297 MET cc_start: 0.7298 (mpp) cc_final: 0.7075 (mpp) REVERT: D 135 MET cc_start: 0.5039 (ppp) cc_final: 0.4483 (ppp) REVERT: D 297 MET cc_start: 0.7304 (mpp) cc_final: 0.7077 (mpp) REVERT: G 135 MET cc_start: 0.5069 (ppp) cc_final: 0.4506 (ppp) REVERT: J 135 MET cc_start: 0.5053 (ppp) cc_final: 0.4494 (ppp) REVERT: L 297 MET cc_start: 0.7326 (mpp) cc_final: 0.6971 (tmm) outliers start: 50 outliers final: 45 residues processed: 325 average time/residue: 0.6462 time to fit residues: 382.9506 Evaluate side-chains 325 residues out of total 8616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 280 time to evaluate : 6.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 570 TYR Chi-restraints excluded: chain A residue 1021 GLU Chi-restraints excluded: chain B residue 396 GLN Chi-restraints excluded: chain B residue 570 TYR Chi-restraints excluded: chain B residue 611 GLU Chi-restraints excluded: chain B residue 872 LEU Chi-restraints excluded: chain B residue 1021 GLU Chi-restraints excluded: chain C residue 876 MET Chi-restraints excluded: chain C residue 1021 GLU Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 570 TYR Chi-restraints excluded: chain D residue 1021 GLU Chi-restraints excluded: chain E residue 396 GLN Chi-restraints excluded: chain E residue 570 TYR Chi-restraints excluded: chain E residue 611 GLU Chi-restraints excluded: chain E residue 872 LEU Chi-restraints excluded: chain E residue 915 TYR Chi-restraints excluded: chain E residue 1021 GLU Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain F residue 876 MET Chi-restraints excluded: chain F residue 1021 GLU Chi-restraints excluded: chain G residue 322 VAL Chi-restraints excluded: chain G residue 570 TYR Chi-restraints excluded: chain G residue 1021 GLU Chi-restraints excluded: chain H residue 396 GLN Chi-restraints excluded: chain H residue 570 TYR Chi-restraints excluded: chain H residue 611 GLU Chi-restraints excluded: chain H residue 630 TYR Chi-restraints excluded: chain H residue 872 LEU Chi-restraints excluded: chain H residue 1021 GLU Chi-restraints excluded: chain I residue 876 MET Chi-restraints excluded: chain I residue 1021 GLU Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain J residue 570 TYR Chi-restraints excluded: chain J residue 1021 GLU Chi-restraints excluded: chain K residue 396 GLN Chi-restraints excluded: chain K residue 570 TYR Chi-restraints excluded: chain K residue 611 GLU Chi-restraints excluded: chain K residue 872 LEU Chi-restraints excluded: chain K residue 915 TYR Chi-restraints excluded: chain K residue 1021 GLU Chi-restraints excluded: chain L residue 343 LEU Chi-restraints excluded: chain L residue 876 MET Chi-restraints excluded: chain L residue 1021 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 936 random chunks: chunk 589 optimal weight: 20.0000 chunk 790 optimal weight: 0.9990 chunk 227 optimal weight: 5.9990 chunk 684 optimal weight: 7.9990 chunk 109 optimal weight: 10.0000 chunk 206 optimal weight: 7.9990 chunk 743 optimal weight: 5.9990 chunk 311 optimal weight: 9.9990 chunk 763 optimal weight: 4.9990 chunk 94 optimal weight: 40.0000 chunk 136 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.061966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.045265 restraints weight = 594490.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.046609 restraints weight = 302862.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.047352 restraints weight = 193930.036| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 78048 Z= 0.182 Angle : 0.691 14.879 105336 Z= 0.319 Chirality : 0.043 0.455 11976 Planarity : 0.003 0.033 13116 Dihedral : 7.636 145.428 10416 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.57 % Allowed : 14.94 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.09), residues: 9300 helix: 1.51 (0.08), residues: 4668 sheet: -1.84 (0.16), residues: 1188 loop : -0.22 (0.11), residues: 3444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP B 621 HIS 0.004 0.001 HIS F 139 PHE 0.013 0.001 PHE G 392 TYR 0.023 0.001 TYR K 132 ARG 0.009 0.000 ARG F1013 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10942.28 seconds wall clock time: 195 minutes 55.20 seconds (11755.20 seconds total)