Starting phenix.real_space_refine on Sat Jan 25 09:20:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vtq_32120/01_2025/7vtq_32120.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vtq_32120/01_2025/7vtq_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/cci-nas-00/data/ceres_data/7vtq_32120/01_2025/7vtq_32120.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vtq_32120/01_2025/7vtq_32120.map" model { file = "/net/cci-nas-00/data/ceres_data/7vtq_32120/01_2025/7vtq_32120.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vtq_32120/01_2025/7vtq_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): 0.19s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 33.48, per 1000 atoms: 0.44 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: 14.87 Conformation dependent library (CDL) restraints added in 7.3 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: 7.34 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: 35.76 Time building geometry restraints manager: 17.57 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: 0.05 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: 1.100 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: 0.080 Extract box with map and model: 2.210 Check model and map are aligned: 0.440 Set scattering table: 0.530 Process input model: 137.220 Find NCS groups from input model: 3.160 Set up NCS constraints: 0.440 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: 0.030 Load rotamer database and sin/cos tables:2.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 147.470 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 4 poor density : 520 time to evaluate : 6.882 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: 0.6547 time to fit residues: 608.2941 Evaluate side-chains 310 residues out of total 8616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 306 time to evaluate : 6.861 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.064117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.046612 restraints weight = 520502.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.047893 restraints weight = 279190.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.048699 restraints weight = 181768.051| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1266 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 12.426 105336 Z= 0.323 Chirality : 0.040 0.335 11976 Planarity : 0.003 0.029 13116 Dihedral : 8.979 140.646 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 : 6.71 % Favored : 92.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 to be fit. rotamer outliers: 78 poor density : 335 time to evaluate : 7.034 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: A 135 MET cc_start: 0.8703 (tmm) cc_final: 0.7861 (ppp) REVERT: A 635 MET cc_start: 0.7977 (ttp) cc_final: 0.6840 (ppp) REVERT: B 297 MET cc_start: 0.8190 (mpp) cc_final: 0.7966 (mpp) REVERT: B 635 MET cc_start: 0.8263 (ttp) cc_final: 0.8037 (ttp) REVERT: C 659 MET cc_start: 0.8135 (mmm) cc_final: 0.7885 (mmm) REVERT: C 872 LEU cc_start: 0.9521 (OUTLIER) cc_final: 0.9296 (mm) REVERT: D 635 MET cc_start: 0.7971 (ttp) cc_final: 0.6839 (ppp) REVERT: E 297 MET cc_start: 0.8187 (mpp) cc_final: 0.7967 (mpp) REVERT: E 523 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.8467 (mt-10) REVERT: E 635 MET cc_start: 0.8237 (ttp) cc_final: 0.8010 (ttp) REVERT: F 297 MET cc_start: 0.7996 (mpp) cc_final: 0.7781 (mpp) REVERT: F 659 MET cc_start: 0.8140 (mmm) cc_final: 0.7887 (mmm) REVERT: F 872 LEU cc_start: 0.9514 (OUTLIER) cc_final: 0.9289 (mm) REVERT: G 635 MET cc_start: 0.7979 (ttp) cc_final: 0.6841 (ppp) REVERT: H 297 MET cc_start: 0.8176 (mpp) cc_final: 0.7956 (mpp) REVERT: H 635 MET cc_start: 0.8224 (ttp) cc_final: 0.7995 (ttp) REVERT: I 297 MET cc_start: 0.8020 (mpp) cc_final: 0.7804 (mpp) REVERT: I 659 MET cc_start: 0.8147 (mmm) cc_final: 0.7892 (mmm) REVERT: I 872 LEU cc_start: 0.9519 (OUTLIER) cc_final: 0.9296 (mm) REVERT: J 635 MET cc_start: 0.7944 (ttp) cc_final: 0.6819 (ppp) REVERT: K 297 MET cc_start: 0.8183 (mpp) cc_final: 0.7964 (mpp) REVERT: K 523 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8477 (mt-10) REVERT: K 635 MET cc_start: 0.8244 (ttp) cc_final: 0.8018 (ttp) REVERT: L 297 MET cc_start: 0.7986 (mpp) cc_final: 0.7769 (mpp) REVERT: L 659 MET cc_start: 0.8130 (mmm) cc_final: 0.7879 (mmm) REVERT: L 872 LEU cc_start: 0.9528 (OUTLIER) cc_final: 0.9303 (mm) outliers start: 78 outliers final: 35 residues processed: 382 average time/residue: 0.6581 time to fit residues: 449.4183 Evaluate side-chains 332 residues out of total 8616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 291 time to evaluate : 6.932 ------------------------------------------------------------------------------- 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 872 LEU 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 523 GLU Chi-restraints excluded: chain E residue 1021 GLU Chi-restraints excluded: chain F residue 872 LEU 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 872 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 523 GLU Chi-restraints excluded: chain K residue 1021 GLU Chi-restraints excluded: chain L residue 231 LEU Chi-restraints excluded: chain L residue 872 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 149 optimal weight: 7.9990 chunk 531 optimal weight: 0.0980 chunk 67 optimal weight: 7.9990 chunk 745 optimal weight: 5.9990 chunk 766 optimal weight: 9.9990 chunk 736 optimal weight: 50.0000 chunk 812 optimal weight: 40.0000 chunk 632 optimal weight: 40.0000 chunk 621 optimal weight: 9.9990 chunk 571 optimal weight: 30.0000 chunk 8 optimal weight: 30.0000 overall best weight: 6.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 600 GLN B 600 GLN C 600 GLN D 600 GLN E 600 GLN F 600 GLN G 600 GLN ** G 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 600 GLN I 600 GLN J 600 GLN K 600 GLN L 600 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.063798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.046834 restraints weight = 583879.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.048224 restraints weight = 301175.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.049008 restraints weight = 193281.305| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 78048 Z= 0.223 Angle : 0.629 11.712 105336 Z= 0.301 Chirality : 0.040 0.355 11976 Planarity : 0.003 0.028 13116 Dihedral : 8.458 141.712 10416 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.09 % Allowed : 9.11 % Favored : 89.80 % 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: 0.34 (0.09), residues: 9300 helix: 1.65 (0.08), residues: 4488 sheet: -1.82 (0.15), residues: 1224 loop : -0.79 (0.11), residues: 3588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 621 HIS 0.004 0.001 HIS A 672 PHE 0.020 0.001 PHE C 378 TYR 0.010 0.001 TYR I 570 ARG 0.003 0.000 ARG H 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 408 residues out of total 8616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 314 time to evaluate : 7.014 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: A 297 MET cc_start: 0.8051 (mpp) cc_final: 0.7850 (mpp) REVERT: A 523 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8363 (mt-10) REVERT: B 135 MET cc_start: 0.8254 (tmm) cc_final: 0.7256 (ppp) REVERT: B 297 MET cc_start: 0.8056 (mpp) cc_final: 0.7288 (mpp) REVERT: B 343 LEU cc_start: 0.9337 (mt) cc_final: 0.8777 (pp) REVERT: B 635 MET cc_start: 0.8400 (ttp) cc_final: 0.8189 (ttp) REVERT: B 942 MET cc_start: 0.8447 (tmm) cc_final: 0.7092 (tmm) REVERT: C 135 MET cc_start: 0.8620 (tmm) cc_final: 0.7855 (ppp) REVERT: C 659 MET cc_start: 0.8218 (mmm) cc_final: 0.7983 (mmm) REVERT: C 872 LEU cc_start: 0.9535 (OUTLIER) cc_final: 0.9312 (mm) REVERT: D 297 MET cc_start: 0.8049 (mpp) cc_final: 0.7846 (mpp) REVERT: D 523 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8361 (mt-10) REVERT: D 1005 MET cc_start: 0.8086 (pmm) cc_final: 0.7421 (pmm) REVERT: E 135 MET cc_start: 0.8256 (tmm) cc_final: 0.7260 (ppp) REVERT: E 297 MET cc_start: 0.7998 (mpp) cc_final: 0.7234 (mpp) REVERT: E 343 LEU cc_start: 0.9338 (mt) cc_final: 0.8851 (pp) REVERT: E 635 MET cc_start: 0.8380 (ttp) cc_final: 0.8163 (ttp) REVERT: E 942 MET cc_start: 0.8430 (tmm) cc_final: 0.7074 (tmm) REVERT: F 135 MET cc_start: 0.8612 (tmm) cc_final: 0.7844 (ppp) REVERT: F 297 MET cc_start: 0.7998 (mpp) cc_final: 0.7652 (mpp) REVERT: F 635 MET cc_start: 0.8045 (tmm) cc_final: 0.7706 (tmm) REVERT: F 659 MET cc_start: 0.8228 (mmm) cc_final: 0.7973 (mmm) REVERT: F 872 LEU cc_start: 0.9527 (OUTLIER) cc_final: 0.9304 (mm) REVERT: G 297 MET cc_start: 0.7929 (mpp) cc_final: 0.7718 (mpp) REVERT: G 523 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8364 (mt-10) REVERT: G 1005 MET cc_start: 0.8068 (pmm) cc_final: 0.7401 (pmm) REVERT: H 135 MET cc_start: 0.8283 (tmm) cc_final: 0.7298 (ppp) REVERT: H 297 MET cc_start: 0.7864 (mpp) cc_final: 0.7096 (mpp) REVERT: H 343 LEU cc_start: 0.9333 (mt) cc_final: 0.8842 (pp) REVERT: H 635 MET cc_start: 0.8340 (ttp) cc_final: 0.8128 (ttp) REVERT: H 942 MET cc_start: 0.8436 (tmm) cc_final: 0.7073 (tmm) REVERT: I 297 MET cc_start: 0.7994 (mpp) cc_final: 0.7644 (mpp) REVERT: I 635 MET cc_start: 0.8058 (tmm) cc_final: 0.7713 (tmm) REVERT: I 659 MET cc_start: 0.8219 (mmm) cc_final: 0.7968 (mmm) REVERT: I 872 LEU cc_start: 0.9532 (OUTLIER) cc_final: 0.9310 (mm) REVERT: J 297 MET cc_start: 0.7938 (mpp) cc_final: 0.7726 (mpp) REVERT: J 523 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8363 (mt-10) REVERT: J 1005 MET cc_start: 0.8071 (pmm) cc_final: 0.7406 (pmm) REVERT: K 135 MET cc_start: 0.8257 (tmm) cc_final: 0.7258 (ppp) REVERT: K 297 MET cc_start: 0.7866 (mpp) cc_final: 0.7103 (mpp) REVERT: K 343 LEU cc_start: 0.9331 (mt) cc_final: 0.8843 (pp) REVERT: K 635 MET cc_start: 0.8384 (ttp) cc_final: 0.8167 (ttp) REVERT: K 942 MET cc_start: 0.8426 (tmm) cc_final: 0.7060 (tmm) REVERT: L 297 MET cc_start: 0.7953 (mpp) cc_final: 0.7591 (mpp) REVERT: L 635 MET cc_start: 0.8063 (tmm) cc_final: 0.7720 (tmm) REVERT: L 659 MET cc_start: 0.8207 (mmm) cc_final: 0.7963 (mmm) REVERT: L 872 LEU cc_start: 0.9535 (OUTLIER) cc_final: 0.9315 (mm) REVERT: L 1005 MET cc_start: 0.7871 (pmm) cc_final: 0.7665 (pmm) outliers start: 94 outliers final: 33 residues processed: 390 average time/residue: 0.6366 time to fit residues: 449.5735 Evaluate side-chains 308 residues out of total 8616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 267 time to evaluate : 6.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 523 GLU 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 1021 GLU Chi-restraints excluded: chain C residue 872 LEU Chi-restraints excluded: chain C residue 876 MET Chi-restraints excluded: chain C residue 1021 GLU Chi-restraints excluded: chain D residue 523 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 1021 GLU Chi-restraints excluded: chain F residue 872 LEU Chi-restraints excluded: chain F residue 876 MET Chi-restraints excluded: chain F residue 1021 GLU Chi-restraints excluded: chain G residue 523 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 1021 GLU Chi-restraints excluded: chain I residue 872 LEU Chi-restraints excluded: chain I residue 876 MET Chi-restraints excluded: chain I residue 1021 GLU Chi-restraints excluded: chain J residue 523 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 1021 GLU Chi-restraints excluded: chain L residue 872 LEU 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 45 optimal weight: 4.9990 chunk 44 optimal weight: 20.0000 chunk 509 optimal weight: 10.0000 chunk 228 optimal weight: 0.8980 chunk 844 optimal weight: 4.9990 chunk 781 optimal weight: 8.9990 chunk 410 optimal weight: 10.0000 chunk 236 optimal weight: 20.0000 chunk 397 optimal weight: 20.0000 chunk 301 optimal weight: 6.9990 chunk 1 optimal weight: 8.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.063578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.046635 restraints weight = 582895.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.047992 restraints weight = 298977.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.048828 restraints weight = 191888.516| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 78048 Z= 0.198 Angle : 0.615 12.095 105336 Z= 0.288 Chirality : 0.040 0.417 11976 Planarity : 0.002 0.030 13116 Dihedral : 8.259 142.585 10416 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.20 % Allowed : 10.40 % Favored : 88.41 % 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: 0.42 (0.09), residues: 9300 helix: 1.63 (0.08), residues: 4644 sheet: -1.83 (0.15), residues: 1224 loop : -0.72 (0.11), residues: 3432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 621 HIS 0.003 0.001 HIS A 781 PHE 0.014 0.001 PHE L 640 TYR 0.008 0.001 TYR H 514 ARG 0.002 0.000 ARG K 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 409 residues out of total 8616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 306 time to evaluate : 6.927 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: A 297 MET cc_start: 0.7916 (mpp) cc_final: 0.7609 (mpp) REVERT: A 523 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8372 (mt-10) REVERT: A 635 MET cc_start: 0.8066 (ttp) cc_final: 0.6922 (ppp) REVERT: B 297 MET cc_start: 0.8034 (mpp) cc_final: 0.7463 (mpp) REVERT: B 343 LEU cc_start: 0.9338 (mt) cc_final: 0.8739 (pp) REVERT: B 942 MET cc_start: 0.8496 (tmm) cc_final: 0.6774 (tmm) REVERT: C 659 MET cc_start: 0.8291 (mmm) cc_final: 0.8016 (mmm) REVERT: C 872 LEU cc_start: 0.9511 (OUTLIER) cc_final: 0.9278 (mm) REVERT: C 1005 MET cc_start: 0.7945 (pmm) cc_final: 0.7686 (pmm) REVERT: D 297 MET cc_start: 0.7919 (mpp) cc_final: 0.7611 (mpp) REVERT: D 523 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8368 (mt-10) REVERT: D 635 MET cc_start: 0.8063 (ttp) cc_final: 0.6920 (ppp) REVERT: D 1005 MET cc_start: 0.8014 (pmm) cc_final: 0.7378 (pmm) REVERT: E 297 MET cc_start: 0.7959 (mpp) cc_final: 0.7352 (mpp) REVERT: E 343 LEU cc_start: 0.9363 (mt) cc_final: 0.8823 (pp) REVERT: E 523 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8476 (mt-10) REVERT: E 635 MET cc_start: 0.8288 (ttp) cc_final: 0.8086 (ttp) REVERT: E 942 MET cc_start: 0.8492 (tmm) cc_final: 0.6786 (tmm) REVERT: F 297 MET cc_start: 0.7997 (mpp) cc_final: 0.7657 (mpp) REVERT: F 635 MET cc_start: 0.8210 (tmm) cc_final: 0.7784 (tmm) REVERT: F 659 MET cc_start: 0.8323 (mmm) cc_final: 0.8120 (mmm) REVERT: F 872 LEU cc_start: 0.9508 (OUTLIER) cc_final: 0.9301 (mm) REVERT: G 523 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8371 (mt-10) REVERT: G 635 MET cc_start: 0.8062 (ttp) cc_final: 0.6921 (ppp) REVERT: G 1005 MET cc_start: 0.8009 (pmm) cc_final: 0.7373 (pmm) REVERT: H 297 MET cc_start: 0.7923 (mpp) cc_final: 0.7314 (mpp) REVERT: H 343 LEU cc_start: 0.9356 (mt) cc_final: 0.8810 (pp) REVERT: H 942 MET cc_start: 0.8497 (tmm) cc_final: 0.6789 (tmm) REVERT: I 297 MET cc_start: 0.7989 (mpp) cc_final: 0.7441 (mpp) REVERT: I 635 MET cc_start: 0.8108 (tmm) cc_final: 0.7680 (tmm) REVERT: I 659 MET cc_start: 0.8321 (mmm) cc_final: 0.8121 (mmm) REVERT: I 872 LEU cc_start: 0.9510 (OUTLIER) cc_final: 0.9277 (mm) REVERT: I 1005 MET cc_start: 0.7968 (pmm) cc_final: 0.7708 (pmm) REVERT: J 523 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8369 (mt-10) REVERT: J 635 MET cc_start: 0.8052 (ttp) cc_final: 0.6913 (ppp) REVERT: J 1005 MET cc_start: 0.8013 (pmm) cc_final: 0.7378 (pmm) REVERT: K 297 MET cc_start: 0.7929 (mpp) cc_final: 0.7319 (mpp) REVERT: K 343 LEU cc_start: 0.9355 (mt) cc_final: 0.8811 (pp) REVERT: K 523 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8454 (mt-10) REVERT: K 635 MET cc_start: 0.8290 (ttp) cc_final: 0.8089 (ttp) REVERT: K 942 MET cc_start: 0.8503 (tmm) cc_final: 0.6795 (tmm) REVERT: L 297 MET cc_start: 0.7968 (mpp) cc_final: 0.7633 (mpp) REVERT: L 635 MET cc_start: 0.8240 (tmm) cc_final: 0.7832 (tmm) REVERT: L 872 LEU cc_start: 0.9518 (OUTLIER) cc_final: 0.9310 (mm) outliers start: 103 outliers final: 46 residues processed: 399 average time/residue: 0.6271 time to fit residues: 456.5390 Evaluate side-chains 315 residues out of total 8616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 259 time to evaluate : 6.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 523 GLU Chi-restraints excluded: chain A residue 570 TYR 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 760 GLU Chi-restraints excluded: chain B residue 872 LEU Chi-restraints excluded: chain B residue 1021 GLU Chi-restraints excluded: chain C residue 872 LEU Chi-restraints excluded: chain C residue 876 MET Chi-restraints excluded: chain C residue 1021 GLU Chi-restraints excluded: chain D residue 523 GLU Chi-restraints excluded: chain D residue 570 TYR 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 523 GLU Chi-restraints excluded: chain E residue 570 TYR Chi-restraints excluded: chain E residue 760 GLU Chi-restraints excluded: chain E residue 872 LEU Chi-restraints excluded: chain E residue 1021 GLU Chi-restraints excluded: chain F residue 872 LEU Chi-restraints excluded: chain F residue 876 MET Chi-restraints excluded: chain F residue 1021 GLU Chi-restraints excluded: chain G residue 523 GLU Chi-restraints excluded: chain G residue 570 TYR 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 760 GLU Chi-restraints excluded: chain H residue 872 LEU Chi-restraints excluded: chain H residue 1021 GLU Chi-restraints excluded: chain I residue 872 LEU Chi-restraints excluded: chain I residue 876 MET Chi-restraints excluded: chain I residue 1021 GLU Chi-restraints excluded: chain J residue 523 GLU Chi-restraints excluded: chain J residue 570 TYR 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 523 GLU Chi-restraints excluded: chain K residue 570 TYR Chi-restraints excluded: chain K residue 760 GLU Chi-restraints excluded: chain K residue 872 LEU Chi-restraints excluded: chain K residue 1021 GLU Chi-restraints excluded: chain L residue 872 LEU 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 772 optimal weight: 20.0000 chunk 88 optimal weight: 7.9990 chunk 541 optimal weight: 5.9990 chunk 618 optimal weight: 0.0370 chunk 283 optimal weight: 30.0000 chunk 396 optimal weight: 7.9990 chunk 580 optimal weight: 40.0000 chunk 803 optimal weight: 5.9990 chunk 577 optimal weight: 0.5980 chunk 358 optimal weight: 30.0000 chunk 871 optimal weight: 50.0000 overall best weight: 4.1264 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.063464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.046629 restraints weight = 580519.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.047877 restraints weight = 300500.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.048666 restraints weight = 193269.231| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 78048 Z= 0.173 Angle : 0.633 13.644 105336 Z= 0.290 Chirality : 0.041 0.484 11976 Planarity : 0.002 0.030 13116 Dihedral : 8.087 143.287 10416 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.21 % Allowed : 11.51 % Favored : 87.28 % 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: 0.52 (0.09), residues: 9300 helix: 1.63 (0.08), residues: 4656 sheet: -1.78 (0.15), residues: 1212 loop : -0.55 (0.11), residues: 3432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 621 HIS 0.003 0.001 HIS C 139 PHE 0.014 0.001 PHE D 392 TYR 0.008 0.001 TYR H 461 ARG 0.002 0.000 ARG K 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 425 residues out of total 8616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 321 time to evaluate : 6.968 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: A 135 MET cc_start: 0.8691 (tmm) cc_final: 0.7934 (ppp) REVERT: A 523 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8406 (mt-10) REVERT: A 635 MET cc_start: 0.8033 (ttp) cc_final: 0.6995 (ppp) REVERT: A 942 MET cc_start: 0.8561 (tmm) cc_final: 0.8022 (tmm) REVERT: B 135 MET cc_start: 0.8350 (tmm) cc_final: 0.7381 (ppp) REVERT: B 297 MET cc_start: 0.8090 (mpp) cc_final: 0.7540 (mpp) REVERT: B 343 LEU cc_start: 0.9267 (mt) cc_final: 0.8616 (pp) REVERT: B 404 MET cc_start: 0.8763 (mtm) cc_final: 0.8546 (mtm) REVERT: B 942 MET cc_start: 0.8533 (tmm) cc_final: 0.6629 (tmm) REVERT: C 135 MET cc_start: 0.8608 (tmm) cc_final: 0.7767 (ppp) REVERT: C 659 MET cc_start: 0.8301 (mmm) cc_final: 0.8085 (mmm) REVERT: C 872 LEU cc_start: 0.9524 (OUTLIER) cc_final: 0.9315 (mm) REVERT: C 1013 ARG cc_start: 0.8502 (ttp-110) cc_final: 0.8071 (ttp-110) REVERT: C 1028 VAL cc_start: 0.9227 (OUTLIER) cc_final: 0.9000 (p) REVERT: D 135 MET cc_start: 0.8768 (tmm) cc_final: 0.8047 (ppp) REVERT: D 523 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8404 (mt-10) REVERT: D 635 MET cc_start: 0.8036 (ttp) cc_final: 0.6998 (ppp) REVERT: D 1005 MET cc_start: 0.8016 (pmm) cc_final: 0.7346 (pmm) REVERT: E 135 MET cc_start: 0.8348 (tmm) cc_final: 0.7378 (ppp) REVERT: E 297 MET cc_start: 0.7928 (mpp) cc_final: 0.7292 (mpp) REVERT: E 343 LEU cc_start: 0.9348 (mt) cc_final: 0.8785 (pp) REVERT: E 523 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8424 (mt-10) REVERT: E 635 MET cc_start: 0.8313 (ttp) cc_final: 0.8110 (ttp) REVERT: E 942 MET cc_start: 0.8512 (tmm) cc_final: 0.6598 (tmm) REVERT: F 135 MET cc_start: 0.8606 (tmm) cc_final: 0.7767 (ppp) REVERT: F 297 MET cc_start: 0.7993 (mpp) cc_final: 0.7620 (mpp) REVERT: F 404 MET cc_start: 0.8246 (mtt) cc_final: 0.7818 (mtm) REVERT: F 635 MET cc_start: 0.8286 (tmm) cc_final: 0.7839 (tmm) REVERT: F 659 MET cc_start: 0.8307 (mmm) cc_final: 0.7971 (mmm) REVERT: F 872 LEU cc_start: 0.9515 (OUTLIER) cc_final: 0.9304 (mm) REVERT: F 1013 ARG cc_start: 0.8497 (ttp-110) cc_final: 0.8071 (ttp-110) REVERT: F 1028 VAL cc_start: 0.9219 (OUTLIER) cc_final: 0.8988 (p) REVERT: G 135 MET cc_start: 0.8776 (tmm) cc_final: 0.8058 (ppp) REVERT: G 523 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8407 (mt-10) REVERT: G 635 MET cc_start: 0.8030 (ttp) cc_final: 0.6993 (ppp) REVERT: G 1005 MET cc_start: 0.8014 (pmm) cc_final: 0.7341 (pmm) REVERT: H 135 MET cc_start: 0.8378 (tmm) cc_final: 0.7423 (ppp) REVERT: H 297 MET cc_start: 0.7919 (mpp) cc_final: 0.7285 (mpp) REVERT: H 343 LEU cc_start: 0.9338 (mt) cc_final: 0.8772 (pp) REVERT: H 942 MET cc_start: 0.8518 (tmm) cc_final: 0.6596 (tmm) REVERT: I 135 MET cc_start: 0.8623 (tmm) cc_final: 0.7792 (ppp) REVERT: I 297 MET cc_start: 0.8001 (mpp) cc_final: 0.7627 (mpp) REVERT: I 404 MET cc_start: 0.8244 (mtt) cc_final: 0.7959 (mtm) REVERT: I 635 MET cc_start: 0.8130 (tmm) cc_final: 0.7660 (tmm) REVERT: I 659 MET cc_start: 0.8306 (mmm) cc_final: 0.8042 (mmm) REVERT: I 872 LEU cc_start: 0.9520 (OUTLIER) cc_final: 0.9318 (mm) REVERT: I 1013 ARG cc_start: 0.8497 (ttp-110) cc_final: 0.8069 (ttp-110) REVERT: I 1028 VAL cc_start: 0.9232 (OUTLIER) cc_final: 0.9000 (p) REVERT: J 135 MET cc_start: 0.8769 (tmm) cc_final: 0.8048 (ppp) REVERT: J 523 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8405 (mt-10) REVERT: J 635 MET cc_start: 0.8010 (ttp) cc_final: 0.6978 (ppp) REVERT: J 1005 MET cc_start: 0.8015 (pmm) cc_final: 0.7346 (pmm) REVERT: K 135 MET cc_start: 0.8356 (tmm) cc_final: 0.7389 (ppp) REVERT: K 297 MET cc_start: 0.7686 (mpp) cc_final: 0.7014 (mpp) REVERT: K 343 LEU cc_start: 0.9338 (mt) cc_final: 0.8770 (pp) REVERT: K 404 MET cc_start: 0.8757 (mtm) cc_final: 0.8541 (mtm) REVERT: K 523 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8457 (mt-10) REVERT: K 635 MET cc_start: 0.8318 (ttp) cc_final: 0.8118 (ttp) REVERT: K 942 MET cc_start: 0.8518 (tmm) cc_final: 0.6607 (tmm) REVERT: L 135 MET cc_start: 0.8624 (tmm) cc_final: 0.7793 (ppp) REVERT: L 297 MET cc_start: 0.7972 (mpp) cc_final: 0.7613 (mpp) REVERT: L 404 MET cc_start: 0.8621 (mtt) cc_final: 0.8059 (mtm) REVERT: L 635 MET cc_start: 0.8307 (tmm) cc_final: 0.7851 (tmm) REVERT: L 872 LEU cc_start: 0.9525 (OUTLIER) cc_final: 0.9316 (mm) REVERT: L 1013 ARG cc_start: 0.8508 (ttp-110) cc_final: 0.8072 (ttp-110) REVERT: L 1028 VAL cc_start: 0.9271 (OUTLIER) cc_final: 0.9055 (p) outliers start: 104 outliers final: 38 residues processed: 415 average time/residue: 0.6373 time to fit residues: 478.2196 Evaluate side-chains 333 residues out of total 8616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 281 time to evaluate : 6.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 523 GLU 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 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 872 LEU Chi-restraints excluded: chain C residue 876 MET Chi-restraints excluded: chain C residue 1021 GLU Chi-restraints excluded: chain C residue 1028 VAL Chi-restraints excluded: chain D residue 523 GLU 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 501 MET Chi-restraints excluded: chain E residue 523 GLU 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 872 LEU Chi-restraints excluded: chain F residue 876 MET Chi-restraints excluded: chain F residue 1021 GLU Chi-restraints excluded: chain F residue 1028 VAL Chi-restraints excluded: chain G residue 523 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 872 LEU Chi-restraints excluded: chain I residue 876 MET Chi-restraints excluded: chain I residue 1021 GLU Chi-restraints excluded: chain I residue 1028 VAL Chi-restraints excluded: chain J residue 523 GLU 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 523 GLU 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 872 LEU Chi-restraints excluded: chain L residue 876 MET Chi-restraints excluded: chain L residue 1021 GLU Chi-restraints excluded: chain L residue 1028 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 936 random chunks: chunk 912 optimal weight: 7.9990 chunk 760 optimal weight: 20.0000 chunk 223 optimal weight: 9.9990 chunk 514 optimal weight: 2.9990 chunk 766 optimal weight: 0.7980 chunk 208 optimal weight: 7.9990 chunk 91 optimal weight: 7.9990 chunk 762 optimal weight: 9.9990 chunk 294 optimal weight: 5.9990 chunk 372 optimal weight: 8.9990 chunk 856 optimal weight: 8.9990 overall best weight: 5.1588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.062931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.046085 restraints weight = 584163.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.047338 restraints weight = 302447.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.048111 restraints weight = 194962.779| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 78048 Z= 0.193 Angle : 0.653 15.620 105336 Z= 0.302 Chirality : 0.041 0.502 11976 Planarity : 0.002 0.031 13116 Dihedral : 7.941 143.484 10416 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.10 % Allowed : 12.34 % Favored : 86.56 % 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: 0.45 (0.09), residues: 9300 helix: 1.48 (0.08), residues: 4740 sheet: -1.96 (0.15), residues: 1296 loop : -0.35 (0.11), residues: 3264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 609 HIS 0.003 0.001 HIS K 647 PHE 0.013 0.001 PHE K 640 TYR 0.008 0.001 TYR H 461 ARG 0.003 0.000 ARG G 756 *********************** 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 394 residues out of total 8616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 299 time to evaluate : 7.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 523 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8396 (mt-10) REVERT: A 635 MET cc_start: 0.8039 (ttp) cc_final: 0.6972 (ppp) REVERT: B 297 MET cc_start: 0.7781 (mpp) cc_final: 0.7188 (mpp) REVERT: B 343 LEU cc_start: 0.9262 (mt) cc_final: 0.8609 (pp) REVERT: B 635 MET cc_start: 0.8296 (ttp) cc_final: 0.7323 (tmm) REVERT: B 942 MET cc_start: 0.8573 (tmm) cc_final: 0.7423 (tmm) REVERT: B 1028 VAL cc_start: 0.9253 (OUTLIER) cc_final: 0.9017 (p) REVERT: C 630 TYR cc_start: 0.8723 (OUTLIER) cc_final: 0.8332 (m-10) REVERT: C 659 MET cc_start: 0.8317 (mmm) cc_final: 0.7992 (mmm) REVERT: C 872 LEU cc_start: 0.9533 (OUTLIER) cc_final: 0.9325 (mm) REVERT: C 986 LEU cc_start: 0.9776 (mt) cc_final: 0.9429 (pp) REVERT: C 1013 ARG cc_start: 0.8545 (ttp-110) cc_final: 0.8095 (ttp-110) REVERT: D 523 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8395 (mt-10) REVERT: D 635 MET cc_start: 0.8043 (ttp) cc_final: 0.6976 (ppp) REVERT: D 942 MET cc_start: 0.8582 (tmm) cc_final: 0.8078 (tmm) REVERT: D 1005 MET cc_start: 0.8062 (pmm) cc_final: 0.7393 (pmm) REVERT: E 297 MET cc_start: 0.7937 (mpp) cc_final: 0.7303 (mpp) REVERT: E 343 LEU cc_start: 0.9390 (mt) cc_final: 0.8841 (pp) REVERT: E 404 MET cc_start: 0.8730 (mtm) cc_final: 0.8180 (mtm) REVERT: E 523 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8458 (mt-10) REVERT: E 645 MET cc_start: 0.8622 (ttp) cc_final: 0.8408 (ttt) REVERT: E 942 MET cc_start: 0.8607 (tmm) cc_final: 0.7383 (tmm) REVERT: E 1028 VAL cc_start: 0.9250 (OUTLIER) cc_final: 0.9012 (p) REVERT: F 635 MET cc_start: 0.8294 (tmm) cc_final: 0.7668 (tmm) REVERT: F 659 MET cc_start: 0.8316 (mmm) cc_final: 0.7980 (mmm) REVERT: F 872 LEU cc_start: 0.9525 (OUTLIER) cc_final: 0.9318 (mm) REVERT: F 986 LEU cc_start: 0.9783 (mt) cc_final: 0.9436 (pp) REVERT: F 1013 ARG cc_start: 0.8542 (ttp-110) cc_final: 0.8098 (ttp-110) REVERT: F 1028 VAL cc_start: 0.9231 (OUTLIER) cc_final: 0.8998 (p) REVERT: G 523 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8396 (mt-10) REVERT: G 635 MET cc_start: 0.8039 (ttp) cc_final: 0.6973 (ppp) REVERT: G 942 MET cc_start: 0.8585 (tmm) cc_final: 0.8078 (tmm) REVERT: G 1005 MET cc_start: 0.8061 (pmm) cc_final: 0.7389 (pmm) REVERT: H 297 MET cc_start: 0.7661 (mpp) cc_final: 0.6985 (mpp) REVERT: H 343 LEU cc_start: 0.9340 (mt) cc_final: 0.8768 (pp) REVERT: H 404 MET cc_start: 0.8697 (mtm) cc_final: 0.8151 (mtm) REVERT: H 635 MET cc_start: 0.8244 (ttp) cc_final: 0.7256 (tmm) REVERT: H 645 MET cc_start: 0.8607 (ttp) cc_final: 0.8390 (ttt) REVERT: H 942 MET cc_start: 0.8612 (tmm) cc_final: 0.7412 (tmm) REVERT: H 1028 VAL cc_start: 0.9254 (OUTLIER) cc_final: 0.9007 (p) REVERT: I 635 MET cc_start: 0.8178 (tmm) cc_final: 0.7708 (tmm) REVERT: I 659 MET cc_start: 0.8316 (mmm) cc_final: 0.7982 (mmm) REVERT: I 872 LEU cc_start: 0.9531 (OUTLIER) cc_final: 0.9323 (mm) REVERT: I 986 LEU cc_start: 0.9784 (mt) cc_final: 0.9438 (pp) REVERT: I 1013 ARG cc_start: 0.8542 (ttp-110) cc_final: 0.8095 (ttp-110) REVERT: I 1028 VAL cc_start: 0.9235 (OUTLIER) cc_final: 0.9002 (p) REVERT: J 523 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8396 (mt-10) REVERT: J 635 MET cc_start: 0.8026 (ttp) cc_final: 0.6964 (ppp) REVERT: J 942 MET cc_start: 0.8590 (tmm) cc_final: 0.8073 (tmm) REVERT: J 1005 MET cc_start: 0.8063 (pmm) cc_final: 0.7392 (pmm) REVERT: K 297 MET cc_start: 0.7673 (mpp) cc_final: 0.6997 (mpp) REVERT: K 343 LEU cc_start: 0.9340 (mt) cc_final: 0.8769 (pp) REVERT: K 523 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8461 (mt-10) REVERT: K 645 MET cc_start: 0.8620 (ttp) cc_final: 0.8406 (ttt) REVERT: K 942 MET cc_start: 0.8637 (tmm) cc_final: 0.7428 (tmm) REVERT: K 1028 VAL cc_start: 0.9253 (OUTLIER) cc_final: 0.9013 (p) REVERT: L 297 MET cc_start: 0.7956 (mpp) cc_final: 0.7586 (mpp) REVERT: L 635 MET cc_start: 0.8310 (tmm) cc_final: 0.7673 (tmm) REVERT: L 659 MET cc_start: 0.8282 (mmm) cc_final: 0.7864 (mmm) REVERT: L 872 LEU cc_start: 0.9534 (OUTLIER) cc_final: 0.9327 (mm) REVERT: L 986 LEU cc_start: 0.9781 (mt) cc_final: 0.9434 (pp) REVERT: L 1013 ARG cc_start: 0.8552 (ttp-110) cc_final: 0.8100 (ttp-110) REVERT: L 1028 VAL cc_start: 0.9237 (OUTLIER) cc_final: 0.8992 (p) outliers start: 95 outliers final: 44 residues processed: 384 average time/residue: 0.6549 time to fit residues: 455.0579 Evaluate side-chains 335 residues out of total 8616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 273 time to evaluate : 6.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 523 GLU 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 B residue 1028 VAL Chi-restraints excluded: chain C residue 630 TYR Chi-restraints excluded: chain C residue 872 LEU Chi-restraints excluded: chain C residue 876 MET Chi-restraints excluded: chain C residue 1021 GLU Chi-restraints excluded: chain D residue 523 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 523 GLU Chi-restraints excluded: chain E residue 570 TYR Chi-restraints excluded: chain E residue 611 GLU Chi-restraints excluded: chain E residue 641 VAL Chi-restraints excluded: chain E residue 872 LEU Chi-restraints excluded: chain E residue 1021 GLU Chi-restraints excluded: chain E residue 1028 VAL Chi-restraints excluded: chain F residue 872 LEU Chi-restraints excluded: chain F residue 876 MET Chi-restraints excluded: chain F residue 1021 GLU Chi-restraints excluded: chain F residue 1028 VAL Chi-restraints excluded: chain G residue 523 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 1021 GLU Chi-restraints excluded: chain H residue 1028 VAL Chi-restraints excluded: chain I residue 872 LEU Chi-restraints excluded: chain I residue 876 MET Chi-restraints excluded: chain I residue 1021 GLU Chi-restraints excluded: chain I residue 1028 VAL Chi-restraints excluded: chain J residue 523 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 523 GLU Chi-restraints excluded: chain K residue 570 TYR Chi-restraints excluded: chain K residue 611 GLU Chi-restraints excluded: chain K residue 641 VAL Chi-restraints excluded: chain K residue 872 LEU Chi-restraints excluded: chain K residue 1021 GLU Chi-restraints excluded: chain K residue 1028 VAL Chi-restraints excluded: chain L residue 872 LEU Chi-restraints excluded: chain L residue 876 MET Chi-restraints excluded: chain L residue 1021 GLU Chi-restraints excluded: chain L residue 1028 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.0459 > 50: distance: 1 - 83: 6.910 distance: 9 - 86: 12.889 distance: 44 - 91: 7.574 distance: 78 - 83: 7.011 distance: 83 - 84: 7.763 distance: 84 - 85: 3.769 distance: 84 - 87: 4.977 distance: 85 - 86: 7.737 distance: 85 - 91: 5.190 distance: 87 - 88: 4.662 distance: 87 - 89: 18.089 distance: 88 - 90: 12.499 distance: 91 - 92: 13.742 distance: 92 - 95: 15.371 distance: 93 - 94: 21.756 distance: 93 - 98: 5.867 distance: 95 - 96: 22.648 distance: 95 - 97: 28.132 distance: 98 - 99: 10.612 distance: 99 - 100: 9.966 distance: 99 - 102: 12.222 distance: 100 - 101: 9.361 distance: 100 - 105: 8.755 distance: 102 - 103: 3.683 distance: 102 - 104: 10.563 distance: 105 - 106: 18.751 distance: 106 - 107: 21.995 distance: 106 - 109: 9.269 distance: 107 - 108: 16.304 distance: 107 - 116: 30.241 distance: 109 - 110: 3.942 distance: 110 - 111: 3.506 distance: 111 - 112: 6.191 distance: 112 - 113: 6.794 distance: 113 - 114: 8.561 distance: 113 - 115: 10.090 distance: 116 - 117: 14.019 distance: 116 - 122: 29.052 distance: 117 - 120: 15.866 distance: 118 - 119: 27.684 distance: 118 - 123: 14.377 distance: 120 - 121: 7.957 distance: 121 - 122: 27.711 distance: 123 - 124: 12.602 distance: 124 - 125: 13.517 distance: 124 - 127: 10.727 distance: 125 - 126: 17.934 distance: 125 - 130: 9.972 distance: 127 - 128: 15.470 distance: 127 - 129: 11.740 distance: 130 - 131: 9.026 distance: 131 - 134: 28.408 distance: 132 - 133: 22.746 distance: 132 - 135: 5.111 distance: 135 - 136: 15.507 distance: 136 - 137: 20.996 distance: 136 - 139: 28.500 distance: 137 - 138: 6.018 distance: 137 - 143: 8.010 distance: 139 - 140: 8.196 distance: 140 - 141: 12.731 distance: 140 - 142: 15.845 distance: 143 - 144: 3.885 distance: 144 - 145: 19.781 distance: 144 - 147: 14.515 distance: 145 - 146: 21.056 distance: 145 - 152: 20.370 distance: 147 - 148: 9.157 distance: 148 - 149: 12.448 distance: 149 - 150: 12.474 distance: 149 - 151: 12.536 distance: 152 - 153: 12.922 distance: 153 - 154: 9.935 distance: 153 - 156: 11.449 distance: 154 - 155: 12.029 distance: 154 - 161: 13.458 distance: 156 - 157: 8.136 distance: 157 - 158: 12.329 distance: 158 - 159: 25.045 distance: 159 - 160: 9.356