Starting phenix.real_space_refine on Fri Apr 12 04:16:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tp1_26045/04_2024/7tp1_26045.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tp1_26045/04_2024/7tp1_26045.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tp1_26045/04_2024/7tp1_26045.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tp1_26045/04_2024/7tp1_26045.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tp1_26045/04_2024/7tp1_26045.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tp1_26045/04_2024/7tp1_26045.pdb" } resolution = 3.81 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= -0.004 sd= 0.128 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: 4 Type Number sf(0) Gaussians S 105 5.16 5 C 15679 2.51 5 N 4030 2.21 5 O 4832 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 24646 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 7916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1013, 7916 Classifications: {'peptide': 1013} Link IDs: {'PTRANS': 48, 'TRANS': 964} Chain breaks: 7 Chain: "B" Number of atoms: 7985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 7985 Classifications: {'peptide': 1022} Link IDs: {'PTRANS': 49, 'TRANS': 972} Chain breaks: 6 Chain: "C" Number of atoms: 7891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1011, 7891 Classifications: {'peptide': 1011} Link IDs: {'PTRANS': 48, 'TRANS': 962} Chain breaks: 7 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 12.28, per 1000 atoms: 0.50 Number of scatterers: 24646 At special positions: 0 Unit cell: (128.52, 133.92, 177.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 105 16.00 O 4832 8.00 N 4030 7.00 C 15679 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.02 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.01 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.01 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.02 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.02 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.05 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.02 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG A1311 " - " ASN A 165 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 343 " " NAG B1303 " - " ASN B 603 " " NAG B1304 " - " ASN B 61 " " NAG B1305 " - " ASN B 657 " " NAG B1306 " - " ASN B 122 " " NAG B1307 " - " ASN B 282 " " NAG B1308 " - " ASN B 165 " " NAG B1309 " - " ASN B 616 " " NAG B1310 " - " ASN B 709 " " NAG B1311 " - " ASN B1074 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 603 " " NAG C1305 " - " ASN C1074 " " NAG C1306 " - " ASN C 343 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 165 " " NAG C1309 " - " ASN C 657 " " NAG C1310 " - " ASN C 709 " " NAG C1311 " - " ASN C 122 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN A1134 " " NAG I 1 " - " ASN B 234 " " NAG J 1 " - " ASN B 801 " " NAG K 1 " - " ASN B1134 " " NAG L 1 " - " ASN B 717 " " NAG M 1 " - " ASN B1098 " " NAG N 1 " - " ASN C 234 " " NAG O 1 " - " ASN C1098 " " NAG P 1 " - " ASN C1134 " " NAG Q 1 " - " ASN C 801 " Time building additional restraints: 9.88 Conformation dependent library (CDL) restraints added in 4.1 seconds 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5708 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 44 sheets defined 27.8% alpha, 29.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.11 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.081A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.079A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 634 through 638 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 755 removed outlier: 4.026A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.517A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.576A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.663A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.805A pdb=" N LEU A 878 " --> pdb=" O THR A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.630A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.999A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.835A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.062A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1145 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 372 Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.862A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 625 through 630 Processing helix chain 'B' and resid 631 through 638 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.844A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 4.065A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.620A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.672A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.531A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.796A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.139A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1127 through 1129 No H-bonds generated for 'chain 'B' and resid 1127 through 1129' Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.133A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 Processing helix chain 'C' and resid 404 through 408 removed outlier: 4.219A pdb=" N ARG C 408 " --> pdb=" O GLY C 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 404 through 408' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 619 through 623 removed outlier: 3.945A pdb=" N VAL C 622 " --> pdb=" O GLU C 619 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.786A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 4.069A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.776A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.643A pdb=" N GLY C 932 " --> pdb=" O ASN C 928 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.585A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.807A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.331A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE C1013 " --> pdb=" O THR C1009 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.270A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.108A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.831A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.728A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.920A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.297A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 4.988A pdb=" N GLU A 583 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP A 578 " --> pdb=" O GLU A 583 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.729A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 451 through 454 removed outlier: 4.440A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.583A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 704 removed outlier: 3.528A pdb=" N LYS B 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.664A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.664A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1123 removed outlier: 3.971A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.520A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.639A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.784A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 5.657A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.667A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.299A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.003A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 334 through 335 removed outlier: 6.731A pdb=" N ASN B 334 " --> pdb=" O VAL B 362 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.164A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.764A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.845A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.738A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.738A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.811A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.632A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.443A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.534A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.999A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.761A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE1, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.438A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE3, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.727A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.480A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.480A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1122 1042 hydrogen bonds defined for protein. 2814 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: 10.99 Time building geometry restraints manager: 10.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7327 1.34 - 1.46: 4414 1.46 - 1.58: 13311 1.58 - 1.70: 0 1.70 - 1.83: 129 Bond restraints: 25181 Sorted by residual: bond pdb=" C4 NAG D 1 " pdb=" O4 NAG D 1 " ideal model delta sigma weight residual 1.409 1.488 -0.079 2.00e-02 2.50e+03 1.54e+01 bond pdb=" C5 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.413 1.490 -0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" CA PRO C 792 " pdb=" C PRO C 792 " ideal model delta sigma weight residual 1.514 1.535 -0.021 5.50e-03 3.31e+04 1.46e+01 bond pdb=" C5 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.413 1.489 -0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" C5 NAG A1311 " pdb=" O5 NAG A1311 " ideal model delta sigma weight residual 1.413 1.489 -0.076 2.00e-02 2.50e+03 1.46e+01 ... (remaining 25176 not shown) Histogram of bond angle deviations from ideal: 97.86 - 105.47: 519 105.47 - 113.07: 12830 113.07 - 120.68: 12478 120.68 - 128.28: 8342 128.28 - 135.89: 88 Bond angle restraints: 34257 Sorted by residual: angle pdb=" CA VAL A 622 " pdb=" CB VAL A 622 " pdb=" CG1 VAL A 622 " ideal model delta sigma weight residual 110.40 127.35 -16.95 1.70e+00 3.46e-01 9.94e+01 angle pdb=" N CYS C 131 " pdb=" CA CYS C 131 " pdb=" C CYS C 131 " ideal model delta sigma weight residual 110.33 120.56 -10.23 1.29e+00 6.01e-01 6.29e+01 angle pdb=" CA PHE C 347 " pdb=" CB PHE C 347 " pdb=" CG PHE C 347 " ideal model delta sigma weight residual 113.80 120.16 -6.36 1.00e+00 1.00e+00 4.04e+01 angle pdb=" CA THR B 630 " pdb=" CB THR B 630 " pdb=" CG2 THR B 630 " ideal model delta sigma weight residual 110.50 121.22 -10.72 1.70e+00 3.46e-01 3.98e+01 angle pdb=" N CYS C 391 " pdb=" CA CYS C 391 " pdb=" C CYS C 391 " ideal model delta sigma weight residual 108.96 118.08 -9.12 1.49e+00 4.50e-01 3.74e+01 ... (remaining 34252 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 14628 17.93 - 35.87: 920 35.87 - 53.80: 150 53.80 - 71.74: 56 71.74 - 89.67: 33 Dihedral angle restraints: 15787 sinusoidal: 6924 harmonic: 8863 Sorted by residual: dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -154.57 68.57 1 1.00e+01 1.00e-02 6.09e+01 dihedral pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " pdb=" SG CYS A 760 " pdb=" CB CYS A 760 " ideal model delta sinusoidal sigma weight residual 93.00 153.69 -60.69 1 1.00e+01 1.00e-02 4.90e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -146.58 60.58 1 1.00e+01 1.00e-02 4.88e+01 ... (remaining 15784 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.283: 4059 0.283 - 0.565: 21 0.565 - 0.848: 0 0.848 - 1.130: 0 1.130 - 1.413: 1 Chirality restraints: 4081 Sorted by residual: chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 1.04e+02 chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 8.46e+01 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 8.24e+01 ... (remaining 4078 not shown) Planarity restraints: 4396 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 165 " -0.144 2.00e-02 2.50e+03 1.49e-01 2.78e+02 pdb=" CG ASN C 165 " 0.091 2.00e-02 2.50e+03 pdb=" OD1 ASN C 165 " 0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN C 165 " 0.224 2.00e-02 2.50e+03 pdb=" C1 NAG C1308 " -0.180 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 122 " 0.135 2.00e-02 2.50e+03 1.49e-01 2.76e+02 pdb=" CG ASN B 122 " -0.066 2.00e-02 2.50e+03 pdb=" OD1 ASN B 122 " -0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN B 122 " -0.236 2.00e-02 2.50e+03 pdb=" C1 NAG B1306 " 0.179 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 603 " -0.138 2.00e-02 2.50e+03 1.48e-01 2.75e+02 pdb=" CG ASN C 603 " 0.073 2.00e-02 2.50e+03 pdb=" OD1 ASN C 603 " 0.016 2.00e-02 2.50e+03 pdb=" ND2 ASN C 603 " 0.230 2.00e-02 2.50e+03 pdb=" C1 NAG C1304 " -0.180 2.00e-02 2.50e+03 ... (remaining 4393 not shown) Histogram of nonbonded interaction distances: 2.52 - 3.00: 13077 3.00 - 3.47: 24638 3.47 - 3.95: 40710 3.95 - 4.42: 45211 4.42 - 4.90: 74619 Nonbonded interactions: 198255 Sorted by model distance: nonbonded pdb=" OD1 ASP C 364 " pdb=" OG SER C 366 " model vdw 2.523 2.440 nonbonded pdb=" OG SER B 813 " pdb=" OE1 GLU B 868 " model vdw 2.547 2.440 nonbonded pdb=" OG SER B 746 " pdb=" OE1 GLU B 748 " model vdw 2.556 2.440 nonbonded pdb=" OE1 GLU A 516 " pdb=" OH TYR B 200 " model vdw 2.557 2.440 nonbonded pdb=" OH TYR B 91 " pdb=" OE1 GLU B 191 " model vdw 2.560 2.440 ... (remaining 198250 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 623 or resid 635 through 1147 or resid 1301 thr \ ough 1311)) selection = (chain 'B' and (resid 27 through 623 or resid 635 through 1147 or resid 1301 thr \ ough 1311)) selection = chain 'C' } ncs_group { reference = 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' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' } 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: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.920 Check model and map are aligned: 0.320 Set scattering table: 0.200 Process input model: 66.380 Find NCS groups from input model: 1.980 Set up NCS constraints: 0.290 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 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 : 0.014 0.079 25181 Z= 0.881 Angle : 1.752 16.948 34257 Z= 1.156 Chirality : 0.101 1.413 4081 Planarity : 0.015 0.163 4349 Dihedral : 13.196 89.672 9962 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 0.21 Ramachandran Plot: Outliers : 0.87 % Allowed : 6.73 % Favored : 92.40 % Rotamer: Outliers : 1.39 % Allowed : 3.42 % Favored : 95.19 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.14), residues: 3000 helix: -0.58 (0.17), residues: 691 sheet: 0.25 (0.22), residues: 481 loop : -1.35 (0.13), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.122 0.021 TRP B 886 HIS 0.017 0.003 HIS A1048 PHE 0.077 0.013 PHE C 59 TYR 0.162 0.021 TYR B 495 ARG 0.011 0.001 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 2661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 59 time to evaluate : 2.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.6832 (OUTLIER) cc_final: 0.6631 (p) REVERT: A 990 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8309 (mt-10) REVERT: B 458 LYS cc_start: 0.9473 (mttt) cc_final: 0.9213 (tptp) REVERT: B 740 MET cc_start: 0.7939 (ttt) cc_final: 0.7413 (tpp) REVERT: C 342 PHE cc_start: 0.9067 (m-80) cc_final: 0.8853 (m-80) outliers start: 37 outliers final: 10 residues processed: 96 average time/residue: 0.3946 time to fit residues: 61.9459 Evaluate side-chains 49 residues out of total 2661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 38 time to evaluate : 3.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 328 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 256 optimal weight: 7.9990 chunk 230 optimal weight: 8.9990 chunk 127 optimal weight: 8.9990 chunk 78 optimal weight: 0.9980 chunk 155 optimal weight: 6.9990 chunk 123 optimal weight: 10.0000 chunk 238 optimal weight: 8.9990 chunk 92 optimal weight: 0.9980 chunk 144 optimal weight: 5.9990 chunk 177 optimal weight: 0.9990 chunk 276 optimal weight: 0.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN B 493 GLN B 628 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN C 751 ASN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 25181 Z= 0.202 Angle : 0.686 9.152 34257 Z= 0.363 Chirality : 0.047 0.478 4081 Planarity : 0.004 0.046 4349 Dihedral : 7.165 56.268 4558 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.30 % Favored : 95.40 % Rotamer: Outliers : 1.20 % Allowed : 4.40 % Favored : 94.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 (0.15), residues: 3000 helix: 1.38 (0.20), residues: 675 sheet: -0.03 (0.19), residues: 649 loop : -0.99 (0.15), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 64 HIS 0.006 0.001 HIS B 207 PHE 0.017 0.002 PHE B 392 TYR 0.018 0.002 TYR C 489 ARG 0.006 0.001 ARG C1019 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 2661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 44 time to evaluate : 2.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 987 VAL cc_start: 0.8669 (p) cc_final: 0.8228 (m) REVERT: B 458 LYS cc_start: 0.9580 (mttt) cc_final: 0.9207 (tptp) REVERT: B 625 HIS cc_start: 0.6869 (OUTLIER) cc_final: 0.6529 (t-170) REVERT: C 342 PHE cc_start: 0.9046 (m-80) cc_final: 0.8676 (m-80) REVERT: C 740 MET cc_start: 0.9241 (OUTLIER) cc_final: 0.8852 (ttp) outliers start: 32 outliers final: 9 residues processed: 74 average time/residue: 0.3712 time to fit residues: 46.8307 Evaluate side-chains 43 residues out of total 2661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 32 time to evaluate : 2.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 625 HIS Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 466 ARG Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 740 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 153 optimal weight: 8.9990 chunk 85 optimal weight: 0.4980 chunk 229 optimal weight: 20.0000 chunk 187 optimal weight: 8.9990 chunk 76 optimal weight: 7.9990 chunk 276 optimal weight: 0.7980 chunk 298 optimal weight: 0.0470 chunk 246 optimal weight: 6.9990 chunk 274 optimal weight: 9.9990 chunk 94 optimal weight: 6.9990 chunk 221 optimal weight: 9.9990 overall best weight: 3.0682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 655 HIS ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25181 Z= 0.211 Angle : 0.614 8.901 34257 Z= 0.319 Chirality : 0.045 0.379 4081 Planarity : 0.003 0.047 4349 Dihedral : 6.280 53.778 4547 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.23 % Favored : 94.57 % Rotamer: Outliers : 0.71 % Allowed : 5.90 % Favored : 93.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.69 % 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: -0.07 (0.15), residues: 3000 helix: 1.75 (0.20), residues: 685 sheet: 0.09 (0.20), residues: 638 loop : -0.87 (0.15), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 633 HIS 0.004 0.001 HIS C 655 PHE 0.016 0.001 PHE B 392 TYR 0.022 0.001 TYR C1067 ARG 0.004 0.000 ARG C1019 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 2661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 36 time to evaluate : 2.753 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 740 MET cc_start: 0.8500 (tpp) cc_final: 0.8295 (tpp) REVERT: A 988 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8170 (mt-10) REVERT: B 122 ASN cc_start: 0.3959 (OUTLIER) cc_final: 0.3604 (m-40) REVERT: B 402 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8493 (pp) REVERT: B 458 LYS cc_start: 0.9571 (mttt) cc_final: 0.9290 (tptp) REVERT: B 625 HIS cc_start: 0.6817 (OUTLIER) cc_final: 0.6584 (t-170) REVERT: B 1126 CYS cc_start: 0.7552 (OUTLIER) cc_final: 0.6801 (m) REVERT: C 342 PHE cc_start: 0.9098 (m-80) cc_final: 0.8737 (m-80) outliers start: 19 outliers final: 9 residues processed: 55 average time/residue: 0.3627 time to fit residues: 35.0550 Evaluate side-chains 46 residues out of total 2661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 33 time to evaluate : 2.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 625 HIS Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 392 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 273 optimal weight: 4.9990 chunk 207 optimal weight: 8.9990 chunk 143 optimal weight: 30.0000 chunk 30 optimal weight: 8.9990 chunk 131 optimal weight: 6.9990 chunk 185 optimal weight: 0.7980 chunk 277 optimal weight: 0.9980 chunk 293 optimal weight: 9.9990 chunk 145 optimal weight: 2.9990 chunk 263 optimal weight: 1.9990 chunk 79 optimal weight: 7.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1036 GLN C 675 GLN C 784 GLN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25181 Z= 0.172 Angle : 0.547 8.904 34257 Z= 0.283 Chirality : 0.044 0.375 4081 Planarity : 0.003 0.045 4349 Dihedral : 5.615 52.664 4542 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.53 % Favored : 95.30 % Rotamer: Outliers : 1.24 % Allowed : 6.61 % Favored : 92.15 % 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: 0.06 (0.15), residues: 3000 helix: 1.93 (0.20), residues: 685 sheet: 0.06 (0.20), residues: 644 loop : -0.78 (0.15), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 633 HIS 0.003 0.001 HIS B 625 PHE 0.014 0.001 PHE B 392 TYR 0.018 0.001 TYR C1067 ARG 0.002 0.000 ARG C1019 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 2661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 37 time to evaluate : 2.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 473 TYR cc_start: 0.9060 (m-10) cc_final: 0.8827 (m-10) REVERT: A 740 MET cc_start: 0.8406 (tpp) cc_final: 0.8112 (tpp) REVERT: B 402 ILE cc_start: 0.8621 (OUTLIER) cc_final: 0.8411 (pp) REVERT: B 985 ASP cc_start: 0.8368 (p0) cc_final: 0.8143 (p0) REVERT: B 1126 CYS cc_start: 0.7458 (OUTLIER) cc_final: 0.6687 (m) REVERT: C 979 ASP cc_start: 0.8843 (m-30) cc_final: 0.8345 (t0) outliers start: 33 outliers final: 13 residues processed: 68 average time/residue: 0.3225 time to fit residues: 39.5648 Evaluate side-chains 48 residues out of total 2661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 33 time to evaluate : 2.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 638 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 244 optimal weight: 7.9990 chunk 166 optimal weight: 1.9990 chunk 4 optimal weight: 20.0000 chunk 218 optimal weight: 20.0000 chunk 121 optimal weight: 5.9990 chunk 250 optimal weight: 4.9990 chunk 203 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 150 optimal weight: 9.9990 chunk 263 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 914 ASN B 519 HIS B 675 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 25181 Z= 0.225 Angle : 0.564 9.107 34257 Z= 0.289 Chirality : 0.044 0.374 4081 Planarity : 0.003 0.043 4349 Dihedral : 5.518 51.876 4540 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.10 % Favored : 94.73 % Rotamer: Outliers : 1.16 % Allowed : 7.78 % Favored : 91.06 % 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 (0.15), residues: 3000 helix: 2.00 (0.20), residues: 683 sheet: 0.06 (0.19), residues: 646 loop : -0.83 (0.15), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 633 HIS 0.005 0.001 HIS B 625 PHE 0.020 0.001 PHE C 392 TYR 0.022 0.001 TYR C1067 ARG 0.010 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 2661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 33 time to evaluate : 2.813 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 794 ILE cc_start: 0.8584 (OUTLIER) cc_final: 0.8377 (pt) REVERT: B 122 ASN cc_start: 0.4185 (OUTLIER) cc_final: 0.3869 (m-40) REVERT: B 402 ILE cc_start: 0.8624 (OUTLIER) cc_final: 0.8422 (pp) REVERT: B 1126 CYS cc_start: 0.7434 (OUTLIER) cc_final: 0.6652 (m) REVERT: C 979 ASP cc_start: 0.8909 (m-30) cc_final: 0.8384 (t0) outliers start: 31 outliers final: 16 residues processed: 62 average time/residue: 0.3173 time to fit residues: 37.2827 Evaluate side-chains 51 residues out of total 2661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 31 time to evaluate : 2.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 638 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 98 optimal weight: 0.9990 chunk 264 optimal weight: 7.9990 chunk 58 optimal weight: 8.9990 chunk 172 optimal weight: 0.0570 chunk 72 optimal weight: 0.4980 chunk 294 optimal weight: 8.9990 chunk 244 optimal weight: 20.0000 chunk 136 optimal weight: 50.0000 chunk 24 optimal weight: 20.0000 chunk 97 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 overall best weight: 1.3104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 25181 Z= 0.142 Angle : 0.514 8.394 34257 Z= 0.267 Chirality : 0.043 0.346 4081 Planarity : 0.003 0.049 4349 Dihedral : 5.161 46.601 4540 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.53 % Favored : 95.30 % Rotamer: Outliers : 0.86 % Allowed : 8.23 % Favored : 90.91 % 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: 0.20 (0.15), residues: 3000 helix: 2.19 (0.20), residues: 677 sheet: 0.16 (0.19), residues: 646 loop : -0.76 (0.15), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP B 633 HIS 0.004 0.001 HIS A1083 PHE 0.017 0.001 PHE C 392 TYR 0.029 0.001 TYR A 473 ARG 0.006 0.000 ARG B 634 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 2661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 34 time to evaluate : 2.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 122 ASN cc_start: 0.3839 (OUTLIER) cc_final: 0.3527 (m-40) REVERT: B 402 ILE cc_start: 0.8612 (OUTLIER) cc_final: 0.8410 (pp) REVERT: B 1126 CYS cc_start: 0.7335 (OUTLIER) cc_final: 0.6536 (m) REVERT: C 979 ASP cc_start: 0.8908 (m-30) cc_final: 0.8402 (t0) outliers start: 23 outliers final: 13 residues processed: 56 average time/residue: 0.3276 time to fit residues: 33.7590 Evaluate side-chains 48 residues out of total 2661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 32 time to evaluate : 2.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 638 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 283 optimal weight: 0.8980 chunk 33 optimal weight: 20.0000 chunk 167 optimal weight: 4.9990 chunk 214 optimal weight: 30.0000 chunk 166 optimal weight: 10.0000 chunk 247 optimal weight: 10.0000 chunk 164 optimal weight: 3.9990 chunk 293 optimal weight: 3.9990 chunk 183 optimal weight: 9.9990 chunk 178 optimal weight: 0.5980 chunk 135 optimal weight: 5.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1142 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 25181 Z= 0.199 Angle : 0.525 8.806 34257 Z= 0.270 Chirality : 0.043 0.360 4081 Planarity : 0.003 0.052 4349 Dihedral : 5.092 43.488 4539 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.90 % Favored : 94.93 % Rotamer: Outliers : 0.94 % Allowed : 8.38 % Favored : 90.68 % 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: 0.23 (0.15), residues: 3000 helix: 2.21 (0.20), residues: 677 sheet: 0.16 (0.19), residues: 653 loop : -0.73 (0.15), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 633 HIS 0.004 0.001 HIS A1083 PHE 0.016 0.001 PHE C 392 TYR 0.020 0.001 TYR C1067 ARG 0.002 0.000 ARG B 319 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 2661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 32 time to evaluate : 2.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 402 ILE cc_start: 0.8621 (OUTLIER) cc_final: 0.8418 (pp) REVERT: B 638 THR cc_start: 0.7232 (OUTLIER) cc_final: 0.6833 (m) REVERT: B 1126 CYS cc_start: 0.7343 (OUTLIER) cc_final: 0.6619 (m) REVERT: C 979 ASP cc_start: 0.8957 (m-30) cc_final: 0.8484 (t0) outliers start: 25 outliers final: 19 residues processed: 56 average time/residue: 0.3200 time to fit residues: 32.7085 Evaluate side-chains 52 residues out of total 2661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 30 time to evaluate : 2.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 638 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 181 optimal weight: 10.0000 chunk 117 optimal weight: 8.9990 chunk 174 optimal weight: 0.8980 chunk 88 optimal weight: 8.9990 chunk 57 optimal weight: 10.0000 chunk 56 optimal weight: 9.9990 chunk 186 optimal weight: 0.9980 chunk 199 optimal weight: 1.9990 chunk 144 optimal weight: 9.9990 chunk 27 optimal weight: 20.0000 chunk 230 optimal weight: 6.9990 overall best weight: 3.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 25181 Z= 0.252 Angle : 0.554 8.973 34257 Z= 0.284 Chirality : 0.043 0.363 4081 Planarity : 0.003 0.053 4349 Dihedral : 5.230 45.317 4539 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.30 % Favored : 94.53 % Rotamer: Outliers : 1.09 % Allowed : 8.64 % Favored : 90.27 % 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: 0.13 (0.15), residues: 3000 helix: 2.14 (0.20), residues: 678 sheet: 0.08 (0.19), residues: 661 loop : -0.78 (0.15), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 633 HIS 0.005 0.001 HIS B 655 PHE 0.017 0.001 PHE C 392 TYR 0.027 0.001 TYR B 380 ARG 0.005 0.000 ARG C 319 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 2661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 31 time to evaluate : 2.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 402 ILE cc_start: 0.8636 (OUTLIER) cc_final: 0.8434 (pp) REVERT: B 638 THR cc_start: 0.7153 (OUTLIER) cc_final: 0.6754 (m) REVERT: C 979 ASP cc_start: 0.8973 (m-30) cc_final: 0.8553 (t0) outliers start: 29 outliers final: 23 residues processed: 59 average time/residue: 0.3087 time to fit residues: 34.4426 Evaluate side-chains 56 residues out of total 2661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 31 time to evaluate : 2.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 625 HIS Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 638 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 266 optimal weight: 10.0000 chunk 280 optimal weight: 1.9990 chunk 256 optimal weight: 9.9990 chunk 273 optimal weight: 10.0000 chunk 164 optimal weight: 6.9990 chunk 118 optimal weight: 20.0000 chunk 214 optimal weight: 30.0000 chunk 83 optimal weight: 8.9990 chunk 246 optimal weight: 5.9990 chunk 258 optimal weight: 10.0000 chunk 272 optimal weight: 0.0770 overall best weight: 4.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 25181 Z= 0.294 Angle : 0.587 10.087 34257 Z= 0.298 Chirality : 0.044 0.362 4081 Planarity : 0.004 0.053 4349 Dihedral : 5.463 47.519 4539 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.20 % Favored : 94.63 % Rotamer: Outliers : 1.16 % Allowed : 8.64 % Favored : 90.19 % 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: 0.01 (0.15), residues: 3000 helix: 1.94 (0.20), residues: 690 sheet: 0.07 (0.19), residues: 653 loop : -0.87 (0.15), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 633 HIS 0.006 0.001 HIS B 655 PHE 0.019 0.001 PHE C 392 TYR 0.024 0.001 TYR A 473 ARG 0.006 0.000 ARG C 319 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 2661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 33 time to evaluate : 2.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 402 ILE cc_start: 0.8697 (OUTLIER) cc_final: 0.8493 (pp) REVERT: B 638 THR cc_start: 0.7188 (OUTLIER) cc_final: 0.6810 (m) REVERT: C 979 ASP cc_start: 0.8957 (m-30) cc_final: 0.8588 (t0) outliers start: 31 outliers final: 24 residues processed: 62 average time/residue: 0.3218 time to fit residues: 36.6710 Evaluate side-chains 57 residues out of total 2661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 31 time to evaluate : 2.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 638 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 179 optimal weight: 6.9990 chunk 288 optimal weight: 1.9990 chunk 176 optimal weight: 6.9990 chunk 136 optimal weight: 30.0000 chunk 200 optimal weight: 9.9990 chunk 302 optimal weight: 0.6980 chunk 278 optimal weight: 6.9990 chunk 241 optimal weight: 20.0000 chunk 25 optimal weight: 0.9990 chunk 186 optimal weight: 0.9990 chunk 147 optimal weight: 20.0000 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 613 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 25181 Z= 0.171 Angle : 0.521 8.394 34257 Z= 0.268 Chirality : 0.043 0.338 4081 Planarity : 0.003 0.052 4349 Dihedral : 5.223 48.294 4539 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.93 % Favored : 94.93 % Rotamer: Outliers : 1.01 % Allowed : 8.72 % Favored : 90.27 % 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: 0.12 (0.15), residues: 3000 helix: 2.10 (0.20), residues: 692 sheet: 0.09 (0.19), residues: 653 loop : -0.81 (0.15), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 633 HIS 0.006 0.001 HIS C1083 PHE 0.018 0.001 PHE C 392 TYR 0.023 0.001 TYR C 396 ARG 0.012 0.000 ARG C 357 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 2661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 32 time to evaluate : 2.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 638 THR cc_start: 0.7230 (OUTLIER) cc_final: 0.6850 (m) REVERT: C 979 ASP cc_start: 0.8941 (m-30) cc_final: 0.8588 (t0) outliers start: 27 outliers final: 24 residues processed: 58 average time/residue: 0.3020 time to fit residues: 32.9114 Evaluate side-chains 57 residues out of total 2661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 32 time to evaluate : 2.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 625 HIS Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 638 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 191 optimal weight: 4.9990 chunk 256 optimal weight: 6.9990 chunk 73 optimal weight: 0.9980 chunk 222 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 241 optimal weight: 50.0000 chunk 101 optimal weight: 30.0000 chunk 248 optimal weight: 5.9990 chunk 30 optimal weight: 20.0000 chunk 44 optimal weight: 8.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 955 ASN B 613 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.045480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.033064 restraints weight = 221699.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.033934 restraints weight = 114871.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.034476 restraints weight = 75980.552| |-----------------------------------------------------------------------------| r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 25181 Z= 0.286 Angle : 0.573 9.020 34257 Z= 0.292 Chirality : 0.044 0.359 4081 Planarity : 0.003 0.047 4349 Dihedral : 5.376 48.541 4539 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.27 % Favored : 94.70 % Rotamer: Outliers : 1.09 % Allowed : 8.76 % Favored : 90.15 % 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: 0.03 (0.15), residues: 3000 helix: 2.02 (0.20), residues: 690 sheet: 0.05 (0.19), residues: 653 loop : -0.87 (0.15), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 633 HIS 0.006 0.001 HIS C1083 PHE 0.021 0.001 PHE C 392 TYR 0.025 0.001 TYR A 473 ARG 0.005 0.000 ARG C 319 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3155.48 seconds wall clock time: 60 minutes 49.59 seconds (3649.59 seconds total)