Starting phenix.real_space_refine on Wed Oct 28 06:11:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11is_75725/10_2026/11is_75725.cif Found real_map, /net/cci-nas-00/data/ceres_data/11is_75725/10_2026/11is_75725.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/11is_75725/10_2026/11is_75725.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11is_75725/10_2026/11is_75725.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/11is_75725/10_2026/11is_75725.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11is_75725/10_2026/11is_75725.map" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 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 111 5.16 5 C 17076 2.51 5 N 4359 2.21 5 O 5196 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 62 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26742 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 8086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8086 Classifications: {'peptide': 1032} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 975} Chain breaks: 6 Chain: "B" Number of atoms: 8086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8086 Classifications: {'peptide': 1032} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 975} Chain breaks: 6 Chain: "C" Number of atoms: 8086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8086 Classifications: {'peptide': 1032} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 975} Chain breaks: 6 Chain: "J" Number of atoms: 962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 962 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "N" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 808 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} 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: "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: "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: "R" 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: "S" 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: "T" 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: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 4.84, per 1000 atoms: 0.18 Number of scatterers: 26742 At special positions: 0 Unit cell: (135.513, 131.211, 212.949, 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 111 16.00 O 5196 8.00 N 4359 7.00 C 17076 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 163 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 163 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 163 " 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=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 95 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 90 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 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 K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG A1301 " - " ASN A 230 " " NAG A1302 " - " ASN A 278 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 354 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A1074 " " NAG A1307 " - " ASN A 343 " " NAG B1301 " - " ASN B 230 " " NAG B1302 " - " ASN B 278 " " NAG B1303 " - " ASN B 331 " " NAG B1304 " - " ASN B 343 " " NAG B1305 " - " ASN B 354 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B1074 " " NAG C1301 " - " ASN C 230 " " NAG C1302 " - " ASN C 278 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 343 " " NAG C1305 " - " ASN C 354 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C1074 " " NAG D 1 " - " ASN A 801 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A1098 " " NAG G 1 " - " ASN A1134 " " NAG H 1 " - " ASN A 709 " " NAG I 1 " - " ASN B 801 " " NAG K 1 " - " ASN B 717 " " NAG M 1 " - " ASN B1134 " " NAG O 1 " - " ASN B 709 " " NAG P 1 " - " ASN C 801 " " NAG Q 1 " - " ASN C 717 " " NAG R 1 " - " ASN C1098 " " NAG S 1 " - " ASN C1134 " " NAG T 1 " - " ASN C 709 " NAG-THR " NAG L 1 " - " THR B1100 " Time building additional restraints: 2.45 Conformation dependent library (CDL) restraints added in 1.1 seconds 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6220 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 51 sheets defined 25.2% alpha, 27.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 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 372 Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.563A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 616 through 626 Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.501A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.175A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.657A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (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 removed outlier: 3.923A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN A 960 " --> pdb=" O ALA A 956 " (cutoff:3.500A) 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: 3.641A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.437A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 372 removed outlier: 4.026A pdb=" N ASN B 370 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 3.791A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.557A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 616 through 626 removed outlier: 3.721A pdb=" N VAL B 620 " --> pdb=" O ASN B 616 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N VAL B 622 " --> pdb=" O THR B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 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 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.743A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.922A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN B 919 " --> pdb=" O VAL B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.712A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.580A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (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 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.186A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1139 through 1147 removed outlier: 3.625A pdb=" N LEU B1143 " --> pdb=" O ASP B1139 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 4.127A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 364 through 372 removed outlier: 3.530A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 389 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.249A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 616 through 626 removed outlier: 3.584A pdb=" N VAL C 620 " --> pdb=" O ASN C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.803A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.147A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.780A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.786A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (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: 3.595A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.333A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1139 through 1146 Processing helix chain 'J' and resid 63 through 65 No H-bonds generated for 'chain 'J' and resid 63 through 65' Processing helix chain 'J' and resid 86 through 90 removed outlier: 3.753A pdb=" N THR J 90 " --> pdb=" O ALA J 87 " (cutoff:3.500A) Processing helix chain 'N' and resid 25 through 29 Processing helix chain 'N' and resid 81 through 85 Processing helix chain 'N' and resid 94 through 97 removed outlier: 3.540A pdb=" N THR N 97 " --> pdb=" O ALA N 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 94 through 97' Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.518A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.011A pdb=" N ASP A 283 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 63 through 67 removed outlier: 3.924A pdb=" N VAL A 223 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N SER A 202 " --> pdb=" O PRO A 221 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 82 through 83 removed outlier: 3.794A pdb=" N GLY A 101 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ARG A 100 " --> pdb=" O ASN A 119 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 132 through 133 Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.981A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.759A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 448 through 454 removed outlier: 5.291A pdb=" N TYR A 449 " --> pdb=" O PHE A 497 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N PHE A 497 " --> pdb=" O TYR A 449 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.010A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.495A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.666A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 789 removed outlier: 5.913A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.517A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.813A pdb=" N ASP B 283 " --> pdb=" O LYS B 274 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 63 through 65 removed outlier: 6.137A pdb=" N SER B 202 " --> pdb=" O PRO B 221 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 82 through 83 removed outlier: 3.695A pdb=" N LEU B 237 " --> pdb=" O GLY B 101 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLY B 101 " --> pdb=" O LEU B 237 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ARG B 100 " --> pdb=" O ASN B 119 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL B 124 " --> pdb=" O TYR B 167 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N TYR B 167 " --> pdb=" O VAL B 124 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE B 126 " --> pdb=" O PHE B 165 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N PHE B 165 " --> pdb=" O ILE B 126 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N VAL B 128 " --> pdb=" O CYS B 163 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N CYS B 163 " --> pdb=" O VAL B 128 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.991A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.814A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.158A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.596A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.263A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 788 through 789 removed outlier: 5.830A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD4, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD5, first strand: chain 'C' and resid 36 through 37 removed outlier: 6.927A pdb=" N VAL C 36 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 9.064A pdb=" N ALA C 218 " --> pdb=" O HIS C 204 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N HIS C 204 " --> pdb=" O ALA C 218 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU C 220 " --> pdb=" O SER C 202 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE C 200 " --> pdb=" O LEU C 222 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ASP C 224 " --> pdb=" O PHE C 198 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N PHE C 198 " --> pdb=" O ASP C 224 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.937A pdb=" N ASP C 283 " --> pdb=" O LYS C 274 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 82 through 83 removed outlier: 7.146A pdb=" N ARG C 233 " --> pdb=" O PHE C 104 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N PHE C 104 " --> pdb=" O ARG C 233 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N GLN C 235 " --> pdb=" O TRP C 102 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N TRP C 102 " --> pdb=" O GLN C 235 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU C 237 " --> pdb=" O ARG C 100 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N ARG C 100 " --> pdb=" O ASN C 119 " (cutoff:3.500A) removed outlier: 11.428A pdb=" N VAL C 124 " --> pdb=" O GLU C 166 " (cutoff:3.500A) removed outlier: 10.051A pdb=" N GLU C 166 " --> pdb=" O VAL C 124 " (cutoff:3.500A) removed outlier: 11.511A pdb=" N ILE C 126 " --> pdb=" O THR C 164 " (cutoff:3.500A) removed outlier: 8.951A pdb=" N THR C 164 " --> pdb=" O ILE C 126 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N VAL C 128 " --> pdb=" O ASN C 162 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ASN C 162 " --> pdb=" O VAL C 128 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N GLU C 130 " --> pdb=" O ALA C 160 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ALA C 160 " --> pdb=" O GLU C 130 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N GLN C 132 " --> pdb=" O SER C 158 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.533A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 325 through 328 Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.739A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.020A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.620A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.620A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.280A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.282A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 4 through 7 removed outlier: 3.694A pdb=" N THR J 21 " --> pdb=" O SER J 7 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.696A pdb=" N GLY J 10 " --> pdb=" O THR J 122 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLY J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.696A pdb=" N GLY J 10 " --> pdb=" O THR J 122 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'N' and resid 9 through 11 removed outlier: 6.429A pdb=" N VAL N 10 " --> pdb=" O THR N 108 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE N 50 " --> pdb=" O TRP N 37 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLN N 39 " --> pdb=" O LEU N 48 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N LEU N 48 " --> pdb=" O GLN N 39 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'N' and resid 9 through 11 removed outlier: 6.429A pdb=" N VAL N 10 " --> pdb=" O THR N 108 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'N' and resid 18 through 23 1074 hydrogen bonds defined for protein. 2871 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.08 Time building geometry restraints manager: 3.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8362 1.34 - 1.46: 6851 1.46 - 1.58: 12025 1.58 - 1.70: 0 1.70 - 1.83: 136 Bond restraints: 27374 Sorted by residual: bond pdb=" CB CYS B 760 " pdb=" SG CYS B 760 " ideal model delta sigma weight residual 1.808 1.737 0.071 3.30e-02 9.18e+02 4.60e+00 bond pdb=" C THR B 630 " pdb=" N PRO B 631 " ideal model delta sigma weight residual 1.333 1.350 -0.017 1.01e-02 9.80e+03 2.69e+00 bond pdb=" CD1 TYR J 32 " pdb=" CE1 TYR J 32 " ideal model delta sigma weight residual 1.382 1.340 0.042 3.00e-02 1.11e+03 1.92e+00 bond pdb=" CB GLU C 988 " pdb=" CG GLU C 988 " ideal model delta sigma weight residual 1.520 1.560 -0.040 3.00e-02 1.11e+03 1.79e+00 bond pdb=" CB ASP B 195 " pdb=" CG ASP B 195 " ideal model delta sigma weight residual 1.516 1.549 -0.033 2.50e-02 1.60e+03 1.76e+00 ... (remaining 27369 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 36678 1.98 - 3.97: 501 3.97 - 5.95: 68 5.95 - 7.94: 12 7.94 - 9.92: 5 Bond angle restraints: 37264 Sorted by residual: angle pdb=" C ASN A 135 " pdb=" N ASP A 136 " pdb=" CA ASP A 136 " ideal model delta sigma weight residual 121.80 131.63 -9.83 2.44e+00 1.68e-01 1.62e+01 angle pdb=" C LYS C1073 " pdb=" N ASN C1074 " pdb=" CA ASN C1074 " ideal model delta sigma weight residual 120.71 125.90 -5.19 1.42e+00 4.96e-01 1.34e+01 angle pdb=" C CYS B 760 " pdb=" N THR B 761 " pdb=" CA THR B 761 " ideal model delta sigma weight residual 120.44 115.75 4.69 1.30e+00 5.92e-01 1.30e+01 angle pdb=" CA LYS J 81 " pdb=" CB LYS J 81 " pdb=" CG LYS J 81 " ideal model delta sigma weight residual 114.10 120.99 -6.89 2.00e+00 2.50e-01 1.19e+01 angle pdb=" C1 NAG C1307 " pdb=" O5 NAG C1307 " pdb=" C5 NAG C1307 " ideal model delta sigma weight residual 113.21 123.13 -9.92 3.00e+00 1.11e-01 1.09e+01 ... (remaining 37259 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 15080 17.58 - 35.16: 1401 35.16 - 52.73: 317 52.73 - 70.31: 81 70.31 - 87.89: 37 Dihedral angle restraints: 16916 sinusoidal: 7231 harmonic: 9685 Sorted by residual: dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -7.22 -78.78 1 1.00e+01 1.00e-02 7.73e+01 dihedral pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sinusoidal sigma weight residual -86.00 -157.79 71.79 1 1.00e+01 1.00e-02 6.60e+01 dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual 93.00 32.45 60.55 1 1.00e+01 1.00e-02 4.88e+01 ... (remaining 16913 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 3449 0.050 - 0.100: 707 0.100 - 0.150: 190 0.150 - 0.200: 9 0.200 - 0.250: 4 Chirality restraints: 4359 Sorted by residual: chirality pdb=" C2 NAG C1307 " pdb=" C1 NAG C1307 " pdb=" C3 NAG C1307 " pdb=" N2 NAG C1307 " both_signs ideal model delta sigma weight residual False -2.49 -2.24 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" C2 NAG G 2 " pdb=" C1 NAG G 2 " pdb=" C3 NAG G 2 " pdb=" N2 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.25 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" C2 NAG T 2 " pdb=" C1 NAG T 2 " pdb=" C3 NAG T 2 " pdb=" N2 NAG T 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.26 -0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 4356 not shown) Planarity restraints: 4767 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP J 34 " -0.037 2.00e-02 2.50e+03 3.41e-02 2.90e+01 pdb=" CG TRP J 34 " 0.086 2.00e-02 2.50e+03 pdb=" CD1 TRP J 34 " -0.048 2.00e-02 2.50e+03 pdb=" CD2 TRP J 34 " 0.013 2.00e-02 2.50e+03 pdb=" NE1 TRP J 34 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP J 34 " 0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP J 34 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 34 " 0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 34 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP J 34 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 985 " -0.038 5.00e-02 4.00e+02 5.70e-02 5.21e+00 pdb=" N PRO B 986 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO B 986 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 986 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN C1074 " -0.018 2.00e-02 2.50e+03 1.65e-02 3.40e+00 pdb=" CG ASN C1074 " 0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN C1074 " -0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN C1074 " 0.017 2.00e-02 2.50e+03 pdb=" C1 NAG C1307 " -0.017 2.00e-02 2.50e+03 ... (remaining 4764 not shown) Histogram of nonbonded interaction distances: 2.46 - 2.95: 12211 2.95 - 3.43: 25569 3.43 - 3.92: 43470 3.92 - 4.41: 48956 4.41 - 4.90: 82860 Nonbonded interactions: 213066 Sorted by model distance: nonbonded pdb=" N GLU C 619 " pdb=" OE1 GLU C 619 " model vdw 2.458 3.120 nonbonded pdb=" OD1 ASN C1074 " pdb=" O5 NAG C1307 " model vdw 2.483 3.040 nonbonded pdb=" N GLU C 988 " pdb=" OE1 GLU C 988 " model vdw 2.492 3.120 nonbonded pdb=" CB GLU B 130 " pdb=" O ASN B 161 " model vdw 2.500 2.752 nonbonded pdb=" O VAL C 570 " pdb=" OD1 ASP C 571 " model vdw 2.536 3.040 ... (remaining 213061 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 14.550 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: 0.630 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 25.500 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.060 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: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 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 : 0.003 0.071 27463 Z= 0.123 Angle : 0.611 18.506 37492 Z= 0.317 Chirality : 0.044 0.250 4359 Planarity : 0.004 0.057 4732 Dihedral : 14.656 87.889 10582 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.01 % Favored : 96.93 % Rotamer: Outliers : 1.68 % Allowed : 15.92 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.15), residues: 3285 helix: 1.98 (0.20), residues: 693 sheet: 0.46 (0.18), residues: 796 loop : -0.53 (0.15), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 498 TYR 0.032 0.001 TYR J 52 PHE 0.021 0.001 PHE A 189 TRP 0.086 0.002 TRP J 34 HIS 0.003 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (27374) covalent geometry : angle 0.58527 / 0.31 (37264) SS BOND : bond 0.00241 / 0.16 ( 38) SS BOND : angle 1.21919 / 0.82 ( 76) hydrogen bonds : bond 0.11672 / 7.41 ( 1056) hydrogen bonds : angle 6.39122 / 4.45 ( 2871) link_BETA1-4 : bond 0.00337 / 0.18 ( 15) link_BETA1-4 : angle 1.08539 / 0.71 ( 45) link_NAG-ASN : bond 0.00543 / 0.24 ( 35) link_NAG-ASN : angle 3.11470 / 1.83 ( 105) link_NAG-THR : bond 0.00800 / 0.42 ( 1) link_NAG-THR : angle 4.02410 / 2.16 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 215 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 PHE cc_start: 0.6636 (p90) cc_final: 0.6349 (p90) REVERT: A 414 GLN cc_start: 0.8107 (mp10) cc_final: 0.7522 (mp10) REVERT: A 428 ASP cc_start: 0.8667 (t0) cc_final: 0.8274 (t0) REVERT: A 460 LYS cc_start: 0.9055 (pttt) cc_final: 0.8788 (mtmm) REVERT: A 498 ARG cc_start: 0.8396 (ttm-80) cc_final: 0.7849 (tpp80) REVERT: A 580 GLN cc_start: 0.8617 (mt0) cc_final: 0.8044 (mt0) REVERT: A 630 THR cc_start: 0.8423 (m) cc_final: 0.8100 (m) REVERT: A 988 GLU cc_start: 0.8370 (pm20) cc_final: 0.7725 (pm20) REVERT: B 199 LYS cc_start: 0.8922 (mttt) cc_final: 0.8646 (mttp) REVERT: B 265 TYR cc_start: 0.8289 (OUTLIER) cc_final: 0.7792 (t80) REVERT: B 630 THR cc_start: 0.8382 (m) cc_final: 0.8102 (m) REVERT: B 990 GLU cc_start: 0.8278 (tm-30) cc_final: 0.8056 (tt0) REVERT: B 1119 ASN cc_start: 0.8213 (t0) cc_final: 0.7583 (t0) REVERT: C 52 GLN cc_start: 0.8700 (tm-30) cc_final: 0.8271 (tm-30) REVERT: C 314 GLN cc_start: 0.9169 (tt0) cc_final: 0.8733 (tm-30) REVERT: C 360 ASN cc_start: 0.8773 (t0) cc_final: 0.8239 (t0) REVERT: C 434 ILE cc_start: 0.6711 (OUTLIER) cc_final: 0.6430 (mm) REVERT: C 451 TYR cc_start: 0.6505 (m-80) cc_final: 0.5993 (m-80) REVERT: C 508 TYR cc_start: 0.6686 (OUTLIER) cc_final: 0.5780 (t80) REVERT: C 856 ASN cc_start: 0.9196 (OUTLIER) cc_final: 0.8780 (p0) REVERT: C 994 ASP cc_start: 0.8749 (t70) cc_final: 0.8209 (t0) REVERT: C 1119 ASN cc_start: 0.8476 (t0) cc_final: 0.8177 (t0) REVERT: J 32 TYR cc_start: 0.6156 (t80) cc_final: 0.5782 (t80) outliers start: 49 outliers final: 38 residues processed: 248 average time/residue: 0.1510 time to fit residues: 62.9359 Evaluate side-chains 248 residues out of total 2909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 206 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 508 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 939 PHE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain N residue 75 LEU Chi-restraints excluded: chain N residue 90 CYS Chi-restraints excluded: chain N residue 92 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 298] chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.0370 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 0.4980 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 3.9990 overall best weight: 2.1064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 339 HIS ** A 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN B1125 ASN C 519 HIS ** J 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.129360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.076844 restraints weight = 53684.295| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 3.21 r_work: 0.2877 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.0996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 27463 Z= 0.236 Angle : 0.610 18.987 37492 Z= 0.302 Chirality : 0.045 0.256 4359 Planarity : 0.004 0.054 4732 Dihedral : 7.164 58.469 4706 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.17 % Favored : 96.77 % Rotamer: Outliers : 2.78 % Allowed : 14.64 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.15), residues: 3285 helix: 1.86 (0.20), residues: 695 sheet: 0.50 (0.18), residues: 774 loop : -0.58 (0.15), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 498 TYR 0.023 0.001 TYR A 261 PHE 0.015 0.001 PHE C 133 TRP 0.028 0.002 TRP J 34 HIS 0.007 0.001 HIS A 954 Details of bonding type rmsd/Z covalent geometry : bond 0.00556 / 0.24 (27374) covalent geometry : angle 0.57818 / 0.29 (37264) SS BOND : bond 0.00369 / 0.23 ( 38) SS BOND : angle 1.63060 / 1.09 ( 76) hydrogen bonds : bond 0.04083 / 2.62 ( 1056) hydrogen bonds : angle 5.35750 / 3.73 ( 2871) link_BETA1-4 : bond 0.00337 / 0.16 ( 15) link_BETA1-4 : angle 1.25474 / 0.79 ( 45) link_NAG-ASN : bond 0.00543 / 0.27 ( 35) link_NAG-ASN : angle 3.36678 / 2.00 ( 105) link_NAG-THR : bond 0.00839 / 0.44 ( 1) link_NAG-THR : angle 2.88645 / 1.52 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 197 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 PHE cc_start: 0.6671 (p90) cc_final: 0.6466 (p90) REVERT: A 414 GLN cc_start: 0.8322 (mp10) cc_final: 0.7743 (mp10) REVERT: A 428 ASP cc_start: 0.8804 (t0) cc_final: 0.8436 (t0) REVERT: A 460 LYS cc_start: 0.9142 (pttt) cc_final: 0.8912 (mtmm) REVERT: A 630 THR cc_start: 0.8449 (m) cc_final: 0.8129 (m) REVERT: B 52 GLN cc_start: 0.8574 (tt0) cc_final: 0.8211 (tm-30) REVERT: B 111 LYS cc_start: 0.8671 (ptmt) cc_final: 0.8387 (pttm) REVERT: B 199 LYS cc_start: 0.9121 (mttt) cc_final: 0.8836 (mttp) REVERT: B 630 THR cc_start: 0.8417 (m) cc_final: 0.8147 (m) REVERT: C 52 GLN cc_start: 0.8842 (tm-30) cc_final: 0.8324 (tm-30) REVERT: C 360 ASN cc_start: 0.8804 (t0) cc_final: 0.8330 (t0) REVERT: C 434 ILE cc_start: 0.7014 (OUTLIER) cc_final: 0.6708 (mm) REVERT: C 451 TYR cc_start: 0.6942 (m-80) cc_final: 0.6303 (m-80) REVERT: C 994 ASP cc_start: 0.8847 (t70) cc_final: 0.8350 (t0) REVERT: C 1119 ASN cc_start: 0.8545 (t0) cc_final: 0.8098 (t0) REVERT: J 32 TYR cc_start: 0.6230 (t80) cc_final: 0.5837 (t80) REVERT: N 95 ASP cc_start: 0.8593 (t70) cc_final: 0.8253 (m-30) outliers start: 81 outliers final: 46 residues processed: 260 average time/residue: 0.1403 time to fit residues: 62.8524 Evaluate side-chains 233 residues out of total 2909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 186 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 508 TYR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 939 PHE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 97 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: [180, 273, 221, 243, 67, 306, 47, 304, 196, 187, 153] chunk 180 optimal weight: 0.9990 chunk 273 optimal weight: 0.7980 chunk 221 optimal weight: 0.0040 chunk 243 optimal weight: 9.9990 chunk 67 optimal weight: 0.9990 chunk 306 optimal weight: 0.6980 chunk 47 optimal weight: 6.9990 chunk 304 optimal weight: 0.9980 chunk 196 optimal weight: 0.8980 chunk 187 optimal weight: 0.8980 chunk 153 optimal weight: 0.9980 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 339 HIS ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN C 751 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.131255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.078801 restraints weight = 53671.722| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 3.19 r_work: 0.2917 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.1028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 27463 Z= 0.111 Angle : 0.548 19.017 37492 Z= 0.268 Chirality : 0.043 0.237 4359 Planarity : 0.003 0.051 4732 Dihedral : 6.718 59.948 4665 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.77 % Favored : 97.17 % Rotamer: Outliers : 2.51 % Allowed : 15.61 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.15), residues: 3285 helix: 2.18 (0.20), residues: 684 sheet: 0.49 (0.18), residues: 759 loop : -0.54 (0.15), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 328 TYR 0.019 0.001 TYR B1067 PHE 0.020 0.001 PHE A 90 TRP 0.018 0.001 TRP A 452 HIS 0.003 0.001 HIS C1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (27374) covalent geometry : angle 0.51893 / 0.26 (37264) SS BOND : bond 0.00284 / 0.18 ( 38) SS BOND : angle 1.24290 / 0.82 ( 76) hydrogen bonds : bond 0.03525 / 2.25 ( 1056) hydrogen bonds : angle 5.11817 / 3.56 ( 2871) link_BETA1-4 : bond 0.00344 / 0.17 ( 15) link_BETA1-4 : angle 1.09741 / 0.71 ( 45) link_NAG-ASN : bond 0.00602 / 0.27 ( 35) link_NAG-ASN : angle 3.12673 / 1.82 ( 105) link_NAG-THR : bond 0.00483 / 0.25 ( 1) link_NAG-THR : angle 2.25517 / 1.19 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 212 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 PHE cc_start: 0.6613 (p90) cc_final: 0.6374 (p90) REVERT: A 414 GLN cc_start: 0.8330 (mp10) cc_final: 0.7634 (mp10) REVERT: A 428 ASP cc_start: 0.8827 (t0) cc_final: 0.8451 (t0) REVERT: A 460 LYS cc_start: 0.9180 (pttt) cc_final: 0.8957 (mtmm) REVERT: A 580 GLN cc_start: 0.8638 (mt0) cc_final: 0.8330 (mt0) REVERT: A 630 THR cc_start: 0.8367 (m) cc_final: 0.8049 (m) REVERT: B 52 GLN cc_start: 0.8576 (tt0) cc_final: 0.8167 (tm-30) REVERT: B 111 LYS cc_start: 0.8684 (ptmt) cc_final: 0.8384 (pttm) REVERT: B 199 LYS cc_start: 0.9033 (mttt) cc_final: 0.8748 (mttp) REVERT: B 287 CYS cc_start: 0.8940 (t) cc_final: 0.8590 (t) REVERT: B 630 THR cc_start: 0.8397 (m) cc_final: 0.8131 (m) REVERT: C 52 GLN cc_start: 0.8826 (tm-30) cc_final: 0.8325 (tm-30) REVERT: C 360 ASN cc_start: 0.8825 (t0) cc_final: 0.8422 (t0) REVERT: C 434 ILE cc_start: 0.6999 (OUTLIER) cc_final: 0.6687 (mm) REVERT: C 451 TYR cc_start: 0.7019 (m-80) cc_final: 0.6454 (m-80) REVERT: C 994 ASP cc_start: 0.8798 (t70) cc_final: 0.8250 (t0) REVERT: C 1119 ASN cc_start: 0.8484 (t0) cc_final: 0.8054 (t0) REVERT: J 32 TYR cc_start: 0.6631 (OUTLIER) cc_final: 0.6175 (t80) REVERT: J 34 TRP cc_start: 0.7005 (m100) cc_final: 0.6410 (m100) REVERT: N 95 ASP cc_start: 0.8596 (t70) cc_final: 0.8303 (m-30) outliers start: 73 outliers final: 46 residues processed: 272 average time/residue: 0.1427 time to fit residues: 66.2910 Evaluate side-chains 245 residues out of total 2909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 197 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 508 TYR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 939 PHE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain J residue 32 TYR Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain N residue 75 LEU Chi-restraints excluded: chain N residue 90 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: [236, 196, 216, 95, 32, 121, 265, 322, 129, 136, 223] chunk 236 optimal weight: 7.9990 chunk 196 optimal weight: 1.9990 chunk 216 optimal weight: 10.0000 chunk 95 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 121 optimal weight: 7.9990 chunk 265 optimal weight: 2.9990 chunk 322 optimal weight: 0.3980 chunk 129 optimal weight: 20.0000 chunk 136 optimal weight: 20.0000 chunk 223 optimal weight: 5.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 267 GLN A 339 HIS ** A 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN B1010 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.127606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.075277 restraints weight = 53585.023| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 3.16 r_work: 0.2863 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 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 : 0.005 0.062 27463 Z= 0.232 Angle : 0.619 19.276 37492 Z= 0.303 Chirality : 0.045 0.227 4359 Planarity : 0.004 0.053 4732 Dihedral : 6.834 58.369 4663 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.47 % Favored : 96.47 % Rotamer: Outliers : 3.44 % Allowed : 15.74 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.15), residues: 3285 helix: 1.90 (0.20), residues: 685 sheet: 0.25 (0.18), residues: 803 loop : -0.64 (0.15), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 498 TYR 0.017 0.001 TYR B1067 PHE 0.015 0.001 PHE C 375 TRP 0.021 0.001 TRP A 452 HIS 0.005 0.001 HIS N 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.23 (27374) covalent geometry : angle 0.58787 / 0.30 (37264) SS BOND : bond 0.00386 / 0.25 ( 38) SS BOND : angle 1.62504 / 1.07 ( 76) hydrogen bonds : bond 0.04022 / 2.57 ( 1056) hydrogen bonds : angle 5.19586 / 3.61 ( 2871) link_BETA1-4 : bond 0.00308 / 0.16 ( 15) link_BETA1-4 : angle 1.28925 / 0.83 ( 45) link_NAG-ASN : bond 0.00585 / 0.30 ( 35) link_NAG-ASN : angle 3.32459 / 1.96 ( 105) link_NAG-THR : bond 0.01337 / 0.70 ( 1) link_NAG-THR : angle 4.39190 / 2.33 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 201 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 PHE cc_start: 0.6800 (p90) cc_final: 0.6394 (p90) REVERT: A 414 GLN cc_start: 0.8463 (mp10) cc_final: 0.7891 (mp10) REVERT: A 428 ASP cc_start: 0.8941 (t0) cc_final: 0.8640 (t0) REVERT: A 460 LYS cc_start: 0.9259 (pttt) cc_final: 0.9044 (mtmm) REVERT: A 630 THR cc_start: 0.8410 (m) cc_final: 0.8117 (m) REVERT: B 52 GLN cc_start: 0.8564 (tt0) cc_final: 0.8246 (tm-30) REVERT: B 56 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8732 (tp) REVERT: B 199 LYS cc_start: 0.9157 (mttt) cc_final: 0.8858 (mttp) REVERT: B 287 CYS cc_start: 0.8938 (t) cc_final: 0.8589 (t) REVERT: B 630 THR cc_start: 0.8414 (m) cc_final: 0.8169 (m) REVERT: B 985 ASP cc_start: 0.8376 (t70) cc_final: 0.8139 (t0) REVERT: C 434 ILE cc_start: 0.7462 (OUTLIER) cc_final: 0.7173 (mm) REVERT: C 451 TYR cc_start: 0.7421 (m-80) cc_final: 0.6839 (m-80) REVERT: C 994 ASP cc_start: 0.8857 (t70) cc_final: 0.8358 (t0) REVERT: C 1119 ASN cc_start: 0.8605 (t0) cc_final: 0.8027 (t0) REVERT: J 32 TYR cc_start: 0.6901 (OUTLIER) cc_final: 0.6611 (t80) outliers start: 100 outliers final: 61 residues processed: 284 average time/residue: 0.1405 time to fit residues: 68.3001 Evaluate side-chains 247 residues out of total 2909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 183 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 508 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 939 PHE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 32 TYR Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain N residue 75 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: [51, 49, 177, 295, 160, 310, 179, 275, 23, 286, 135] chunk 51 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 177 optimal weight: 1.9990 chunk 295 optimal weight: 0.5980 chunk 160 optimal weight: 0.9980 chunk 310 optimal weight: 0.3980 chunk 179 optimal weight: 0.8980 chunk 275 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 286 optimal weight: 0.6980 chunk 135 optimal weight: 20.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 544 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 505 HIS B 762 GLN B1010 GLN C 751 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.129828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.077838 restraints weight = 53115.727| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 3.17 r_work: 0.2892 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27463 Z= 0.112 Angle : 0.552 19.164 37492 Z= 0.270 Chirality : 0.043 0.238 4359 Planarity : 0.003 0.052 4732 Dihedral : 6.686 58.733 4661 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.59 % Favored : 97.35 % Rotamer: Outliers : 2.68 % Allowed : 16.67 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.15), residues: 3285 helix: 2.17 (0.20), residues: 682 sheet: 0.27 (0.18), residues: 779 loop : -0.57 (0.15), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 498 TYR 0.023 0.001 TYR C 495 PHE 0.020 0.001 PHE A 90 TRP 0.018 0.001 TRP A 452 HIS 0.004 0.001 HIS B1101 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (27374) covalent geometry : angle 0.52456 / 0.26 (37264) SS BOND : bond 0.00274 / 0.18 ( 38) SS BOND : angle 1.25506 / 0.81 ( 76) hydrogen bonds : bond 0.03399 / 2.17 ( 1056) hydrogen bonds : angle 4.99430 / 3.48 ( 2871) link_BETA1-4 : bond 0.00313 / 0.16 ( 15) link_BETA1-4 : angle 1.05961 / 0.69 ( 45) link_NAG-ASN : bond 0.00587 / 0.26 ( 35) link_NAG-ASN : angle 3.05185 / 1.77 ( 105) link_NAG-THR : bond 0.00615 / 0.32 ( 1) link_NAG-THR : angle 4.21099 / 2.27 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 194 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 234 PHE cc_start: 0.6859 (p90) cc_final: 0.6494 (p90) REVERT: A 378 LYS cc_start: 0.8842 (ptmt) cc_final: 0.8595 (pttt) REVERT: A 414 GLN cc_start: 0.8442 (mp10) cc_final: 0.7623 (mp10) REVERT: A 428 ASP cc_start: 0.8936 (t0) cc_final: 0.8645 (t0) REVERT: A 630 THR cc_start: 0.8408 (m) cc_final: 0.8115 (m) REVERT: A 663 ASP cc_start: 0.8811 (t0) cc_final: 0.8567 (t0) REVERT: B 52 GLN cc_start: 0.8538 (tt0) cc_final: 0.8216 (tm-30) REVERT: B 111 LYS cc_start: 0.8707 (ptmt) cc_final: 0.8485 (pttm) REVERT: B 199 LYS cc_start: 0.9149 (mttt) cc_final: 0.8858 (mttp) REVERT: B 287 CYS cc_start: 0.8895 (t) cc_final: 0.8593 (t) REVERT: B 511 VAL cc_start: 0.6674 (OUTLIER) cc_final: 0.6166 (m) REVERT: B 630 THR cc_start: 0.8443 (m) cc_final: 0.8195 (m) REVERT: B 985 ASP cc_start: 0.8234 (OUTLIER) cc_final: 0.8016 (t0) REVERT: C 396 TYR cc_start: 0.8815 (m-80) cc_final: 0.8594 (m-80) REVERT: C 434 ILE cc_start: 0.7524 (OUTLIER) cc_final: 0.7260 (mm) REVERT: C 451 TYR cc_start: 0.7338 (m-80) cc_final: 0.6844 (m-80) REVERT: C 619 GLU cc_start: 0.8279 (mp0) cc_final: 0.8057 (mp0) REVERT: C 994 ASP cc_start: 0.8825 (t70) cc_final: 0.8278 (t0) REVERT: C 1050 MET cc_start: 0.8990 (ptm) cc_final: 0.8507 (ptm) REVERT: C 1119 ASN cc_start: 0.8487 (t0) cc_final: 0.7996 (t0) REVERT: J 32 TYR cc_start: 0.6899 (OUTLIER) cc_final: 0.6530 (t80) REVERT: N 20 ILE cc_start: 0.3483 (OUTLIER) cc_final: 0.2958 (tp) outliers start: 78 outliers final: 54 residues processed: 257 average time/residue: 0.1512 time to fit residues: 66.1053 Evaluate side-chains 243 residues out of total 2909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 184 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 508 TYR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 939 PHE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 32 TYR Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 90 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: [255, 57, 312, 224, 76, 195, 5, 212, 288, 241, 236] chunk 255 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 312 optimal weight: 5.9990 chunk 224 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 195 optimal weight: 0.2980 chunk 5 optimal weight: 0.9980 chunk 212 optimal weight: 0.0000 chunk 288 optimal weight: 0.9980 chunk 241 optimal weight: 5.9990 chunk 236 optimal weight: 3.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 339 HIS A 405 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN C1010 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.130343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.078096 restraints weight = 53385.707| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 3.20 r_work: 0.2905 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 27463 Z= 0.109 Angle : 0.548 19.062 37492 Z= 0.267 Chirality : 0.043 0.242 4359 Planarity : 0.003 0.052 4732 Dihedral : 6.585 58.680 4661 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.77 % Favored : 97.17 % Rotamer: Outliers : 2.99 % Allowed : 16.98 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.15), residues: 3285 helix: 2.24 (0.20), residues: 678 sheet: 0.35 (0.18), residues: 767 loop : -0.53 (0.14), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 498 TYR 0.025 0.001 TYR B 904 PHE 0.013 0.001 PHE A 198 TRP 0.016 0.001 TRP A 452 HIS 0.003 0.001 HIS B1101 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (27374) covalent geometry : angle 0.51980 / 0.26 (37264) SS BOND : bond 0.00237 / 0.15 ( 38) SS BOND : angle 1.14831 / 0.75 ( 76) hydrogen bonds : bond 0.03256 / 2.08 ( 1056) hydrogen bonds : angle 4.87694 / 3.39 ( 2871) link_BETA1-4 : bond 0.00292 / 0.15 ( 15) link_BETA1-4 : angle 1.09349 / 0.70 ( 45) link_NAG-ASN : bond 0.00518 / 0.22 ( 35) link_NAG-ASN : angle 3.10933 / 1.81 ( 105) link_NAG-THR : bond 0.00586 / 0.31 ( 1) link_NAG-THR : angle 3.46920 / 1.85 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 201 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 PHE cc_start: 0.6841 (p90) cc_final: 0.6433 (p90) REVERT: A 414 GLN cc_start: 0.8483 (mp10) cc_final: 0.7893 (mp10) REVERT: A 420 ASP cc_start: 0.7450 (m-30) cc_final: 0.7015 (m-30) REVERT: A 428 ASP cc_start: 0.8921 (t0) cc_final: 0.8653 (t0) REVERT: A 630 THR cc_start: 0.8454 (m) cc_final: 0.8175 (m) REVERT: A 663 ASP cc_start: 0.8824 (t0) cc_final: 0.8596 (t0) REVERT: B 52 GLN cc_start: 0.8545 (tt0) cc_final: 0.8261 (tm-30) REVERT: B 199 LYS cc_start: 0.9162 (mttt) cc_final: 0.8876 (mttp) REVERT: B 287 CYS cc_start: 0.8920 (t) cc_final: 0.8594 (t) REVERT: B 511 VAL cc_start: 0.6697 (OUTLIER) cc_final: 0.6210 (m) REVERT: B 630 THR cc_start: 0.8449 (m) cc_final: 0.8204 (m) REVERT: B 985 ASP cc_start: 0.8214 (OUTLIER) cc_final: 0.7994 (t0) REVERT: B 1119 ASN cc_start: 0.8201 (t0) cc_final: 0.7539 (t0) REVERT: C 98 ILE cc_start: 0.7845 (OUTLIER) cc_final: 0.7287 (tp) REVERT: C 360 ASN cc_start: 0.8777 (t0) cc_final: 0.8461 (t0) REVERT: C 396 TYR cc_start: 0.8818 (m-80) cc_final: 0.8554 (m-80) REVERT: C 434 ILE cc_start: 0.7531 (OUTLIER) cc_final: 0.7296 (mm) REVERT: C 451 TYR cc_start: 0.7365 (m-80) cc_final: 0.6851 (m-80) REVERT: C 574 ASP cc_start: 0.8586 (t0) cc_final: 0.8130 (t0) REVERT: C 985 ASP cc_start: 0.8820 (m-30) cc_final: 0.8603 (m-30) REVERT: C 994 ASP cc_start: 0.8812 (t70) cc_final: 0.8275 (t0) REVERT: C 1050 MET cc_start: 0.8979 (ptm) cc_final: 0.8500 (ptm) REVERT: C 1119 ASN cc_start: 0.8450 (t0) cc_final: 0.8030 (t0) REVERT: J 32 TYR cc_start: 0.7043 (OUTLIER) cc_final: 0.6617 (t80) REVERT: J 34 TRP cc_start: 0.7312 (m100) cc_final: 0.6031 (m100) REVERT: N 20 ILE cc_start: 0.3506 (OUTLIER) cc_final: 0.2975 (tp) outliers start: 87 outliers final: 65 residues processed: 270 average time/residue: 0.1449 time to fit residues: 66.3385 Evaluate side-chains 259 residues out of total 2909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 188 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 132 GLN Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 939 PHE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 32 TYR Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 75 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: [27, 213, 250, 111, 82, 80, 181, 101, 218, 325, 0] chunk 27 optimal weight: 6.9990 chunk 213 optimal weight: 0.9990 chunk 250 optimal weight: 9.9990 chunk 111 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 101 optimal weight: 0.0370 chunk 218 optimal weight: 0.7980 chunk 325 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.9664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 339 HIS ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN C 690 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.131585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.079278 restraints weight = 54303.069| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 3.29 r_work: 0.3003 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 27463 Z= 0.130 Angle : 0.552 19.079 37492 Z= 0.269 Chirality : 0.043 0.239 4359 Planarity : 0.003 0.052 4732 Dihedral : 6.501 59.195 4658 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.83 % Favored : 97.11 % Rotamer: Outliers : 3.03 % Allowed : 17.29 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.15), residues: 3285 helix: 2.26 (0.20), residues: 677 sheet: 0.30 (0.18), residues: 770 loop : -0.51 (0.14), residues: 1838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 498 TYR 0.019 0.001 TYR A 380 PHE 0.022 0.001 PHE A 90 TRP 0.016 0.001 TRP A 452 HIS 0.003 0.001 HIS B1101 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (27374) covalent geometry : angle 0.52446 / 0.26 (37264) SS BOND : bond 0.00268 / 0.16 ( 38) SS BOND : angle 1.22088 / 0.79 ( 76) hydrogen bonds : bond 0.03287 / 2.11 ( 1056) hydrogen bonds : angle 4.85328 / 3.37 ( 2871) link_BETA1-4 : bond 0.00239 / 0.12 ( 15) link_BETA1-4 : angle 1.09028 / 0.70 ( 45) link_NAG-ASN : bond 0.00526 / 0.25 ( 35) link_NAG-ASN : angle 3.09114 / 1.79 ( 105) link_NAG-THR : bond 0.00571 / 0.30 ( 1) link_NAG-THR : angle 3.14217 / 1.66 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 201 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 PHE cc_start: 0.6771 (p90) cc_final: 0.6557 (p90) REVERT: A 378 LYS cc_start: 0.8813 (ptmt) cc_final: 0.8527 (pptt) REVERT: A 414 GLN cc_start: 0.8513 (mp10) cc_final: 0.7753 (mp10) REVERT: A 428 ASP cc_start: 0.8922 (t0) cc_final: 0.8685 (t0) REVERT: A 630 THR cc_start: 0.8422 (m) cc_final: 0.8144 (m) REVERT: A 663 ASP cc_start: 0.8824 (t0) cc_final: 0.8618 (t0) REVERT: B 52 GLN cc_start: 0.8577 (tt0) cc_final: 0.8292 (tm-30) REVERT: B 111 LYS cc_start: 0.8751 (ptmt) cc_final: 0.8489 (pttm) REVERT: B 199 LYS cc_start: 0.9158 (mttt) cc_final: 0.8870 (mttp) REVERT: B 287 CYS cc_start: 0.8949 (t) cc_final: 0.8622 (t) REVERT: B 511 VAL cc_start: 0.6719 (OUTLIER) cc_final: 0.6243 (m) REVERT: B 630 THR cc_start: 0.8431 (m) cc_final: 0.8188 (m) REVERT: B 985 ASP cc_start: 0.8260 (OUTLIER) cc_final: 0.8002 (t70) REVERT: B 1119 ASN cc_start: 0.8212 (t0) cc_final: 0.7564 (t0) REVERT: C 98 ILE cc_start: 0.7840 (OUTLIER) cc_final: 0.7409 (tp) REVERT: C 360 ASN cc_start: 0.8796 (t0) cc_final: 0.8503 (t0) REVERT: C 396 TYR cc_start: 0.8789 (m-80) cc_final: 0.8510 (m-80) REVERT: C 434 ILE cc_start: 0.7539 (OUTLIER) cc_final: 0.7319 (mm) REVERT: C 451 TYR cc_start: 0.7443 (m-80) cc_final: 0.6922 (m-80) REVERT: C 574 ASP cc_start: 0.8610 (t0) cc_final: 0.8147 (t0) REVERT: C 985 ASP cc_start: 0.8807 (m-30) cc_final: 0.8595 (m-30) REVERT: C 994 ASP cc_start: 0.8815 (t70) cc_final: 0.8267 (t0) REVERT: C 1050 MET cc_start: 0.9070 (ptm) cc_final: 0.8618 (ptm) REVERT: C 1119 ASN cc_start: 0.8393 (t0) cc_final: 0.8041 (t0) REVERT: J 32 TYR cc_start: 0.7110 (OUTLIER) cc_final: 0.6689 (t80) REVERT: J 34 TRP cc_start: 0.7403 (m100) cc_final: 0.6194 (m100) REVERT: N 20 ILE cc_start: 0.3610 (OUTLIER) cc_final: 0.3076 (tp) outliers start: 88 outliers final: 70 residues processed: 271 average time/residue: 0.1425 time to fit residues: 65.3194 Evaluate side-chains 270 residues out of total 2909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 194 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 132 GLN Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 939 PHE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 32 TYR Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 75 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: [62, 42, 297, 194, 231, 142, 53, 313, 319, 47, 174] chunk 62 optimal weight: 0.3980 chunk 42 optimal weight: 7.9990 chunk 297 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 231 optimal weight: 0.9990 chunk 142 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 313 optimal weight: 0.5980 chunk 319 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 174 optimal weight: 0.9980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 339 HIS ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.131483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.079486 restraints weight = 54762.108| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 3.28 r_work: 0.2977 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 27463 Z= 0.132 Angle : 0.556 19.102 37492 Z= 0.272 Chirality : 0.043 0.238 4359 Planarity : 0.003 0.052 4732 Dihedral : 6.479 57.361 4658 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.14 % Favored : 96.80 % Rotamer: Outliers : 3.03 % Allowed : 17.19 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.15), residues: 3285 helix: 2.26 (0.20), residues: 676 sheet: 0.31 (0.18), residues: 754 loop : -0.52 (0.14), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 498 TYR 0.019 0.001 TYR A 453 PHE 0.014 0.001 PHE A 198 TRP 0.015 0.001 TRP A 452 HIS 0.003 0.001 HIS B1101 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (27374) covalent geometry : angle 0.52878 / 0.27 (37264) SS BOND : bond 0.00255 / 0.16 ( 38) SS BOND : angle 1.30747 / 0.87 ( 76) hydrogen bonds : bond 0.03312 / 2.12 ( 1056) hydrogen bonds : angle 4.84362 / 3.36 ( 2871) link_BETA1-4 : bond 0.00245 / 0.13 ( 15) link_BETA1-4 : angle 1.09182 / 0.70 ( 45) link_NAG-ASN : bond 0.00487 / 0.20 ( 35) link_NAG-ASN : angle 3.03918 / 1.75 ( 105) link_NAG-THR : bond 0.00511 / 0.27 ( 1) link_NAG-THR : angle 3.05210 / 1.61 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 202 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 PHE cc_start: 0.6728 (p90) cc_final: 0.6470 (p90) REVERT: A 378 LYS cc_start: 0.8813 (ptmt) cc_final: 0.8497 (pptt) REVERT: A 414 GLN cc_start: 0.8506 (mp10) cc_final: 0.7732 (mp10) REVERT: A 428 ASP cc_start: 0.8950 (t0) cc_final: 0.8730 (t0) REVERT: A 630 THR cc_start: 0.8371 (m) cc_final: 0.8093 (m) REVERT: A 663 ASP cc_start: 0.8864 (t0) cc_final: 0.8634 (t0) REVERT: B 52 GLN cc_start: 0.8594 (tt0) cc_final: 0.8277 (tm-30) REVERT: B 111 LYS cc_start: 0.8758 (ptmt) cc_final: 0.8475 (pttm) REVERT: B 199 LYS cc_start: 0.9100 (mttt) cc_final: 0.8801 (mttp) REVERT: B 287 CYS cc_start: 0.8991 (t) cc_final: 0.8650 (t) REVERT: B 511 VAL cc_start: 0.6734 (OUTLIER) cc_final: 0.6267 (m) REVERT: B 630 THR cc_start: 0.8435 (m) cc_final: 0.8181 (m) REVERT: B 985 ASP cc_start: 0.8270 (OUTLIER) cc_final: 0.7997 (t70) REVERT: B 1119 ASN cc_start: 0.8231 (t0) cc_final: 0.7578 (t0) REVERT: C 98 ILE cc_start: 0.7900 (OUTLIER) cc_final: 0.7473 (tp) REVERT: C 360 ASN cc_start: 0.8815 (t0) cc_final: 0.8572 (t0) REVERT: C 396 TYR cc_start: 0.8755 (m-80) cc_final: 0.8248 (m-80) REVERT: C 434 ILE cc_start: 0.7497 (OUTLIER) cc_final: 0.7296 (mm) REVERT: C 451 TYR cc_start: 0.7542 (m-80) cc_final: 0.7065 (m-80) REVERT: C 495 TYR cc_start: 0.5851 (m-80) cc_final: 0.5635 (m-10) REVERT: C 574 ASP cc_start: 0.8573 (t0) cc_final: 0.8085 (t0) REVERT: C 985 ASP cc_start: 0.8783 (m-30) cc_final: 0.8578 (m-30) REVERT: C 994 ASP cc_start: 0.8825 (t70) cc_final: 0.8260 (t0) REVERT: C 1050 MET cc_start: 0.9112 (ptm) cc_final: 0.8671 (ptm) REVERT: C 1119 ASN cc_start: 0.8390 (t0) cc_final: 0.8011 (t0) REVERT: J 32 TYR cc_start: 0.7121 (OUTLIER) cc_final: 0.6777 (t80) REVERT: J 120 MET cc_start: 0.8544 (tpp) cc_final: 0.7864 (ptt) REVERT: N 20 ILE cc_start: 0.3692 (OUTLIER) cc_final: 0.3157 (tp) outliers start: 88 outliers final: 72 residues processed: 270 average time/residue: 0.1435 time to fit residues: 66.0548 Evaluate side-chains 273 residues out of total 2909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 195 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 132 GLN Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 939 PHE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 32 TYR Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 75 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: [78, 125, 62, 250, 185, 264, 228, 270, 251, 148, 60] chunk 78 optimal weight: 0.5980 chunk 125 optimal weight: 3.9990 chunk 62 optimal weight: 0.0970 chunk 250 optimal weight: 0.9980 chunk 185 optimal weight: 0.6980 chunk 264 optimal weight: 0.5980 chunk 228 optimal weight: 0.9990 chunk 270 optimal weight: 3.9990 chunk 251 optimal weight: 8.9990 chunk 148 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 GLN B 762 GLN B1010 GLN B1125 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.132166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.080200 restraints weight = 54641.859| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 3.28 r_work: 0.2997 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 27463 Z= 0.106 Angle : 0.546 19.015 37492 Z= 0.267 Chirality : 0.043 0.241 4359 Planarity : 0.003 0.052 4732 Dihedral : 6.407 57.844 4658 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.95 % Favored : 96.99 % Rotamer: Outliers : 2.58 % Allowed : 18.05 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.15), residues: 3285 helix: 2.27 (0.20), residues: 682 sheet: 0.36 (0.18), residues: 747 loop : -0.49 (0.14), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 328 TYR 0.020 0.001 TYR A 453 PHE 0.023 0.001 PHE A 90 TRP 0.013 0.001 TRP A 452 HIS 0.003 0.001 HIS C1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (27374) covalent geometry : angle 0.51992 / 0.26 (37264) SS BOND : bond 0.00241 / 0.16 ( 38) SS BOND : angle 1.17888 / 0.84 ( 76) hydrogen bonds : bond 0.03164 / 2.03 ( 1056) hydrogen bonds : angle 4.76495 / 3.30 ( 2871) link_BETA1-4 : bond 0.00289 / 0.15 ( 15) link_BETA1-4 : angle 1.06238 / 0.69 ( 45) link_NAG-ASN : bond 0.00485 / 0.19 ( 35) link_NAG-ASN : angle 2.95907 / 1.69 ( 105) link_NAG-THR : bond 0.00431 / 0.23 ( 1) link_NAG-THR : angle 2.93793 / 1.55 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 206 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 VAL cc_start: 0.5997 (OUTLIER) cc_final: 0.5756 (p) REVERT: A 234 PHE cc_start: 0.6698 (p90) cc_final: 0.6434 (p90) REVERT: A 414 GLN cc_start: 0.8495 (mp10) cc_final: 0.7704 (mp10) REVERT: A 428 ASP cc_start: 0.8968 (t0) cc_final: 0.8749 (t0) REVERT: A 493 GLU cc_start: 0.8686 (tm-30) cc_final: 0.8436 (tm-30) REVERT: A 630 THR cc_start: 0.8389 (m) cc_final: 0.8114 (m) REVERT: A 663 ASP cc_start: 0.8836 (t0) cc_final: 0.8609 (t0) REVERT: B 52 GLN cc_start: 0.8587 (tt0) cc_final: 0.8243 (tm-30) REVERT: B 111 LYS cc_start: 0.8776 (ptmt) cc_final: 0.8483 (pttm) REVERT: B 199 LYS cc_start: 0.9095 (mttt) cc_final: 0.8802 (mttp) REVERT: B 287 CYS cc_start: 0.8977 (t) cc_final: 0.8649 (t) REVERT: B 511 VAL cc_start: 0.6858 (OUTLIER) cc_final: 0.6394 (m) REVERT: B 630 THR cc_start: 0.8460 (m) cc_final: 0.8212 (m) REVERT: B 985 ASP cc_start: 0.8249 (OUTLIER) cc_final: 0.8002 (t70) REVERT: B 1119 ASN cc_start: 0.8211 (t0) cc_final: 0.7632 (t0) REVERT: B 1125 ASN cc_start: 0.8484 (OUTLIER) cc_final: 0.8230 (p0) REVERT: C 98 ILE cc_start: 0.7918 (OUTLIER) cc_final: 0.7492 (tp) REVERT: C 220 GLU cc_start: 0.8804 (mt-10) cc_final: 0.8333 (mp0) REVERT: C 360 ASN cc_start: 0.8790 (t0) cc_final: 0.8575 (t0) REVERT: C 451 TYR cc_start: 0.7538 (m-80) cc_final: 0.7067 (m-80) REVERT: C 495 TYR cc_start: 0.5881 (m-80) cc_final: 0.5666 (m-10) REVERT: C 574 ASP cc_start: 0.8424 (t0) cc_final: 0.7990 (t0) REVERT: C 985 ASP cc_start: 0.8749 (m-30) cc_final: 0.8544 (m-30) REVERT: C 994 ASP cc_start: 0.8782 (t70) cc_final: 0.8196 (t0) REVERT: C 1050 MET cc_start: 0.9103 (ptm) cc_final: 0.8626 (ptm) REVERT: C 1119 ASN cc_start: 0.8359 (t0) cc_final: 0.8072 (t0) REVERT: J 32 TYR cc_start: 0.7100 (OUTLIER) cc_final: 0.6727 (t80) REVERT: J 120 MET cc_start: 0.8607 (tpp) cc_final: 0.7886 (ptt) REVERT: N 20 ILE cc_start: 0.3554 (OUTLIER) cc_final: 0.3008 (tp) outliers start: 75 outliers final: 63 residues processed: 266 average time/residue: 0.1459 time to fit residues: 65.2390 Evaluate side-chains 268 residues out of total 2909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 198 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 132 GLN Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 939 PHE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 32 TYR Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 75 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: [60, 169, 240, 186, 5, 249, 192, 180, 241, 198, 202] chunk 60 optimal weight: 2.9990 chunk 169 optimal weight: 0.7980 chunk 240 optimal weight: 10.0000 chunk 186 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 249 optimal weight: 9.9990 chunk 192 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 chunk 241 optimal weight: 6.9990 chunk 198 optimal weight: 2.9990 chunk 202 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 GLN B 394 ASN B1010 GLN C 506 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.127109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.075132 restraints weight = 53355.928| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 3.15 r_work: 0.2843 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 27463 Z= 0.241 Angle : 0.621 19.315 37492 Z= 0.306 Chirality : 0.045 0.224 4359 Planarity : 0.004 0.052 4732 Dihedral : 6.516 58.518 4656 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.62 % Favored : 96.32 % Rotamer: Outliers : 2.68 % Allowed : 17.94 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.15), residues: 3285 helix: 2.08 (0.20), residues: 681 sheet: 0.23 (0.18), residues: 776 loop : -0.55 (0.15), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C1019 TYR 0.019 0.001 TYR B 904 PHE 0.016 0.001 PHE A 198 TRP 0.020 0.002 TRP J 115 HIS 0.004 0.001 HIS A1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00567 / 0.24 (27374) covalent geometry : angle 0.59345 / 0.30 (37264) SS BOND : bond 0.00342 / 0.21 ( 38) SS BOND : angle 1.64323 / 1.15 ( 76) hydrogen bonds : bond 0.03779 / 2.42 ( 1056) hydrogen bonds : angle 4.97910 / 3.45 ( 2871) link_BETA1-4 : bond 0.00150 / 0.08 ( 15) link_BETA1-4 : angle 1.24730 / 0.81 ( 45) link_NAG-ASN : bond 0.00577 / 0.29 ( 35) link_NAG-ASN : angle 3.12395 / 1.79 ( 105) link_NAG-THR : bond 0.00609 / 0.32 ( 1) link_NAG-THR : angle 2.83149 / 1.49 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 201 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 VAL cc_start: 0.6088 (OUTLIER) cc_final: 0.5852 (p) REVERT: A 234 PHE cc_start: 0.6831 (p90) cc_final: 0.6523 (p90) REVERT: A 396 TYR cc_start: 0.8297 (m-80) cc_final: 0.8025 (m-80) REVERT: A 414 GLN cc_start: 0.8552 (mp10) cc_final: 0.7810 (mp10) REVERT: A 630 THR cc_start: 0.8434 (m) cc_final: 0.8158 (m) REVERT: B 52 GLN cc_start: 0.8560 (tt0) cc_final: 0.8255 (tm-30) REVERT: B 199 LYS cc_start: 0.9169 (mttt) cc_final: 0.8876 (mttp) REVERT: B 511 VAL cc_start: 0.6899 (OUTLIER) cc_final: 0.6445 (m) REVERT: B 630 THR cc_start: 0.8428 (m) cc_final: 0.8189 (m) REVERT: B 985 ASP cc_start: 0.8326 (OUTLIER) cc_final: 0.8040 (t0) REVERT: B 1119 ASN cc_start: 0.8351 (t0) cc_final: 0.7620 (t0) REVERT: C 98 ILE cc_start: 0.8040 (OUTLIER) cc_final: 0.7565 (tp) REVERT: C 451 TYR cc_start: 0.7759 (m-80) cc_final: 0.7276 (m-80) REVERT: C 495 TYR cc_start: 0.6024 (m-80) cc_final: 0.5776 (m-10) REVERT: C 994 ASP cc_start: 0.8883 (t70) cc_final: 0.8334 (t0) REVERT: C 1119 ASN cc_start: 0.8526 (t0) cc_final: 0.8049 (t0) REVERT: J 32 TYR cc_start: 0.7207 (OUTLIER) cc_final: 0.6819 (t80) REVERT: N 20 ILE cc_start: 0.3419 (OUTLIER) cc_final: 0.2866 (tp) outliers start: 78 outliers final: 65 residues processed: 262 average time/residue: 0.1454 time to fit residues: 65.2308 Evaluate side-chains 264 residues out of total 2909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 193 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 132 GLN Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 939 PHE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 32 TYR Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 75 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: [134, 130, 259, 118, 172, 325, 197, 138, 92, 70, 113] chunk 134 optimal weight: 5.9990 chunk 130 optimal weight: 7.9990 chunk 259 optimal weight: 0.7980 chunk 118 optimal weight: 0.0070 chunk 172 optimal weight: 2.9990 chunk 325 optimal weight: 0.5980 chunk 197 optimal weight: 0.9990 chunk 138 optimal weight: 5.9990 chunk 92 optimal weight: 0.9990 chunk 70 optimal weight: 0.3980 chunk 113 optimal weight: 10.0000 overall best weight: 0.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 GLN B1010 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.129347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.078026 restraints weight = 52497.545| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 3.13 r_work: 0.2905 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 27463 Z= 0.108 Angle : 0.563 19.044 37492 Z= 0.278 Chirality : 0.043 0.236 4359 Planarity : 0.003 0.052 4732 Dihedral : 6.387 57.173 4654 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.95 % Favored : 96.99 % Rotamer: Outliers : 2.44 % Allowed : 18.18 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.15), residues: 3285 helix: 2.22 (0.20), residues: 682 sheet: 0.26 (0.18), residues: 768 loop : -0.50 (0.15), residues: 1835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1019 TYR 0.023 0.001 TYR A 453 PHE 0.024 0.001 PHE A 90 TRP 0.017 0.001 TRP J 115 HIS 0.003 0.001 HIS C1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (27374) covalent geometry : angle 0.53863 / 0.27 (37264) SS BOND : bond 0.00243 / 0.15 ( 38) SS BOND : angle 1.18134 / 0.82 ( 76) hydrogen bonds : bond 0.03286 / 2.11 ( 1056) hydrogen bonds : angle 4.81280 / 3.33 ( 2871) link_BETA1-4 : bond 0.00300 / 0.15 ( 15) link_BETA1-4 : angle 1.05050 / 0.68 ( 45) link_NAG-ASN : bond 0.00491 / 0.19 ( 35) link_NAG-ASN : angle 2.94185 / 1.67 ( 105) link_NAG-THR : bond 0.00337 / 0.18 ( 1) link_NAG-THR : angle 2.84024 / 1.50 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6839.11 seconds wall clock time: 117 minutes 48.70 seconds (7068.70 seconds total)