Starting phenix.real_space_refine on Mon Jul 6 18:49:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hfz_34729/07_2026/8hfz_34729.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hfz_34729/07_2026/8hfz_34729.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hfz_34729/07_2026/8hfz_34729.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hfz_34729/07_2026/8hfz_34729.map" model { file = "/net/cci-nas-00/data/ceres_data/8hfz_34729/07_2026/8hfz_34729.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hfz_34729/07_2026/8hfz_34729.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8hfz_34729/07_2026/8hfz_34729.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hfz_34729/07_2026/8hfz_34729.cif" } resolution = 2.71 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= -0.001 sd= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 8986 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 143 5.16 5 C 19538 2.51 5 N 5023 2.21 5 O 5999 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.19s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30704 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 8290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8290 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 58, 'TRANS': 1002} Chain breaks: 6 Chain: "B" Number of atoms: 8292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8292 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 58, 'TRANS': 1002} Chain breaks: 6 Chain: "C" Number of atoms: 8322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1065, 8322 Classifications: {'peptide': 1065} Link IDs: {'PTRANS': 58, 'TRANS': 1006} Chain breaks: 6 Chain: "E" Number of atoms: 4889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4889 Classifications: {'peptide': 595} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 570} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 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 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 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 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 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 chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 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 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 chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 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 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 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 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 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 chiralities: 2 Chain: "U" 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 chiralities: 2 Chain: "V" 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 chiralities: 2 Chain: "W" 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 chiralities: 2 Chain: "X" 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 chiralities: 2 Chain: "Y" 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 chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 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 chiralities: 7 Chain: "E" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' ZN': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 5.85, per 1000 atoms: 0.19 Number of scatterers: 30704 At special positions: 0 Unit cell: (130.9, 146.2, 249.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 143 16.00 O 5999 8.00 N 5023 7.00 C 19538 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 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=2.04 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 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " 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=2.04 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=2.04 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=2.04 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 15 " - pdb=" SG CYS C 136 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 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 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 344 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " 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 F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A1074 " " NAG A1304 " - " ASN A 616 " " NAG B1301 " - " ASN B 122 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 17 " " NAG B1308 " - " ASN B 61 " " NAG B1309 " - " ASN B 165 " " NAG C1301 " - " ASN C 17 " " NAG C1302 " - " ASN C 61 " " NAG C1303 " - " ASN C 122 " " NAG C1304 " - " ASN C 165 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 343 " " NAG C1307 " - " ASN C 616 " " NAG D 1 " - " ASN A 234 " " NAG E 701 " - " ASN E 54 " " NAG E 702 " - " ASN E 432 " " NAG E 703 " - " ASN E 91 " " NAG F 1 " - " ASN A 282 " " NAG G 1 " - " ASN A 331 " " NAG H 1 " - " ASN A 709 " " NAG I 1 " - " ASN A 717 " " NAG J 1 " - " ASN A 801 " " NAG K 1 " - " ASN A1098 " " NAG L 1 " - " ASN A1134 " " NAG M 1 " - " ASN B 709 " " NAG N 1 " - " ASN B 717 " " NAG O 1 " - " ASN B 801 " " NAG P 1 " - " ASN B1074 " " NAG Q 1 " - " ASN B1098 " " NAG R 1 " - " ASN B1134 " " NAG S 1 " - " ASN C 709 " " NAG T 1 " - " ASN C 717 " " NAG U 1 " - " ASN C 801 " " NAG V 1 " - " ASN C1074 " " NAG W 1 " - " ASN C1098 " " NAG X 1 " - " ASN C1134 " " NAG Y 1 " - " ASN E 546 " Time building additional restraints: 2.87 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E 704 " pdb="ZN ZN E 704 " - pdb=" ND1 HIS E 378 " pdb="ZN ZN E 704 " - pdb=" NE2 HIS E 374 " 7476 Ramachandran restraints generated. 3738 Oldfield, 0 Emsley, 3738 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7114 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 43 sheets defined 29.6% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.53 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.752A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 371 removed outlier: 3.643A pdb=" N ASN A 370 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N SER A 371 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 423 Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.652A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 753 Processing helix chain 'A' and resid 754 through 756 No H-bonds generated for 'chain 'A' and resid 754 through 756' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.541A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 826 removed outlier: 3.738A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS A 825 " --> pdb=" O LEU A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 856 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.664A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.205A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.745A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.640A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (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 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.824A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 4.273A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 removed outlier: 4.081A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 390 removed outlier: 4.005A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 407 Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.754A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.667A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.806A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 759 through 783 removed outlier: 3.508A pdb=" N ILE B 770 " --> pdb=" O ALA B 766 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 849 through 855 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.869A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.810A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.276A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 4.273A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.136A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.712A 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 983 removed outlier: 3.920A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.773A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 4.488A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN C 343 " --> pdb=" O GLY C 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 337 through 343' Processing helix chain 'C' and resid 366 through 371 removed outlier: 3.724A pdb=" N TYR C 369 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER C 371 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 5.986A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.642A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.577A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 849 through 855 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.353A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.567A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.920A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.637A 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 982 removed outlier: 3.788A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.826A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.189A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 45 removed outlier: 4.252A pdb=" N GLN E 25 " --> pdb=" O THR E 21 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS E 32 " --> pdb=" O THR E 28 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N HIS E 35 " --> pdb=" O GLU E 31 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU E 40 " --> pdb=" O GLU E 36 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN E 43 " --> pdb=" O ASP E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 82 removed outlier: 4.180A pdb=" N MET E 63 " --> pdb=" O ASN E 59 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA E 66 " --> pdb=" O LYS E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 102 removed outlier: 3.618A pdb=" N LEU E 101 " --> pdb=" O GLN E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 109 removed outlier: 4.076A pdb=" N VAL E 108 " --> pdb=" O GLY E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 122 removed outlier: 4.027A pdb=" N ARG E 116 " --> pdb=" O GLU E 112 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU E 117 " --> pdb=" O LYS E 113 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASN E 118 " --> pdb=" O SER E 114 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N THR E 119 " --> pdb=" O LYS E 115 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE E 120 " --> pdb=" O ARG E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 128 removed outlier: 4.279A pdb=" N ILE E 127 " --> pdb=" O THR E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 139 removed outlier: 3.741A pdb=" N GLN E 139 " --> pdb=" O PRO E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 155 removed outlier: 3.985A pdb=" N MET E 152 " --> pdb=" O LEU E 148 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLU E 153 " --> pdb=" O ASP E 149 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASN E 154 " --> pdb=" O ASP E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 171 removed outlier: 3.879A pdb=" N ARG E 161 " --> pdb=" O ASP E 157 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU E 162 " --> pdb=" O TYR E 158 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N TRP E 165 " --> pdb=" O ARG E 161 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU E 166 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ARG E 169 " --> pdb=" O TRP E 165 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLU E 171 " --> pdb=" O GLY E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 180 removed outlier: 3.592A pdb=" N LEU E 176 " --> pdb=" O VAL E 172 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG E 177 " --> pdb=" O GLY E 173 " (cutoff:3.500A) Proline residue: E 178 - end of helix No H-bonds generated for 'chain 'E' and resid 172 through 180' Processing helix chain 'E' and resid 180 through 186 Processing helix chain 'E' and resid 188 through 194 Processing helix chain 'E' and resid 198 through 204 Processing helix chain 'E' and resid 219 through 223 Processing helix chain 'E' and resid 224 through 230 removed outlier: 3.875A pdb=" N ASN E 228 " --> pdb=" O LYS E 224 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR E 229 " --> pdb=" O ASP E 225 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N PHE E 230 " --> pdb=" O VAL E 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 224 through 230' Processing helix chain 'E' and resid 232 through 247 removed outlier: 3.990A pdb=" N LEU E 236 " --> pdb=" O GLU E 232 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN E 239 " --> pdb=" O PRO E 235 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA E 242 " --> pdb=" O GLU E 238 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR E 243 " --> pdb=" O GLN E 239 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS E 247 " --> pdb=" O TYR E 243 " (cutoff:3.500A) Processing helix chain 'E' and resid 263 through 267 removed outlier: 3.628A pdb=" N LEU E 267 " --> pdb=" O ALA E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 283 removed outlier: 3.951A pdb=" N SER E 280 " --> pdb=" O ASN E 277 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU E 281 " --> pdb=" O LEU E 278 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL E 283 " --> pdb=" O SER E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 316 removed outlier: 3.519A pdb=" N ILE E 307 " --> pdb=" O ASP E 303 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LYS E 313 " --> pdb=" O LYS E 309 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N PHE E 314 " --> pdb=" O GLU E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 319 No H-bonds generated for 'chain 'E' and resid 317 through 319' Processing helix chain 'E' and resid 324 through 330 removed outlier: 4.524A pdb=" N TRP E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 371 removed outlier: 3.502A pdb=" N PHE E 369 " --> pdb=" O THR E 365 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR E 371 " --> pdb=" O ASP E 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 371 through 376 Processing helix chain 'E' and resid 378 through 382 Processing helix chain 'E' and resid 397 through 405 removed outlier: 4.235A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 407 No H-bonds generated for 'chain 'E' and resid 406 through 407' Processing helix chain 'E' and resid 408 through 412 Processing helix chain 'E' and resid 414 through 422 removed outlier: 3.550A pdb=" N LEU E 418 " --> pdb=" O THR E 414 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA E 420 " --> pdb=" O HIS E 416 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU E 421 " --> pdb=" O TYR E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 436 through 449 removed outlier: 4.253A pdb=" N LEU E 440 " --> pdb=" O ILE E 436 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA E 443 " --> pdb=" O LEU E 439 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR E 445 " --> pdb=" O LYS E 441 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE E 446 " --> pdb=" O GLN E 442 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR E 449 " --> pdb=" O THR E 445 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 463 removed outlier: 4.158A pdb=" N GLU E 457 " --> pdb=" O THR E 453 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LYS E 458 " --> pdb=" O TYR E 454 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG E 460 " --> pdb=" O LEU E 456 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N MET E 462 " --> pdb=" O LYS E 458 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL E 463 " --> pdb=" O TRP E 459 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 483 removed outlier: 5.272A pdb=" N MET E 480 " --> pdb=" O TRP E 477 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LYS E 481 " --> pdb=" O TRP E 478 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG E 482 " --> pdb=" O GLU E 479 " (cutoff:3.500A) Processing helix chain 'E' and resid 499 through 503 removed outlier: 4.047A pdb=" N LEU E 503 " --> pdb=" O PRO E 500 " (cutoff:3.500A) Processing helix chain 'E' and resid 513 through 533 removed outlier: 4.279A pdb=" N THR E 517 " --> pdb=" O ILE E 513 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ILE E 520 " --> pdb=" O TYR E 516 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN E 522 " --> pdb=" O ARG E 518 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N PHE E 523 " --> pdb=" O THR E 519 " (cutoff:3.500A) Processing helix chain 'E' and resid 554 through 561 removed outlier: 3.814A pdb=" N LEU E 558 " --> pdb=" O LEU E 554 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER E 559 " --> pdb=" O LEU E 555 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY E 561 " --> pdb=" O MET E 557 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 571 removed outlier: 3.657A pdb=" N ALA E 569 " --> pdb=" O PRO E 565 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU E 571 " --> pdb=" O THR E 567 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 588 removed outlier: 3.816A pdb=" N LEU E 585 " --> pdb=" O VAL E 581 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASN E 586 " --> pdb=" O LYS E 582 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE E 588 " --> pdb=" O LEU E 584 " (cutoff:3.500A) Processing helix chain 'E' and resid 588 through 597 removed outlier: 4.030A pdb=" N TRP E 594 " --> pdb=" O PRO E 590 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N GLU E 597 " --> pdb=" O THR E 593 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 8.559A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG A 190 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE A 197 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.917A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 10.726A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.040A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.695A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU A 117 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE A 128 " --> pdb=" O TYR A 170 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.180A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.238A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.637A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ASN A 437 " --> pdb=" O PHE A 374 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N PHE A 374 " --> pdb=" O ASN A 437 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AA8, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.741A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB1, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.564A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA A1070 " --> pdb=" O ASN A 717 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.564A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA A1070 " --> pdb=" O ASN A 717 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.716A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB6, first strand: chain 'B' and resid 28 through 31 Processing sheet with id=AB7, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.298A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.532A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 9.309A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.813A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.896A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 135 through 141 removed outlier: 7.809A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 12.287A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 11.076A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.864A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.638A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.028A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 removed outlier: 3.812A pdb=" N TYR B 453 " --> pdb=" O GLN B 493 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 538 through 541 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.545A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.872A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.848A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.848A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.735A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD4, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.802A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 9.088A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.883A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.550A pdb=" N GLN C 239 " --> pdb=" O ILE C 105 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.156A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.856A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE C 400 " --> pdb=" O VAL C 510 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.025A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE2, first strand: chain 'C' and resid 538 through 543 removed outlier: 3.655A pdb=" N PHE C 543 " --> pdb=" O LEU C 546 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.832A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 712 removed outlier: 3.652A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 715 through 728 removed outlier: 6.066A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.724A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.433A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1067 hydrogen bonds defined for protein. 2910 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.22 Time building geometry restraints manager: 3.79 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: 9707 1.34 - 1.46: 7609 1.46 - 1.58: 13908 1.58 - 1.71: 2 1.71 - 1.83: 191 Bond restraints: 31417 Sorted by residual: bond pdb=" CG PRO E 469 " pdb=" CD PRO E 469 " ideal model delta sigma weight residual 1.503 1.327 0.176 3.40e-02 8.65e+02 2.68e+01 bond pdb=" C1 NAG B1306 " pdb=" O5 NAG B1306 " ideal model delta sigma weight residual 1.406 1.486 -0.080 2.00e-02 2.50e+03 1.59e+01 bond pdb=" C1 NAG M 2 " pdb=" O5 NAG M 2 " ideal model delta sigma weight residual 1.406 1.478 -0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" C1 NAG E 701 " pdb=" O5 NAG E 701 " ideal model delta sigma weight residual 1.406 1.475 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C1 NAG C1307 " pdb=" O5 NAG C1307 " ideal model delta sigma weight residual 1.406 1.475 -0.069 2.00e-02 2.50e+03 1.20e+01 ... (remaining 31412 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.77: 42576 3.77 - 7.54: 161 7.54 - 11.32: 14 11.32 - 15.09: 2 15.09 - 18.86: 1 Bond angle restraints: 42754 Sorted by residual: angle pdb=" CA PRO E 469 " pdb=" N PRO E 469 " pdb=" CD PRO E 469 " ideal model delta sigma weight residual 112.00 93.14 18.86 1.40e+00 5.10e-01 1.82e+02 angle pdb=" N PRO E 469 " pdb=" CD PRO E 469 " pdb=" CG PRO E 469 " ideal model delta sigma weight residual 103.20 90.72 12.48 1.50e+00 4.44e-01 6.92e+01 angle pdb=" CA PRO E 469 " pdb=" CB PRO E 469 " pdb=" CG PRO E 469 " ideal model delta sigma weight residual 104.50 95.42 9.08 1.90e+00 2.77e-01 2.28e+01 angle pdb=" CA PRO A 25 " pdb=" N PRO A 25 " pdb=" CD PRO A 25 " ideal model delta sigma weight residual 112.00 105.77 6.23 1.40e+00 5.10e-01 1.98e+01 angle pdb=" N PRO E 469 " pdb=" CA PRO E 469 " pdb=" CB PRO E 469 " ideal model delta sigma weight residual 103.25 99.10 4.15 1.05e+00 9.07e-01 1.56e+01 ... (remaining 42749 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 15904 17.89 - 35.78: 1790 35.78 - 53.67: 429 53.67 - 71.56: 65 71.56 - 89.45: 31 Dihedral angle restraints: 18219 sinusoidal: 7178 harmonic: 11041 Sorted by residual: dihedral pdb=" CB CYS C 15 " pdb=" SG CYS C 15 " pdb=" SG CYS C 136 " pdb=" CB CYS C 136 " ideal model delta sinusoidal sigma weight residual 93.00 -177.55 -89.45 1 1.00e+01 1.00e-02 9.51e+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 93.00 140.48 -47.48 1 1.00e+01 1.00e-02 3.11e+01 dihedral pdb=" C THR A 676 " pdb=" N THR A 676 " pdb=" CA THR A 676 " pdb=" CB THR A 676 " ideal model delta harmonic sigma weight residual -122.00 -134.84 12.84 0 2.50e+00 1.60e-01 2.64e+01 ... (remaining 18216 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 4763 0.110 - 0.219: 210 0.219 - 0.329: 10 0.329 - 0.439: 1 0.439 - 0.549: 2 Chirality restraints: 4986 Sorted by residual: chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-02 2.50e+03 8.88e+01 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 8.36e+01 chirality pdb=" C1 NAG W 2 " pdb=" O4 NAG W 1 " pdb=" C2 NAG W 2 " pdb=" O5 NAG W 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.31 -0.09 2.00e-02 2.50e+03 1.83e+01 ... (remaining 4983 not shown) Planarity restraints: 5493 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE E 468 " -0.127 5.00e-02 4.00e+02 1.73e-01 4.77e+01 pdb=" N PRO E 469 " 0.298 5.00e-02 4.00e+02 pdb=" CA PRO E 469 " -0.089 5.00e-02 4.00e+02 pdb=" CD PRO E 469 " -0.081 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 24 " -0.080 5.00e-02 4.00e+02 1.19e-01 2.26e+01 pdb=" N PRO A 25 " 0.205 5.00e-02 4.00e+02 pdb=" CA PRO A 25 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO A 25 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 24 " 0.054 5.00e-02 4.00e+02 8.09e-02 1.05e+01 pdb=" N PRO B 25 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO B 25 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 25 " 0.044 5.00e-02 4.00e+02 ... (remaining 5490 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 526 2.65 - 3.21: 27999 3.21 - 3.78: 45563 3.78 - 4.34: 62496 4.34 - 4.90: 102821 Nonbonded interactions: 239405 Sorted by model distance: nonbonded pdb=" OH TYR A 756 " pdb=" OD1 ASP A 994 " model vdw 2.088 3.040 nonbonded pdb=" O GLU E 24 " pdb=" OG1 THR E 28 " model vdw 2.157 3.040 nonbonded pdb=" O ASP C 80 " pdb=" OH TYR C 265 " model vdw 2.166 3.040 nonbonded pdb=" NH1 ARG C 457 " pdb=" OG SER C 459 " model vdw 2.169 3.120 nonbonded pdb=" O GLU C 661 " pdb=" OH TYR C 695 " model vdw 2.207 3.040 ... (remaining 239400 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 257 or resid 262 through 1304)) selection = (chain 'B' and (resid 14 through 141 or resid 154 through 176 or resid 188 throu \ gh 1304)) selection = (chain 'C' and (resid 14 through 141 or resid 154 through 176 or resid 188 throu \ gh 257 or resid 262 through 1304)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' } 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: 5.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 33.550 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.120 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:7.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 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 : 0.008 0.833 31527 Z= 0.332 Angle : 0.794 18.862 43035 Z= 0.402 Chirality : 0.055 0.549 4986 Planarity : 0.006 0.173 5449 Dihedral : 15.916 89.400 10976 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.22 % Favored : 94.76 % Rotamer: Outliers : 1.45 % Allowed : 23.64 % Favored : 74.92 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.51 % 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: -0.67 (0.13), residues: 3738 helix: 0.31 (0.17), residues: 871 sheet: 0.44 (0.21), residues: 655 loop : -1.06 (0.13), residues: 2212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 78 TYR 0.033 0.002 TYR C 170 PHE 0.042 0.003 PHE C 168 TRP 0.026 0.003 TRP C 633 HIS 0.011 0.003 HIS A 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00653 / 0.29 (31417) covalent geometry : angle 0.76682 / 0.40 (42754) SS BOND : bond 0.00362 / 0.23 ( 43) SS BOND : angle 1.01766 / 0.68 ( 86) hydrogen bonds : bond 0.27423 / 17.74 ( 1044) hydrogen bonds : angle 8.61707 / 5.99 ( 2910) metal coordination : bond 0.58925 / 28.06 ( 2) link_BETA1-4 : bond 0.01041 / 0.64 ( 21) link_BETA1-4 : angle 2.45946 / 1.74 ( 63) link_NAG-ASN : bond 0.00818 / 0.57 ( 44) link_NAG-ASN : angle 3.36442 / 2.35 ( 132) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7476 Ramachandran restraints generated. 3738 Oldfield, 0 Emsley, 3738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7476 Ramachandran restraints generated. 3738 Oldfield, 0 Emsley, 3738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 83 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 54 ASN cc_start: 0.3584 (OUTLIER) cc_final: 0.2288 (p0) REVERT: E 270 MET cc_start: 0.2095 (mmm) cc_final: -0.0061 (ppp) REVERT: E 323 MET cc_start: 0.0742 (tmt) cc_final: 0.0333 (tmt) REVERT: E 360 MET cc_start: 0.5443 (ptt) cc_final: 0.4899 (mmt) REVERT: E 366 MET cc_start: 0.1316 (mmm) cc_final: 0.0049 (tpt) REVERT: E 462 MET cc_start: 0.7391 (mpm) cc_final: 0.6424 (ppp) outliers start: 48 outliers final: 38 residues processed: 129 average time/residue: 0.4996 time to fit residues: 81.0392 Evaluate side-chains 112 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 73 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 170 TYR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 800 PHE Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain E residue 83 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 30.0000 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 0.0370 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 4.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN A 314 GLN A 343 ASN A 414 GLN A 437 ASN A 613 GLN A 804 GLN A 907 ASN A 935 GLN A 953 ASN A 957 GLN A1142 GLN B 14 GLN B 173 GLN B 218 GLN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 ASN B 360 ASN B 394 ASN B 422 ASN B 448 ASN B 493 GLN B 544 ASN B 613 GLN B 628 GLN B 658 ASN B 901 GLN B 955 ASN B1002 GLN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN C 207 HIS C 314 GLN C 321 GLN C 422 ASN C 450 ASN C 519 HIS C 613 GLN C 658 ASN C 675 GLN C 804 GLN C 901 GLN C1002 GLN E 43 GLN E 59 ASN E 64 ASN E 228 ASN E 345 HIS E 493 HIS E 524 GLN E 586 ASN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.104535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.061617 restraints weight = 106069.372| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 4.86 r_work: 0.2846 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 31527 Z= 0.119 Angle : 0.605 9.711 43035 Z= 0.299 Chirality : 0.045 0.321 4986 Planarity : 0.004 0.085 5449 Dihedral : 4.665 57.612 4111 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.92 % Allowed : 21.44 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % 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 (0.14), residues: 3738 helix: 1.28 (0.18), residues: 893 sheet: 0.60 (0.20), residues: 662 loop : -0.97 (0.13), residues: 2183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 983 TYR 0.020 0.001 TYR B1067 PHE 0.021 0.001 PHE C 168 TRP 0.014 0.001 TRP C 633 HIS 0.005 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 (31417) covalent geometry : angle 0.58568 / 0.29 (42754) SS BOND : bond 0.00190 / 0.12 ( 43) SS BOND : angle 0.67501 / 0.50 ( 86) hydrogen bonds : bond 0.05635 / 3.78 ( 1044) hydrogen bonds : angle 5.87686 / 4.13 ( 2910) metal coordination : bond 0.00368 / 0.19 ( 2) link_BETA1-4 : bond 0.00553 / 0.31 ( 21) link_BETA1-4 : angle 1.65593 / 1.14 ( 63) link_NAG-ASN : bond 0.00621 / 0.44 ( 44) link_NAG-ASN : angle 2.55372 / 1.82 ( 132) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7476 Ramachandran restraints generated. 3738 Oldfield, 0 Emsley, 3738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7476 Ramachandran restraints generated. 3738 Oldfield, 0 Emsley, 3738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 77 time to evaluate : 1.198 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 421 TYR cc_start: 0.8261 (OUTLIER) cc_final: 0.7208 (t80) REVERT: B 981 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8709 (mt) REVERT: C 314 GLN cc_start: 0.9087 (OUTLIER) cc_final: 0.8600 (tm-30) REVERT: C 456 PHE cc_start: 0.8667 (m-80) cc_final: 0.8199 (m-80) REVERT: E 54 ASN cc_start: 0.7901 (OUTLIER) cc_final: 0.6900 (p0) REVERT: E 332 MET cc_start: 0.7521 (pp-130) cc_final: 0.7217 (pp-130) REVERT: E 360 MET cc_start: 0.6156 (OUTLIER) cc_final: 0.5498 (mmt) REVERT: E 366 MET cc_start: 0.4329 (mmm) cc_final: 0.3732 (mmm) REVERT: E 462 MET cc_start: 0.7635 (mpm) cc_final: 0.6956 (ppp) REVERT: E 579 MET cc_start: 0.8018 (mmt) cc_final: 0.7777 (mmt) outliers start: 97 outliers final: 29 residues processed: 167 average time/residue: 0.4872 time to fit residues: 101.6745 Evaluate side-chains 109 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 75 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 800 PHE Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain E residue 261 CYS Chi-restraints excluded: chain E residue 360 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 124 optimal weight: 4.9990 chunk 42 optimal weight: 50.0000 chunk 130 optimal weight: 1.9990 chunk 229 optimal weight: 5.9990 chunk 190 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 chunk 207 optimal weight: 5.9990 chunk 356 optimal weight: 50.0000 chunk 373 optimal weight: 5.9990 chunk 220 optimal weight: 20.0000 chunk 136 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN A 188 ASN A 422 ASN A 957 GLN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN B 992 GLN B1002 GLN C 125 ASN C 501 ASN C 965 GLN C1002 GLN ** E 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.102694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.059008 restraints weight = 106697.596| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 5.00 r_work: 0.2736 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8940 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.106 31527 Z= 0.296 Angle : 0.667 9.766 43035 Z= 0.329 Chirality : 0.048 0.310 4986 Planarity : 0.004 0.060 5449 Dihedral : 4.483 47.453 4077 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.82 % Allowed : 20.11 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % 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: -0.20 (0.14), residues: 3738 helix: 1.42 (0.18), residues: 911 sheet: 0.36 (0.19), residues: 718 loop : -1.04 (0.13), residues: 2109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 983 TYR 0.021 0.002 TYR A1067 PHE 0.022 0.002 PHE C 800 TRP 0.024 0.001 TRP A 633 HIS 0.005 0.001 HIS E 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00706 / 0.30 (31417) covalent geometry : angle 0.64774 / 0.33 (42754) SS BOND : bond 0.00336 / 0.24 ( 43) SS BOND : angle 0.98111 / 0.69 ( 86) hydrogen bonds : bond 0.06409 / 4.27 ( 1044) hydrogen bonds : angle 5.63809 / 3.96 ( 2910) metal coordination : bond 0.00372 / 0.18 ( 2) link_BETA1-4 : bond 0.00462 / 0.29 ( 21) link_BETA1-4 : angle 1.83584 / 1.28 ( 63) link_NAG-ASN : bond 0.00599 / 0.38 ( 44) link_NAG-ASN : angle 2.58778 / 1.83 ( 132) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7476 Ramachandran restraints generated. 3738 Oldfield, 0 Emsley, 3738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7476 Ramachandran restraints generated. 3738 Oldfield, 0 Emsley, 3738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 77 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 421 TYR cc_start: 0.8317 (OUTLIER) cc_final: 0.7325 (t80) REVERT: A 900 MET cc_start: 0.9444 (OUTLIER) cc_final: 0.9230 (mtp) REVERT: B 34 ARG cc_start: 0.9209 (OUTLIER) cc_final: 0.8957 (mtp85) REVERT: B 981 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8691 (mt) REVERT: B 994 ASP cc_start: 0.8882 (OUTLIER) cc_final: 0.8664 (t0) REVERT: C 347 PHE cc_start: 0.8135 (OUTLIER) cc_final: 0.7684 (m-10) REVERT: C 456 PHE cc_start: 0.8836 (m-80) cc_final: 0.8299 (m-80) REVERT: C 492 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.7894 (mm) REVERT: E 112 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.8647 (tp30) REVERT: E 116 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7043 (ppt170) REVERT: E 332 MET cc_start: 0.7868 (pp-130) cc_final: 0.7637 (pp-130) REVERT: E 366 MET cc_start: 0.4514 (mmm) cc_final: 0.4170 (mmm) outliers start: 127 outliers final: 51 residues processed: 197 average time/residue: 0.4286 time to fit residues: 108.1092 Evaluate side-chains 137 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 77 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 800 PHE Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain E residue 116 ARG Chi-restraints excluded: chain E residue 261 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 50 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 chunk 334 optimal weight: 40.0000 chunk 211 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 251 optimal weight: 6.9990 chunk 164 optimal weight: 9.9990 chunk 333 optimal weight: 10.0000 chunk 134 optimal weight: 30.0000 chunk 172 optimal weight: 0.8980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 ASN A 957 GLN A 965 GLN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN B 544 ASN C 314 GLN ** E 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.105241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.066157 restraints weight = 114692.603| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 4.20 r_work: 0.2759 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 31527 Z= 0.159 Angle : 0.585 10.339 43035 Z= 0.283 Chirality : 0.045 0.291 4986 Planarity : 0.004 0.053 5449 Dihedral : 4.232 46.164 4075 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.10 % Allowed : 20.78 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % 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: -0.09 (0.14), residues: 3738 helix: 1.59 (0.18), residues: 901 sheet: 0.38 (0.19), residues: 710 loop : -0.98 (0.13), residues: 2127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 357 TYR 0.019 0.001 TYR A1067 PHE 0.018 0.001 PHE E 29 TRP 0.016 0.001 TRP A 633 HIS 0.004 0.001 HIS B 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (31417) covalent geometry : angle 0.56658 / 0.28 (42754) SS BOND : bond 0.00288 / 0.21 ( 43) SS BOND : angle 0.78723 / 0.59 ( 86) hydrogen bonds : bond 0.05021 / 3.37 ( 1044) hydrogen bonds : angle 5.24469 / 3.69 ( 2910) metal coordination : bond 0.00177 / 0.08 ( 2) link_BETA1-4 : bond 0.00405 / 0.22 ( 21) link_BETA1-4 : angle 1.55849 / 1.08 ( 63) link_NAG-ASN : bond 0.00392 / 0.27 ( 44) link_NAG-ASN : angle 2.43152 / 1.82 ( 132) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7476 Ramachandran restraints generated. 3738 Oldfield, 0 Emsley, 3738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7476 Ramachandran restraints generated. 3738 Oldfield, 0 Emsley, 3738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 77 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 421 TYR cc_start: 0.8390 (OUTLIER) cc_final: 0.7403 (t80) REVERT: A 900 MET cc_start: 0.9417 (OUTLIER) cc_final: 0.9147 (mtp) REVERT: B 981 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8581 (mt) REVERT: B 994 ASP cc_start: 0.8839 (OUTLIER) cc_final: 0.8623 (t0) REVERT: C 153 MET cc_start: 0.7367 (pmm) cc_final: 0.6645 (tpt) REVERT: C 347 PHE cc_start: 0.8051 (OUTLIER) cc_final: 0.7632 (m-10) REVERT: C 456 PHE cc_start: 0.8805 (m-80) cc_final: 0.8239 (m-80) REVERT: E 112 GLU cc_start: 0.8974 (OUTLIER) cc_final: 0.8583 (tp30) REVERT: E 116 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7232 (ppt170) REVERT: E 270 MET cc_start: -0.0693 (mpt) cc_final: -0.1556 (ptp) REVERT: E 332 MET cc_start: 0.7759 (pp-130) cc_final: 0.7499 (pp-130) REVERT: E 366 MET cc_start: 0.4486 (mmm) cc_final: 0.4139 (mmm) REVERT: E 462 MET cc_start: 0.7955 (mpm) cc_final: 0.6982 (ppp) outliers start: 103 outliers final: 47 residues processed: 173 average time/residue: 0.4227 time to fit residues: 93.2433 Evaluate side-chains 129 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 75 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 800 PHE Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain E residue 116 ARG Chi-restraints excluded: chain E residue 306 ARG Chi-restraints excluded: chain E residue 362 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 19 optimal weight: 2.9990 chunk 247 optimal weight: 9.9990 chunk 154 optimal weight: 6.9990 chunk 138 optimal weight: 10.0000 chunk 81 optimal weight: 1.9990 chunk 0 optimal weight: 40.0000 chunk 228 optimal weight: 6.9990 chunk 342 optimal weight: 50.0000 chunk 324 optimal weight: 40.0000 chunk 376 optimal weight: 50.0000 chunk 282 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 165 ASN A 957 GLN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN B 544 ASN B1135 ASN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 ASN C 450 ASN C 907 ASN ** E 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.102654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.063065 restraints weight = 116243.409| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 4.26 r_work: 0.2725 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.115 31527 Z= 0.319 Angle : 0.666 9.856 43035 Z= 0.326 Chirality : 0.048 0.314 4986 Planarity : 0.004 0.051 5449 Dihedral : 4.496 46.827 4075 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 3.61 % Allowed : 21.02 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % 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: -0.27 (0.14), residues: 3738 helix: 1.53 (0.18), residues: 899 sheet: 0.21 (0.19), residues: 723 loop : -1.11 (0.13), residues: 2116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 319 TYR 0.019 0.001 TYR A1067 PHE 0.026 0.002 PHE C 759 TRP 0.022 0.001 TRP A 633 HIS 0.004 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00763 / 0.32 (31417) covalent geometry : angle 0.64732 / 0.32 (42754) SS BOND : bond 0.00434 / 0.32 ( 43) SS BOND : angle 0.97948 / 0.69 ( 86) hydrogen bonds : bond 0.05984 / 3.98 ( 1044) hydrogen bonds : angle 5.40471 / 3.80 ( 2910) metal coordination : bond 0.00053 / 0.03 ( 2) link_BETA1-4 : bond 0.00486 / 0.31 ( 21) link_BETA1-4 : angle 1.78690 / 1.22 ( 63) link_NAG-ASN : bond 0.00598 / 0.38 ( 44) link_NAG-ASN : angle 2.56930 / 1.83 ( 132) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7476 Ramachandran restraints generated. 3738 Oldfield, 0 Emsley, 3738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7476 Ramachandran restraints generated. 3738 Oldfield, 0 Emsley, 3738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 78 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 421 TYR cc_start: 0.8415 (OUTLIER) cc_final: 0.7457 (t80) REVERT: B 981 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8563 (mt) REVERT: B 994 ASP cc_start: 0.8889 (OUTLIER) cc_final: 0.8672 (t0) REVERT: C 153 MET cc_start: 0.7760 (pmm) cc_final: 0.7223 (tpt) REVERT: C 347 PHE cc_start: 0.8358 (OUTLIER) cc_final: 0.7936 (m-10) REVERT: C 456 PHE cc_start: 0.8880 (m-80) cc_final: 0.8284 (m-80) REVERT: C 492 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7853 (mm) REVERT: C 515 PHE cc_start: 0.8821 (OUTLIER) cc_final: 0.8298 (p90) REVERT: C 614 ASP cc_start: 0.8325 (t0) cc_final: 0.8116 (t0) REVERT: E 112 GLU cc_start: 0.8956 (OUTLIER) cc_final: 0.8553 (tp30) REVERT: E 116 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7165 (ppt170) REVERT: E 270 MET cc_start: -0.0730 (mpt) cc_final: -0.1494 (ptp) REVERT: E 332 MET cc_start: 0.7645 (pp-130) cc_final: 0.7385 (pp-130) REVERT: E 351 LEU cc_start: 0.2125 (OUTLIER) cc_final: 0.1505 (mt) REVERT: E 366 MET cc_start: 0.4393 (mmm) cc_final: 0.4020 (mmm) outliers start: 120 outliers final: 70 residues processed: 194 average time/residue: 0.4045 time to fit residues: 101.7871 Evaluate side-chains 158 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 79 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 800 PHE Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain E residue 116 ARG Chi-restraints excluded: chain E residue 306 ARG Chi-restraints excluded: chain E residue 351 LEU Chi-restraints excluded: chain E residue 362 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 4 optimal weight: 4.9990 chunk 267 optimal weight: 2.9990 chunk 235 optimal weight: 4.9990 chunk 358 optimal weight: 50.0000 chunk 352 optimal weight: 6.9990 chunk 278 optimal weight: 2.9990 chunk 333 optimal weight: 30.0000 chunk 369 optimal weight: 30.0000 chunk 83 optimal weight: 0.9980 chunk 310 optimal weight: 0.9980 chunk 222 optimal weight: 6.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 ASN A 957 GLN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN B 544 ASN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 ASN C 450 ASN C 907 ASN ** E 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.102880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.062713 restraints weight = 116213.941| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 3.73 r_work: 0.2781 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8915 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 31527 Z= 0.185 Angle : 0.599 9.680 43035 Z= 0.290 Chirality : 0.046 0.299 4986 Planarity : 0.004 0.049 5449 Dihedral : 4.372 45.870 4075 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.22 % Allowed : 21.47 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % 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 (0.14), residues: 3738 helix: 1.61 (0.18), residues: 904 sheet: 0.25 (0.19), residues: 716 loop : -1.05 (0.13), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1091 TYR 0.019 0.001 TYR A1067 PHE 0.024 0.001 PHE C 168 TRP 0.017 0.001 TRP A 633 HIS 0.005 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.18 (31417) covalent geometry : angle 0.58172 / 0.29 (42754) SS BOND : bond 0.00310 / 0.18 ( 43) SS BOND : angle 0.93169 / 0.67 ( 86) hydrogen bonds : bond 0.05106 / 3.41 ( 1044) hydrogen bonds : angle 5.17741 / 3.64 ( 2910) metal coordination : bond 0.00069 / 0.03 ( 2) link_BETA1-4 : bond 0.00388 / 0.21 ( 21) link_BETA1-4 : angle 1.60599 / 1.11 ( 63) link_NAG-ASN : bond 0.00395 / 0.27 ( 44) link_NAG-ASN : angle 2.33256 / 1.65 ( 132) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7476 Ramachandran restraints generated. 3738 Oldfield, 0 Emsley, 3738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7476 Ramachandran restraints generated. 3738 Oldfield, 0 Emsley, 3738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 81 time to evaluate : 1.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 421 TYR cc_start: 0.8409 (OUTLIER) cc_final: 0.7464 (t80) REVERT: B 981 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8546 (mt) REVERT: B 984 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7420 (tm) REVERT: B 994 ASP cc_start: 0.8872 (OUTLIER) cc_final: 0.8649 (t0) REVERT: C 153 MET cc_start: 0.7496 (pmm) cc_final: 0.7191 (tpt) REVERT: C 456 PHE cc_start: 0.8838 (m-80) cc_final: 0.8259 (m-80) REVERT: C 492 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.7973 (mm) REVERT: C 614 ASP cc_start: 0.8157 (t0) cc_final: 0.7865 (t0) REVERT: E 112 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.8568 (tp30) REVERT: E 116 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.7111 (ppt170) REVERT: E 270 MET cc_start: -0.0821 (mpt) cc_final: -0.1586 (ptp) REVERT: E 332 MET cc_start: 0.7817 (pp-130) cc_final: 0.7563 (pp-130) REVERT: E 366 MET cc_start: 0.4681 (mmm) cc_final: 0.4293 (mmm) REVERT: E 462 MET cc_start: 0.7775 (mmt) cc_final: 0.6797 (ppp) outliers start: 107 outliers final: 64 residues processed: 184 average time/residue: 0.4280 time to fit residues: 101.8307 Evaluate side-chains 150 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 79 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 800 PHE Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain E residue 116 ARG Chi-restraints excluded: chain E residue 306 ARG Chi-restraints excluded: chain E residue 362 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 323 optimal weight: 20.0000 chunk 346 optimal weight: 0.0270 chunk 336 optimal weight: 8.9990 chunk 264 optimal weight: 10.0000 chunk 0 optimal weight: 40.0000 chunk 99 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 258 optimal weight: 1.9990 chunk 138 optimal weight: 10.0000 chunk 267 optimal weight: 2.9990 chunk 69 optimal weight: 0.4980 overall best weight: 1.9044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 ASN A 957 GLN B 245 HIS B 360 ASN B 544 ASN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.103072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.063742 restraints weight = 115528.442| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 4.32 r_work: 0.2766 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 31527 Z= 0.147 Angle : 0.580 9.656 43035 Z= 0.279 Chirality : 0.045 0.297 4986 Planarity : 0.004 0.048 5449 Dihedral : 4.264 45.289 4075 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.13 % Allowed : 21.80 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % 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: -0.13 (0.14), residues: 3738 helix: 1.64 (0.18), residues: 905 sheet: 0.29 (0.19), residues: 716 loop : -1.03 (0.13), residues: 2117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 983 TYR 0.019 0.001 TYR A1067 PHE 0.017 0.001 PHE C 392 TRP 0.015 0.001 TRP A 633 HIS 0.004 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (31417) covalent geometry : angle 0.56398 / 0.28 (42754) SS BOND : bond 0.00215 / 0.14 ( 43) SS BOND : angle 0.82225 / 0.59 ( 86) hydrogen bonds : bond 0.04731 / 3.17 ( 1044) hydrogen bonds : angle 5.03936 / 3.55 ( 2910) metal coordination : bond 0.00029 / 0.01 ( 2) link_BETA1-4 : bond 0.00398 / 0.21 ( 21) link_BETA1-4 : angle 1.52388 / 1.05 ( 63) link_NAG-ASN : bond 0.00378 / 0.25 ( 44) link_NAG-ASN : angle 2.25210 / 1.59 ( 132) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7476 Ramachandran restraints generated. 3738 Oldfield, 0 Emsley, 3738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7476 Ramachandran restraints generated. 3738 Oldfield, 0 Emsley, 3738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 80 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8444 (pm20) REVERT: A 421 TYR cc_start: 0.8401 (OUTLIER) cc_final: 0.7436 (t80) REVERT: B 981 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8509 (mt) REVERT: B 984 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.7280 (tm) REVERT: B 994 ASP cc_start: 0.8894 (OUTLIER) cc_final: 0.8676 (t0) REVERT: C 347 PHE cc_start: 0.8369 (OUTLIER) cc_final: 0.7924 (m-10) REVERT: C 456 PHE cc_start: 0.8838 (m-80) cc_final: 0.8248 (m-80) REVERT: C 492 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.7993 (mm) REVERT: C 515 PHE cc_start: 0.8969 (OUTLIER) cc_final: 0.8255 (p90) REVERT: C 614 ASP cc_start: 0.8228 (t0) cc_final: 0.7901 (t0) REVERT: E 112 GLU cc_start: 0.8981 (OUTLIER) cc_final: 0.8559 (tp30) REVERT: E 116 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7187 (ppt170) REVERT: E 270 MET cc_start: -0.0888 (mpt) cc_final: -0.1611 (ptp) REVERT: E 323 MET cc_start: 0.6826 (tmt) cc_final: 0.6280 (tmm) REVERT: E 332 MET cc_start: 0.7880 (pp-130) cc_final: 0.7612 (pp-130) REVERT: E 351 LEU cc_start: 0.2268 (OUTLIER) cc_final: 0.1579 (mt) REVERT: E 366 MET cc_start: 0.4824 (mmm) cc_final: 0.4510 (mmm) REVERT: E 462 MET cc_start: 0.7751 (mmt) cc_final: 0.6777 (ppp) outliers start: 104 outliers final: 59 residues processed: 176 average time/residue: 0.4567 time to fit residues: 102.1024 Evaluate side-chains 150 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 80 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 800 PHE Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain E residue 116 ARG Chi-restraints excluded: chain E residue 261 CYS Chi-restraints excluded: chain E residue 306 ARG Chi-restraints excluded: chain E residue 351 LEU Chi-restraints excluded: chain E residue 362 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 268 optimal weight: 0.6980 chunk 33 optimal weight: 9.9990 chunk 106 optimal weight: 30.0000 chunk 100 optimal weight: 1.9990 chunk 233 optimal weight: 9.9990 chunk 123 optimal weight: 1.9990 chunk 300 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 140 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 109 optimal weight: 7.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 ASN A 957 GLN B 360 ASN B 394 ASN B 544 ASN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN E 330 ASN ** E 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.102798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.062826 restraints weight = 115938.919| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 3.74 r_work: 0.2785 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 31527 Z= 0.192 Angle : 0.601 9.696 43035 Z= 0.289 Chirality : 0.045 0.296 4986 Planarity : 0.004 0.048 5449 Dihedral : 4.276 45.294 4074 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.28 % Allowed : 21.59 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % 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: -0.16 (0.14), residues: 3738 helix: 1.65 (0.18), residues: 909 sheet: 0.26 (0.19), residues: 716 loop : -1.06 (0.13), residues: 2113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 357 TYR 0.030 0.001 TYR C 170 PHE 0.020 0.001 PHE C 168 TRP 0.017 0.001 TRP A 633 HIS 0.004 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.19 (31417) covalent geometry : angle 0.58487 / 0.29 (42754) SS BOND : bond 0.00245 / 0.16 ( 43) SS BOND : angle 0.82709 / 0.59 ( 86) hydrogen bonds : bond 0.04943 / 3.31 ( 1044) hydrogen bonds : angle 5.05608 / 3.56 ( 2910) metal coordination : bond 0.00061 / 0.03 ( 2) link_BETA1-4 : bond 0.00385 / 0.21 ( 21) link_BETA1-4 : angle 1.53930 / 1.05 ( 63) link_NAG-ASN : bond 0.00407 / 0.27 ( 44) link_NAG-ASN : angle 2.28928 / 1.61 ( 132) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7476 Ramachandran restraints generated. 3738 Oldfield, 0 Emsley, 3738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7476 Ramachandran restraints generated. 3738 Oldfield, 0 Emsley, 3738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 81 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 421 TYR cc_start: 0.8463 (OUTLIER) cc_final: 0.7494 (t80) REVERT: B 277 LEU cc_start: 0.9519 (OUTLIER) cc_final: 0.9304 (mt) REVERT: B 981 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8535 (mt) REVERT: B 984 LEU cc_start: 0.7631 (OUTLIER) cc_final: 0.7405 (tm) REVERT: B 994 ASP cc_start: 0.8892 (OUTLIER) cc_final: 0.8665 (t0) REVERT: C 347 PHE cc_start: 0.8452 (OUTLIER) cc_final: 0.8023 (m-10) REVERT: C 492 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8122 (mm) REVERT: C 508 TYR cc_start: 0.8051 (m-80) cc_final: 0.7815 (m-80) REVERT: C 515 PHE cc_start: 0.9010 (OUTLIER) cc_final: 0.8291 (p90) REVERT: C 614 ASP cc_start: 0.8176 (t0) cc_final: 0.7842 (t0) REVERT: E 112 GLU cc_start: 0.8957 (OUTLIER) cc_final: 0.8485 (tp30) REVERT: E 270 MET cc_start: -0.0655 (OUTLIER) cc_final: -0.1503 (ptp) REVERT: E 332 MET cc_start: 0.7367 (pp-130) cc_final: 0.7016 (pp-130) REVERT: E 351 LEU cc_start: 0.1859 (OUTLIER) cc_final: 0.1186 (mt) REVERT: E 366 MET cc_start: 0.4493 (mmm) cc_final: 0.4062 (mmm) outliers start: 109 outliers final: 70 residues processed: 184 average time/residue: 0.4385 time to fit residues: 104.1766 Evaluate side-chains 161 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 80 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 800 PHE Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain E residue 261 CYS Chi-restraints excluded: chain E residue 270 MET Chi-restraints excluded: chain E residue 306 ARG Chi-restraints excluded: chain E residue 351 LEU Chi-restraints excluded: chain E residue 362 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 145 optimal weight: 40.0000 chunk 122 optimal weight: 4.9990 chunk 231 optimal weight: 8.9990 chunk 87 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 88 optimal weight: 5.9990 chunk 47 optimal weight: 20.0000 chunk 78 optimal weight: 0.7980 chunk 99 optimal weight: 0.0020 chunk 363 optimal weight: 20.0000 chunk 326 optimal weight: 6.9990 overall best weight: 1.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 ASN A 957 GLN B 544 ASN B1002 GLN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN C1002 GLN ** E 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 526 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.103319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.064491 restraints weight = 115944.605| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 4.45 r_work: 0.2767 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 31527 Z= 0.129 Angle : 0.584 12.388 43035 Z= 0.279 Chirality : 0.045 0.287 4986 Planarity : 0.004 0.048 5449 Dihedral : 4.163 44.827 4074 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.47 % Allowed : 22.34 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % 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: -0.08 (0.14), residues: 3738 helix: 1.71 (0.18), residues: 906 sheet: 0.30 (0.19), residues: 722 loop : -1.00 (0.13), residues: 2110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 190 TYR 0.018 0.001 TYR A1067 PHE 0.015 0.001 PHE C 392 TRP 0.013 0.001 TRP A 633 HIS 0.003 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (31417) covalent geometry : angle 0.56926 / 0.28 (42754) SS BOND : bond 0.00235 / 0.14 ( 43) SS BOND : angle 0.79527 / 0.56 ( 86) hydrogen bonds : bond 0.04435 / 2.98 ( 1044) hydrogen bonds : angle 4.91865 / 3.47 ( 2910) metal coordination : bond 0.00052 / 0.03 ( 2) link_BETA1-4 : bond 0.00408 / 0.22 ( 21) link_BETA1-4 : angle 1.46675 / 1.01 ( 63) link_NAG-ASN : bond 0.00372 / 0.25 ( 44) link_NAG-ASN : angle 2.19007 / 1.54 ( 132) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7476 Ramachandran restraints generated. 3738 Oldfield, 0 Emsley, 3738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7476 Ramachandran restraints generated. 3738 Oldfield, 0 Emsley, 3738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 83 time to evaluate : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 421 TYR cc_start: 0.8445 (OUTLIER) cc_final: 0.7514 (t80) REVERT: B 981 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8524 (mt) REVERT: B 984 LEU cc_start: 0.7465 (OUTLIER) cc_final: 0.7216 (tm) REVERT: B 994 ASP cc_start: 0.8871 (OUTLIER) cc_final: 0.8653 (t0) REVERT: C 153 MET cc_start: 0.7853 (pmm) cc_final: 0.6822 (tpt) REVERT: C 347 PHE cc_start: 0.8334 (OUTLIER) cc_final: 0.7910 (m-10) REVERT: C 456 PHE cc_start: 0.8877 (m-80) cc_final: 0.8297 (m-80) REVERT: C 492 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8014 (mm) REVERT: C 508 TYR cc_start: 0.7893 (m-80) cc_final: 0.7674 (m-80) REVERT: C 614 ASP cc_start: 0.8260 (t0) cc_final: 0.7921 (t0) REVERT: E 54 ASN cc_start: 0.7834 (OUTLIER) cc_final: 0.6914 (p0) REVERT: E 112 GLU cc_start: 0.8968 (OUTLIER) cc_final: 0.8518 (tp30) REVERT: E 270 MET cc_start: -0.0742 (OUTLIER) cc_final: -0.1517 (ptp) REVERT: E 323 MET cc_start: 0.6473 (tmt) cc_final: 0.5944 (tmm) REVERT: E 332 MET cc_start: 0.7646 (pp-130) cc_final: 0.7342 (pp-130) REVERT: E 351 LEU cc_start: 0.2008 (OUTLIER) cc_final: 0.1309 (mt) REVERT: E 366 MET cc_start: 0.4698 (mmm) cc_final: 0.4363 (mmm) REVERT: E 516 TYR cc_start: 0.6514 (OUTLIER) cc_final: 0.6081 (m-80) outliers start: 82 outliers final: 57 residues processed: 162 average time/residue: 0.4822 time to fit residues: 99.7397 Evaluate side-chains 149 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 81 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 800 PHE Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain E residue 261 CYS Chi-restraints excluded: chain E residue 270 MET Chi-restraints excluded: chain E residue 306 ARG Chi-restraints excluded: chain E residue 351 LEU Chi-restraints excluded: chain E residue 362 THR Chi-restraints excluded: chain E residue 516 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 111 optimal weight: 8.9990 chunk 365 optimal weight: 0.7980 chunk 175 optimal weight: 7.9990 chunk 206 optimal weight: 0.7980 chunk 154 optimal weight: 9.9990 chunk 70 optimal weight: 5.9990 chunk 360 optimal weight: 30.0000 chunk 94 optimal weight: 3.9990 chunk 267 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 146 optimal weight: 0.2980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 ASN A 957 GLN B 360 ASN B 544 ASN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** E 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.103223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.063947 restraints weight = 115011.468| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 4.17 r_work: 0.2788 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 31527 Z= 0.141 Angle : 0.583 10.091 43035 Z= 0.279 Chirality : 0.045 0.290 4986 Planarity : 0.004 0.048 5449 Dihedral : 4.125 44.350 4073 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.56 % Allowed : 22.28 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % 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: -0.07 (0.14), residues: 3738 helix: 1.72 (0.18), residues: 913 sheet: 0.32 (0.19), residues: 707 loop : -1.00 (0.13), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1091 TYR 0.034 0.001 TYR C 170 PHE 0.021 0.001 PHE C 168 TRP 0.014 0.001 TRP A 633 HIS 0.003 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (31417) covalent geometry : angle 0.56835 / 0.28 (42754) SS BOND : bond 0.00228 / 0.14 ( 43) SS BOND : angle 0.78385 / 0.56 ( 86) hydrogen bonds : bond 0.04430 / 2.97 ( 1044) hydrogen bonds : angle 4.87054 / 3.44 ( 2910) metal coordination : bond 0.00036 / 0.02 ( 2) link_BETA1-4 : bond 0.00401 / 0.21 ( 21) link_BETA1-4 : angle 1.43661 / 0.98 ( 63) link_NAG-ASN : bond 0.00369 / 0.25 ( 44) link_NAG-ASN : angle 2.17784 / 1.53 ( 132) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7476 Ramachandran restraints generated. 3738 Oldfield, 0 Emsley, 3738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7476 Ramachandran restraints generated. 3738 Oldfield, 0 Emsley, 3738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 82 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 421 TYR cc_start: 0.8380 (OUTLIER) cc_final: 0.7421 (t80) REVERT: B 981 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8516 (mt) REVERT: B 984 LEU cc_start: 0.7535 (OUTLIER) cc_final: 0.7288 (tm) REVERT: C 153 MET cc_start: 0.7862 (pmm) cc_final: 0.6926 (tpt) REVERT: C 347 PHE cc_start: 0.8334 (OUTLIER) cc_final: 0.7904 (m-10) REVERT: C 456 PHE cc_start: 0.8921 (m-80) cc_final: 0.8356 (m-80) REVERT: C 492 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8092 (mm) REVERT: C 508 TYR cc_start: 0.7922 (m-80) cc_final: 0.7720 (m-80) REVERT: C 515 PHE cc_start: 0.8980 (OUTLIER) cc_final: 0.8213 (p90) REVERT: C 614 ASP cc_start: 0.8186 (t0) cc_final: 0.7834 (t0) REVERT: E 54 ASN cc_start: 0.7813 (OUTLIER) cc_final: 0.6899 (p0) REVERT: E 112 GLU cc_start: 0.8965 (OUTLIER) cc_final: 0.8482 (tp30) REVERT: E 270 MET cc_start: -0.0723 (OUTLIER) cc_final: -0.1491 (ptp) REVERT: E 323 MET cc_start: 0.6506 (tmt) cc_final: 0.6079 (tmm) REVERT: E 332 MET cc_start: 0.7554 (pp-130) cc_final: 0.7254 (pp-130) REVERT: E 351 LEU cc_start: 0.2071 (OUTLIER) cc_final: 0.1371 (mt) REVERT: E 366 MET cc_start: 0.4744 (mmm) cc_final: 0.4423 (mmm) outliers start: 85 outliers final: 59 residues processed: 162 average time/residue: 0.4707 time to fit residues: 97.6217 Evaluate side-chains 148 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 79 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 800 PHE Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain E residue 261 CYS Chi-restraints excluded: chain E residue 270 MET Chi-restraints excluded: chain E residue 306 ARG Chi-restraints excluded: chain E residue 351 LEU Chi-restraints excluded: chain E residue 362 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 58 optimal weight: 7.9990 chunk 178 optimal weight: 0.6980 chunk 145 optimal weight: 40.0000 chunk 164 optimal weight: 9.9990 chunk 304 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 34 optimal weight: 9.9990 chunk 354 optimal weight: 20.0000 chunk 140 optimal weight: 7.9990 chunk 199 optimal weight: 3.9990 chunk 362 optimal weight: 30.0000 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 ASN A 360 ASN A 957 GLN B 360 ASN B 544 ASN B1002 GLN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 ASN C 450 ASN C 907 ASN C1002 GLN ** E 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.101846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.061998 restraints weight = 116910.699| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 3.46 r_work: 0.2772 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.106 31527 Z= 0.289 Angle : 0.655 10.239 43035 Z= 0.318 Chirality : 0.047 0.301 4986 Planarity : 0.004 0.048 5449 Dihedral : 4.350 45.074 4073 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.68 % Allowed : 22.19 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % 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: -0.20 (0.14), residues: 3738 helix: 1.64 (0.18), residues: 912 sheet: 0.23 (0.19), residues: 713 loop : -1.09 (0.13), residues: 2113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 319 TYR 0.018 0.001 TYR B1067 PHE 0.023 0.002 PHE C 759 TRP 0.020 0.001 TRP A 633 HIS 0.005 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00691 / 0.29 (31417) covalent geometry : angle 0.63963 / 0.31 (42754) SS BOND : bond 0.00314 / 0.22 ( 43) SS BOND : angle 0.96161 / 0.66 ( 86) hydrogen bonds : bond 0.05413 / 3.61 ( 1044) hydrogen bonds : angle 5.11678 / 3.61 ( 2910) metal coordination : bond 0.00157 / 0.08 ( 2) link_BETA1-4 : bond 0.00409 / 0.25 ( 21) link_BETA1-4 : angle 1.61036 / 1.09 ( 63) link_NAG-ASN : bond 0.00508 / 0.33 ( 44) link_NAG-ASN : angle 2.37931 / 1.66 ( 132) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14633.87 seconds wall clock time: 248 minutes 51.59 seconds (14931.59 seconds total)