Starting phenix.real_space_refine on Sun Sep 13 20:22:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6xm5_22256/09_2026/6xm5_22256.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xm5_22256/09_2026/6xm5_22256.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6xm5_22256/09_2026/6xm5_22256.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6xm5_22256/09_2026/6xm5_22256.cif" model { file = "/net/cci-nas-00/data/ceres_data/6xm5_22256/09_2026/6xm5_22256.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xm5_22256/09_2026/6xm5_22256.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6xm5_22256/09_2026/6xm5_22256.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xm5_22256/09_2026/6xm5_22256.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 110 5.16 5 C 16154 2.51 5 N 4148 2.21 5 O 4981 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 138 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25393 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 8249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1057, 8249 Classifications: {'peptide': 1057} Link IDs: {'PTRANS': 51, 'TRANS': 1005} Chain breaks: 6 Chain: "B" Number of atoms: 8242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1056, 8242 Classifications: {'peptide': 1056} Link IDs: {'PTRANS': 52, 'TRANS': 1003} Chain breaks: 6 Chain: "C" Number of atoms: 8090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1036, 8090 Classifications: {'peptide': 1036} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 52, 'TRANS': 983} Chain breaks: 7 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 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: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 5.56, per 1000 atoms: 0.22 Number of scatterers: 25393 At special positions: 0 Unit cell: (142.8, 138.55, 180.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 110 16.00 O 4981 8.00 N 4148 7.00 C 16154 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 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=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " 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 131 " - pdb=" SG CYS C 166 " distance=2.03 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=2.06 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=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 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 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG 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-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A 165 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 603 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 657 " " NAG B1306 " - " ASN B 709 " " NAG B1307 " - " ASN B1074 " " NAG B1308 " - " ASN B 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 343 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 657 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C1074 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1074 " " NAG H 1 " - " ASN A1098 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN B 234 " " NAG K 1 " - " ASN B 331 " " NAG L 1 " - " ASN B 717 " " NAG M 1 " - " ASN B 801 " " NAG N 1 " - " ASN B1098 " " NAG O 1 " - " ASN B1134 " " NAG P 1 " - " ASN C 717 " " NAG Q 1 " - " ASN C 801 " " NAG R 1 " - " ASN C1098 " " NAG S 1 " - " ASN C1134 " Time building additional restraints: 2.23 Conformation dependent library (CDL) restraints added in 1.0 seconds 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5908 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 48 sheets defined 23.8% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.546A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 411 removed outlier: 4.018A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 618 No H-bonds generated for 'chain 'A' and resid 616 through 618' Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 625 through 629 Processing helix chain 'A' and resid 634 through 638 removed outlier: 4.048A pdb=" N THR A 638 " --> pdb=" O VAL A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.646A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.773A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 removed outlier: 3.639A pdb=" N ASP A 820 " --> pdb=" O SER A 816 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 855 removed outlier: 4.328A pdb=" N ALA A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 882 removed outlier: 3.704A pdb=" N ALA A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 878 " --> pdb=" O THR A 874 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY A 880 " --> pdb=" O ALA A 876 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR A 881 " --> pdb=" O LEU A 877 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE A 882 " --> pdb=" O LEU A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 891 removed outlier: 4.126A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.517A pdb=" N ASN A 907 " --> pdb=" O ALA A 903 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY A 908 " --> pdb=" O TYR A 904 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.658A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.587A pdb=" N GLY A 932 " --> pdb=" O ASN A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.574A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.659A pdb=" N ARG A 983 " --> pdb=" O ASP A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 1032 removed outlier: 4.322A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR A 998 " --> pdb=" O ASP A 994 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY A 999 " --> pdb=" O ARG A 995 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER A1003 " --> pdb=" O GLY A 999 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE A1013 " --> pdb=" O THR A1009 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER A1021 " --> pdb=" O GLU A1017 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A1024 " --> pdb=" O ALA A1020 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR A1027 " --> pdb=" O ASN A1023 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER A1030 " --> pdb=" O ALA A1026 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 283 No H-bonds generated for 'chain 'B' and resid 281 through 283' Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 removed outlier: 4.403A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 368 removed outlier: 3.750A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 3.671A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 4.239A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 737 through 744 removed outlier: 3.549A pdb=" N GLY B 744 " --> pdb=" O MET B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.567A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.719A 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 760 through 783 removed outlier: 4.115A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 832 through 839 removed outlier: 3.524A pdb=" N GLN B 836 " --> pdb=" O GLY B 832 " (cutoff:3.500A) Processing helix chain 'B' and resid 851 through 855 removed outlier: 3.527A pdb=" N LYS B 854 " --> pdb=" O CYS B 851 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N PHE B 855 " --> pdb=" O ALA B 852 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 851 through 855' Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.782A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA B 876 " --> pdb=" O GLN B 872 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.521A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 886 through 891' Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.747A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.837A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 removed outlier: 3.528A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.500A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA B 958 " --> pdb=" O GLN B 954 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR B 961 " --> pdb=" O GLN B 957 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.721A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 990 removed outlier: 4.347A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 1016 Processing helix chain 'B' and resid 1017 through 1033 removed outlier: 3.735A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER B1030 " --> pdb=" O ALA B1026 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 368 removed outlier: 3.990A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.593A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.949A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.510A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 635 removed outlier: 3.507A pdb=" N TRP C 633 " --> pdb=" O THR C 630 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL C 635 " --> pdb=" O THR C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.789A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.590A 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 760 through 783 removed outlier: 3.736A pdb=" N ALA C 766 " --> pdb=" O GLN C 762 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 removed outlier: 3.507A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 869 through 885 removed outlier: 3.572A pdb=" N LEU C 878 " --> pdb=" O THR C 874 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 887 through 891 removed outlier: 4.040A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.701A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.815A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.758A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER C 937 " --> pdb=" O LYS C 933 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 965 removed outlier: 3.849A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN C 957 " --> pdb=" O ASN C 953 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU C 962 " --> pdb=" O ALA C 958 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.637A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 988 through 993 removed outlier: 4.050A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 1032 removed outlier: 3.663A pdb=" N THR C 998 " --> pdb=" O ASP C 994 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLY C 999 " --> pdb=" O ARG C 995 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA C1020 " --> pdb=" O ALA C1016 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR C1027 " --> pdb=" O ASN C1023 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER C1030 " --> pdb=" O ALA C1026 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.759A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG A 190 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.030A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.339A 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: 7.472A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 5.491A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.534A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 315 removed outlier: 4.639A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.549A pdb=" N ALA A 397 " --> pdb=" O LYS A 356 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'A' and resid 541 through 543 removed outlier: 3.609A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 551 through 554 removed outlier: 5.861A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.692A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.696A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.838A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.838A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL A1104 " --> pdb=" O GLN A1113 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.684A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.439A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 29 through 31 removed outlier: 7.930A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE B 197 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 50 through 51 removed outlier: 6.623A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 5.822A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.536A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE B 106 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 312 removed outlier: 3.819A pdb=" N GLY B 593 " --> pdb=" O PHE B 318 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 312 removed outlier: 3.670A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.515A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.514A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP B 398 " --> pdb=" O VAL B 512 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.925A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.984A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.569A pdb=" N ILE B 712 " --> pdb=" O PHE B1075 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.577A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 734 through 736 removed outlier: 3.539A pdb=" N SER B 735 " --> pdb=" O THR B 859 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD7, first strand: chain 'C' and resid 28 through 30 removed outlier: 3.746A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N TYR C 266 " --> pdb=" O ALA C 93 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ARG C 190 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.565A pdb=" N THR C 51 " --> pdb=" O PHE C 275 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE1, first strand: chain 'C' and resid 115 through 119 Processing sheet with id=AE2, first strand: chain 'C' and resid 141 through 142 removed outlier: 6.621A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.173A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR C 612 " --> pdb=" O CYS C 649 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.706A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE7, first strand: chain 'C' and resid 539 through 540 removed outlier: 5.339A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.819A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.755A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF2, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF3, first strand: chain 'C' and resid 1094 through 1097 784 hydrogen bonds defined for protein. 2136 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: 5.58 Time building geometry restraints manager: 3.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 8061 1.35 - 1.48: 6922 1.48 - 1.61: 10836 1.61 - 1.74: 1 1.74 - 1.87: 133 Bond restraints: 25953 Sorted by residual: bond pdb=" C LYS A 790 " pdb=" N THR A 791 " ideal model delta sigma weight residual 1.331 1.258 0.073 2.07e-02 2.33e+03 1.23e+01 bond pdb=" C1 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 1.406 1.464 -0.058 2.00e-02 2.50e+03 8.35e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.36e+00 bond pdb=" C1 NAG C1302 " pdb=" O5 NAG C1302 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 6.94e+00 bond pdb=" C1 NAG J 2 " pdb=" O5 NAG J 2 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.40e+00 ... (remaining 25948 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 34494 2.39 - 4.79: 746 4.79 - 7.18: 71 7.18 - 9.58: 16 9.58 - 11.97: 3 Bond angle restraints: 35330 Sorted by residual: angle pdb=" C PHE A 392 " pdb=" N THR A 393 " pdb=" CA THR A 393 " ideal model delta sigma weight residual 121.54 132.67 -11.13 1.91e+00 2.74e-01 3.39e+01 angle pdb=" C SER C 31 " pdb=" N PHE C 32 " pdb=" CA PHE C 32 " ideal model delta sigma weight residual 121.54 131.71 -10.17 1.91e+00 2.74e-01 2.84e+01 angle pdb=" C GLY A 744 " pdb=" N ASP A 745 " pdb=" CA ASP A 745 " ideal model delta sigma weight residual 121.54 130.57 -9.03 1.91e+00 2.74e-01 2.24e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 116.25 -5.55 1.22e+00 6.72e-01 2.07e+01 angle pdb=" N GLU B1144 " pdb=" CA GLU B1144 " pdb=" C GLU B1144 " ideal model delta sigma weight residual 114.56 109.09 5.47 1.27e+00 6.20e-01 1.85e+01 ... (remaining 35325 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 13306 17.82 - 35.64: 1374 35.64 - 53.45: 257 53.45 - 71.27: 40 71.27 - 89.09: 19 Dihedral angle restraints: 14996 sinusoidal: 5821 harmonic: 9175 Sorted by residual: dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual 93.00 171.03 -78.03 1 1.00e+01 1.00e-02 7.61e+01 dihedral pdb=" CB CYS C 617 " pdb=" SG CYS C 617 " pdb=" SG CYS C 649 " pdb=" CB CYS C 649 " ideal model delta sinusoidal sigma weight residual 93.00 163.21 -70.21 1 1.00e+01 1.00e-02 6.35e+01 dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -16.23 -69.77 1 1.00e+01 1.00e-02 6.28e+01 ... (remaining 14993 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 3395 0.073 - 0.147: 728 0.147 - 0.220: 65 0.220 - 0.293: 5 0.293 - 0.367: 3 Chirality restraints: 4196 Sorted by residual: chirality pdb=" C2 NAG B1301 " pdb=" C1 NAG B1301 " pdb=" C3 NAG B1301 " pdb=" N2 NAG B1301 " both_signs ideal model delta sigma weight residual False -2.49 -2.13 -0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CB THR C 33 " pdb=" CA THR C 33 " pdb=" OG1 THR C 33 " pdb=" CG2 THR C 33 " both_signs ideal model delta sigma weight residual False 2.55 2.20 0.35 2.00e-01 2.50e+01 3.14e+00 chirality pdb=" C1 NAG L 2 " pdb=" O4 NAG L 1 " pdb=" C2 NAG L 2 " pdb=" O5 NAG L 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.37 -0.03 2.00e-02 2.50e+03 2.62e+00 ... (remaining 4193 not shown) Planarity restraints: 4539 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 986 " 0.076 5.00e-02 4.00e+02 1.15e-01 2.11e+01 pdb=" N PRO A 987 " -0.199 5.00e-02 4.00e+02 pdb=" CA PRO A 987 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO A 987 " 0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 986 " 0.063 5.00e-02 4.00e+02 9.41e-02 1.42e+01 pdb=" N PRO B 987 " -0.163 5.00e-02 4.00e+02 pdb=" CA PRO B 987 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO B 987 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 986 " -0.059 5.00e-02 4.00e+02 8.77e-02 1.23e+01 pdb=" N PRO C 987 " 0.152 5.00e-02 4.00e+02 pdb=" CA PRO C 987 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO C 987 " -0.049 5.00e-02 4.00e+02 ... (remaining 4536 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 6893 2.80 - 3.32: 20417 3.32 - 3.85: 39812 3.85 - 4.37: 44770 4.37 - 4.90: 81320 Nonbonded interactions: 193212 Sorted by model distance: nonbonded pdb=" OH TYR A 91 " pdb=" OE2 GLU A 191 " model vdw 2.275 3.040 nonbonded pdb=" OD1 ASP B 568 " pdb=" OG1 THR B 572 " model vdw 2.276 3.040 nonbonded pdb=" OG1 THR C 676 " pdb=" OE1 GLN C 690 " model vdw 2.282 3.040 nonbonded pdb=" OG1 THR C 645 " pdb=" O GLY C 648 " model vdw 2.290 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.294 3.040 ... (remaining 193207 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 27 through 172 or resid 186 through 250 or resid 265 throu \ gh 828 or (resid 850 and (name N or name CA or name C or name O or name CB )) or \ resid 851 through 1308)) selection = (chain 'B' and (resid 27 through 250 or resid 265 through 828 or (resid 850 and \ (name N or name CA or name C or name O or name CB )) or resid 851 through 1308)) \ selection = (chain 'C' and (resid 27 through 250 or resid 265 through 1308)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } 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: 6.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 23.920 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 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 0.091 26052 Z= 0.333 Angle : 0.885 11.970 35586 Z= 0.464 Chirality : 0.059 0.367 4196 Planarity : 0.007 0.115 4497 Dihedral : 14.772 89.088 8965 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 0.51 % Allowed : 8.88 % Favored : 90.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -4.06 (0.12), residues: 3105 helix: -2.87 (0.15), residues: 641 sheet: -1.53 (0.19), residues: 651 loop : -3.22 (0.11), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 102 TYR 0.031 0.002 TYR C 453 PHE 0.049 0.002 PHE B 906 TRP 0.017 0.002 TRP C 886 HIS 0.006 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00790 / 0.33 (25953) covalent geometry : angle 0.85616 / 0.46 (35330) SS BOND : bond 0.00787 / 0.43 ( 41) SS BOND : angle 3.03012 / 1.98 ( 82) hydrogen bonds : bond 0.22789 / 15.00 ( 766) hydrogen bonds : angle 8.65753 / 5.98 ( 2136) link_BETA1-4 : bond 0.00881 / 0.60 ( 16) link_BETA1-4 : angle 1.93850 / 1.20 ( 48) link_NAG-ASN : bond 0.00508 / 0.31 ( 42) link_NAG-ASN : angle 2.88861 / 1.99 ( 126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 229 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 351 TYR cc_start: 0.8261 (p90) cc_final: 0.7806 (p90) REVERT: A 452 LEU cc_start: 0.8429 (tp) cc_final: 0.8144 (tp) REVERT: A 540 ASN cc_start: 0.7949 (m110) cc_final: 0.7702 (m110) REVERT: B 201 PHE cc_start: 0.7841 (t80) cc_final: 0.7611 (t80) REVERT: B 266 TYR cc_start: 0.5569 (m-80) cc_final: 0.5272 (m-80) REVERT: B 282 ASN cc_start: 0.7356 (OUTLIER) cc_final: 0.6990 (p0) REVERT: B 375 SER cc_start: 0.7665 (p) cc_final: 0.7392 (p) REVERT: C 238 PHE cc_start: 0.6192 (p90) cc_final: 0.5562 (p90) outliers start: 14 outliers final: 4 residues processed: 242 average time/residue: 0.1647 time to fit residues: 65.9676 Evaluate side-chains 175 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 170 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain C residue 294 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.5980 chunk 298 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A 81 ASN A 354 ASN A 360 ASN A 613 GLN A 710 ASN A 935 GLN B 81 ASN B 334 ASN B 487 ASN B 519 HIS B 764 ASN B 901 GLN B 957 GLN B 965 GLN C 196 ASN C 321 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 532 ASN C 901 GLN C 935 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.157864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.100503 restraints weight = 39408.802| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.92 r_work: 0.2993 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9005 moved from start: 0.0986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 26052 Z= 0.147 Angle : 0.611 11.693 35586 Z= 0.315 Chirality : 0.045 0.250 4196 Planarity : 0.005 0.095 4497 Dihedral : 5.492 56.596 3379 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 1.31 % Allowed : 11.35 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -3.02 (0.13), residues: 3105 helix: -1.13 (0.19), residues: 628 sheet: -1.10 (0.19), residues: 679 loop : -2.83 (0.12), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 328 TYR 0.021 0.001 TYR A1067 PHE 0.024 0.001 PHE C 92 TRP 0.011 0.001 TRP C 886 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (25953) covalent geometry : angle 0.58875 / 0.31 (35330) SS BOND : bond 0.00426 / 0.25 ( 41) SS BOND : angle 1.76236 / 1.14 ( 82) hydrogen bonds : bond 0.05329 / 3.54 ( 766) hydrogen bonds : angle 6.07701 / 4.17 ( 2136) link_BETA1-4 : bond 0.00401 / 0.25 ( 16) link_BETA1-4 : angle 1.13756 / 0.71 ( 48) link_NAG-ASN : bond 0.00332 / 0.23 ( 42) link_NAG-ASN : angle 2.40166 / 1.57 ( 126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 191 time to evaluate : 0.892 Fit side-chains revert: symmetry clash REVERT: A 141 LEU cc_start: 0.7857 (tp) cc_final: 0.7395 (tp) REVERT: A 351 TYR cc_start: 0.8376 (p90) cc_final: 0.8058 (p90) REVERT: A 452 LEU cc_start: 0.8505 (tp) cc_final: 0.8302 (tp) REVERT: A 508 TYR cc_start: 0.7891 (m-80) cc_final: 0.7630 (m-80) REVERT: A 987 PRO cc_start: 0.9020 (Cg_exo) cc_final: 0.8814 (Cg_endo) REVERT: B 201 PHE cc_start: 0.7847 (t80) cc_final: 0.7595 (t80) REVERT: B 266 TYR cc_start: 0.5936 (m-80) cc_final: 0.5477 (m-80) REVERT: B 338 PHE cc_start: 0.8046 (m-10) cc_final: 0.7515 (m-80) REVERT: B 353 TRP cc_start: 0.7909 (p-90) cc_final: 0.7521 (p-90) REVERT: B 365 TYR cc_start: 0.8305 (m-80) cc_final: 0.7983 (m-80) REVERT: C 238 PHE cc_start: 0.6247 (p90) cc_final: 0.5579 (p90) REVERT: C 867 ASP cc_start: 0.8000 (t0) cc_final: 0.7775 (t0) outliers start: 36 outliers final: 17 residues processed: 219 average time/residue: 0.1590 time to fit residues: 57.8990 Evaluate side-chains 186 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 169 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 441 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 230 optimal weight: 0.7980 chunk 118 optimal weight: 5.9990 chunk 168 optimal weight: 0.9990 chunk 297 optimal weight: 0.3980 chunk 22 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 201 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 236 optimal weight: 0.0370 chunk 93 optimal weight: 0.8980 overall best weight: 0.6260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.159311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.098504 restraints weight = 39542.664| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.89 r_work: 0.3030 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8973 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 26052 Z= 0.109 Angle : 0.544 10.662 35586 Z= 0.279 Chirality : 0.044 0.356 4196 Planarity : 0.005 0.082 4497 Dihedral : 4.931 46.238 3375 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.86 % Allowed : 12.81 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.42 (0.14), residues: 3105 helix: -0.36 (0.21), residues: 629 sheet: -0.73 (0.19), residues: 698 loop : -2.57 (0.12), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 454 TYR 0.019 0.001 TYR A1067 PHE 0.037 0.001 PHE A 562 TRP 0.010 0.001 TRP A 436 HIS 0.003 0.000 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (25953) covalent geometry : angle 0.52779 / 0.28 (35330) SS BOND : bond 0.00384 / 0.23 ( 41) SS BOND : angle 1.52914 / 0.98 ( 82) hydrogen bonds : bond 0.04274 / 2.83 ( 766) hydrogen bonds : angle 5.52495 / 3.76 ( 2136) link_BETA1-4 : bond 0.00361 / 0.22 ( 16) link_BETA1-4 : angle 1.05707 / 0.67 ( 48) link_NAG-ASN : bond 0.00296 / 0.20 ( 42) link_NAG-ASN : angle 1.84822 / 1.25 ( 126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 195 time to evaluate : 0.949 Fit side-chains revert: symmetry clash REVERT: A 137 ASN cc_start: 0.7151 (m-40) cc_final: 0.6284 (t0) REVERT: A 141 LEU cc_start: 0.7815 (tp) cc_final: 0.7370 (tp) REVERT: A 351 TYR cc_start: 0.8360 (p90) cc_final: 0.8017 (p90) REVERT: A 452 LEU cc_start: 0.8567 (tp) cc_final: 0.8325 (tp) REVERT: A 525 CYS cc_start: 0.4856 (OUTLIER) cc_final: 0.4184 (m) REVERT: A 878 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.9094 (tt) REVERT: B 140 PHE cc_start: 0.5317 (p90) cc_final: 0.4889 (p90) REVERT: B 266 TYR cc_start: 0.5801 (m-80) cc_final: 0.5325 (m-80) REVERT: B 353 TRP cc_start: 0.7913 (p-90) cc_final: 0.7622 (p-90) REVERT: B 357 ARG cc_start: 0.7890 (tpp80) cc_final: 0.7454 (tpp80) REVERT: B 365 TYR cc_start: 0.8284 (m-80) cc_final: 0.8024 (m-80) REVERT: B 429 PHE cc_start: 0.7863 (t80) cc_final: 0.7570 (t80) REVERT: B 508 TYR cc_start: 0.8122 (m-80) cc_final: 0.7402 (m-80) REVERT: C 238 PHE cc_start: 0.6234 (p90) cc_final: 0.5852 (p90) REVERT: C 867 ASP cc_start: 0.8102 (t0) cc_final: 0.7875 (t0) outliers start: 51 outliers final: 24 residues processed: 240 average time/residue: 0.1543 time to fit residues: 62.2552 Evaluate side-chains 206 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 180 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 791 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 25 optimal weight: 4.9990 chunk 236 optimal weight: 0.9990 chunk 201 optimal weight: 0.6980 chunk 162 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 228 optimal weight: 9.9990 chunk 83 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 chunk 271 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.158409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.100337 restraints weight = 39320.275| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 3.03 r_work: 0.2999 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9001 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 26052 Z= 0.147 Angle : 0.561 9.492 35586 Z= 0.287 Chirality : 0.045 0.347 4196 Planarity : 0.004 0.062 4497 Dihedral : 4.812 33.297 3375 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.26 % Allowed : 13.32 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.17 (0.14), residues: 3105 helix: -0.00 (0.21), residues: 635 sheet: -0.64 (0.19), residues: 693 loop : -2.44 (0.13), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 34 TYR 0.020 0.001 TYR A1067 PHE 0.026 0.001 PHE C 92 TRP 0.010 0.001 TRP C 886 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 (25953) covalent geometry : angle 0.54387 / 0.28 (35330) SS BOND : bond 0.00383 / 0.23 ( 41) SS BOND : angle 1.85765 / 1.19 ( 82) hydrogen bonds : bond 0.04530 / 2.99 ( 766) hydrogen bonds : angle 5.37295 / 3.65 ( 2136) link_BETA1-4 : bond 0.00332 / 0.20 ( 16) link_BETA1-4 : angle 1.06256 / 0.67 ( 48) link_NAG-ASN : bond 0.00244 / 0.16 ( 42) link_NAG-ASN : angle 1.80568 / 1.22 ( 126) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 186 time to evaluate : 1.025 Fit side-chains revert: symmetry clash REVERT: A 137 ASN cc_start: 0.7170 (m-40) cc_final: 0.6243 (t0) REVERT: A 141 LEU cc_start: 0.7834 (tp) cc_final: 0.7354 (tp) REVERT: A 351 TYR cc_start: 0.8386 (p90) cc_final: 0.7864 (p90) REVERT: A 452 LEU cc_start: 0.8585 (tp) cc_final: 0.8212 (tp) REVERT: A 533 LEU cc_start: 0.5012 (OUTLIER) cc_final: 0.4164 (mp) REVERT: A 878 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9117 (tt) REVERT: B 140 PHE cc_start: 0.5227 (p90) cc_final: 0.4775 (p90) REVERT: B 212 LEU cc_start: 0.3475 (OUTLIER) cc_final: 0.2797 (mm) REVERT: B 266 TYR cc_start: 0.5846 (m-80) cc_final: 0.5358 (m-80) REVERT: B 353 TRP cc_start: 0.7901 (p-90) cc_final: 0.7588 (p-90) REVERT: B 365 TYR cc_start: 0.8309 (m-80) cc_final: 0.8034 (m-80) REVERT: B 429 PHE cc_start: 0.7838 (t80) cc_final: 0.7477 (t80) REVERT: B 508 TYR cc_start: 0.8182 (m-80) cc_final: 0.7335 (m-80) REVERT: C 238 PHE cc_start: 0.6310 (p90) cc_final: 0.5975 (p90) REVERT: C 867 ASP cc_start: 0.8162 (t0) cc_final: 0.7910 (t0) outliers start: 62 outliers final: 38 residues processed: 239 average time/residue: 0.1567 time to fit residues: 63.4751 Evaluate side-chains 220 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 179 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1125 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 4 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 288 optimal weight: 0.6980 chunk 85 optimal weight: 0.9990 chunk 205 optimal weight: 0.8980 chunk 297 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 35 optimal weight: 9.9990 chunk 142 optimal weight: 10.0000 chunk 287 optimal weight: 0.7980 chunk 144 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS B 394 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.157605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.099207 restraints weight = 38439.522| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.75 r_work: 0.2992 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8973 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 26052 Z= 0.123 Angle : 0.533 9.436 35586 Z= 0.272 Chirality : 0.044 0.303 4196 Planarity : 0.004 0.060 4497 Dihedral : 4.618 36.556 3374 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.37 % Allowed : 13.86 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.86 (0.14), residues: 3105 helix: 0.37 (0.21), residues: 635 sheet: -0.41 (0.19), residues: 695 loop : -2.31 (0.13), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 357 TYR 0.019 0.001 TYR A1067 PHE 0.020 0.001 PHE C 92 TRP 0.009 0.001 TRP A 436 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.12 (25953) covalent geometry : angle 0.51687 / 0.27 (35330) SS BOND : bond 0.00440 / 0.26 ( 41) SS BOND : angle 1.71673 / 1.11 ( 82) hydrogen bonds : bond 0.04147 / 2.73 ( 766) hydrogen bonds : angle 5.18271 / 3.52 ( 2136) link_BETA1-4 : bond 0.00340 / 0.21 ( 16) link_BETA1-4 : angle 1.00513 / 0.64 ( 48) link_NAG-ASN : bond 0.00236 / 0.15 ( 42) link_NAG-ASN : angle 1.69847 / 1.14 ( 126) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 197 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 LEU cc_start: 0.7821 (tp) cc_final: 0.7354 (tp) REVERT: A 351 TYR cc_start: 0.8359 (p90) cc_final: 0.7800 (p90) REVERT: A 452 LEU cc_start: 0.8610 (tp) cc_final: 0.8228 (tp) REVERT: A 533 LEU cc_start: 0.5058 (OUTLIER) cc_final: 0.4216 (mp) REVERT: A 878 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.9104 (tt) REVERT: B 140 PHE cc_start: 0.5168 (p90) cc_final: 0.4731 (p90) REVERT: B 212 LEU cc_start: 0.3152 (OUTLIER) cc_final: 0.2584 (mm) REVERT: B 239 GLN cc_start: 0.5400 (tm-30) cc_final: 0.4746 (tm-30) REVERT: B 266 TYR cc_start: 0.5837 (m-80) cc_final: 0.5325 (m-80) REVERT: B 353 TRP cc_start: 0.7843 (p-90) cc_final: 0.7545 (p-90) REVERT: B 357 ARG cc_start: 0.7630 (tpp80) cc_final: 0.7292 (tpp80) REVERT: B 365 TYR cc_start: 0.8309 (m-80) cc_final: 0.8051 (m-80) REVERT: B 508 TYR cc_start: 0.8192 (m-80) cc_final: 0.7184 (m-80) REVERT: B 992 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.7344 (mm-40) REVERT: C 238 PHE cc_start: 0.6314 (p90) cc_final: 0.6004 (p90) REVERT: C 474 GLN cc_start: 0.7147 (pp30) cc_final: 0.6551 (pp30) REVERT: C 505 TYR cc_start: 0.8075 (m-80) cc_final: 0.7827 (m-80) REVERT: C 867 ASP cc_start: 0.8249 (t0) cc_final: 0.8002 (t0) REVERT: C 1138 TYR cc_start: 0.8504 (t80) cc_final: 0.8260 (t80) outliers start: 65 outliers final: 46 residues processed: 251 average time/residue: 0.1529 time to fit residues: 64.5764 Evaluate side-chains 231 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 181 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 992 GLN Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1125 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 221 optimal weight: 9.9990 chunk 40 optimal weight: 8.9990 chunk 200 optimal weight: 1.9990 chunk 180 optimal weight: 8.9990 chunk 30 optimal weight: 0.9990 chunk 257 optimal weight: 0.7980 chunk 122 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 298 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 901 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.156549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.099615 restraints weight = 38683.333| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.81 r_work: 0.2965 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8992 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 26052 Z= 0.164 Angle : 0.560 9.479 35586 Z= 0.285 Chirality : 0.045 0.259 4196 Planarity : 0.004 0.062 4497 Dihedral : 4.667 34.845 3374 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.69 % Allowed : 13.86 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.81 (0.14), residues: 3105 helix: 0.42 (0.21), residues: 638 sheet: -0.44 (0.19), residues: 693 loop : -2.24 (0.13), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 357 TYR 0.020 0.001 TYR A1067 PHE 0.019 0.001 PHE B 318 TRP 0.011 0.001 TRP C 886 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.16 (25953) covalent geometry : angle 0.54390 / 0.28 (35330) SS BOND : bond 0.00433 / 0.26 ( 41) SS BOND : angle 1.78594 / 1.14 ( 82) hydrogen bonds : bond 0.04650 / 3.06 ( 766) hydrogen bonds : angle 5.22775 / 3.55 ( 2136) link_BETA1-4 : bond 0.00325 / 0.20 ( 16) link_BETA1-4 : angle 1.05168 / 0.66 ( 48) link_NAG-ASN : bond 0.00236 / 0.15 ( 42) link_NAG-ASN : angle 1.76036 / 1.19 ( 126) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 189 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 249 LEU cc_start: 0.5401 (OUTLIER) cc_final: 0.4890 (mp) REVERT: A 351 TYR cc_start: 0.8348 (p90) cc_final: 0.7802 (p90) REVERT: A 452 LEU cc_start: 0.8632 (tp) cc_final: 0.8254 (tp) REVERT: A 533 LEU cc_start: 0.5106 (OUTLIER) cc_final: 0.4279 (mp) REVERT: A 878 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9127 (tt) REVERT: B 140 PHE cc_start: 0.5045 (p90) cc_final: 0.4630 (p90) REVERT: B 212 LEU cc_start: 0.3224 (OUTLIER) cc_final: 0.2666 (mm) REVERT: B 266 TYR cc_start: 0.5839 (m-80) cc_final: 0.5335 (m-80) REVERT: B 353 TRP cc_start: 0.7900 (p-90) cc_final: 0.7602 (p-90) REVERT: B 365 TYR cc_start: 0.8337 (m-80) cc_final: 0.8055 (m-80) REVERT: B 508 TYR cc_start: 0.8241 (m-80) cc_final: 0.7217 (m-80) REVERT: C 238 PHE cc_start: 0.6305 (p90) cc_final: 0.6028 (p90) REVERT: C 474 GLN cc_start: 0.7161 (pp30) cc_final: 0.6554 (pp30) REVERT: C 505 TYR cc_start: 0.8067 (m-80) cc_final: 0.7840 (m-80) REVERT: C 697 MET cc_start: 0.9119 (ptm) cc_final: 0.8879 (ptm) REVERT: C 867 ASP cc_start: 0.8304 (t0) cc_final: 0.8069 (t0) REVERT: C 1138 TYR cc_start: 0.8526 (t80) cc_final: 0.8296 (t80) outliers start: 74 outliers final: 55 residues processed: 252 average time/residue: 0.1503 time to fit residues: 63.7148 Evaluate side-chains 241 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 182 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1125 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 268 optimal weight: 0.5980 chunk 101 optimal weight: 1.9990 chunk 140 optimal weight: 0.9990 chunk 276 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 89 optimal weight: 0.0570 chunk 249 optimal weight: 10.0000 chunk 149 optimal weight: 10.0000 chunk 92 optimal weight: 0.8980 chunk 222 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.9102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 354 ASN B 563 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.157537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.101268 restraints weight = 38567.335| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.78 r_work: 0.2988 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8972 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 26052 Z= 0.124 Angle : 0.532 9.415 35586 Z= 0.272 Chirality : 0.044 0.240 4196 Planarity : 0.004 0.061 4497 Dihedral : 4.518 34.665 3374 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.55 % Allowed : 14.52 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.61 (0.14), residues: 3105 helix: 0.67 (0.22), residues: 635 sheet: -0.33 (0.19), residues: 690 loop : -2.14 (0.13), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 357 TYR 0.019 0.001 TYR A1067 PHE 0.020 0.001 PHE C 92 TRP 0.010 0.001 TRP A 436 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.12 (25953) covalent geometry : angle 0.51755 / 0.27 (35330) SS BOND : bond 0.00399 / 0.24 ( 41) SS BOND : angle 1.57726 / 1.00 ( 82) hydrogen bonds : bond 0.04113 / 2.71 ( 766) hydrogen bonds : angle 5.09713 / 3.47 ( 2136) link_BETA1-4 : bond 0.00346 / 0.22 ( 16) link_BETA1-4 : angle 0.99360 / 0.63 ( 48) link_NAG-ASN : bond 0.00221 / 0.14 ( 42) link_NAG-ASN : angle 1.66272 / 1.12 ( 126) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 192 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 LEU cc_start: 0.5405 (OUTLIER) cc_final: 0.4901 (mp) REVERT: A 351 TYR cc_start: 0.8332 (p90) cc_final: 0.7738 (p90) REVERT: A 452 LEU cc_start: 0.8614 (tp) cc_final: 0.8204 (tp) REVERT: A 533 LEU cc_start: 0.5146 (OUTLIER) cc_final: 0.4359 (mp) REVERT: A 878 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.9123 (tt) REVERT: B 140 PHE cc_start: 0.5009 (p90) cc_final: 0.4632 (p90) REVERT: B 212 LEU cc_start: 0.3017 (OUTLIER) cc_final: 0.2550 (mm) REVERT: B 266 TYR cc_start: 0.5872 (m-80) cc_final: 0.5356 (m-80) REVERT: B 353 TRP cc_start: 0.7849 (p-90) cc_final: 0.7572 (p-90) REVERT: B 355 ARG cc_start: 0.7643 (tpp-160) cc_final: 0.7336 (tpp-160) REVERT: B 365 TYR cc_start: 0.8335 (m-80) cc_final: 0.8072 (m-80) REVERT: B 429 PHE cc_start: 0.7692 (t80) cc_final: 0.7455 (t80) REVERT: B 508 TYR cc_start: 0.8251 (m-10) cc_final: 0.7271 (m-80) REVERT: B 992 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.7413 (mm-40) REVERT: C 128 ILE cc_start: 0.7120 (OUTLIER) cc_final: 0.6908 (tp) REVERT: C 237 ARG cc_start: 0.6891 (mmt180) cc_final: 0.6426 (ptm-80) REVERT: C 474 GLN cc_start: 0.7202 (pp30) cc_final: 0.6598 (pp30) REVERT: C 505 TYR cc_start: 0.7952 (m-80) cc_final: 0.7740 (m-80) REVERT: C 697 MET cc_start: 0.9129 (ptm) cc_final: 0.8909 (ptm) REVERT: C 1138 TYR cc_start: 0.8499 (t80) cc_final: 0.8255 (t80) outliers start: 70 outliers final: 53 residues processed: 252 average time/residue: 0.1576 time to fit residues: 66.1541 Evaluate side-chains 242 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 183 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 992 GLN Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1125 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 165 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 194 optimal weight: 3.9990 chunk 136 optimal weight: 0.6980 chunk 90 optimal weight: 0.5980 chunk 102 optimal weight: 0.7980 chunk 15 optimal weight: 6.9990 chunk 310 optimal weight: 0.9990 chunk 289 optimal weight: 0.9990 chunk 282 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.158062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.101526 restraints weight = 38569.996| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.78 r_work: 0.2995 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8963 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 26052 Z= 0.113 Angle : 0.527 12.716 35586 Z= 0.268 Chirality : 0.044 0.243 4196 Planarity : 0.004 0.062 4497 Dihedral : 4.400 34.579 3374 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.58 % Allowed : 14.52 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.44 (0.15), residues: 3105 helix: 0.83 (0.22), residues: 632 sheet: -0.19 (0.19), residues: 677 loop : -2.04 (0.13), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 357 TYR 0.019 0.001 TYR A1067 PHE 0.022 0.001 PHE C 92 TRP 0.009 0.001 TRP C 64 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.11 (25953) covalent geometry : angle 0.51407 / 0.26 (35330) SS BOND : bond 0.00411 / 0.24 ( 41) SS BOND : angle 1.49495 / 0.96 ( 82) hydrogen bonds : bond 0.03920 / 2.58 ( 766) hydrogen bonds : angle 5.01760 / 3.41 ( 2136) link_BETA1-4 : bond 0.00333 / 0.20 ( 16) link_BETA1-4 : angle 0.98011 / 0.62 ( 48) link_NAG-ASN : bond 0.00215 / 0.14 ( 42) link_NAG-ASN : angle 1.60662 / 1.08 ( 126) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 196 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 LEU cc_start: 0.5407 (OUTLIER) cc_final: 0.4927 (mp) REVERT: A 508 TYR cc_start: 0.7914 (m-80) cc_final: 0.7605 (m-80) REVERT: A 533 LEU cc_start: 0.5104 (OUTLIER) cc_final: 0.4328 (mp) REVERT: A 878 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.9120 (tt) REVERT: B 140 PHE cc_start: 0.4935 (p90) cc_final: 0.4561 (p90) REVERT: B 212 LEU cc_start: 0.2943 (OUTLIER) cc_final: 0.2555 (mm) REVERT: B 266 TYR cc_start: 0.5901 (m-80) cc_final: 0.5376 (m-80) REVERT: B 353 TRP cc_start: 0.7804 (p-90) cc_final: 0.7542 (p-90) REVERT: B 355 ARG cc_start: 0.7652 (tpp-160) cc_final: 0.7332 (tpp-160) REVERT: B 365 TYR cc_start: 0.8337 (m-80) cc_final: 0.8088 (m-80) REVERT: B 429 PHE cc_start: 0.7739 (t80) cc_final: 0.7463 (t80) REVERT: B 434 ILE cc_start: 0.8249 (OUTLIER) cc_final: 0.8040 (mm) REVERT: B 508 TYR cc_start: 0.8250 (m-10) cc_final: 0.7277 (m-80) REVERT: B 992 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.7347 (mm-40) REVERT: C 47 VAL cc_start: 0.7606 (OUTLIER) cc_final: 0.7316 (m) REVERT: C 128 ILE cc_start: 0.7059 (OUTLIER) cc_final: 0.6832 (tp) REVERT: C 237 ARG cc_start: 0.6904 (mmt180) cc_final: 0.6427 (ptm-80) REVERT: C 324 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7199 (pm20) REVERT: C 474 GLN cc_start: 0.7181 (pp30) cc_final: 0.6581 (pp30) REVERT: C 697 MET cc_start: 0.9125 (ptm) cc_final: 0.8918 (ptm) REVERT: C 867 ASP cc_start: 0.8242 (t0) cc_final: 0.8009 (t0) outliers start: 71 outliers final: 54 residues processed: 256 average time/residue: 0.1526 time to fit residues: 65.5691 Evaluate side-chains 246 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 183 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 992 GLN Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1125 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 274 optimal weight: 2.9990 chunk 140 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 chunk 266 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 147 optimal weight: 0.7980 chunk 145 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 271 optimal weight: 3.9990 chunk 71 optimal weight: 0.1980 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 354 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.158604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.100220 restraints weight = 39031.515| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.84 r_work: 0.3000 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8970 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 26052 Z= 0.117 Angle : 0.558 19.700 35586 Z= 0.280 Chirality : 0.045 0.290 4196 Planarity : 0.004 0.061 4497 Dihedral : 4.425 37.753 3374 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.40 % Allowed : 14.96 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.36 (0.15), residues: 3105 helix: 0.93 (0.22), residues: 633 sheet: -0.13 (0.19), residues: 677 loop : -2.00 (0.13), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 355 TYR 0.019 0.001 TYR A1067 PHE 0.024 0.001 PHE C 92 TRP 0.008 0.001 TRP A 436 HIS 0.003 0.000 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (25953) covalent geometry : angle 0.54056 / 0.27 (35330) SS BOND : bond 0.00458 / 0.29 ( 41) SS BOND : angle 2.16962 / 1.58 ( 82) hydrogen bonds : bond 0.03928 / 2.59 ( 766) hydrogen bonds : angle 4.98177 / 3.39 ( 2136) link_BETA1-4 : bond 0.00338 / 0.21 ( 16) link_BETA1-4 : angle 0.97547 / 0.62 ( 48) link_NAG-ASN : bond 0.00211 / 0.14 ( 42) link_NAG-ASN : angle 1.58913 / 1.07 ( 126) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 187 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 LEU cc_start: 0.5404 (OUTLIER) cc_final: 0.4926 (mp) REVERT: A 351 TYR cc_start: 0.8125 (p90) cc_final: 0.7604 (p90) REVERT: A 533 LEU cc_start: 0.4992 (OUTLIER) cc_final: 0.4255 (mp) REVERT: A 878 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.9102 (tt) REVERT: B 140 PHE cc_start: 0.4916 (p90) cc_final: 0.4547 (p90) REVERT: B 212 LEU cc_start: 0.2939 (OUTLIER) cc_final: 0.2559 (mm) REVERT: B 266 TYR cc_start: 0.5922 (m-80) cc_final: 0.5372 (m-80) REVERT: B 353 TRP cc_start: 0.7821 (p-90) cc_final: 0.7555 (p-90) REVERT: B 355 ARG cc_start: 0.7644 (tpp-160) cc_final: 0.7317 (tpp-160) REVERT: B 365 TYR cc_start: 0.8343 (m-80) cc_final: 0.8037 (m-80) REVERT: B 429 PHE cc_start: 0.7714 (t80) cc_final: 0.7417 (t80) REVERT: B 434 ILE cc_start: 0.8271 (OUTLIER) cc_final: 0.8054 (mm) REVERT: B 508 TYR cc_start: 0.8244 (m-10) cc_final: 0.7273 (m-80) REVERT: B 992 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.7380 (mm-40) REVERT: C 47 VAL cc_start: 0.7597 (OUTLIER) cc_final: 0.7306 (m) REVERT: C 128 ILE cc_start: 0.7014 (OUTLIER) cc_final: 0.6782 (tp) REVERT: C 237 ARG cc_start: 0.6923 (mmt180) cc_final: 0.6415 (ptm-80) REVERT: C 324 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7213 (pm20) REVERT: C 474 GLN cc_start: 0.7186 (pp30) cc_final: 0.6580 (pp30) REVERT: C 697 MET cc_start: 0.9108 (ptm) cc_final: 0.8908 (ptm) outliers start: 66 outliers final: 56 residues processed: 242 average time/residue: 0.1555 time to fit residues: 63.0257 Evaluate side-chains 249 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 184 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 992 GLN Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1125 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 17 optimal weight: 1.9990 chunk 239 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 170 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 203 optimal weight: 0.8980 chunk 206 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 308 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 163 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 354 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 493 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.158697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.099392 restraints weight = 39046.509| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.93 r_work: 0.2994 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8975 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 26052 Z= 0.116 Angle : 0.551 15.728 35586 Z= 0.278 Chirality : 0.045 0.243 4196 Planarity : 0.004 0.061 4497 Dihedral : 4.389 39.161 3374 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.44 % Allowed : 15.03 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.31 (0.15), residues: 3105 helix: 0.98 (0.22), residues: 639 sheet: -0.10 (0.19), residues: 680 loop : -1.99 (0.13), residues: 1786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 765 TYR 0.043 0.001 TYR C 453 PHE 0.025 0.001 PHE C 92 TRP 0.008 0.001 TRP A 886 HIS 0.003 0.000 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (25953) covalent geometry : angle 0.53549 / 0.27 (35330) SS BOND : bond 0.00415 / 0.25 ( 41) SS BOND : angle 1.97719 / 1.40 ( 82) hydrogen bonds : bond 0.03910 / 2.57 ( 766) hydrogen bonds : angle 4.96816 / 3.37 ( 2136) link_BETA1-4 : bond 0.00343 / 0.21 ( 16) link_BETA1-4 : angle 0.97412 / 0.62 ( 48) link_NAG-ASN : bond 0.00211 / 0.14 ( 42) link_NAG-ASN : angle 1.57022 / 1.06 ( 126) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 191 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 LEU cc_start: 0.5417 (OUTLIER) cc_final: 0.4937 (mp) REVERT: A 351 TYR cc_start: 0.8135 (p90) cc_final: 0.7626 (p90) REVERT: A 533 LEU cc_start: 0.4967 (OUTLIER) cc_final: 0.4367 (mp) REVERT: A 585 LEU cc_start: 0.7696 (mt) cc_final: 0.7430 (mt) REVERT: A 592 PHE cc_start: 0.7239 (t80) cc_final: 0.6671 (t80) REVERT: A 878 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9103 (tt) REVERT: A 988 GLU cc_start: 0.8846 (pm20) cc_final: 0.8340 (pm20) REVERT: B 140 PHE cc_start: 0.4912 (p90) cc_final: 0.4550 (p90) REVERT: B 212 LEU cc_start: 0.2911 (OUTLIER) cc_final: 0.2573 (mm) REVERT: B 266 TYR cc_start: 0.5924 (m-80) cc_final: 0.5340 (m-80) REVERT: B 353 TRP cc_start: 0.7827 (p-90) cc_final: 0.7577 (p-90) REVERT: B 355 ARG cc_start: 0.7635 (tpp-160) cc_final: 0.7289 (tpp-160) REVERT: B 365 TYR cc_start: 0.8365 (m-80) cc_final: 0.8051 (m-80) REVERT: B 429 PHE cc_start: 0.7701 (t80) cc_final: 0.7394 (t80) REVERT: B 434 ILE cc_start: 0.8276 (OUTLIER) cc_final: 0.8056 (mm) REVERT: B 508 TYR cc_start: 0.8234 (m-10) cc_final: 0.7324 (m-80) REVERT: B 516 GLU cc_start: 0.7942 (pm20) cc_final: 0.7652 (pm20) REVERT: B 992 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.7395 (mm-40) REVERT: C 47 VAL cc_start: 0.7598 (OUTLIER) cc_final: 0.7297 (m) REVERT: C 128 ILE cc_start: 0.7030 (OUTLIER) cc_final: 0.6792 (tp) REVERT: C 324 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7200 (pm20) REVERT: C 474 GLN cc_start: 0.7220 (pp30) cc_final: 0.6610 (pp30) REVERT: C 493 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7713 (mm110) REVERT: C 867 ASP cc_start: 0.8272 (t0) cc_final: 0.8037 (t0) outliers start: 67 outliers final: 55 residues processed: 246 average time/residue: 0.1581 time to fit residues: 64.9739 Evaluate side-chains 249 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 184 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 992 GLN Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1125 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 149 optimal weight: 0.5980 chunk 108 optimal weight: 0.2980 chunk 96 optimal weight: 1.9990 chunk 27 optimal weight: 10.0000 chunk 16 optimal weight: 0.8980 chunk 142 optimal weight: 8.9990 chunk 204 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 236 optimal weight: 0.0970 chunk 83 optimal weight: 2.9990 chunk 266 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 354 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 493 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.158704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.099402 restraints weight = 39004.064| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.90 r_work: 0.2994 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8972 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.218 26052 Z= 0.168 Angle : 0.679 59.182 35586 Z= 0.372 Chirality : 0.046 0.778 4196 Planarity : 0.004 0.061 4497 Dihedral : 4.392 39.260 3374 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.40 % Allowed : 15.21 % Favored : 82.39 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.31 (0.15), residues: 3105 helix: 0.98 (0.22), residues: 639 sheet: -0.10 (0.19), residues: 680 loop : -1.99 (0.13), residues: 1786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 765 TYR 0.037 0.001 TYR C 453 PHE 0.023 0.001 PHE C 92 TRP 0.007 0.001 TRP C 886 HIS 0.003 0.000 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 (25953) covalent geometry : angle 0.66527 / 0.37 (35330) SS BOND : bond 0.00413 / 0.25 ( 41) SS BOND : angle 2.27731 / 1.74 ( 82) hydrogen bonds : bond 0.03946 / 2.62 ( 766) hydrogen bonds : angle 4.97006 / 3.38 ( 2136) link_BETA1-4 : bond 0.00317 / 0.19 ( 16) link_BETA1-4 : angle 0.98391 / 0.62 ( 48) link_NAG-ASN : bond 0.00210 / 0.14 ( 42) link_NAG-ASN : angle 1.57031 / 1.06 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8750.36 seconds wall clock time: 149 minutes 53.81 seconds (8993.81 seconds total)