Starting phenix.real_space_refine on Thu Mar 5 22:50:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jwy_22515/03_2026/7jwy_22515.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jwy_22515/03_2026/7jwy_22515.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7jwy_22515/03_2026/7jwy_22515.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jwy_22515/03_2026/7jwy_22515.map" model { file = "/net/cci-nas-00/data/ceres_data/7jwy_22515/03_2026/7jwy_22515.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jwy_22515/03_2026/7jwy_22515.cif" } resolution = 2.5 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 111 5.16 5 C 16366 2.51 5 N 4200 2.21 5 O 5183 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 115 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25860 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 8267 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1057, 8262 Classifications: {'peptide': 1057} Link IDs: {'PTRANS': 51, 'TRANS': 1005} Chain breaks: 7 Conformer: "B" Number of residues, atoms: 1057, 8262 Classifications: {'peptide': 1057} Link IDs: {'PTRANS': 51, 'TRANS': 1005} Chain breaks: 7 bond proxies already assigned to first conformer: 8442 Chain: "B" Number of atoms: 8293 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1061, 8288 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 52, 'TRANS': 1008} Chain breaks: 6 Conformer: "B" Number of residues, atoms: 1061, 8288 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 52, 'TRANS': 1008} Chain breaks: 6 bond proxies already assigned to first conformer: 8471 Chain: "C" Number of atoms: 8285 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1060, 8280 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 52, 'TRANS': 1007} Chain breaks: 7 Conformer: "B" Number of residues, atoms: 1060, 8280 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 52, 'TRANS': 1007} Chain breaks: 7 bond proxies already assigned to first conformer: 8462 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" 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 dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Time building chain proxies: 9.58, per 1000 atoms: 0.37 Number of scatterers: 25860 At special positions: 0 Unit cell: (139.68, 130.077, 178.965, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 111 16.00 O 5183 8.00 N 4200 7.00 C 16366 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.06 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=2.02 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=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.05 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.05 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.07 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.05 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=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.06 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=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.06 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 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=2.05 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 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 T 1 " - " NAG T 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG A1311 " - " ASN A 165 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 343 " " NAG C1306 " - " ASN C 603 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C 709 " " NAG C1310 " - " ASN C 165 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN A1134 " " NAG I 1 " - " ASN B 234 " " NAG J 1 " - " ASN B 717 " " NAG K 1 " - " ASN B 801 " " NAG L 1 " - " ASN B1074 " " NAG M 1 " - " ASN B1098 " " NAG N 1 " - " ASN B1134 " " NAG O 1 " - " ASN C 234 " " NAG P 1 " - " ASN C 717 " " NAG Q 1 " - " ASN C 801 " " NAG R 1 " - " ASN C1074 " " NAG S 1 " - " ASN C1098 " " NAG T 1 " - " ASN C1134 " Time building additional restraints: 1.72 Conformation dependent library (CDL) restraints added in 1.8 seconds 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5968 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 47 sheets defined 24.8% alpha, 25.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.159A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.547A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.553A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN A 409 " --> pdb=" O GLU A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 625 through 629 removed outlier: 3.661A pdb=" N LEU A 629 " --> pdb=" O ALA A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 637 removed outlier: 3.555A pdb=" N SER A 637 " --> pdb=" O ARG A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.811A 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: 3.942A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 848 through 855 removed outlier: 4.180A pdb=" N ALA A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.125A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.009A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.840A pdb=" N ARG A 983 " --> pdb=" O ASP A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.541A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.502A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.647A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 629 Processing helix chain 'B' and resid 633 through 637 removed outlier: 3.624A pdb=" N SER B 637 " --> pdb=" O ARG B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.773A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.957A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 848 through 855 removed outlier: 4.097A pdb=" N ALA B 852 " --> pdb=" O ASP B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.167A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.953A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.730A pdb=" N ARG B 983 " --> pdb=" O ASP B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.545A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.170A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 616 through 618 No H-bonds generated for 'chain 'C' and resid 616 through 618' Processing helix chain 'C' and resid 619 through 624 Processing helix chain 'C' and resid 630 through 634 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.681A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.930A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 848 through 855 removed outlier: 3.665A pdb=" N ALA C 852 " --> pdb=" O ASP C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.505A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.150A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.960A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.711A pdb=" N ARG C 983 " --> pdb=" O ASP C 979 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.732A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.835A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.021A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.331A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.321A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.219A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN A 613 " --> pdb=" O GLY A 594 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 325 removed outlier: 6.806A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.184A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.184A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 660 removed outlier: 5.441A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.624A 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 703 removed outlier: 6.834A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (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 715 removed outlier: 3.697A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.535A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.619A 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 789 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.432A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.083A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.547A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 13.461A pdb=" N PHE B 238 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 12.647A pdb=" N ASN B 137 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 9.688A pdb=" N THR B 240 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N LEU B 242 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 11.565A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 10.720A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.559A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.193A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 324 through 325 removed outlier: 6.816A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.117A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.117A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 542 through 543 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.643A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 701 through 703 removed outlier: 6.849A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.701A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.582A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.703A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD6, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.397A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 9.015A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.237A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.579A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 135 through 141 removed outlier: 7.380A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 11.478A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 10.671A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.294A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.134A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.134A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 538 through 539 removed outlier: 5.181A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 542 through 543 Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.583A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.678A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.694A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.600A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1120 through 1122 978 hydrogen bonds defined for protein. 2678 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: 6.38 Time building geometry restraints manager: 2.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 8120 1.34 - 1.48: 7503 1.48 - 1.62: 10549 1.62 - 1.76: 16 1.76 - 1.91: 119 Bond restraints: 26307 Sorted by residual: bond pdb=" CG LEU C 916 " pdb=" CD1 LEU C 916 " ideal model delta sigma weight residual 1.521 1.350 0.171 3.30e-02 9.18e+02 2.70e+01 bond pdb=" C VAL B 620 " pdb=" N PRO B 621 " ideal model delta sigma weight residual 1.337 1.393 -0.057 1.11e-02 8.12e+03 2.60e+01 bond pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " ideal model delta sigma weight residual 1.808 1.648 0.160 3.30e-02 9.18e+02 2.34e+01 bond pdb=" CG LEU A 916 " pdb=" CD1 LEU A 916 " ideal model delta sigma weight residual 1.521 1.394 0.127 3.30e-02 9.18e+02 1.49e+01 bond pdb=" CG LEU B 916 " pdb=" CD1 LEU B 916 " ideal model delta sigma weight residual 1.521 1.397 0.124 3.30e-02 9.18e+02 1.42e+01 ... (remaining 26302 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.68: 35289 3.68 - 7.37: 462 7.37 - 11.05: 48 11.05 - 14.74: 3 14.74 - 18.42: 5 Bond angle restraints: 35807 Sorted by residual: angle pdb=" C ASP B 215 " pdb=" N LEU B 216 " pdb=" CA LEU B 216 " ideal model delta sigma weight residual 120.39 132.63 -12.24 1.39e+00 5.18e-01 7.75e+01 angle pdb=" CA CYS C 166 " pdb=" CB CYS C 166 " pdb=" SG CYS C 166 " ideal model delta sigma weight residual 114.40 132.82 -18.42 2.30e+00 1.89e-01 6.42e+01 angle pdb=" CA CYS B 525 " pdb=" CB CYS B 525 " pdb=" SG CYS B 525 " ideal model delta sigma weight residual 114.40 131.64 -17.24 2.30e+00 1.89e-01 5.62e+01 angle pdb=" C SER B 31 " pdb=" N PHE B 32 " pdb=" CA PHE B 32 " ideal model delta sigma weight residual 121.54 135.28 -13.74 1.91e+00 2.74e-01 5.18e+01 angle pdb=" CA CYS A 525 " pdb=" CB CYS A 525 " pdb=" SG CYS A 525 " ideal model delta sigma weight residual 114.40 130.43 -16.03 2.30e+00 1.89e-01 4.86e+01 ... (remaining 35802 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 14954 17.57 - 35.14: 1259 35.14 - 52.70: 212 52.70 - 70.27: 59 70.27 - 87.84: 31 Dihedral angle restraints: 16515 sinusoidal: 7245 harmonic: 9270 Sorted by residual: dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 23.36 69.64 1 1.00e+01 1.00e-02 6.26e+01 dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual -86.00 -149.42 63.42 1 1.00e+01 1.00e-02 5.30e+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 -147.90 61.90 1 1.00e+01 1.00e-02 5.08e+01 ... (remaining 16512 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 3090 0.077 - 0.153: 1029 0.153 - 0.230: 117 0.230 - 0.307: 13 0.307 - 0.384: 12 Chirality restraints: 4261 Sorted by residual: chirality pdb=" C1 NAG A1304 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG A1304 " pdb=" O5 NAG A1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.68e+00 chirality pdb=" C2 NAG A1311 " pdb=" C1 NAG A1311 " pdb=" C3 NAG A1311 " pdb=" N2 NAG A1311 " both_signs ideal model delta sigma weight residual False -2.49 -2.11 -0.38 2.00e-01 2.50e+01 3.66e+00 chirality pdb=" C1 NAG B1301 " pdb=" ND2 ASN B 61 " pdb=" C2 NAG B1301 " pdb=" O5 NAG B1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.12e+00 ... (remaining 4258 not shown) Planarity restraints: 4601 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 886 " -0.030 2.00e-02 2.50e+03 2.63e-02 1.72e+01 pdb=" CG TRP A 886 " 0.065 2.00e-02 2.50e+03 pdb=" CD1 TRP A 886 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 TRP A 886 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 886 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP A 886 " 0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP A 886 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 886 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 886 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 886 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 886 " -0.027 2.00e-02 2.50e+03 2.58e-02 1.66e+01 pdb=" CG TRP C 886 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP C 886 " -0.038 2.00e-02 2.50e+03 pdb=" CD2 TRP C 886 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 886 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP C 886 " 0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP C 886 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 886 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 886 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 886 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 886 " 0.030 2.00e-02 2.50e+03 2.51e-02 1.58e+01 pdb=" CG TRP B 886 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 TRP B 886 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 TRP B 886 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 886 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP B 886 " -0.009 2.00e-02 2.50e+03 pdb=" CE3 TRP B 886 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 886 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 886 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 886 " 0.018 2.00e-02 2.50e+03 ... (remaining 4598 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4938 2.78 - 3.31: 20928 3.31 - 3.84: 41292 3.84 - 4.37: 48725 4.37 - 4.90: 84365 Nonbonded interactions: 200248 Sorted by model distance: nonbonded pdb=" OG SER A 469 " pdb=" O LYS B 113 " model vdw 2.248 3.040 nonbonded pdb=" OE2 GLU B1017 " pdb=" O HOH B1401 " model vdw 2.254 3.040 nonbonded pdb=" OG1 THR A 599 " pdb=" O PRO A 600 " model vdw 2.261 3.040 nonbonded pdb=" OG1 THR C 599 " pdb=" O PRO C 600 " model vdw 2.275 3.040 nonbonded pdb=" OD1 ASP C 294 " pdb=" OG SER C 297 " model vdw 2.284 3.040 ... (remaining 200243 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 954 or resid 956 through 1309)) selection = (chain 'B' and (resid 27 through 250 or resid 265 through 828 or resid 834 throu \ gh 954 or resid 956 through 1309)) selection = (chain 'C' and (resid 27 through 250 or resid 265 through 828 or resid 834 throu \ gh 954 or resid 956 through 1309)) } 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' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 7.350 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: 0.320 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 29.510 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.080 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:8.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 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 : 0.011 0.171 26413 Z= 0.487 Angle : 1.249 18.456 36083 Z= 0.685 Chirality : 0.073 0.384 4261 Planarity : 0.008 0.072 4554 Dihedral : 13.664 87.839 10421 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 0.11 % Allowed : 3.28 % Favored : 96.62 % 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: -2.72 (0.12), residues: 3135 helix: -1.38 (0.17), residues: 722 sheet: -0.50 (0.20), residues: 637 loop : -2.60 (0.11), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 328 TYR 0.023 0.004 TYR C 369 PHE 0.038 0.004 PHE B 238 TRP 0.065 0.006 TRP A 886 HIS 0.011 0.002 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.01137 (26307) covalent geometry : angle 1.19910 (35807) SS BOND : bond 0.01279 ( 42) SS BOND : angle 3.81092 ( 84) hydrogen bonds : bond 0.21377 ( 959) hydrogen bonds : angle 7.33309 ( 2678) link_BETA1-4 : bond 0.01134 ( 17) link_BETA1-4 : angle 3.17314 ( 51) link_NAG-ASN : bond 0.00805 ( 47) link_NAG-ASN : angle 4.64447 ( 141) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 276 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 614 ASP cc_start: 0.7181 (p0) cc_final: 0.6966 (p0) REVERT: B 985 ASP cc_start: 0.6743 (p0) cc_final: 0.6424 (p0) REVERT: C 904 TYR cc_start: 0.7328 (p90) cc_final: 0.6941 (p90) outliers start: 3 outliers final: 0 residues processed: 279 average time/residue: 0.6862 time to fit residues: 221.4858 Evaluate side-chains 204 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 211 ASN A 218 GLN A 370 ASN A 414 GLN A 501 ASN A 779 GLN A 901 GLN A1002 GLN A1113 GLN B 99 ASN B 519 HIS B 901 GLN B1113 GLN C 52 GLN C 81 ASN C 99 ASN C 121 ASN C 188 ASN C 218 GLN C 440 ASN C 501 ASN C 779 GLN C 901 GLN C1005 GLN C1113 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.199707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.151508 restraints weight = 34869.530| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 2.20 r_work: 0.3152 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3122 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3122 r_free = 0.3122 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3122 r_free = 0.3122 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3122 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 26413 Z= 0.158 Angle : 0.732 15.406 36083 Z= 0.381 Chirality : 0.048 0.219 4261 Planarity : 0.005 0.064 4554 Dihedral : 7.571 59.676 4754 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.04 % Allowed : 7.45 % Favored : 91.50 % 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: -1.43 (0.14), residues: 3135 helix: 0.48 (0.20), residues: 725 sheet: 0.17 (0.20), residues: 652 loop : -2.13 (0.12), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 319 TYR 0.030 0.002 TYR C 904 PHE 0.029 0.001 PHE A 32 TRP 0.033 0.002 TRP B 886 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00346 (26307) covalent geometry : angle 0.68105 (35807) SS BOND : bond 0.00773 ( 42) SS BOND : angle 2.55567 ( 84) hydrogen bonds : bond 0.07747 ( 959) hydrogen bonds : angle 5.80786 ( 2678) link_BETA1-4 : bond 0.00481 ( 17) link_BETA1-4 : angle 1.71558 ( 51) link_NAG-ASN : bond 0.00417 ( 47) link_NAG-ASN : angle 3.79323 ( 141) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 229 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 613 GLN cc_start: 0.7847 (OUTLIER) cc_final: 0.7618 (mp10) REVERT: A 614 ASP cc_start: 0.7712 (p0) cc_final: 0.7429 (p0) REVERT: A 921 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.8104 (mppt) REVERT: B 453 TYR cc_start: 0.7949 (p90) cc_final: 0.7715 (p90) REVERT: B 776 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8504 (tmtm) REVERT: B 834 ILE cc_start: 0.1078 (OUTLIER) cc_final: 0.0821 (mm) REVERT: C 586 ASP cc_start: 0.6986 (m-30) cc_final: 0.6743 (m-30) REVERT: C 603 ASN cc_start: 0.8185 (m110) cc_final: 0.7389 (t0) REVERT: C 614 ASP cc_start: 0.7509 (p0) cc_final: 0.7231 (p0) REVERT: C 904 TYR cc_start: 0.7801 (p90) cc_final: 0.7367 (p90) outliers start: 29 outliers final: 12 residues processed: 249 average time/residue: 0.5554 time to fit residues: 163.6430 Evaluate side-chains 221 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 205 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 808 ASP Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 204 optimal weight: 2.9990 chunk 316 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 142 optimal weight: 9.9990 chunk 153 optimal weight: 1.9990 chunk 180 optimal weight: 9.9990 chunk 235 optimal weight: 0.4980 chunk 118 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 chunk 56 optimal weight: 7.9990 chunk 303 optimal weight: 1.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN A1101 HIS A1135 ASN B 99 ASN C 99 ASN C 121 ASN C 218 GLN C 779 GLN C1135 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.197855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.149207 restraints weight = 32629.902| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 2.11 r_work: 0.3123 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2904 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2904 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 26413 Z= 0.222 Angle : 0.790 12.842 36083 Z= 0.412 Chirality : 0.052 0.234 4261 Planarity : 0.005 0.059 4554 Dihedral : 7.281 58.883 4754 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.76 % Allowed : 8.35 % Favored : 89.88 % 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: -1.16 (0.14), residues: 3135 helix: 0.70 (0.20), residues: 721 sheet: 0.43 (0.20), residues: 655 loop : -1.99 (0.12), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 567 TYR 0.032 0.002 TYR C 904 PHE 0.028 0.002 PHE A 32 TRP 0.022 0.002 TRP C 886 HIS 0.006 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00526 (26307) covalent geometry : angle 0.74279 (35807) SS BOND : bond 0.00643 ( 42) SS BOND : angle 3.07862 ( 84) hydrogen bonds : bond 0.08960 ( 959) hydrogen bonds : angle 5.72405 ( 2678) link_BETA1-4 : bond 0.00543 ( 17) link_BETA1-4 : angle 1.93202 ( 51) link_NAG-ASN : bond 0.00463 ( 47) link_NAG-ASN : angle 3.52614 ( 141) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 202 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 453 TYR cc_start: 0.7871 (p90) cc_final: 0.7651 (p90) REVERT: A 564 GLN cc_start: 0.7546 (OUTLIER) cc_final: 0.7285 (tp40) REVERT: A 613 GLN cc_start: 0.8029 (OUTLIER) cc_final: 0.7786 (mp10) REVERT: A 614 ASP cc_start: 0.7927 (p0) cc_final: 0.7640 (p0) REVERT: A 776 LYS cc_start: 0.8997 (OUTLIER) cc_final: 0.8744 (tmtm) REVERT: A 790 LYS cc_start: 0.8681 (tttm) cc_final: 0.8396 (ttmm) REVERT: A 1005 GLN cc_start: 0.9059 (OUTLIER) cc_final: 0.8771 (mm-40) REVERT: B 453 TYR cc_start: 0.7894 (p90) cc_final: 0.7622 (p90) REVERT: C 239 GLN cc_start: 0.7830 (tm-30) cc_final: 0.7328 (tm-30) REVERT: C 271 GLN cc_start: 0.7572 (OUTLIER) cc_final: 0.7052 (mt0) REVERT: C 453 TYR cc_start: 0.7751 (p90) cc_final: 0.7500 (p90) REVERT: C 564 GLN cc_start: 0.7532 (OUTLIER) cc_final: 0.5765 (tm-30) REVERT: C 603 ASN cc_start: 0.8481 (m110) cc_final: 0.7548 (t0) REVERT: C 613 GLN cc_start: 0.8150 (mt0) cc_final: 0.7884 (mp10) REVERT: C 904 TYR cc_start: 0.8092 (p90) cc_final: 0.7797 (p90) outliers start: 49 outliers final: 24 residues processed: 234 average time/residue: 0.5944 time to fit residues: 164.4204 Evaluate side-chains 223 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 193 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 808 ASP Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 48 optimal weight: 10.0000 chunk 143 optimal weight: 2.9990 chunk 101 optimal weight: 0.2980 chunk 203 optimal weight: 0.9990 chunk 194 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 35 optimal weight: 0.0670 chunk 168 optimal weight: 0.6980 chunk 167 optimal weight: 0.7980 chunk 174 optimal weight: 0.9980 chunk 225 optimal weight: 4.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN A1101 HIS B 99 ASN C 66 HIS C 99 ASN C 779 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.201664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.154278 restraints weight = 35694.653| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.28 r_work: 0.3179 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3150 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3150 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 26413 Z= 0.124 Angle : 0.628 11.262 36083 Z= 0.327 Chirality : 0.046 0.214 4261 Planarity : 0.004 0.054 4554 Dihedral : 6.439 57.637 4754 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.22 % Allowed : 9.32 % Favored : 89.45 % 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: -0.64 (0.15), residues: 3135 helix: 1.31 (0.21), residues: 729 sheet: 0.86 (0.20), residues: 664 loop : -1.83 (0.13), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 567 TYR 0.029 0.001 TYR C 904 PHE 0.030 0.001 PHE A 32 TRP 0.016 0.001 TRP A 886 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00262 (26307) covalent geometry : angle 0.58906 (35807) SS BOND : bond 0.00459 ( 42) SS BOND : angle 2.24553 ( 84) hydrogen bonds : bond 0.06327 ( 959) hydrogen bonds : angle 5.30975 ( 2678) link_BETA1-4 : bond 0.00394 ( 17) link_BETA1-4 : angle 1.48558 ( 51) link_NAG-ASN : bond 0.00408 ( 47) link_NAG-ASN : angle 3.01443 ( 141) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 229 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 417 LYS cc_start: 0.6631 (pttm) cc_final: 0.6405 (ptpt) REVERT: A 453 TYR cc_start: 0.7966 (p90) cc_final: 0.7742 (p90) REVERT: A 614 ASP cc_start: 0.7852 (p0) cc_final: 0.7592 (p0) REVERT: A 979 ASP cc_start: 0.7941 (t0) cc_final: 0.7636 (t0) REVERT: B 453 TYR cc_start: 0.8029 (p90) cc_final: 0.7787 (p90) REVERT: B 603 ASN cc_start: 0.7902 (m110) cc_final: 0.7197 (t0) REVERT: B 776 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8364 (tmtm) REVERT: C 118 LEU cc_start: 0.8147 (tt) cc_final: 0.7888 (tp) REVERT: C 239 GLN cc_start: 0.7740 (OUTLIER) cc_final: 0.7173 (tm-30) REVERT: C 271 GLN cc_start: 0.7531 (OUTLIER) cc_final: 0.7035 (mt0) REVERT: C 453 TYR cc_start: 0.7840 (p90) cc_final: 0.7556 (p90) REVERT: C 603 ASN cc_start: 0.8234 (m110) cc_final: 0.7401 (t0) outliers start: 34 outliers final: 14 residues processed: 248 average time/residue: 0.5723 time to fit residues: 168.0369 Evaluate side-chains 219 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 202 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 808 ASP Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 171 optimal weight: 0.8980 chunk 107 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 chunk 119 optimal weight: 5.9990 chunk 162 optimal weight: 0.0000 chunk 66 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 227 optimal weight: 9.9990 chunk 143 optimal weight: 0.0980 chunk 154 optimal weight: 6.9990 chunk 244 optimal weight: 7.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN A1101 HIS B 99 ASN C 99 ASN C 121 ASN C 779 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.200219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.152398 restraints weight = 27930.363| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 1.94 r_work: 0.3187 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2934 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2934 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 26413 Z= 0.181 Angle : 0.702 11.224 36083 Z= 0.367 Chirality : 0.049 0.221 4261 Planarity : 0.005 0.049 4554 Dihedral : 6.448 58.852 4754 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.73 % Allowed : 9.58 % Favored : 88.70 % 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: -0.64 (0.14), residues: 3135 helix: 1.27 (0.20), residues: 725 sheet: 0.80 (0.20), residues: 655 loop : -1.76 (0.13), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 403 TYR 0.024 0.002 TYR B 904 PHE 0.025 0.002 PHE A 32 TRP 0.019 0.002 TRP C 886 HIS 0.021 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00420 (26307) covalent geometry : angle 0.66369 (35807) SS BOND : bond 0.00587 ( 42) SS BOND : angle 2.58123 ( 84) hydrogen bonds : bond 0.08003 ( 959) hydrogen bonds : angle 5.41948 ( 2678) link_BETA1-4 : bond 0.00432 ( 17) link_BETA1-4 : angle 1.67603 ( 51) link_NAG-ASN : bond 0.00424 ( 47) link_NAG-ASN : angle 3.07285 ( 141) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 204 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 417 LYS cc_start: 0.6523 (pttm) cc_final: 0.6280 (ptpt) REVERT: A 453 TYR cc_start: 0.7896 (p90) cc_final: 0.7648 (p90) REVERT: A 613 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.6646 (mp10) REVERT: A 614 ASP cc_start: 0.8010 (p0) cc_final: 0.7719 (p0) REVERT: A 776 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8706 (tmtm) REVERT: A 850 ILE cc_start: 0.6796 (OUTLIER) cc_final: 0.6442 (tp) REVERT: A 979 ASP cc_start: 0.8139 (t0) cc_final: 0.7911 (t0) REVERT: A 1005 GLN cc_start: 0.9012 (OUTLIER) cc_final: 0.8726 (mm-40) REVERT: A 1092 GLU cc_start: 0.7939 (tp30) cc_final: 0.7221 (pp20) REVERT: B 453 TYR cc_start: 0.7915 (p90) cc_final: 0.7661 (p90) REVERT: B 564 GLN cc_start: 0.7493 (OUTLIER) cc_final: 0.6572 (tp40) REVERT: B 776 LYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8598 (tmtm) REVERT: B 1017 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8098 (tp30) REVERT: C 239 GLN cc_start: 0.7752 (OUTLIER) cc_final: 0.7198 (tm-30) REVERT: C 271 GLN cc_start: 0.7509 (OUTLIER) cc_final: 0.7008 (mt0) REVERT: C 453 TYR cc_start: 0.7739 (p90) cc_final: 0.7472 (p90) REVERT: C 564 GLN cc_start: 0.7451 (OUTLIER) cc_final: 0.5594 (tm-30) REVERT: C 603 ASN cc_start: 0.8405 (m110) cc_final: 0.7498 (t0) REVERT: C 613 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.6123 (mp10) outliers start: 48 outliers final: 25 residues processed: 235 average time/residue: 0.5911 time to fit residues: 164.7561 Evaluate side-chains 233 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 197 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 808 ASP Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 108 optimal weight: 6.9990 chunk 236 optimal weight: 0.9990 chunk 306 optimal weight: 0.7980 chunk 153 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 60 optimal weight: 0.1980 chunk 286 optimal weight: 0.3980 chunk 27 optimal weight: 0.4980 chunk 208 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN A1101 HIS B 99 ASN B1005 GLN C 99 ASN C 779 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.203724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.158056 restraints weight = 41754.429| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 2.37 r_work: 0.3187 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3147 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3147 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 26413 Z= 0.117 Angle : 0.590 10.275 36083 Z= 0.308 Chirality : 0.045 0.246 4261 Planarity : 0.004 0.048 4554 Dihedral : 5.821 55.464 4754 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.33 % Allowed : 10.26 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.15), residues: 3135 helix: 1.68 (0.21), residues: 721 sheet: 0.95 (0.20), residues: 694 loop : -1.64 (0.13), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 567 TYR 0.023 0.001 TYR B 904 PHE 0.028 0.001 PHE A 32 TRP 0.019 0.001 TRP C 886 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00245 (26307) covalent geometry : angle 0.55697 (35807) SS BOND : bond 0.00464 ( 42) SS BOND : angle 1.96921 ( 84) hydrogen bonds : bond 0.05842 ( 959) hydrogen bonds : angle 5.08310 ( 2678) link_BETA1-4 : bond 0.00403 ( 17) link_BETA1-4 : angle 1.35616 ( 51) link_NAG-ASN : bond 0.00387 ( 47) link_NAG-ASN : angle 2.72374 ( 141) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 214 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 ILE cc_start: 0.7752 (pt) cc_final: 0.7532 (pt) REVERT: A 417 LYS cc_start: 0.6582 (pttm) cc_final: 0.6369 (ptpt) REVERT: A 453 TYR cc_start: 0.7983 (p90) cc_final: 0.7743 (p90) REVERT: A 614 ASP cc_start: 0.7887 (p0) cc_final: 0.7599 (p0) REVERT: A 1092 GLU cc_start: 0.7858 (tp30) cc_final: 0.7286 (pp20) REVERT: B 239 GLN cc_start: 0.7798 (OUTLIER) cc_final: 0.7475 (tm-30) REVERT: B 453 TYR cc_start: 0.8069 (p90) cc_final: 0.7796 (p90) REVERT: B 529 LYS cc_start: 0.6933 (OUTLIER) cc_final: 0.6648 (ptmm) REVERT: B 614 ASP cc_start: 0.7720 (p0) cc_final: 0.7300 (p0) REVERT: B 776 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8324 (tmtm) REVERT: C 88 ASP cc_start: 0.7810 (m-30) cc_final: 0.7598 (m-30) REVERT: C 118 LEU cc_start: 0.8180 (tt) cc_final: 0.7815 (tm) REVERT: C 239 GLN cc_start: 0.7745 (OUTLIER) cc_final: 0.7168 (tm-30) REVERT: C 453 TYR cc_start: 0.7820 (p90) cc_final: 0.7557 (p90) REVERT: C 564 GLN cc_start: 0.7395 (OUTLIER) cc_final: 0.5603 (tm-30) REVERT: C 586 ASP cc_start: 0.7268 (OUTLIER) cc_final: 0.6939 (m-30) REVERT: C 603 ASN cc_start: 0.8230 (m110) cc_final: 0.7396 (t0) REVERT: C 933 LYS cc_start: 0.8625 (mttp) cc_final: 0.8119 (mmtm) outliers start: 37 outliers final: 15 residues processed: 239 average time/residue: 0.6197 time to fit residues: 174.4725 Evaluate side-chains 225 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 204 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 808 ASP Chi-restraints excluded: chain C residue 921 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 115 optimal weight: 10.0000 chunk 214 optimal weight: 6.9990 chunk 185 optimal weight: 2.9990 chunk 271 optimal weight: 2.9990 chunk 225 optimal weight: 6.9990 chunk 227 optimal weight: 8.9990 chunk 163 optimal weight: 4.9990 chunk 286 optimal weight: 8.9990 chunk 231 optimal weight: 6.9990 chunk 196 optimal weight: 0.8980 chunk 251 optimal weight: 40.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN A1101 HIS B 99 ASN B1135 ASN C 99 ASN C 121 ASN C 779 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.195841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.142800 restraints weight = 29326.038| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.11 r_work: 0.3096 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2882 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2882 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.135 26413 Z= 0.346 Angle : 0.902 13.065 36083 Z= 0.472 Chirality : 0.059 0.274 4261 Planarity : 0.006 0.052 4554 Dihedral : 6.802 59.353 4754 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 2.05 % Allowed : 10.37 % Favored : 87.58 % 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: -0.92 (0.14), residues: 3135 helix: 0.78 (0.20), residues: 711 sheet: 0.74 (0.20), residues: 659 loop : -1.84 (0.13), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 214 TYR 0.034 0.003 TYR A 904 PHE 0.030 0.003 PHE C 823 TRP 0.017 0.003 TRP A 104 HIS 0.009 0.002 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00846 (26307) covalent geometry : angle 0.86225 (35807) SS BOND : bond 0.00786 ( 42) SS BOND : angle 3.31336 ( 84) hydrogen bonds : bond 0.10384 ( 959) hydrogen bonds : angle 5.73761 ( 2678) link_BETA1-4 : bond 0.00612 ( 17) link_BETA1-4 : angle 2.14134 ( 51) link_NAG-ASN : bond 0.00543 ( 47) link_NAG-ASN : angle 3.37789 ( 141) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 207 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 417 LYS cc_start: 0.6638 (pttm) cc_final: 0.6353 (ptpt) REVERT: A 453 TYR cc_start: 0.7928 (p90) cc_final: 0.7653 (p90) REVERT: A 580 GLN cc_start: 0.7560 (OUTLIER) cc_final: 0.7129 (mt0) REVERT: A 613 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.6760 (mp10) REVERT: A 614 ASP cc_start: 0.8081 (p0) cc_final: 0.7796 (p0) REVERT: A 850 ILE cc_start: 0.6907 (OUTLIER) cc_final: 0.6533 (tp) REVERT: A 916 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8157 (tt) REVERT: A 1005 GLN cc_start: 0.9043 (OUTLIER) cc_final: 0.8769 (mm-40) REVERT: A 1092 GLU cc_start: 0.8034 (tp30) cc_final: 0.7287 (pp20) REVERT: B 453 TYR cc_start: 0.7920 (p90) cc_final: 0.7549 (p90) REVERT: B 529 LYS cc_start: 0.7015 (OUTLIER) cc_final: 0.6690 (ptmm) REVERT: B 564 GLN cc_start: 0.7621 (OUTLIER) cc_final: 0.6758 (tp40) REVERT: B 1017 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8164 (tp30) REVERT: C 239 GLN cc_start: 0.7759 (OUTLIER) cc_final: 0.7265 (tm-30) REVERT: C 271 GLN cc_start: 0.7590 (OUTLIER) cc_final: 0.7053 (mt0) REVERT: C 453 TYR cc_start: 0.7849 (p90) cc_final: 0.7585 (p90) REVERT: C 564 GLN cc_start: 0.7503 (OUTLIER) cc_final: 0.5582 (tm-30) REVERT: C 586 ASP cc_start: 0.7230 (OUTLIER) cc_final: 0.6619 (m-30) REVERT: C 603 ASN cc_start: 0.8427 (m110) cc_final: 0.7630 (t0) REVERT: C 613 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.6210 (mp10) outliers start: 57 outliers final: 27 residues processed: 246 average time/residue: 0.5707 time to fit residues: 166.5129 Evaluate side-chains 243 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 203 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 808 ASP Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 198 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 233 optimal weight: 0.4980 chunk 284 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 chunk 164 optimal weight: 0.7980 chunk 209 optimal weight: 3.9990 chunk 211 optimal weight: 7.9990 chunk 302 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN A1101 HIS B 99 ASN C 99 ASN C 779 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.200978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.141388 restraints weight = 27432.585| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 2.36 r_work: 0.3183 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3046 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3046 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 26413 Z= 0.135 Angle : 0.644 10.325 36083 Z= 0.336 Chirality : 0.047 0.233 4261 Planarity : 0.004 0.053 4554 Dihedral : 5.987 56.170 4754 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.22 % Allowed : 11.45 % Favored : 87.33 % 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: -0.48 (0.15), residues: 3135 helix: 1.38 (0.20), residues: 725 sheet: 0.93 (0.20), residues: 652 loop : -1.65 (0.13), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 567 TYR 0.024 0.001 TYR B 904 PHE 0.031 0.001 PHE B 318 TRP 0.018 0.002 TRP C 886 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00293 (26307) covalent geometry : angle 0.60780 (35807) SS BOND : bond 0.00560 ( 42) SS BOND : angle 2.30335 ( 84) hydrogen bonds : bond 0.06893 ( 959) hydrogen bonds : angle 5.31145 ( 2678) link_BETA1-4 : bond 0.00392 ( 17) link_BETA1-4 : angle 1.57722 ( 51) link_NAG-ASN : bond 0.00399 ( 47) link_NAG-ASN : angle 2.85022 ( 141) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 203 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 417 LYS cc_start: 0.6507 (pttm) cc_final: 0.6235 (ptmt) REVERT: A 453 TYR cc_start: 0.7732 (p90) cc_final: 0.7434 (p90) REVERT: A 614 ASP cc_start: 0.7962 (p0) cc_final: 0.7668 (p0) REVERT: A 979 ASP cc_start: 0.8127 (t0) cc_final: 0.7800 (t0) REVERT: A 1092 GLU cc_start: 0.7867 (tp30) cc_final: 0.7189 (pp20) REVERT: B 453 TYR cc_start: 0.7850 (p90) cc_final: 0.7539 (p90) REVERT: B 614 ASP cc_start: 0.7726 (p0) cc_final: 0.7299 (p0) REVERT: B 776 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8445 (tmtm) REVERT: C 118 LEU cc_start: 0.7835 (tt) cc_final: 0.7577 (tp) REVERT: C 239 GLN cc_start: 0.7571 (OUTLIER) cc_final: 0.7035 (tm-30) REVERT: C 271 GLN cc_start: 0.7408 (OUTLIER) cc_final: 0.6920 (mt0) REVERT: C 403 ARG cc_start: 0.6198 (mtp-110) cc_final: 0.5980 (mtp-110) REVERT: C 453 TYR cc_start: 0.7683 (p90) cc_final: 0.7388 (p90) REVERT: C 564 GLN cc_start: 0.7272 (OUTLIER) cc_final: 0.5371 (tm-30) REVERT: C 586 ASP cc_start: 0.7175 (OUTLIER) cc_final: 0.6539 (m-30) REVERT: C 603 ASN cc_start: 0.8352 (m110) cc_final: 0.7448 (t0) outliers start: 34 outliers final: 20 residues processed: 228 average time/residue: 0.6024 time to fit residues: 162.7287 Evaluate side-chains 224 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 199 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 808 ASP Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 191 optimal weight: 1.9990 chunk 266 optimal weight: 0.1980 chunk 88 optimal weight: 2.9990 chunk 293 optimal weight: 2.9990 chunk 82 optimal weight: 0.2980 chunk 28 optimal weight: 7.9990 chunk 249 optimal weight: 7.9990 chunk 60 optimal weight: 0.5980 chunk 218 optimal weight: 2.9990 chunk 147 optimal weight: 0.9980 chunk 288 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 211 ASN A1101 HIS B 99 ASN B 121 ASN B1005 GLN C 66 HIS C 99 ASN C 218 GLN C 779 GLN C1005 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.202959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.153975 restraints weight = 33080.082| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 2.09 r_work: 0.3228 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3005 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3005 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 26413 Z= 0.119 Angle : 0.590 9.787 36083 Z= 0.309 Chirality : 0.045 0.222 4261 Planarity : 0.004 0.052 4554 Dihedral : 5.437 54.720 4754 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.90 % Allowed : 11.92 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.15), residues: 3135 helix: 1.76 (0.21), residues: 722 sheet: 1.00 (0.20), residues: 700 loop : -1.52 (0.14), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 567 TYR 0.024 0.001 TYR B 904 PHE 0.027 0.001 PHE A 32 TRP 0.017 0.001 TRP C 886 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00253 (26307) covalent geometry : angle 0.56026 (35807) SS BOND : bond 0.00471 ( 42) SS BOND : angle 1.78691 ( 84) hydrogen bonds : bond 0.05955 ( 959) hydrogen bonds : angle 5.04071 ( 2678) link_BETA1-4 : bond 0.00405 ( 17) link_BETA1-4 : angle 1.38348 ( 51) link_NAG-ASN : bond 0.00372 ( 47) link_NAG-ASN : angle 2.60764 ( 141) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 212 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 417 LYS cc_start: 0.6528 (pttm) cc_final: 0.6298 (ptmt) REVERT: A 453 TYR cc_start: 0.7855 (p90) cc_final: 0.7529 (p90) REVERT: A 614 ASP cc_start: 0.8076 (p0) cc_final: 0.7766 (p0) REVERT: A 827 THR cc_start: 0.7881 (OUTLIER) cc_final: 0.7647 (p) REVERT: A 979 ASP cc_start: 0.8227 (t0) cc_final: 0.7933 (t0) REVERT: A 1092 GLU cc_start: 0.7994 (tp30) cc_final: 0.7229 (pp20) REVERT: B 239 GLN cc_start: 0.7835 (tm-30) cc_final: 0.7599 (tm-30) REVERT: B 453 TYR cc_start: 0.7977 (p90) cc_final: 0.7689 (p90) REVERT: B 614 ASP cc_start: 0.7813 (p0) cc_final: 0.7346 (p0) REVERT: B 776 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8474 (tmtm) REVERT: C 239 GLN cc_start: 0.7786 (OUTLIER) cc_final: 0.7281 (tm-30) REVERT: C 453 TYR cc_start: 0.7766 (p90) cc_final: 0.7433 (p90) REVERT: C 564 GLN cc_start: 0.7292 (OUTLIER) cc_final: 0.5427 (tm-30) REVERT: C 586 ASP cc_start: 0.7288 (OUTLIER) cc_final: 0.6880 (m-30) REVERT: C 603 ASN cc_start: 0.8374 (m110) cc_final: 0.7485 (t0) REVERT: C 933 LYS cc_start: 0.8719 (mttp) cc_final: 0.8156 (mmtm) outliers start: 25 outliers final: 14 residues processed: 232 average time/residue: 0.5979 time to fit residues: 162.8138 Evaluate side-chains 223 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 204 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 808 ASP Chi-restraints excluded: chain C residue 921 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 6 optimal weight: 0.6980 chunk 42 optimal weight: 0.0030 chunk 95 optimal weight: 2.9990 chunk 294 optimal weight: 4.9990 chunk 289 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 33 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 chunk 191 optimal weight: 0.5980 chunk 129 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.8594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 211 ASN A1101 HIS B 99 ASN B 121 ASN B1005 GLN C 66 HIS C 99 ASN C 218 GLN C 779 GLN C1005 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.203009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.159161 restraints weight = 45878.065| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 2.46 r_work: 0.3145 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3093 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3093 r_free = 0.3093 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3093 r_free = 0.3093 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3093 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 26413 Z= 0.134 Angle : 0.614 9.842 36083 Z= 0.322 Chirality : 0.046 0.225 4261 Planarity : 0.004 0.051 4554 Dihedral : 5.385 55.601 4754 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.04 % Allowed : 12.10 % Favored : 86.86 % 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: -0.19 (0.15), residues: 3135 helix: 1.72 (0.20), residues: 728 sheet: 0.93 (0.20), residues: 687 loop : -1.49 (0.14), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 567 TYR 0.025 0.001 TYR B 904 PHE 0.025 0.001 PHE B 318 TRP 0.016 0.002 TRP C 886 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00295 (26307) covalent geometry : angle 0.58355 (35807) SS BOND : bond 0.00496 ( 42) SS BOND : angle 2.05551 ( 84) hydrogen bonds : bond 0.06566 ( 959) hydrogen bonds : angle 5.09751 ( 2678) link_BETA1-4 : bond 0.00402 ( 17) link_BETA1-4 : angle 1.43989 ( 51) link_NAG-ASN : bond 0.00367 ( 47) link_NAG-ASN : angle 2.60617 ( 141) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 205 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 335 LEU cc_start: 0.7514 (OUTLIER) cc_final: 0.7287 (mm) REVERT: A 417 LYS cc_start: 0.6586 (pttm) cc_final: 0.6362 (ptmt) REVERT: A 453 TYR cc_start: 0.7995 (p90) cc_final: 0.7683 (p90) REVERT: A 614 ASP cc_start: 0.7989 (p0) cc_final: 0.7681 (p0) REVERT: A 979 ASP cc_start: 0.8107 (t0) cc_final: 0.7768 (t0) REVERT: A 1092 GLU cc_start: 0.7874 (tp30) cc_final: 0.7242 (pp20) REVERT: B 453 TYR cc_start: 0.8075 (p90) cc_final: 0.7803 (p90) REVERT: B 614 ASP cc_start: 0.7763 (p0) cc_final: 0.7319 (p0) REVERT: B 776 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8464 (tmtm) REVERT: C 118 LEU cc_start: 0.8200 (tt) cc_final: 0.7806 (tm) REVERT: C 239 GLN cc_start: 0.7792 (OUTLIER) cc_final: 0.7261 (tm-30) REVERT: C 271 GLN cc_start: 0.7499 (OUTLIER) cc_final: 0.7028 (mt0) REVERT: C 453 TYR cc_start: 0.7876 (p90) cc_final: 0.7534 (p90) REVERT: C 564 GLN cc_start: 0.7330 (OUTLIER) cc_final: 0.5477 (tm-30) REVERT: C 586 ASP cc_start: 0.7262 (OUTLIER) cc_final: 0.6901 (m-30) REVERT: C 603 ASN cc_start: 0.8237 (m110) cc_final: 0.7456 (t0) REVERT: C 613 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.6058 (mp10) REVERT: C 933 LYS cc_start: 0.8669 (mttp) cc_final: 0.8145 (mmtm) outliers start: 29 outliers final: 15 residues processed: 227 average time/residue: 0.6000 time to fit residues: 161.5635 Evaluate side-chains 223 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 201 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 808 ASP Chi-restraints excluded: chain C residue 868 GLU Chi-restraints excluded: chain C residue 921 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 172 optimal weight: 0.9980 chunk 312 optimal weight: 0.8980 chunk 310 optimal weight: 0.0570 chunk 201 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 117 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 169 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 233 optimal weight: 0.9990 chunk 112 optimal weight: 9.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 211 ASN A1101 HIS B 99 ASN B 121 ASN B1005 GLN C 30 ASN C 66 HIS C 99 ASN C 779 GLN C1005 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.203927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.159780 restraints weight = 45891.087| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 2.42 r_work: 0.3178 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3116 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3116 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 26413 Z= 0.121 Angle : 0.584 9.842 36083 Z= 0.305 Chirality : 0.045 0.233 4261 Planarity : 0.004 0.050 4554 Dihedral : 5.128 54.707 4754 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.12 % Allowed : 12.06 % Favored : 86.83 % 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: -0.12 (0.15), residues: 3135 helix: 1.81 (0.20), residues: 728 sheet: 0.95 (0.20), residues: 677 loop : -1.43 (0.14), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 567 TYR 0.025 0.001 TYR B 904 PHE 0.025 0.001 PHE A 32 TRP 0.016 0.001 TRP C 886 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00261 (26307) covalent geometry : angle 0.55579 (35807) SS BOND : bond 0.00469 ( 42) SS BOND : angle 1.85173 ( 84) hydrogen bonds : bond 0.06144 ( 959) hydrogen bonds : angle 4.98871 ( 2678) link_BETA1-4 : bond 0.00403 ( 17) link_BETA1-4 : angle 1.37470 ( 51) link_NAG-ASN : bond 0.00353 ( 47) link_NAG-ASN : angle 2.48867 ( 141) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12366.10 seconds wall clock time: 210 minutes 20.62 seconds (12620.62 seconds total)