Starting phenix.real_space_refine on Thu Mar 5 14:15:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vsb_21375/03_2026/6vsb_21375.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vsb_21375/03_2026/6vsb_21375.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vsb_21375/03_2026/6vsb_21375.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vsb_21375/03_2026/6vsb_21375.map" model { file = "/net/cci-nas-00/data/ceres_data/6vsb_21375/03_2026/6vsb_21375.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vsb_21375/03_2026/6vsb_21375.cif" } resolution = 3.46 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= 0.023 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 101 5.16 5 C 14551 2.51 5 N 3712 2.21 5 O 4490 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 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: 22854 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 7311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 959, 7311 Classifications: {'peptide': 959} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 46, 'TRANS': 912} Chain breaks: 13 Unresolved non-hydrogen bonds: 183 Unresolved non-hydrogen angles: 229 Unresolved non-hydrogen dihedrals: 148 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'PHE:plan': 3, 'ASN:plan1': 2, 'GLN:plan1': 5, 'GLU:plan': 5, 'TYR:plan': 1, 'ARG:plan': 5, 'ASP:plan': 8, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 125 Chain: "B" Number of atoms: 7362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 973, 7362 Classifications: {'peptide': 973} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 48, 'TRANS': 924} Chain breaks: 13 Unresolved non-hydrogen bonds: 260 Unresolved non-hydrogen angles: 330 Unresolved non-hydrogen dihedrals: 214 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ASN:plan1': 6, 'GLU:plan': 8, 'ARG:plan': 5, 'GLN:plan1': 5, 'PHE:plan': 2, 'TYR:plan': 6, 'ASP:plan': 7, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 175 Chain: "C" Number of atoms: 7327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 973, 7327 Classifications: {'peptide': 973} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 47, 'TRANS': 925} Chain breaks: 13 Unresolved non-hydrogen bonds: 296 Unresolved non-hydrogen angles: 372 Unresolved non-hydrogen dihedrals: 244 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'ASN:plan1': 5, 'ARG:plan': 10, 'GLN:plan1': 6, 'PHE:plan': 5, 'TYR:plan': 4, 'ASP:plan': 11, 'GLU:plan': 6, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 209 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: 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: "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: 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 Time building chain proxies: 5.50, per 1000 atoms: 0.24 Number of scatterers: 22854 At special positions: 0 Unit cell: (132.969, 131.922, 182.178, 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 101 16.00 O 4490 8.00 N 3712 7.00 C 14551 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.01 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.05 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 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 603 " " NAG A1302 " - " ASN A 616 " " NAG A1303 " - " ASN A 657 " " NAG A1304 " - " ASN A 709 " " NAG A1315 " - " ASN A 122 " " NAG A1316 " - " ASN A 165 " " NAG A1317 " - " ASN A 234 " " NAG A1318 " - " ASN A 282 " " NAG A1319 " - " ASN A 343 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 603 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B 657 " " NAG B1315 " - " ASN B 343 " " NAG B1316 " - " ASN B 282 " " NAG B1317 " - " ASN B 234 " " NAG B1318 " - " ASN B 165 " " NAG B1319 " - " ASN B 122 " " NAG C1313 " - " ASN C 657 " " NAG C1314 " - " ASN C 616 " " NAG C1315 " - " ASN C 603 " " NAG C1316 " - " ASN C 122 " " NAG C1317 " - " ASN C 165 " " NAG C1318 " - " ASN C 234 " " NAG C1319 " - " ASN C 282 " " NAG C1320 " - " ASN C 331 " " NAG C1321 " - " ASN C 343 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A 801 " " NAG F 1 " - " ASN A1074 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN A1134 " " NAG I 1 " - " ASN B 709 " " NAG J 1 " - " ASN B 717 " " NAG K 1 " - " ASN B 801 " " NAG L 1 " - " ASN B1098 " " NAG M 1 " - " ASN B1134 " " NAG N 1 " - " ASN B1074 " " NAG O 1 " - " ASN C1134 " " NAG P 1 " - " ASN C1098 " " NAG Q 1 " - " ASN C1074 " " NAG R 1 " - " ASN C 801 " " NAG S 1 " - " ASN C 717 " " NAG T 1 " - " ASN C 709 " Time building additional restraints: 2.04 Conformation dependent library (CDL) restraints added in 1.0 seconds 5642 Ramachandran restraints generated. 2821 Oldfield, 0 Emsley, 2821 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5466 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 42 sheets defined 26.4% alpha, 26.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 296 through 304 removed outlier: 3.650A pdb=" N THR A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.613A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.637A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.679A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (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: 3.656A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.776A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR A 873 " --> pdb=" O MET A 869 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE A 882 " --> pdb=" O LEU A 878 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 890 removed outlier: 3.533A pdb=" N PHE A 888 " --> pdb=" O GLY A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 removed outlier: 3.510A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.830A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.637A pdb=" N LYS A 933 " --> pdb=" O SER A 929 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.950A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.751A 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 983 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.680A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1140 through 1145 Processing helix chain 'B' and resid 296 through 304 removed outlier: 3.516A pdb=" N CYS B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N THR B 302 " --> pdb=" O GLU B 298 " (cutoff:3.500A) 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 390 removed outlier: 3.600A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.061A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.876A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.605A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 866 through 884 removed outlier: 4.439A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR B 873 " --> pdb=" O MET B 869 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA B 879 " --> pdb=" O SER B 875 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE B 882 " --> pdb=" O LEU B 878 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 885 through 890 removed outlier: 3.982A pdb=" N PHE B 888 " --> pdb=" O GLY B 885 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.844A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.610A pdb=" N LYS B 933 " --> pdb=" O SER B 929 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.907A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.625A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1120 Processing helix chain 'B' and resid 1140 through 1145 Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.527A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 383 through 390 removed outlier: 5.280A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.810A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 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: 3.691A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.554A pdb=" N SER C 875 " --> pdb=" O ALA C 871 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU C 878 " --> pdb=" O THR C 874 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR C 881 " --> pdb=" O LEU C 877 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 885 through 888 removed outlier: 3.525A pdb=" N PHE C 888 " --> pdb=" O GLY C 885 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 885 through 888' Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.593A pdb=" N LYS C 933 " --> pdb=" O SER C 929 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.655A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (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 983 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.336A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1145 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.925A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 51 removed outlier: 6.734A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 172 removed outlier: 3.840A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.415A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.627A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.557A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AA9, first strand: chain 'A' and resid 538 through 540 removed outlier: 5.288A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.361A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.754A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.120A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.120A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N HIS A1101 " --> pdb=" O ASN A1098 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.112A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.901A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.672A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.599A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 106 through 107 Processing sheet with id=AB9, first strand: chain 'B' and resid 120 through 121 Processing sheet with id=AC1, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.122A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 323 through 328 removed outlier: 6.327A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ASN B 540 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ARG B 328 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.501A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.725A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 451 through 453 removed outlier: 4.321A pdb=" N TYR B 451 " --> pdb=" O TYR B 495 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.404A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 9.001A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.443A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.443A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N TRP B1102 " --> pdb=" O GLN B1113 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLN B1113 " --> pdb=" O TRP B1102 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N VAL B1104 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N GLU B1111 " --> pdb=" O VAL B1104 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN B1106 " --> pdb=" O PHE B1109 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.223A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1122 through 1125 removed outlier: 5.423A pdb=" N GLY B1124 " --> pdb=" O ALA B1087 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE B1081 " --> pdb=" O HIS B1088 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 29 through 31 removed outlier: 3.726A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.036A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 224 through 227 removed outlier: 6.760A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE C 194 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 169 through 172 removed outlier: 3.597A pdb=" N TYR C 170 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL C 127 " --> pdb=" O VAL C 120 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.530A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.506A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N PHE C 515 " --> pdb=" O THR C 430 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N THR C 430 " --> pdb=" O PHE C 515 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N GLY C 431 " --> pdb=" O TYR C 380 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.878A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'C' and resid 451 through 453 removed outlier: 4.070A pdb=" N TYR C 451 " --> pdb=" O TYR C 495 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 538 through 543 Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.383A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.877A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.040A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.040A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR C1105 " --> pdb=" O VAL C1094 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.184A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.785A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N CYS C1082 " --> pdb=" O VAL C1133 " (cutoff:3.500A) 905 hydrogen bonds defined for protein. 2472 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: 4.61 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.35: 7231 1.35 - 1.48: 6170 1.48 - 1.61: 9796 1.61 - 1.75: 5 1.75 - 1.88: 120 Bond restraints: 23322 Sorted by residual: bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.468 -0.062 2.00e-02 2.50e+03 9.59e+00 bond pdb=" CA ASN A 709 " pdb=" C ASN A 709 " ideal model delta sigma weight residual 1.523 1.481 0.042 1.41e-02 5.03e+03 8.69e+00 bond pdb=" CB CYS B 166 " pdb=" SG CYS B 166 " ideal model delta sigma weight residual 1.808 1.716 0.092 3.30e-02 9.18e+02 7.76e+00 bond pdb=" C1 NAG A1316 " pdb=" O5 NAG A1316 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.35e+00 bond pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " ideal model delta sigma weight residual 1.808 1.721 0.087 3.30e-02 9.18e+02 6.97e+00 ... (remaining 23317 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.13: 31363 3.13 - 6.27: 380 6.27 - 9.40: 37 9.40 - 12.53: 7 12.53 - 15.67: 2 Bond angle restraints: 31789 Sorted by residual: angle pdb=" C SER A 708 " pdb=" N ASN A 709 " pdb=" CA ASN A 709 " ideal model delta sigma weight residual 122.38 111.45 10.93 1.81e+00 3.05e-01 3.65e+01 angle pdb=" CA CYS A 525 " pdb=" CB CYS A 525 " pdb=" SG CYS A 525 " ideal model delta sigma weight residual 114.40 127.47 -13.07 2.30e+00 1.89e-01 3.23e+01 angle pdb=" CB MET C 697 " pdb=" CG MET C 697 " pdb=" SD MET C 697 " ideal model delta sigma weight residual 112.70 97.03 15.67 3.00e+00 1.11e-01 2.73e+01 angle pdb=" N ILE A 805 " pdb=" CA ILE A 805 " pdb=" C ILE A 805 " ideal model delta sigma weight residual 112.96 107.77 5.19 1.00e+00 1.00e+00 2.70e+01 angle pdb=" C ASN B 542 " pdb=" N PHE B 543 " pdb=" CA PHE B 543 " ideal model delta sigma weight residual 121.54 131.17 -9.63 1.91e+00 2.74e-01 2.54e+01 ... (remaining 31784 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 13567 17.99 - 35.97: 802 35.97 - 53.96: 186 53.96 - 71.95: 44 71.95 - 89.94: 21 Dihedral angle restraints: 14620 sinusoidal: 6176 harmonic: 8444 Sorted by residual: dihedral pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " pdb=" SG CYS B 649 " pdb=" CB CYS B 649 " ideal model delta sinusoidal sigma weight residual -86.00 -172.86 86.86 1 1.00e+01 1.00e-02 9.07e+01 dihedral pdb=" CB CYS B 131 " pdb=" SG CYS B 131 " pdb=" SG CYS B 166 " pdb=" CB CYS B 166 " ideal model delta sinusoidal sigma weight residual 93.00 10.32 82.68 1 1.00e+01 1.00e-02 8.38e+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 -15.39 -70.61 1 1.00e+01 1.00e-02 6.41e+01 ... (remaining 14617 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.253: 3867 0.253 - 0.506: 16 0.506 - 0.759: 5 0.759 - 1.012: 0 1.012 - 1.265: 1 Chirality restraints: 3889 Sorted by residual: chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.13 -1.27 2.00e-02 2.50e+03 4.00e+03 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.67 -0.73 2.00e-02 2.50e+03 1.31e+03 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-02 2.50e+03 6.98e+02 ... (remaining 3886 not shown) Planarity restraints: 4064 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG P 2 " 0.359 2.00e-02 2.50e+03 3.09e-01 1.19e+03 pdb=" C7 NAG P 2 " -0.085 2.00e-02 2.50e+03 pdb=" C8 NAG P 2 " 0.096 2.00e-02 2.50e+03 pdb=" N2 NAG P 2 " -0.547 2.00e-02 2.50e+03 pdb=" O7 NAG P 2 " 0.177 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 2 " -0.346 2.00e-02 2.50e+03 2.92e-01 1.07e+03 pdb=" C7 NAG N 2 " 0.090 2.00e-02 2.50e+03 pdb=" C8 NAG N 2 " -0.187 2.00e-02 2.50e+03 pdb=" N2 NAG N 2 " 0.509 2.00e-02 2.50e+03 pdb=" O7 NAG N 2 " -0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 1 " 0.339 2.00e-02 2.50e+03 2.91e-01 1.05e+03 pdb=" C7 NAG I 1 " -0.087 2.00e-02 2.50e+03 pdb=" C8 NAG I 1 " 0.166 2.00e-02 2.50e+03 pdb=" N2 NAG I 1 " -0.513 2.00e-02 2.50e+03 pdb=" O7 NAG I 1 " 0.094 2.00e-02 2.50e+03 ... (remaining 4061 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 340 2.62 - 3.19: 21225 3.19 - 3.76: 33627 3.76 - 4.33: 46869 4.33 - 4.90: 76492 Nonbonded interactions: 178553 Sorted by model distance: nonbonded pdb=" O3 NAG I 2 " pdb=" O7 NAG I 2 " model vdw 2.054 3.040 nonbonded pdb=" OG SER B 708 " pdb=" OD1 ASN B 710 " model vdw 2.093 3.040 nonbonded pdb=" OG SER A 708 " pdb=" OD1 ASN A 710 " model vdw 2.093 3.040 nonbonded pdb=" N GLU B1072 " pdb=" OE1 GLU B1072 " model vdw 2.100 3.120 nonbonded pdb=" OG1 THR A 645 " pdb=" O GLY A 648 " model vdw 2.109 3.040 ... (remaining 178548 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 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB )) or resid 42 through 66 or resid 81 through 95 or (resi \ d 99 through 100 and (name N or name CA or name C or name O or name CB )) or res \ id 101 or (resid 102 and (name N or name CA or name C or name O or name CB )) or \ resid 103 through 104 or (resid 105 and (name N or name CA or name C or name O \ or name CB )) or resid 106 through 128 or (resid 129 and (name N or name CA or n \ ame C or name O or name CB )) or resid 130 through 140 or (resid 157 through 160 \ and (name N or name CA or name C or name O or name CB )) or resid 161 through 1 \ 87 or (resid 188 and (name N or name CA or name C or name O or name CB )) or res \ id 189 through 194 or (resid 195 through 198 and (name N or name CA or name C or \ name O or name CB )) or resid 199 or (resid 200 and (name N or name CA or name \ C or name O or name CB )) or resid 201 through 209 or resid 217 through 236 or ( \ resid 237 and (name N or name CA or name C or name O or name CB )) or resid 238 \ or (resid 239 and (name N or name CA or name C or name O or name CB )) or resid \ 240 through 243 or resid 264 through 344 or (resid 345 through 346 and (name N o \ r name CA or name C or name O or name CB )) or resid 347 through 350 or (resid 3 \ 51 through 352 and (name N or name CA or name C or name O or name CB )) or resid \ 353 through 363 or (resid 364 and (name N or name CA or name C or name O or nam \ e CB )) or resid 365 through 368 or (resid 369 and (name N or name CA or name C \ or name O or name CB )) or resid 370 through 373 or (resid 374 and (name N or na \ me CA or name C or name O or name CB )) or resid 375 through 407 or (resid 408 a \ nd (name N or name CA or name C or name O or name CB )) or resid 409 through 441 \ or (resid 442 and (name N or name CA or name C or name O or name CB )) or resid \ 443 or (resid 449 and (name N or name CA or name C or name O or name CB )) or r \ esid 450 through 496 or (resid 497 through 498 and (name N or name CA or name C \ or name O or name CB )) or resid 503 through 504 or (resid 505 and (name N or na \ me CA or name C or name O or name CB )) or resid 506 through 508 or (resid 509 a \ nd (name N or name CA or name C or name O or name CB )) or resid 510 through 620 \ or resid 641 through 1319)) selection = (chain 'B' and (resid 27 through 95 or resid 99 through 128 or (resid 129 and (n \ ame N or name CA or name C or name O or name CB )) or resid 130 through 140 or ( \ resid 157 through 160 and (name N or name CA or name C or name O or name CB )) o \ r resid 161 through 175 or (resid 176 through 188 and (name N or name CA or name \ C or name O or name CB )) or resid 189 or (resid 190 and (name N or name CA or \ name C or name O or name CB )) or resid 191 through 236 or (resid 237 and (name \ N or name CA or name C or name O or name CB )) or resid 238 or (resid 239 and (n \ ame N or name CA or name C or name O or name CB )) or resid 240 through 289 or ( \ resid 290 and (name N or name CA or name C or name O or name CB )) or resid 291 \ through 328 or resid 335 through 350 or (resid 351 through 352 and (name N or na \ me CA or name C or name O or name CB )) or resid 353 through 363 or (resid 364 a \ nd (name N or name CA or name C or name O or name CB )) or resid 365 through 373 \ or (resid 374 and (name N or name CA or name C or name O or name CB )) or resid \ 375 through 441 or (resid 442 and (name N or name CA or name C or name O or nam \ e CB )) or resid 443 through 454 or resid 491 through 496 or (resid 497 through \ 498 and (name N or name CA or name C or name O or name CB )) or resid 503 throug \ h 508 or (resid 509 and (name N or name CA or name C or name O or name CB )) or \ resid 510 through 527 or (resid 528 through 529 and (name N or name CA or name C \ or name O or name CB )) or resid 530 through 620 or resid 641 through 1319)) selection = (chain 'C' and (resid 27 through 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB )) or resid 42 through 59 or (resid 60 and (name N or nam \ e CA or name C or name O or name CB )) or resid 61 through 66 or resid 81 throug \ h 95 or (resid 99 through 100 and (name N or name CA or name C or name O or name \ CB )) or resid 101 through 104 or (resid 105 and (name N or name CA or name C o \ r name O or name CB )) or resid 106 through 187 or (resid 188 and (name N or nam \ e CA or name C or name O or name CB )) or resid 189 through 199 or (resid 200 an \ d (name N or name CA or name C or name O or name CB )) or resid 201 through 209 \ or resid 217 through 243 or resid 264 through 328 or resid 335 through 344 or (r \ esid 345 through 346 and (name N or name CA or name C or name O or name CB )) or \ resid 347 through 454 or resid 491 through 504 or (resid 505 and (name N or nam \ e CA or name C or name O or name CB )) or resid 506 through 1321)) } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 21.710 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 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 : 0.005 0.106 23418 Z= 0.242 Angle : 1.075 57.515 32042 Z= 0.544 Chirality : 0.066 1.265 3889 Planarity : 0.015 0.309 4020 Dihedral : 12.569 89.935 9049 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.18 % Favored : 94.65 % Rotamer: Outliers : 0.59 % Allowed : 3.39 % Favored : 96.02 % 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: -1.66 (0.15), residues: 2821 helix: -0.34 (0.19), residues: 646 sheet: -0.73 (0.22), residues: 519 loop : -1.57 (0.14), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C1014 TYR 0.032 0.002 TYR B 660 PHE 0.033 0.002 PHE C 888 TRP 0.015 0.001 TRP B1102 HIS 0.011 0.002 HIS B 655 Details of bonding type rmsd covalent geometry : bond 0.00516 (23322) covalent geometry : angle 0.91948 (31789) SS BOND : bond 0.00816 ( 35) SS BOND : angle 3.35489 ( 70) hydrogen bonds : bond 0.24991 ( 876) hydrogen bonds : angle 9.70141 ( 2472) link_BETA1-4 : bond 0.04492 ( 17) link_BETA1-4 : angle 12.30232 ( 51) link_NAG-ASN : bond 0.00566 ( 44) link_NAG-ASN : angle 3.50325 ( 132) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5642 Ramachandran restraints generated. 2821 Oldfield, 0 Emsley, 2821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5642 Ramachandran restraints generated. 2821 Oldfield, 0 Emsley, 2821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 258 time to evaluate : 0.783 Fit side-chains revert: symmetry clash REVERT: B 562 PHE cc_start: 0.7284 (p90) cc_final: 0.7018 (p90) REVERT: B 763 LEU cc_start: 0.9105 (mt) cc_final: 0.8206 (mt) REVERT: B 1050 MET cc_start: 0.8074 (ptm) cc_final: 0.7817 (ptp) REVERT: C 42 VAL cc_start: 0.9198 (m) cc_final: 0.8968 (m) REVERT: C 646 ARG cc_start: 0.7111 (tpt90) cc_final: 0.6837 (tpt-90) REVERT: C 867 ASP cc_start: 0.7910 (m-30) cc_final: 0.7625 (m-30) REVERT: C 902 MET cc_start: 0.8873 (tpt) cc_final: 0.8563 (tpt) REVERT: C 904 TYR cc_start: 0.6915 (t80) cc_final: 0.6676 (t80) outliers start: 14 outliers final: 4 residues processed: 272 average time/residue: 0.1441 time to fit residues: 62.1385 Evaluate side-chains 143 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 139 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 GLN A 644 GLN A 655 HIS A 755 GLN A 762 GLN ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A 955 ASN A 957 GLN A 965 GLN ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS B 207 HIS B 394 ASN B 542 ASN B 564 GLN B 655 HIS B 755 GLN B 804 GLN B 901 GLN B 935 GLN B 954 GLN B 955 ASN B 965 GLN B1119 ASN C 61 ASN C 66 HIS C 536 ASN C 606 ASN C 644 GLN C 751 ASN C 755 GLN C 955 ASN C 965 GLN C1113 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.097767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.068372 restraints weight = 59749.163| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 3.63 r_work: 0.2976 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.107 23418 Z= 0.268 Angle : 0.801 13.831 32042 Z= 0.395 Chirality : 0.052 0.334 3889 Planarity : 0.005 0.053 4020 Dihedral : 8.224 59.823 4338 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.91 % Allowed : 9.58 % Favored : 88.52 % 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: -1.06 (0.15), residues: 2821 helix: 0.80 (0.20), residues: 667 sheet: -0.66 (0.21), residues: 546 loop : -1.41 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 237 TYR 0.032 0.002 TYR A1067 PHE 0.025 0.002 PHE C 377 TRP 0.014 0.002 TRP A 436 HIS 0.007 0.002 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00626 (23322) covalent geometry : angle 0.76668 (31789) SS BOND : bond 0.00693 ( 35) SS BOND : angle 2.29382 ( 70) hydrogen bonds : bond 0.05837 ( 876) hydrogen bonds : angle 6.59281 ( 2472) link_BETA1-4 : bond 0.00306 ( 17) link_BETA1-4 : angle 3.10786 ( 51) link_NAG-ASN : bond 0.00573 ( 44) link_NAG-ASN : angle 2.74582 ( 132) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5642 Ramachandran restraints generated. 2821 Oldfield, 0 Emsley, 2821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5642 Ramachandran restraints generated. 2821 Oldfield, 0 Emsley, 2821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 151 time to evaluate : 0.847 Fit side-chains revert: symmetry clash REVERT: A 656 VAL cc_start: 0.9128 (OUTLIER) cc_final: 0.8906 (p) REVERT: A 957 GLN cc_start: 0.8696 (OUTLIER) cc_final: 0.8359 (tm-30) REVERT: B 394 ASN cc_start: 0.8893 (OUTLIER) cc_final: 0.8585 (p0) REVERT: B 543 PHE cc_start: 0.7303 (t80) cc_final: 0.6944 (t80) REVERT: B 562 PHE cc_start: 0.7565 (p90) cc_final: 0.7146 (p90) REVERT: B 1005 GLN cc_start: 0.9373 (tp40) cc_final: 0.8961 (tp40) REVERT: B 1132 ILE cc_start: 0.8958 (OUTLIER) cc_final: 0.8733 (pt) REVERT: C 525 CYS cc_start: 0.5398 (OUTLIER) cc_final: 0.4765 (m) REVERT: C 756 TYR cc_start: 0.8717 (m-80) cc_final: 0.8176 (m-10) REVERT: C 867 ASP cc_start: 0.8484 (m-30) cc_final: 0.8152 (m-30) REVERT: C 882 ILE cc_start: 0.9619 (mt) cc_final: 0.9376 (mp) REVERT: C 902 MET cc_start: 0.9222 (tpt) cc_final: 0.8761 (tpt) REVERT: C 904 TYR cc_start: 0.8043 (t80) cc_final: 0.7837 (t80) REVERT: C 1031 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8012 (mp0) REVERT: C 1050 MET cc_start: 0.8474 (ttp) cc_final: 0.8248 (mtp) outliers start: 45 outliers final: 11 residues processed: 189 average time/residue: 0.1336 time to fit residues: 42.6361 Evaluate side-chains 136 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1116 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 204 optimal weight: 0.8980 chunk 215 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 277 optimal weight: 0.6980 chunk 131 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 219 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN C 764 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.098650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.069175 restraints weight = 59278.543| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 3.65 r_work: 0.2997 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 23418 Z= 0.157 Angle : 0.668 14.948 32042 Z= 0.330 Chirality : 0.047 0.279 3889 Planarity : 0.004 0.045 4020 Dihedral : 7.547 57.893 4336 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.12 % Allowed : 11.36 % Favored : 86.53 % 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: -0.77 (0.15), residues: 2821 helix: 1.17 (0.21), residues: 663 sheet: -0.50 (0.21), residues: 573 loop : -1.28 (0.15), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 237 TYR 0.022 0.001 TYR A1067 PHE 0.019 0.001 PHE C 168 TRP 0.013 0.001 TRP B 353 HIS 0.003 0.001 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00354 (23322) covalent geometry : angle 0.64034 (31789) SS BOND : bond 0.00541 ( 35) SS BOND : angle 2.07844 ( 70) hydrogen bonds : bond 0.05134 ( 876) hydrogen bonds : angle 5.97377 ( 2472) link_BETA1-4 : bond 0.00348 ( 17) link_BETA1-4 : angle 2.46416 ( 51) link_NAG-ASN : bond 0.00361 ( 44) link_NAG-ASN : angle 2.20452 ( 132) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5642 Ramachandran restraints generated. 2821 Oldfield, 0 Emsley, 2821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5642 Ramachandran restraints generated. 2821 Oldfield, 0 Emsley, 2821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 156 time to evaluate : 0.821 Fit side-chains REVERT: A 515 PHE cc_start: 0.8688 (m-10) cc_final: 0.8397 (m-10) REVERT: A 957 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.8463 (tm-30) REVERT: B 543 PHE cc_start: 0.7518 (t80) cc_final: 0.7078 (t80) REVERT: B 562 PHE cc_start: 0.7582 (p90) cc_final: 0.7126 (p90) REVERT: B 740 MET cc_start: 0.9196 (tpp) cc_final: 0.8824 (tpp) REVERT: B 1005 GLN cc_start: 0.9257 (tp40) cc_final: 0.8912 (tp40) REVERT: B 1132 ILE cc_start: 0.8935 (OUTLIER) cc_final: 0.8709 (pt) REVERT: C 269 TYR cc_start: 0.7183 (m-80) cc_final: 0.6964 (m-80) REVERT: C 394 ASN cc_start: 0.8498 (m-40) cc_final: 0.8253 (m-40) REVERT: C 525 CYS cc_start: 0.5430 (OUTLIER) cc_final: 0.4809 (m) REVERT: C 756 TYR cc_start: 0.8751 (m-80) cc_final: 0.8340 (m-10) REVERT: C 867 ASP cc_start: 0.8447 (m-30) cc_final: 0.8102 (m-30) REVERT: C 882 ILE cc_start: 0.9616 (mt) cc_final: 0.9377 (mp) REVERT: C 888 PHE cc_start: 0.9211 (OUTLIER) cc_final: 0.8709 (p90) REVERT: C 902 MET cc_start: 0.9171 (tpt) cc_final: 0.8837 (tpt) REVERT: C 904 TYR cc_start: 0.7900 (t80) cc_final: 0.7679 (t80) REVERT: C 1005 GLN cc_start: 0.9081 (tp40) cc_final: 0.8787 (mm-40) REVERT: C 1031 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.7892 (mp0) outliers start: 50 outliers final: 18 residues processed: 197 average time/residue: 0.1337 time to fit residues: 44.5054 Evaluate side-chains 147 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1031 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 77 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 170 optimal weight: 0.6980 chunk 160 optimal weight: 1.9990 chunk 21 optimal weight: 0.0270 chunk 235 optimal weight: 7.9990 chunk 128 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 118 optimal weight: 0.0970 chunk 123 optimal weight: 6.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.5236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.099627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.070250 restraints weight = 58976.350| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 3.64 r_work: 0.3023 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 23418 Z= 0.121 Angle : 0.614 10.714 32042 Z= 0.302 Chirality : 0.046 0.279 3889 Planarity : 0.004 0.049 4020 Dihedral : 7.135 59.958 4336 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.61 % Allowed : 12.92 % Favored : 85.47 % 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: -0.54 (0.16), residues: 2821 helix: 1.42 (0.21), residues: 657 sheet: -0.31 (0.21), residues: 580 loop : -1.18 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 509 TYR 0.021 0.001 TYR A1067 PHE 0.022 0.001 PHE B 643 TRP 0.014 0.001 TRP A 436 HIS 0.003 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00268 (23322) covalent geometry : angle 0.59233 (31789) SS BOND : bond 0.00588 ( 35) SS BOND : angle 1.74522 ( 70) hydrogen bonds : bond 0.04416 ( 876) hydrogen bonds : angle 5.61297 ( 2472) link_BETA1-4 : bond 0.00365 ( 17) link_BETA1-4 : angle 2.14062 ( 51) link_NAG-ASN : bond 0.00292 ( 44) link_NAG-ASN : angle 1.92441 ( 132) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5642 Ramachandran restraints generated. 2821 Oldfield, 0 Emsley, 2821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5642 Ramachandran restraints generated. 2821 Oldfield, 0 Emsley, 2821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 151 time to evaluate : 0.660 Fit side-chains revert: symmetry clash REVERT: B 53 ASP cc_start: 0.7537 (t0) cc_final: 0.7321 (t0) REVERT: B 543 PHE cc_start: 0.7408 (t80) cc_final: 0.6936 (t80) REVERT: B 562 PHE cc_start: 0.7550 (p90) cc_final: 0.7020 (p90) REVERT: B 1005 GLN cc_start: 0.9218 (tp40) cc_final: 0.8850 (tp40) REVERT: B 1050 MET cc_start: 0.8434 (ptm) cc_final: 0.8210 (ptp) REVERT: B 1132 ILE cc_start: 0.8882 (OUTLIER) cc_final: 0.8630 (pt) REVERT: C 200 TYR cc_start: 0.7890 (m-80) cc_final: 0.7391 (m-80) REVERT: C 306 PHE cc_start: 0.7975 (m-80) cc_final: 0.7767 (m-80) REVERT: C 394 ASN cc_start: 0.8480 (m-40) cc_final: 0.8245 (m-40) REVERT: C 525 CYS cc_start: 0.5528 (OUTLIER) cc_final: 0.4919 (m) REVERT: C 598 ILE cc_start: 0.8676 (mm) cc_final: 0.8404 (mm) REVERT: C 756 TYR cc_start: 0.8747 (m-80) cc_final: 0.8366 (m-10) REVERT: C 770 ILE cc_start: 0.8878 (pt) cc_final: 0.8651 (mt) REVERT: C 773 GLU cc_start: 0.8772 (tt0) cc_final: 0.8494 (tt0) REVERT: C 867 ASP cc_start: 0.8375 (m-30) cc_final: 0.8013 (m-30) REVERT: C 882 ILE cc_start: 0.9561 (mt) cc_final: 0.9311 (mp) REVERT: C 888 PHE cc_start: 0.9265 (OUTLIER) cc_final: 0.8676 (p90) REVERT: C 902 MET cc_start: 0.9157 (tpt) cc_final: 0.8883 (tpt) REVERT: C 904 TYR cc_start: 0.7866 (t80) cc_final: 0.7614 (t80) REVERT: C 957 GLN cc_start: 0.8802 (tp40) cc_final: 0.8436 (tt0) REVERT: C 1005 GLN cc_start: 0.9045 (tp40) cc_final: 0.8768 (mm-40) REVERT: C 1031 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.7934 (mp0) outliers start: 38 outliers final: 18 residues processed: 185 average time/residue: 0.1311 time to fit residues: 40.8364 Evaluate side-chains 151 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1031 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 254 optimal weight: 0.7980 chunk 80 optimal weight: 0.9980 chunk 136 optimal weight: 3.9990 chunk 152 optimal weight: 0.6980 chunk 203 optimal weight: 9.9990 chunk 94 optimal weight: 0.8980 chunk 210 optimal weight: 4.9990 chunk 126 optimal weight: 0.7980 chunk 143 optimal weight: 1.9990 chunk 267 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.098682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.068875 restraints weight = 58901.035| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 3.61 r_work: 0.3010 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 23418 Z= 0.132 Angle : 0.601 9.725 32042 Z= 0.295 Chirality : 0.046 0.268 3889 Planarity : 0.004 0.052 4020 Dihedral : 6.829 57.091 4336 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.82 % Allowed : 13.35 % Favored : 84.83 % 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: -0.42 (0.16), residues: 2821 helix: 1.57 (0.21), residues: 641 sheet: -0.23 (0.21), residues: 581 loop : -1.09 (0.15), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 765 TYR 0.020 0.001 TYR A1067 PHE 0.022 0.001 PHE A 374 TRP 0.014 0.001 TRP A 436 HIS 0.006 0.001 HIS B 655 Details of bonding type rmsd covalent geometry : bond 0.00301 (23322) covalent geometry : angle 0.57912 (31789) SS BOND : bond 0.00396 ( 35) SS BOND : angle 1.86657 ( 70) hydrogen bonds : bond 0.04223 ( 876) hydrogen bonds : angle 5.38258 ( 2472) link_BETA1-4 : bond 0.00320 ( 17) link_BETA1-4 : angle 2.02650 ( 51) link_NAG-ASN : bond 0.00284 ( 44) link_NAG-ASN : angle 1.83950 ( 132) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5642 Ramachandran restraints generated. 2821 Oldfield, 0 Emsley, 2821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5642 Ramachandran restraints generated. 2821 Oldfield, 0 Emsley, 2821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 145 time to evaluate : 0.901 Fit side-chains revert: symmetry clash REVERT: A 515 PHE cc_start: 0.8604 (m-10) cc_final: 0.8269 (m-10) REVERT: A 902 MET cc_start: 0.9106 (tpt) cc_final: 0.8836 (tpt) REVERT: A 950 ASP cc_start: 0.8824 (OUTLIER) cc_final: 0.8584 (t0) REVERT: A 957 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.8328 (tm-30) REVERT: A 1017 GLU cc_start: 0.9038 (tm-30) cc_final: 0.8779 (tm-30) REVERT: B 133 PHE cc_start: 0.7200 (m-80) cc_final: 0.6990 (m-80) REVERT: B 166 CYS cc_start: 0.7184 (OUTLIER) cc_final: 0.6419 (t) REVERT: B 562 PHE cc_start: 0.7496 (p90) cc_final: 0.6943 (p90) REVERT: B 990 GLU cc_start: 0.8676 (tm-30) cc_final: 0.8437 (tm-30) REVERT: B 1005 GLN cc_start: 0.9215 (tp40) cc_final: 0.8802 (tp40) REVERT: B 1019 ARG cc_start: 0.8920 (tpp-160) cc_final: 0.8642 (tpp-160) REVERT: B 1132 ILE cc_start: 0.8909 (OUTLIER) cc_final: 0.8669 (pt) REVERT: C 200 TYR cc_start: 0.8046 (m-80) cc_final: 0.7604 (m-80) REVERT: C 269 TYR cc_start: 0.7255 (OUTLIER) cc_final: 0.6185 (t80) REVERT: C 505 TYR cc_start: 0.9154 (m-10) cc_final: 0.8429 (p90) REVERT: C 525 CYS cc_start: 0.5688 (OUTLIER) cc_final: 0.5063 (m) REVERT: C 598 ILE cc_start: 0.8701 (mm) cc_final: 0.8421 (mm) REVERT: C 756 TYR cc_start: 0.8870 (m-80) cc_final: 0.8608 (m-10) REVERT: C 773 GLU cc_start: 0.8791 (tt0) cc_final: 0.8506 (tt0) REVERT: C 867 ASP cc_start: 0.8380 (m-30) cc_final: 0.8032 (m-30) REVERT: C 882 ILE cc_start: 0.9564 (mt) cc_final: 0.9320 (mp) REVERT: C 888 PHE cc_start: 0.9290 (OUTLIER) cc_final: 0.8580 (p90) REVERT: C 902 MET cc_start: 0.9142 (tpt) cc_final: 0.8898 (tpt) REVERT: C 904 TYR cc_start: 0.7841 (t80) cc_final: 0.7597 (t80) REVERT: C 1005 GLN cc_start: 0.9065 (tp40) cc_final: 0.8784 (mm-40) REVERT: C 1031 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8000 (mp0) outliers start: 43 outliers final: 20 residues processed: 183 average time/residue: 0.1304 time to fit residues: 40.5434 Evaluate side-chains 153 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 125 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 269 TYR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1031 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 220 optimal weight: 0.8980 chunk 259 optimal weight: 2.9990 chunk 201 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 chunk 174 optimal weight: 0.9990 chunk 16 optimal weight: 0.0570 chunk 39 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 266 optimal weight: 1.9990 chunk 27 optimal weight: 8.9990 overall best weight: 1.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.098463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.067840 restraints weight = 59686.565| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 3.90 r_work: 0.2957 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 23418 Z= 0.179 Angle : 0.618 9.652 32042 Z= 0.303 Chirality : 0.046 0.262 3889 Planarity : 0.004 0.053 4020 Dihedral : 6.822 59.715 4336 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.91 % Allowed : 13.77 % Favored : 84.32 % 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: -0.47 (0.16), residues: 2821 helix: 1.48 (0.21), residues: 646 sheet: -0.30 (0.21), residues: 585 loop : -1.10 (0.15), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 765 TYR 0.021 0.001 TYR A1067 PHE 0.016 0.001 PHE C 377 TRP 0.014 0.001 TRP C 886 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00417 (23322) covalent geometry : angle 0.59862 (31789) SS BOND : bond 0.00421 ( 35) SS BOND : angle 1.69846 ( 70) hydrogen bonds : bond 0.04329 ( 876) hydrogen bonds : angle 5.40490 ( 2472) link_BETA1-4 : bond 0.00274 ( 17) link_BETA1-4 : angle 1.99223 ( 51) link_NAG-ASN : bond 0.00315 ( 44) link_NAG-ASN : angle 1.85707 ( 132) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5642 Ramachandran restraints generated. 2821 Oldfield, 0 Emsley, 2821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5642 Ramachandran restraints generated. 2821 Oldfield, 0 Emsley, 2821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 132 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 515 PHE cc_start: 0.8676 (m-10) cc_final: 0.8421 (m-10) REVERT: A 917 TYR cc_start: 0.8933 (m-80) cc_final: 0.8716 (m-80) REVERT: A 950 ASP cc_start: 0.8866 (OUTLIER) cc_final: 0.8627 (t0) REVERT: B 133 PHE cc_start: 0.7224 (m-80) cc_final: 0.6871 (m-80) REVERT: B 562 PHE cc_start: 0.7475 (p90) cc_final: 0.6967 (p90) REVERT: B 740 MET cc_start: 0.9197 (tpp) cc_final: 0.8748 (tpp) REVERT: B 1005 GLN cc_start: 0.9252 (tp40) cc_final: 0.8924 (tp40) REVERT: B 1019 ARG cc_start: 0.8985 (tpp-160) cc_final: 0.8705 (tpp-160) REVERT: B 1132 ILE cc_start: 0.8931 (OUTLIER) cc_final: 0.8706 (pt) REVERT: C 200 TYR cc_start: 0.8096 (m-80) cc_final: 0.7651 (m-80) REVERT: C 505 TYR cc_start: 0.9161 (m-10) cc_final: 0.8422 (p90) REVERT: C 525 CYS cc_start: 0.5697 (OUTLIER) cc_final: 0.5086 (m) REVERT: C 756 TYR cc_start: 0.8999 (m-80) cc_final: 0.8653 (m-10) REVERT: C 867 ASP cc_start: 0.8426 (m-30) cc_final: 0.8067 (m-30) REVERT: C 882 ILE cc_start: 0.9588 (mt) cc_final: 0.9334 (mp) REVERT: C 888 PHE cc_start: 0.9356 (OUTLIER) cc_final: 0.8425 (p90) REVERT: C 902 MET cc_start: 0.9177 (tpt) cc_final: 0.8851 (tpt) REVERT: C 904 TYR cc_start: 0.7899 (t80) cc_final: 0.7676 (t80) REVERT: C 1005 GLN cc_start: 0.9080 (tp40) cc_final: 0.8793 (mm-40) REVERT: C 1031 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8053 (mp0) outliers start: 45 outliers final: 29 residues processed: 173 average time/residue: 0.1329 time to fit residues: 38.7021 Evaluate side-chains 156 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 122 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 6 optimal weight: 0.8980 chunk 215 optimal weight: 0.0770 chunk 133 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 85 optimal weight: 0.5980 chunk 197 optimal weight: 4.9990 chunk 127 optimal weight: 0.7980 chunk 184 optimal weight: 0.9990 chunk 275 optimal weight: 0.6980 chunk 251 optimal weight: 0.0270 chunk 265 optimal weight: 1.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.099566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.070246 restraints weight = 59431.827| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 3.61 r_work: 0.3018 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 23418 Z= 0.111 Angle : 0.585 9.708 32042 Z= 0.287 Chirality : 0.045 0.264 3889 Planarity : 0.004 0.056 4020 Dihedral : 6.602 57.336 4335 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.91 % Allowed : 14.36 % Favored : 83.73 % 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: -0.35 (0.16), residues: 2821 helix: 1.61 (0.21), residues: 645 sheet: -0.14 (0.21), residues: 579 loop : -1.07 (0.15), residues: 1597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C1107 TYR 0.020 0.001 TYR A1067 PHE 0.014 0.001 PHE B 238 TRP 0.022 0.002 TRP B 353 HIS 0.003 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00247 (23322) covalent geometry : angle 0.56599 (31789) SS BOND : bond 0.00449 ( 35) SS BOND : angle 1.81947 ( 70) hydrogen bonds : bond 0.04057 ( 876) hydrogen bonds : angle 5.25365 ( 2472) link_BETA1-4 : bond 0.00360 ( 17) link_BETA1-4 : angle 1.89154 ( 51) link_NAG-ASN : bond 0.00254 ( 44) link_NAG-ASN : angle 1.64786 ( 132) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5642 Ramachandran restraints generated. 2821 Oldfield, 0 Emsley, 2821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5642 Ramachandran restraints generated. 2821 Oldfield, 0 Emsley, 2821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 141 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8851 (tm-30) cc_final: 0.8566 (tm-30) REVERT: A 515 PHE cc_start: 0.8661 (m-10) cc_final: 0.8355 (m-10) REVERT: A 917 TYR cc_start: 0.8881 (m-80) cc_final: 0.8585 (m-80) REVERT: A 955 ASN cc_start: 0.8918 (OUTLIER) cc_final: 0.8686 (t0) REVERT: A 1092 GLU cc_start: 0.8293 (pm20) cc_final: 0.8042 (pm20) REVERT: B 133 PHE cc_start: 0.7192 (m-80) cc_final: 0.6710 (m-80) REVERT: B 562 PHE cc_start: 0.7415 (p90) cc_final: 0.6937 (p90) REVERT: B 1005 GLN cc_start: 0.9193 (tp40) cc_final: 0.8716 (tp-100) REVERT: B 1019 ARG cc_start: 0.8915 (tpp-160) cc_final: 0.8617 (tpp-160) REVERT: B 1132 ILE cc_start: 0.8928 (OUTLIER) cc_final: 0.8692 (pt) REVERT: C 200 TYR cc_start: 0.7997 (m-80) cc_final: 0.7574 (m-80) REVERT: C 505 TYR cc_start: 0.9120 (m-10) cc_final: 0.8406 (p90) REVERT: C 525 CYS cc_start: 0.5690 (OUTLIER) cc_final: 0.5033 (m) REVERT: C 598 ILE cc_start: 0.8704 (mm) cc_final: 0.8408 (mm) REVERT: C 867 ASP cc_start: 0.8343 (m-30) cc_final: 0.7978 (m-30) REVERT: C 882 ILE cc_start: 0.9571 (mt) cc_final: 0.9317 (mp) REVERT: C 888 PHE cc_start: 0.9346 (OUTLIER) cc_final: 0.8411 (p90) REVERT: C 902 MET cc_start: 0.9127 (tpt) cc_final: 0.8858 (tpt) REVERT: C 904 TYR cc_start: 0.7817 (t80) cc_final: 0.7561 (t80) REVERT: C 957 GLN cc_start: 0.8791 (tp40) cc_final: 0.8494 (tt0) REVERT: C 1005 GLN cc_start: 0.9036 (tp40) cc_final: 0.8775 (mm-40) outliers start: 45 outliers final: 26 residues processed: 181 average time/residue: 0.1420 time to fit residues: 43.3209 Evaluate side-chains 159 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 129 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 26 optimal weight: 8.9990 chunk 151 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 134 optimal weight: 7.9990 chunk 123 optimal weight: 0.9990 chunk 213 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 180 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 4 optimal weight: 0.0010 chunk 182 optimal weight: 0.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.098559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.068943 restraints weight = 58652.239| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 3.53 r_work: 0.3023 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 23418 Z= 0.119 Angle : 0.576 9.687 32042 Z= 0.282 Chirality : 0.045 0.261 3889 Planarity : 0.004 0.057 4020 Dihedral : 6.469 57.194 4335 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.65 % Allowed : 15.13 % Favored : 83.22 % 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 (0.16), residues: 2821 helix: 1.62 (0.21), residues: 647 sheet: -0.07 (0.21), residues: 576 loop : -1.05 (0.15), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 273 TYR 0.022 0.001 TYR B 904 PHE 0.017 0.001 PHE B 238 TRP 0.016 0.001 TRP A 436 HIS 0.003 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00272 (23322) covalent geometry : angle 0.55995 (31789) SS BOND : bond 0.00537 ( 35) SS BOND : angle 1.54129 ( 70) hydrogen bonds : bond 0.03934 ( 876) hydrogen bonds : angle 5.16788 ( 2472) link_BETA1-4 : bond 0.00344 ( 17) link_BETA1-4 : angle 1.83112 ( 51) link_NAG-ASN : bond 0.00231 ( 44) link_NAG-ASN : angle 1.58840 ( 132) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5642 Ramachandran restraints generated. 2821 Oldfield, 0 Emsley, 2821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5642 Ramachandran restraints generated. 2821 Oldfield, 0 Emsley, 2821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 134 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8849 (tm-30) cc_final: 0.8582 (tm-30) REVERT: A 515 PHE cc_start: 0.8670 (m-10) cc_final: 0.8289 (m-10) REVERT: B 562 PHE cc_start: 0.7389 (p90) cc_final: 0.6914 (p90) REVERT: B 1005 GLN cc_start: 0.9193 (tp40) cc_final: 0.8692 (tp-100) REVERT: B 1019 ARG cc_start: 0.8933 (tpp-160) cc_final: 0.8635 (tpp-160) REVERT: B 1132 ILE cc_start: 0.8920 (OUTLIER) cc_final: 0.8683 (pt) REVERT: C 65 PHE cc_start: 0.7011 (m-80) cc_final: 0.6701 (m-10) REVERT: C 200 TYR cc_start: 0.7898 (m-80) cc_final: 0.7478 (m-80) REVERT: C 392 PHE cc_start: 0.8556 (m-80) cc_final: 0.8290 (m-80) REVERT: C 505 TYR cc_start: 0.9077 (m-10) cc_final: 0.8355 (p90) REVERT: C 525 CYS cc_start: 0.5756 (OUTLIER) cc_final: 0.5102 (m) REVERT: C 598 ILE cc_start: 0.8736 (mm) cc_final: 0.8444 (mm) REVERT: C 867 ASP cc_start: 0.8348 (m-30) cc_final: 0.7981 (m-30) REVERT: C 882 ILE cc_start: 0.9577 (mt) cc_final: 0.9330 (mp) REVERT: C 888 PHE cc_start: 0.9341 (OUTLIER) cc_final: 0.8372 (p90) REVERT: C 902 MET cc_start: 0.9122 (tpt) cc_final: 0.8905 (tpt) REVERT: C 904 TYR cc_start: 0.7811 (t80) cc_final: 0.7564 (t80) REVERT: C 1005 GLN cc_start: 0.9049 (tp40) cc_final: 0.8793 (mm-40) outliers start: 39 outliers final: 30 residues processed: 168 average time/residue: 0.1347 time to fit residues: 38.5570 Evaluate side-chains 158 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 125 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 65 optimal weight: 3.9990 chunk 107 optimal weight: 8.9990 chunk 168 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 143 optimal weight: 0.9990 chunk 204 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 152 optimal weight: 0.5980 chunk 197 optimal weight: 2.9990 chunk 194 optimal weight: 9.9990 chunk 201 optimal weight: 3.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.096265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.066643 restraints weight = 60216.381| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 3.65 r_work: 0.2933 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.103 23418 Z= 0.261 Angle : 0.680 9.571 32042 Z= 0.334 Chirality : 0.047 0.265 3889 Planarity : 0.004 0.057 4020 Dihedral : 6.832 57.469 4335 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.65 % Allowed : 15.64 % Favored : 82.71 % 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: -0.55 (0.16), residues: 2821 helix: 1.30 (0.21), residues: 649 sheet: -0.30 (0.21), residues: 590 loop : -1.11 (0.15), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 273 TYR 0.030 0.002 TYR B 904 PHE 0.019 0.002 PHE C 92 TRP 0.015 0.002 TRP C 886 HIS 0.007 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00611 (23322) covalent geometry : angle 0.66242 (31789) SS BOND : bond 0.00549 ( 35) SS BOND : angle 1.79499 ( 70) hydrogen bonds : bond 0.04575 ( 876) hydrogen bonds : angle 5.49946 ( 2472) link_BETA1-4 : bond 0.00262 ( 17) link_BETA1-4 : angle 1.98126 ( 51) link_NAG-ASN : bond 0.00422 ( 44) link_NAG-ASN : angle 1.85350 ( 132) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5642 Ramachandran restraints generated. 2821 Oldfield, 0 Emsley, 2821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5642 Ramachandran restraints generated. 2821 Oldfield, 0 Emsley, 2821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 131 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8915 (tm-30) cc_final: 0.8580 (tm-30) REVERT: A 515 PHE cc_start: 0.8659 (m-10) cc_final: 0.8338 (m-10) REVERT: A 950 ASP cc_start: 0.8863 (m-30) cc_final: 0.8621 (t0) REVERT: B 365 TYR cc_start: 0.8466 (m-80) cc_final: 0.8140 (m-10) REVERT: B 562 PHE cc_start: 0.7460 (p90) cc_final: 0.6947 (p90) REVERT: B 1005 GLN cc_start: 0.9305 (tp40) cc_final: 0.8902 (tp40) REVERT: B 1019 ARG cc_start: 0.9011 (tpp-160) cc_final: 0.8714 (tpp-160) REVERT: B 1132 ILE cc_start: 0.9050 (OUTLIER) cc_final: 0.8849 (pt) REVERT: C 200 TYR cc_start: 0.8044 (m-80) cc_final: 0.7550 (m-80) REVERT: C 392 PHE cc_start: 0.8560 (m-80) cc_final: 0.8351 (m-80) REVERT: C 505 TYR cc_start: 0.9160 (m-10) cc_final: 0.8389 (p90) REVERT: C 525 CYS cc_start: 0.5839 (OUTLIER) cc_final: 0.5220 (m) REVERT: C 563 GLN cc_start: 0.9060 (OUTLIER) cc_final: 0.8457 (mp10) REVERT: C 661 GLU cc_start: 0.8715 (tp30) cc_final: 0.8474 (tp30) REVERT: C 867 ASP cc_start: 0.8566 (m-30) cc_final: 0.8244 (m-30) REVERT: C 882 ILE cc_start: 0.9609 (mt) cc_final: 0.9347 (mp) REVERT: C 888 PHE cc_start: 0.9409 (OUTLIER) cc_final: 0.8681 (p90) REVERT: C 902 MET cc_start: 0.9139 (tpt) cc_final: 0.8773 (tpt) REVERT: C 904 TYR cc_start: 0.7955 (t80) cc_final: 0.7747 (t80) REVERT: C 1005 GLN cc_start: 0.9100 (tp40) cc_final: 0.8747 (mm-40) outliers start: 39 outliers final: 28 residues processed: 167 average time/residue: 0.1269 time to fit residues: 36.0800 Evaluate side-chains 158 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 126 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 978 ASN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 56 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 178 optimal weight: 0.9990 chunk 127 optimal weight: 3.9990 chunk 277 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 154 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 chunk 97 optimal weight: 0.6980 chunk 83 optimal weight: 0.6980 chunk 286 optimal weight: 0.7980 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 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.098215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.068788 restraints weight = 59842.312| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 3.67 r_work: 0.2984 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 23418 Z= 0.135 Angle : 0.601 9.561 32042 Z= 0.293 Chirality : 0.045 0.302 3889 Planarity : 0.004 0.057 4020 Dihedral : 6.578 57.287 4335 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.44 % Allowed : 16.02 % Favored : 82.54 % 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: -0.38 (0.16), residues: 2821 helix: 1.58 (0.21), residues: 640 sheet: -0.18 (0.21), residues: 576 loop : -1.07 (0.15), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 273 TYR 0.024 0.001 TYR B 904 PHE 0.019 0.001 PHE B 238 TRP 0.015 0.001 TRP C 886 HIS 0.003 0.001 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00312 (23322) covalent geometry : angle 0.58608 (31789) SS BOND : bond 0.00466 ( 35) SS BOND : angle 1.42257 ( 70) hydrogen bonds : bond 0.04079 ( 876) hydrogen bonds : angle 5.27849 ( 2472) link_BETA1-4 : bond 0.00332 ( 17) link_BETA1-4 : angle 1.79914 ( 51) link_NAG-ASN : bond 0.00255 ( 44) link_NAG-ASN : angle 1.58510 ( 132) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5642 Ramachandran restraints generated. 2821 Oldfield, 0 Emsley, 2821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5642 Ramachandran restraints generated. 2821 Oldfield, 0 Emsley, 2821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 130 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8909 (tm-30) cc_final: 0.8643 (tm-30) REVERT: A 515 PHE cc_start: 0.8666 (m-10) cc_final: 0.8348 (m-10) REVERT: A 740 MET cc_start: 0.8951 (tpp) cc_final: 0.8673 (tpp) REVERT: A 917 TYR cc_start: 0.8965 (m-10) cc_final: 0.8689 (m-80) REVERT: A 950 ASP cc_start: 0.8811 (m-30) cc_final: 0.8558 (t0) REVERT: A 1092 GLU cc_start: 0.8302 (pm20) cc_final: 0.8050 (pm20) REVERT: B 53 ASP cc_start: 0.7382 (t0) cc_final: 0.7168 (t0) REVERT: B 365 TYR cc_start: 0.8486 (m-80) cc_final: 0.8190 (m-10) REVERT: B 562 PHE cc_start: 0.7302 (p90) cc_final: 0.6831 (p90) REVERT: B 1019 ARG cc_start: 0.8962 (tpp-160) cc_final: 0.8670 (tpp-160) REVERT: B 1132 ILE cc_start: 0.9000 (OUTLIER) cc_final: 0.8793 (pt) REVERT: C 200 TYR cc_start: 0.7864 (m-80) cc_final: 0.7480 (m-80) REVERT: C 505 TYR cc_start: 0.9121 (m-10) cc_final: 0.8407 (p90) REVERT: C 598 ILE cc_start: 0.8721 (mm) cc_final: 0.8412 (mm) REVERT: C 661 GLU cc_start: 0.8733 (tp30) cc_final: 0.8486 (tp30) REVERT: C 867 ASP cc_start: 0.8441 (m-30) cc_final: 0.8085 (m-30) REVERT: C 882 ILE cc_start: 0.9584 (mt) cc_final: 0.9328 (mp) REVERT: C 888 PHE cc_start: 0.9400 (OUTLIER) cc_final: 0.8671 (p90) REVERT: C 902 MET cc_start: 0.9137 (tpt) cc_final: 0.8821 (tpt) REVERT: C 904 TYR cc_start: 0.7897 (t80) cc_final: 0.7670 (t80) REVERT: C 1005 GLN cc_start: 0.9061 (tp40) cc_final: 0.8784 (mm-40) outliers start: 34 outliers final: 27 residues processed: 162 average time/residue: 0.1348 time to fit residues: 37.3073 Evaluate side-chains 153 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 93 optimal weight: 1.9990 chunk 170 optimal weight: 0.6980 chunk 35 optimal weight: 20.0000 chunk 4 optimal weight: 4.9990 chunk 159 optimal weight: 2.9990 chunk 172 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 286 optimal weight: 0.9980 chunk 47 optimal weight: 0.0970 chunk 95 optimal weight: 10.0000 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.098121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.068642 restraints weight = 59688.978| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 3.65 r_work: 0.2981 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 23418 Z= 0.143 Angle : 0.596 9.584 32042 Z= 0.292 Chirality : 0.045 0.298 3889 Planarity : 0.004 0.057 4020 Dihedral : 6.495 57.096 4334 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.61 % Allowed : 15.68 % Favored : 82.71 % 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: -0.32 (0.16), residues: 2821 helix: 1.63 (0.21), residues: 641 sheet: -0.12 (0.21), residues: 574 loop : -1.04 (0.15), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 273 TYR 0.024 0.001 TYR B 904 PHE 0.014 0.001 PHE C 377 TRP 0.014 0.001 TRP A 436 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00332 (23322) covalent geometry : angle 0.58204 (31789) SS BOND : bond 0.00416 ( 35) SS BOND : angle 1.38927 ( 70) hydrogen bonds : bond 0.04043 ( 876) hydrogen bonds : angle 5.21783 ( 2472) link_BETA1-4 : bond 0.00301 ( 17) link_BETA1-4 : angle 1.79295 ( 51) link_NAG-ASN : bond 0.00256 ( 44) link_NAG-ASN : angle 1.58044 ( 132) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5168.75 seconds wall clock time: 89 minutes 26.83 seconds (5366.83 seconds total)