Starting phenix.real_space_refine on Sun Jul 5 08:39:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xiw_33210/07_2026/7xiw_33210.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xiw_33210/07_2026/7xiw_33210.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7xiw_33210/07_2026/7xiw_33210.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xiw_33210/07_2026/7xiw_33210.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7xiw_33210/07_2026/7xiw_33210.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xiw_33210/07_2026/7xiw_33210.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xiw_33210/07_2026/7xiw_33210.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xiw_33210/07_2026/7xiw_33210.map" } resolution = 3.62 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.063 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 112 5.16 5 C 16971 2.51 5 N 4358 2.21 5 O 5183 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26624 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 8610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1103, 8610 Classifications: {'peptide': 1103} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 58, 'TRANS': 1044} Chain breaks: 2 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 8604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1102, 8604 Classifications: {'peptide': 1102} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 58, 'TRANS': 1043} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 8626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1105, 8626 Classifications: {'peptide': 1105} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 58, 'TRANS': 1046} Chain breaks: 2 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 chiralities: 9 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "D" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 5.50, per 1000 atoms: 0.21 Number of scatterers: 26624 At special positions: 0 Unit cell: (157.29, 153.01, 206.51, 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 112 16.00 O 5183 8.00 N 4358 7.00 C 16971 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, 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=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.03 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.03 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.03 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.03 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 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-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 657 " " NAG A1308 " - " ASN A 709 " " NAG A1309 " - " ASN A1074 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " NAG C 1 " - " ASN A 343 " " NAG D1301 " - " ASN D 61 " " NAG D1302 " - " ASN D 122 " " NAG D1303 " - " ASN D 165 " " NAG D1304 " - " ASN D 234 " " NAG D1305 " - " ASN D 282 " " NAG D1306 " - " ASN D 616 " " NAG D1307 " - " ASN D 657 " " NAG D1308 " - " ASN D 709 " " NAG D1309 " - " ASN D 801 " " NAG D1311 " - " ASN D1074 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN A1134 " " NAG I 1 " - " ASN B 343 " " 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 D 717 " " NAG O 1 " - " ASN D1098 " " NAG P 1 " - " ASN D1134 " Time building additional restraints: 2.13 Conformation dependent library (CDL) restraints added in 866.6 milliseconds 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6186 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 49 sheets defined 22.5% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 4.086A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.758A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 372 removed outlier: 4.170A pdb=" N PHE A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ALA A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 367 through 372' Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.670A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.709A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.559A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 762 through 783 removed outlier: 3.749A pdb=" N ALA A 766 " --> pdb=" O GLN A 762 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR A 768 " --> pdb=" O LYS A 764 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 850 through 854 Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.505A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.681A pdb=" N ALA A 890 " --> pdb=" O THR A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.587A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.765A pdb=" N LYS A 933 " --> pdb=" O SER A 929 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.716A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP A 950 " --> pdb=" O GLY A 946 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.544A pdb=" N LEU A 984 " --> pdb=" O ILE A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.206A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR A1006 " --> pdb=" O GLN A1002 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TYR A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL A1008 " --> pdb=" O LEU A1004 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE A1013 " --> pdb=" O THR A1009 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1150 removed outlier: 3.780A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N PHE A1148 " --> pdb=" O GLU A1144 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU A1150 " --> pdb=" O ASP A1146 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.932A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.610A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 765 through 783 removed outlier: 3.860A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 850 through 854 removed outlier: 3.773A pdb=" N LYS B 854 " --> pdb=" O CYS B 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.861A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 933 Processing helix chain 'B' and resid 933 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.593A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP B 950 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.589A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.344A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE B 997 " --> pdb=" O ILE B 993 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR B 998 " --> pdb=" O ASP B 994 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLY B 999 " --> pdb=" O ARG B 995 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR B1006 " --> pdb=" O GLN B1002 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N TYR B1007 " --> pdb=" O SER B1003 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL B1008 " --> pdb=" O LEU B1004 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE B1013 " --> pdb=" O THR B1009 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA B1016 " --> pdb=" O LEU B1012 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1150 removed outlier: 3.963A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 304 Processing helix chain 'D' and resid 338 through 343 Processing helix chain 'D' and resid 367 through 372 removed outlier: 3.780A pdb=" N ASN D 370 " --> pdb=" O VAL D 367 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ALA D 372 " --> pdb=" O TYR D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 407 No H-bonds generated for 'chain 'D' and resid 405 through 407' Processing helix chain 'D' and resid 619 through 623 Processing helix chain 'D' and resid 737 through 742 Processing helix chain 'D' and resid 747 through 754 Processing helix chain 'D' and resid 755 through 757 No H-bonds generated for 'chain 'D' and resid 755 through 757' Processing helix chain 'D' and resid 760 through 783 removed outlier: 3.893A pdb=" N THR D 778 " --> pdb=" O GLN D 774 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLN D 779 " --> pdb=" O ASP D 775 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU D 780 " --> pdb=" O LYS D 776 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL D 781 " --> pdb=" O ASN D 777 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE D 782 " --> pdb=" O THR D 778 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 826 Processing helix chain 'D' and resid 849 through 854 removed outlier: 3.885A pdb=" N LYS D 854 " --> pdb=" O CYS D 851 " (cutoff:3.500A) Processing helix chain 'D' and resid 866 through 884 Processing helix chain 'D' and resid 886 through 890 Processing helix chain 'D' and resid 897 through 908 Processing helix chain 'D' and resid 913 through 919 removed outlier: 3.735A pdb=" N TYR D 917 " --> pdb=" O GLN D 913 " (cutoff:3.500A) Processing helix chain 'D' and resid 919 through 941 removed outlier: 3.719A pdb=" N LYS D 933 " --> pdb=" O SER D 929 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE D 934 " --> pdb=" O ALA D 930 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLN D 935 " --> pdb=" O ILE D 931 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ASP D 936 " --> pdb=" O GLY D 932 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 965 removed outlier: 3.580A pdb=" N GLN D 949 " --> pdb=" O LEU D 945 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP D 950 " --> pdb=" O GLY D 946 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL D 951 " --> pdb=" O LYS D 947 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL D 952 " --> pdb=" O LEU D 948 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN D 955 " --> pdb=" O VAL D 951 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA D 956 " --> pdb=" O VAL D 952 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN D 957 " --> pdb=" O ASN D 953 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA D 958 " --> pdb=" O HIS D 954 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU D 959 " --> pdb=" O ASN D 955 " (cutoff:3.500A) Processing helix chain 'D' and resid 966 through 968 No H-bonds generated for 'chain 'D' and resid 966 through 968' Processing helix chain 'D' and resid 976 through 984 Processing helix chain 'D' and resid 985 through 1033 removed outlier: 4.242A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ASP D 994 " --> pdb=" O GLU D 990 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ARG D 995 " --> pdb=" O VAL D 991 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LEU D 996 " --> pdb=" O GLN D 992 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE D 997 " --> pdb=" O ILE D 993 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR D1007 " --> pdb=" O SER D1003 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE D1013 " --> pdb=" O THR D1009 " (cutoff:3.500A) Processing helix chain 'D' and resid 1140 through 1150 removed outlier: 3.932A pdb=" N GLU D1144 " --> pdb=" O PRO D1140 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE D1148 " --> pdb=" O GLU D1144 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU D1150 " --> pdb=" O ASP D1146 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 31 removed outlier: 3.605A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.621A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 84 removed outlier: 4.278A pdb=" N LEU A 241 " --> pdb=" O GLY A 103 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE A 106 " --> pdb=" O LEU A 117 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 84 removed outlier: 4.278A pdb=" N LEU A 241 " --> pdb=" O GLY A 103 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE A 106 " --> pdb=" O LEU A 117 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 3.600A pdb=" N THR A 315 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.371A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.371A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.238A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 573 through 576 removed outlier: 6.906A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 660 removed outlier: 3.828A pdb=" N VAL A 656 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR A 695 " --> pdb=" O CYS A 671 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N CYS A 671 " --> pdb=" O TYR A 695 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 713 Processing sheet with id=AB4, first strand: chain 'A' and resid 717 through 722 removed outlier: 6.492A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 717 through 722 removed outlier: 6.492A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.855A pdb=" N ILE A 788 " --> pdb=" O ASN D 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB9, first strand: chain 'B' and resid 26 through 31 removed outlier: 3.599A pdb=" N SER B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER B 94 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.483A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.943A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.558A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 125 through 127 removed outlier: 3.842A pdb=" N ASN B 125 " --> pdb=" O ASN B 122 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 125 through 127 removed outlier: 3.842A pdb=" N ASN B 125 " --> pdb=" O ASN B 122 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE B 106 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 3.559A pdb=" N THR B 315 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 324 through 325 removed outlier: 7.593A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.005A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP B 398 " --> pdb=" O VAL B 512 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 391 through 392 removed outlier: 3.824A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 removed outlier: 3.824A pdb=" N ARG B 493 " --> pdb=" O TYR B 453 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD1, first strand: chain 'B' and resid 659 through 660 removed outlier: 4.196A pdb=" N TYR B 660 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 712 through 713 Processing sheet with id=AD3, first strand: chain 'B' and resid 718 through 719 Processing sheet with id=AD4, first strand: chain 'B' and resid 722 through 728 removed outlier: 3.543A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD6, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD7, first strand: chain 'D' and resid 28 through 31 removed outlier: 3.618A pdb=" N THR D 29 " --> pdb=" O VAL D 62 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR D 63 " --> pdb=" O VAL D 267 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL D 267 " --> pdb=" O THR D 63 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL D 193 " --> pdb=" O TYR D 204 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS D 195 " --> pdb=" O LYS D 202 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL D 227 " --> pdb=" O ILE D 203 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N SER D 205 " --> pdb=" O PRO D 225 " (cutoff:3.500A) removed outlier: 9.723A pdb=" N HIS D 207 " --> pdb=" O LEU D 223 " (cutoff:3.500A) removed outlier: 9.539A pdb=" N LEU D 223 " --> pdb=" O HIS D 207 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL D 36 " --> pdb=" O LEU D 223 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 51 through 55 removed outlier: 3.595A pdb=" N PHE D 275 " --> pdb=" O THR D 51 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP D 53 " --> pdb=" O ARG D 273 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG D 273 " --> pdb=" O ASP D 53 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 116 through 117 Processing sheet with id=AE1, first strand: chain 'D' and resid 120 through 121 Processing sheet with id=AE2, first strand: chain 'D' and resid 278 through 279 removed outlier: 3.941A pdb=" N ASP D 287 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 311 through 312 removed outlier: 4.178A pdb=" N PHE D 318 " --> pdb=" O GLY D 593 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 311 through 312 removed outlier: 3.819A pdb=" N GLY D 594 " --> pdb=" O GLN D 613 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU D 650 " --> pdb=" O PHE D 643 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE D 643 " --> pdb=" O LEU D 650 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 325 through 327 removed outlier: 6.884A pdb=" N ILE D 326 " --> pdb=" O ASN D 542 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY D 550 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 356 through 358 removed outlier: 3.683A pdb=" N ALA D 397 " --> pdb=" O LYS D 356 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 378 through 379 removed outlier: 3.834A pdb=" N CYS D 432 " --> pdb=" O LEU D 513 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE D 402 " --> pdb=" O TYR D 508 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N VAL D 510 " --> pdb=" O PHE D 400 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N PHE D 400 " --> pdb=" O VAL D 510 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AE9, first strand: chain 'D' and resid 654 through 655 removed outlier: 6.145A pdb=" N GLU D 654 " --> pdb=" O ALA D 694 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N THR D 696 " --> pdb=" O GLU D 654 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN D 675 " --> pdb=" O SER D 691 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 712 through 719 removed outlier: 6.440A pdb=" N ALA D 713 " --> pdb=" O ASN D1074 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ASN D1074 " --> pdb=" O ALA D 713 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLU D1072 " --> pdb=" O PRO D 715 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ASN D 717 " --> pdb=" O ALA D1070 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 722 through 728 removed outlier: 3.635A pdb=" N GLY D1059 " --> pdb=" O ALA D1056 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 1120 through 1122 Processing sheet with id=AF4, first strand: chain 'D' and resid 1094 through 1097 771 hydrogen bonds defined for protein. 2073 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: 2.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 8454 1.35 - 1.47: 6930 1.47 - 1.59: 11734 1.59 - 1.71: 0 1.71 - 1.83: 140 Bond restraints: 27258 Sorted by residual: bond pdb=" C1 NAG B1309 " pdb=" O5 NAG B1309 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.42e+00 bond pdb=" C1 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.24e+00 bond pdb=" N PHE D 157 " pdb=" CA PHE D 157 " ideal model delta sigma weight residual 1.457 1.480 -0.023 1.29e-02 6.01e+03 3.20e+00 bond pdb=" CB PRO A 373 " pdb=" CG PRO A 373 " ideal model delta sigma weight residual 1.492 1.579 -0.087 5.00e-02 4.00e+02 3.02e+00 bond pdb=" C1 NAG B1308 " pdb=" O5 NAG B1308 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.86e+00 ... (remaining 27253 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 36156 1.67 - 3.34: 844 3.34 - 5.01: 87 5.01 - 6.68: 29 6.68 - 8.35: 4 Bond angle restraints: 37120 Sorted by residual: angle pdb=" C GLY B 232 " pdb=" N ILE B 233 " pdb=" CA ILE B 233 " ideal model delta sigma weight residual 121.97 128.61 -6.64 1.80e+00 3.09e-01 1.36e+01 angle pdb=" N GLY A 757 " pdb=" CA GLY A 757 " pdb=" C GLY A 757 " ideal model delta sigma weight residual 111.35 115.48 -4.13 1.20e+00 6.94e-01 1.18e+01 angle pdb=" OG1 THR A 95 " pdb=" CB THR A 95 " pdb=" CG2 THR A 95 " ideal model delta sigma weight residual 109.30 103.29 6.01 2.00e+00 2.50e-01 9.04e+00 angle pdb=" OG1 THR B 547 " pdb=" CB THR B 547 " pdb=" CG2 THR B 547 " ideal model delta sigma weight residual 109.30 103.29 6.01 2.00e+00 2.50e-01 9.04e+00 angle pdb=" N VAL D 620 " pdb=" CA VAL D 620 " pdb=" C VAL D 620 " ideal model delta sigma weight residual 108.88 115.37 -6.49 2.16e+00 2.14e-01 9.02e+00 ... (remaining 37115 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 14259 17.91 - 35.83: 1193 35.83 - 53.74: 218 53.74 - 71.65: 38 71.65 - 89.57: 31 Dihedral angle restraints: 15739 sinusoidal: 6104 harmonic: 9635 Sorted by residual: dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 -10.49 -75.51 1 1.00e+01 1.00e-02 7.20e+01 dihedral pdb=" CB CYS D1082 " pdb=" SG CYS D1082 " pdb=" SG CYS D1126 " pdb=" CB CYS D1126 " ideal model delta sinusoidal sigma weight residual -86.00 -157.76 71.76 1 1.00e+01 1.00e-02 6.60e+01 dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 -16.16 -69.84 1 1.00e+01 1.00e-02 6.29e+01 ... (remaining 15736 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 3676 0.061 - 0.122: 608 0.122 - 0.183: 43 0.183 - 0.244: 8 0.244 - 0.305: 2 Chirality restraints: 4337 Sorted by residual: chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A 165 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" C1 NAG B1308 " pdb=" ND2 ASN B 657 " pdb=" C2 NAG B1308 " pdb=" O5 NAG B1308 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 343 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 4334 not shown) Planarity restraints: 4784 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 294 " 0.038 5.00e-02 4.00e+02 5.81e-02 5.40e+00 pdb=" N PRO D 295 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO D 295 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 295 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 620 " -0.037 5.00e-02 4.00e+02 5.57e-02 4.96e+00 pdb=" N PRO B 621 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 621 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 621 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D1056 " -0.028 5.00e-02 4.00e+02 4.24e-02 2.87e+00 pdb=" N PRO D1057 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO D1057 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO D1057 " -0.023 5.00e-02 4.00e+02 ... (remaining 4781 not shown) Histogram of nonbonded interaction distances: 1.35 - 2.06: 2 2.06 - 2.77: 4705 2.77 - 3.48: 34608 3.48 - 4.19: 56099 4.19 - 4.90: 100406 Nonbonded interactions: 195820 Sorted by model distance: nonbonded pdb=" CE MET B 153 " pdb=" CD2 HIS B 245 " model vdw 1.353 3.680 nonbonded pdb=" O ASN B 185 " pdb=" CD2 LEU B 212 " model vdw 1.945 3.460 nonbonded pdb=" O ALA B 67 " pdb=" OG1 THR B 250 " model vdw 2.132 3.040 nonbonded pdb=" OH TYR D 655 " pdb=" OG1 THR D 696 " model vdw 2.184 3.040 nonbonded pdb=" O ALA A 292 " pdb=" OG1 THR A 632 " model vdw 2.191 3.040 ... (remaining 195815 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 25 through 835 or resid 849 through 1309)) selection = (chain 'B' and (resid 25 through 152 or (resid 153 and (name N or name CA or nam \ e C or name O or name CB )) or resid 154 through 1309)) selection = (chain 'D' and (resid 25 through 835 or resid 849 through 1309)) } ncs_group { reference = chain 'C' 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' } 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 group one per residue 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: 2.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 21.590 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.050 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 27348 Z= 0.158 Angle : 0.611 12.219 37354 Z= 0.302 Chirality : 0.046 0.305 4337 Planarity : 0.004 0.058 4743 Dihedral : 13.857 89.567 9445 Min Nonbonded Distance : 1.353 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.26 % Favored : 93.35 % Rotamer: Outliers : 0.03 % Allowed : 0.31 % Favored : 99.65 % 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: -1.29 (0.15), residues: 3292 helix: 0.96 (0.23), residues: 628 sheet: -0.57 (0.22), residues: 631 loop : -1.62 (0.13), residues: 2033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 457 TYR 0.019 0.001 TYR B 904 PHE 0.019 0.001 PHE D 65 TRP 0.011 0.001 TRP A 64 HIS 0.003 0.000 HIS B 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.16 (27258) covalent geometry : angle 0.58852 / 0.30 (37120) SS BOND : bond 0.00303 / 0.21 ( 36) SS BOND : angle 1.17592 / 0.70 ( 72) hydrogen bonds : bond 0.22876 / 14.78 ( 750) hydrogen bonds : angle 8.23490 / 5.73 ( 2073) link_BETA1-4 : bond 0.00411 / 0.25 ( 13) link_BETA1-4 : angle 1.57324 / 1.01 ( 39) link_NAG-ASN : bond 0.00465 / 0.27 ( 41) link_NAG-ASN : angle 2.66795 / 1.73 ( 123) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 466 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 PHE cc_start: 0.3809 (p90) cc_final: 0.3598 (p90) REVERT: D 979 ASP cc_start: 0.7210 (t70) cc_final: 0.6778 (t70) outliers start: 1 outliers final: 0 residues processed: 467 average time/residue: 0.1690 time to fit residues: 122.1523 Evaluate side-chains 220 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 1.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 GLN A 405 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A 675 GLN A 751 ASN A 955 ASN A 957 GLN A1071 GLN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 641 ASN B1005 GLN B1088 HIS ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 GLN D 613 GLN D 955 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.136911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.092547 restraints weight = 75863.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.095347 restraints weight = 36507.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.097180 restraints weight = 23465.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.097930 restraints weight = 17737.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.098905 restraints weight = 15409.783| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 27348 Z= 0.181 Angle : 0.688 11.743 37354 Z= 0.347 Chirality : 0.047 0.380 4337 Planarity : 0.005 0.084 4743 Dihedral : 4.299 20.298 3554 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.80 % Favored : 92.80 % Rotamer: Outliers : 1.22 % Allowed : 10.14 % Favored : 88.64 % 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: -1.32 (0.14), residues: 3292 helix: 1.07 (0.22), residues: 635 sheet: -0.72 (0.20), residues: 676 loop : -1.67 (0.13), residues: 1981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 355 TYR 0.024 0.001 TYR A 170 PHE 0.022 0.002 PHE A 490 TRP 0.025 0.001 TRP A 353 HIS 0.005 0.001 HIS A1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 (27258) covalent geometry : angle 0.66507 / 0.34 (37120) SS BOND : bond 0.00347 / 0.21 ( 36) SS BOND : angle 1.59870 / 0.99 ( 72) hydrogen bonds : bond 0.04663 / 3.11 ( 750) hydrogen bonds : angle 5.92083 / 4.08 ( 2073) link_BETA1-4 : bond 0.00337 / 0.20 ( 13) link_BETA1-4 : angle 1.43540 / 0.91 ( 39) link_NAG-ASN : bond 0.00382 / 0.20 ( 41) link_NAG-ASN : angle 2.82016 / 1.82 ( 123) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 229 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 PHE cc_start: 0.7307 (m-80) cc_final: 0.7089 (m-10) REVERT: A 1002 GLN cc_start: 0.9106 (tp40) cc_final: 0.8640 (tp40) REVERT: B 191 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7182 (mp0) REVERT: B 957 GLN cc_start: 0.7893 (tm-30) cc_final: 0.7658 (tm-30) REVERT: B 1002 GLN cc_start: 0.8385 (tm-30) cc_final: 0.7997 (tm-30) REVERT: D 52 GLN cc_start: 0.7985 (tp-100) cc_final: 0.7752 (tp40) REVERT: D 576 VAL cc_start: 0.7228 (OUTLIER) cc_final: 0.6922 (p) REVERT: D 636 TYR cc_start: 0.4984 (p90) cc_final: 0.4737 (p90) REVERT: D 955 ASN cc_start: 0.8728 (m110) cc_final: 0.8509 (t0) REVERT: D 979 ASP cc_start: 0.8310 (t70) cc_final: 0.7943 (t0) outliers start: 35 outliers final: 20 residues processed: 255 average time/residue: 0.1560 time to fit residues: 64.5577 Evaluate side-chains 199 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 178 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 750 SER Chi-restraints excluded: chain D residue 752 LEU Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 963 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 173 optimal weight: 9.9990 chunk 249 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 204 optimal weight: 2.9990 chunk 213 optimal weight: 0.9980 chunk 321 optimal weight: 3.9990 chunk 293 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 230 optimal weight: 20.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 HIS A 196 ASN A 211 ASN A 405 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A 913 GLN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN D 148 ASN D 448 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.131555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.087457 restraints weight = 75800.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.090081 restraints weight = 37841.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.091747 restraints weight = 24762.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 69)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.092809 restraints weight = 19114.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.093458 restraints weight = 16292.848| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 27348 Z= 0.216 Angle : 0.694 11.399 37354 Z= 0.351 Chirality : 0.048 0.417 4337 Planarity : 0.005 0.072 4743 Dihedral : 4.495 20.826 3554 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.43 % Allowed : 6.50 % Favored : 93.07 % Rotamer: Outliers : 1.99 % Allowed : 14.15 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.14), residues: 3292 helix: 1.15 (0.22), residues: 625 sheet: -0.78 (0.20), residues: 693 loop : -1.77 (0.13), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 509 TYR 0.021 0.002 TYR D 266 PHE 0.031 0.002 PHE B 133 TRP 0.033 0.002 TRP A 64 HIS 0.010 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.22 (27258) covalent geometry : angle 0.67170 / 0.35 (37120) SS BOND : bond 0.00514 / 0.29 ( 36) SS BOND : angle 1.58100 / 0.98 ( 72) hydrogen bonds : bond 0.05476 / 3.56 ( 750) hydrogen bonds : angle 5.61604 / 3.85 ( 2073) link_BETA1-4 : bond 0.00484 / 0.37 ( 13) link_BETA1-4 : angle 1.60752 / 1.03 ( 39) link_NAG-ASN : bond 0.00426 / 0.23 ( 41) link_NAG-ASN : angle 2.79853 / 1.82 ( 123) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 210 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 869 MET cc_start: 0.9108 (mtm) cc_final: 0.8467 (mtm) REVERT: A 983 ARG cc_start: 0.8087 (mtm110) cc_final: 0.7847 (mtm110) REVERT: A 1002 GLN cc_start: 0.9176 (tp40) cc_final: 0.8768 (tp40) REVERT: B 118 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.8044 (mp) REVERT: B 152 TRP cc_start: 0.2626 (m-10) cc_final: 0.2055 (m100) REVERT: B 191 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7220 (mp0) REVERT: B 565 PHE cc_start: 0.6732 (m-80) cc_final: 0.6148 (m-80) REVERT: B 957 GLN cc_start: 0.8083 (tm-30) cc_final: 0.7782 (tm-30) REVERT: B 985 ASP cc_start: 0.7680 (t70) cc_final: 0.7395 (t0) REVERT: B 1002 GLN cc_start: 0.8669 (tm-30) cc_final: 0.7985 (tm-30) REVERT: D 186 PHE cc_start: 0.6079 (m-80) cc_final: 0.5692 (m-80) REVERT: D 955 ASN cc_start: 0.8782 (m110) cc_final: 0.8497 (t0) REVERT: D 979 ASP cc_start: 0.8348 (t70) cc_final: 0.7960 (t0) outliers start: 57 outliers final: 31 residues processed: 256 average time/residue: 0.1443 time to fit residues: 60.7435 Evaluate side-chains 213 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 181 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 752 LEU Chi-restraints excluded: chain D residue 787 GLN Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 973 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 190 optimal weight: 10.0000 chunk 276 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 229 optimal weight: 4.9990 chunk 118 optimal weight: 0.5980 chunk 95 optimal weight: 4.9990 chunk 156 optimal weight: 0.5980 chunk 204 optimal weight: 3.9990 chunk 323 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 405 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1005 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.132397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.088609 restraints weight = 75298.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.091260 restraints weight = 37264.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.092941 restraints weight = 24176.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.094015 restraints weight = 18547.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.094634 restraints weight = 15762.162| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 27348 Z= 0.127 Angle : 0.617 11.630 37354 Z= 0.306 Chirality : 0.045 0.407 4337 Planarity : 0.004 0.054 4743 Dihedral : 4.322 19.156 3554 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.43 % Allowed : 6.01 % Favored : 93.56 % Rotamer: Outliers : 2.09 % Allowed : 15.30 % Favored : 82.61 % 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: -1.24 (0.14), residues: 3292 helix: 1.40 (0.22), residues: 627 sheet: -0.64 (0.19), residues: 709 loop : -1.72 (0.13), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 346 TYR 0.019 0.001 TYR A1067 PHE 0.022 0.001 PHE D 92 TRP 0.030 0.001 TRP A 64 HIS 0.003 0.001 HIS B 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (27258) covalent geometry : angle 0.59542 / 0.30 (37120) SS BOND : bond 0.00328 / 0.22 ( 36) SS BOND : angle 1.20867 / 0.74 ( 72) hydrogen bonds : bond 0.04406 / 2.88 ( 750) hydrogen bonds : angle 5.34848 / 3.66 ( 2073) link_BETA1-4 : bond 0.00338 / 0.21 ( 13) link_BETA1-4 : angle 1.26719 / 0.83 ( 39) link_NAG-ASN : bond 0.00356 / 0.20 ( 41) link_NAG-ASN : angle 2.68150 / 1.72 ( 123) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 193 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 ILE cc_start: 0.7825 (mp) cc_final: 0.7485 (pt) REVERT: A 212 LEU cc_start: 0.6640 (OUTLIER) cc_final: 0.6182 (tp) REVERT: A 569 ILE cc_start: 0.8210 (OUTLIER) cc_final: 0.7968 (tp) REVERT: A 990 GLU cc_start: 0.9134 (tm-30) cc_final: 0.8829 (tt0) REVERT: A 1002 GLN cc_start: 0.9182 (tp40) cc_final: 0.8762 (tp40) REVERT: B 118 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7832 (mp) REVERT: B 152 TRP cc_start: 0.2684 (m-10) cc_final: 0.2113 (m100) REVERT: B 186 PHE cc_start: 0.4474 (OUTLIER) cc_final: 0.3908 (m-10) REVERT: B 191 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7057 (mp0) REVERT: B 371 PHE cc_start: 0.7329 (OUTLIER) cc_final: 0.7126 (t80) REVERT: B 565 PHE cc_start: 0.6679 (m-80) cc_final: 0.6117 (m-80) REVERT: B 918 GLU cc_start: 0.8681 (mm-30) cc_final: 0.8473 (mt-10) REVERT: B 957 GLN cc_start: 0.8070 (tm-30) cc_final: 0.7755 (tm-30) REVERT: B 1002 GLN cc_start: 0.8690 (tm-30) cc_final: 0.7974 (tm-30) REVERT: D 186 PHE cc_start: 0.6053 (m-80) cc_final: 0.5628 (m-80) REVERT: D 955 ASN cc_start: 0.8738 (m110) cc_final: 0.8417 (t0) REVERT: D 979 ASP cc_start: 0.8342 (t70) cc_final: 0.8017 (t0) outliers start: 60 outliers final: 32 residues processed: 239 average time/residue: 0.1448 time to fit residues: 57.4369 Evaluate side-chains 215 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 178 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 752 LEU Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 878 LEU Chi-restraints excluded: chain D residue 882 ILE Chi-restraints excluded: chain D residue 906 PHE Chi-restraints excluded: chain D residue 1096 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 34 optimal weight: 10.0000 chunk 180 optimal weight: 0.8980 chunk 30 optimal weight: 8.9990 chunk 167 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 14 optimal weight: 20.0000 chunk 143 optimal weight: 5.9990 chunk 238 optimal weight: 5.9990 chunk 206 optimal weight: 0.9980 chunk 195 optimal weight: 0.7980 chunk 78 optimal weight: 4.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 450 ASN D 762 GLN D1005 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.131021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.087253 restraints weight = 75649.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.089953 restraints weight = 36754.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.091665 restraints weight = 23712.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.092796 restraints weight = 18149.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.093432 restraints weight = 15372.800| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27348 Z= 0.149 Angle : 0.625 12.074 37354 Z= 0.309 Chirality : 0.045 0.407 4337 Planarity : 0.004 0.055 4743 Dihedral : 4.300 25.218 3554 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.93 % Favored : 92.68 % Rotamer: Outliers : 2.75 % Allowed : 15.86 % Favored : 81.39 % 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: -1.25 (0.14), residues: 3292 helix: 1.40 (0.22), residues: 633 sheet: -0.62 (0.19), residues: 702 loop : -1.75 (0.13), residues: 1957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 78 TYR 0.019 0.001 TYR A 170 PHE 0.015 0.001 PHE A 823 TRP 0.025 0.001 TRP A 64 HIS 0.004 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (27258) covalent geometry : angle 0.60419 / 0.30 (37120) SS BOND : bond 0.00384 / 0.24 ( 36) SS BOND : angle 1.29306 / 0.82 ( 72) hydrogen bonds : bond 0.04321 / 2.84 ( 750) hydrogen bonds : angle 5.22227 / 3.58 ( 2073) link_BETA1-4 : bond 0.00344 / 0.19 ( 13) link_BETA1-4 : angle 1.28908 / 0.85 ( 39) link_NAG-ASN : bond 0.00348 / 0.18 ( 41) link_NAG-ASN : angle 2.63208 / 1.71 ( 123) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 190 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 ILE cc_start: 0.7839 (mp) cc_final: 0.7578 (pt) REVERT: A 212 LEU cc_start: 0.6854 (OUTLIER) cc_final: 0.6495 (tp) REVERT: A 858 LEU cc_start: 0.9703 (OUTLIER) cc_final: 0.9454 (mp) REVERT: A 869 MET cc_start: 0.8996 (mtm) cc_final: 0.8652 (mtm) REVERT: A 990 GLU cc_start: 0.9160 (tm-30) cc_final: 0.8723 (tt0) REVERT: A 1002 GLN cc_start: 0.9188 (tp40) cc_final: 0.8759 (tp40) REVERT: B 152 TRP cc_start: 0.2167 (m-10) cc_final: 0.1322 (m100) REVERT: B 186 PHE cc_start: 0.4642 (OUTLIER) cc_final: 0.4141 (m-10) REVERT: B 191 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7097 (mp0) REVERT: B 515 PHE cc_start: 0.7084 (m-80) cc_final: 0.6772 (m-80) REVERT: B 565 PHE cc_start: 0.6729 (m-80) cc_final: 0.6182 (m-80) REVERT: B 957 GLN cc_start: 0.8029 (tm-30) cc_final: 0.7677 (tm-30) REVERT: B 984 LEU cc_start: 0.9024 (mt) cc_final: 0.8504 (tp) REVERT: B 985 ASP cc_start: 0.7948 (t70) cc_final: 0.7429 (t0) REVERT: B 1002 GLN cc_start: 0.8777 (tm-30) cc_final: 0.8042 (tm-30) REVERT: D 186 PHE cc_start: 0.6079 (m-80) cc_final: 0.5682 (m-80) REVERT: D 754 LEU cc_start: 0.9392 (tt) cc_final: 0.9137 (mt) REVERT: D 955 ASN cc_start: 0.8739 (m110) cc_final: 0.8437 (t0) REVERT: D 979 ASP cc_start: 0.8402 (t70) cc_final: 0.8117 (t0) outliers start: 79 outliers final: 45 residues processed: 256 average time/residue: 0.1302 time to fit residues: 54.8003 Evaluate side-chains 227 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 179 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 204 TYR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 833 PHE Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 752 LEU Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 878 LEU Chi-restraints excluded: chain D residue 882 ILE Chi-restraints excluded: chain D residue 952 VAL Chi-restraints excluded: chain D residue 991 VAL Chi-restraints excluded: chain D residue 1096 VAL Chi-restraints excluded: chain D residue 1104 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 135 optimal weight: 4.9990 chunk 224 optimal weight: 10.0000 chunk 291 optimal weight: 0.0050 chunk 236 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 277 optimal weight: 7.9990 chunk 22 optimal weight: 7.9990 chunk 158 optimal weight: 0.9980 chunk 211 optimal weight: 2.9990 chunk 194 optimal weight: 0.5980 chunk 268 optimal weight: 10.0000 overall best weight: 1.1198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN A1106 GLN B 148 ASN ** D1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.131541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.088033 restraints weight = 75656.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.090732 restraints weight = 37090.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.092437 restraints weight = 23992.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.093536 restraints weight = 18354.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.094220 restraints weight = 15591.094| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27348 Z= 0.115 Angle : 0.599 14.262 37354 Z= 0.295 Chirality : 0.045 0.400 4337 Planarity : 0.004 0.057 4743 Dihedral : 4.168 30.531 3554 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.43 % Allowed : 5.71 % Favored : 93.86 % Rotamer: Outliers : 2.30 % Allowed : 17.01 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.15), residues: 3292 helix: 1.40 (0.22), residues: 651 sheet: -0.54 (0.19), residues: 704 loop : -1.71 (0.13), residues: 1937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 983 TYR 0.018 0.001 TYR A1067 PHE 0.022 0.001 PHE D 92 TRP 0.018 0.001 TRP A 64 HIS 0.002 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (27258) covalent geometry : angle 0.57943 / 0.29 (37120) SS BOND : bond 0.00292 / 0.19 ( 36) SS BOND : angle 1.23900 / 0.79 ( 72) hydrogen bonds : bond 0.03860 / 2.51 ( 750) hydrogen bonds : angle 5.03456 / 3.44 ( 2073) link_BETA1-4 : bond 0.00368 / 0.24 ( 13) link_BETA1-4 : angle 1.20247 / 0.78 ( 39) link_NAG-ASN : bond 0.00358 / 0.20 ( 41) link_NAG-ASN : angle 2.49782 / 1.61 ( 123) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 186 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 ILE cc_start: 0.7938 (mp) cc_final: 0.7725 (pt) REVERT: A 212 LEU cc_start: 0.6919 (OUTLIER) cc_final: 0.6589 (tp) REVERT: A 725 GLU cc_start: 0.7976 (tp30) cc_final: 0.7723 (tt0) REVERT: A 858 LEU cc_start: 0.9688 (OUTLIER) cc_final: 0.9422 (mp) REVERT: A 990 GLU cc_start: 0.9051 (tm-30) cc_final: 0.8782 (tt0) REVERT: A 1002 GLN cc_start: 0.9162 (tp40) cc_final: 0.8734 (tp40) REVERT: B 118 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7792 (mp) REVERT: B 186 PHE cc_start: 0.4610 (OUTLIER) cc_final: 0.4169 (m-10) REVERT: B 191 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7041 (mp0) REVERT: B 515 PHE cc_start: 0.6998 (m-80) cc_final: 0.6719 (m-80) REVERT: B 565 PHE cc_start: 0.6661 (m-80) cc_final: 0.6127 (m-80) REVERT: B 590 CYS cc_start: 0.8068 (OUTLIER) cc_final: 0.7802 (m) REVERT: B 957 GLN cc_start: 0.8030 (tm-30) cc_final: 0.7703 (tm-30) REVERT: B 984 LEU cc_start: 0.9015 (mt) cc_final: 0.8510 (tp) REVERT: B 985 ASP cc_start: 0.7980 (t70) cc_final: 0.7522 (t0) REVERT: B 1002 GLN cc_start: 0.8762 (tm-30) cc_final: 0.8037 (tm-30) REVERT: D 754 LEU cc_start: 0.9390 (tt) cc_final: 0.9149 (mt) REVERT: D 955 ASN cc_start: 0.8692 (m110) cc_final: 0.8424 (t0) REVERT: D 979 ASP cc_start: 0.8345 (t70) cc_final: 0.8091 (t0) outliers start: 66 outliers final: 48 residues processed: 238 average time/residue: 0.1612 time to fit residues: 63.8381 Evaluate side-chains 226 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 173 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 204 TYR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 833 PHE Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 581 THR Chi-restraints excluded: chain D residue 587 ILE Chi-restraints excluded: chain D residue 633 TRP Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 752 LEU Chi-restraints excluded: chain D residue 770 ILE Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 878 LEU Chi-restraints excluded: chain D residue 882 ILE Chi-restraints excluded: chain D residue 991 VAL Chi-restraints excluded: chain D residue 1104 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 159 optimal weight: 9.9990 chunk 102 optimal weight: 5.9990 chunk 221 optimal weight: 9.9990 chunk 112 optimal weight: 3.9990 chunk 2 optimal weight: 8.9990 chunk 8 optimal weight: 7.9990 chunk 54 optimal weight: 7.9990 chunk 165 optimal weight: 10.0000 chunk 240 optimal weight: 0.3980 chunk 239 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 ASN ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 ASN A 405 ASN B 245 HIS B1108 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.127564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.084411 restraints weight = 75394.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.087004 restraints weight = 36833.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.088693 restraints weight = 23961.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.089709 restraints weight = 18387.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.090408 restraints weight = 15668.253| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.5107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 27348 Z= 0.203 Angle : 0.687 13.597 37354 Z= 0.341 Chirality : 0.047 0.420 4337 Planarity : 0.005 0.056 4743 Dihedral : 4.535 29.265 3554 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.84 % Favored : 91.71 % Rotamer: Outliers : 3.00 % Allowed : 17.53 % Favored : 79.47 % 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: -1.34 (0.14), residues: 3292 helix: 1.30 (0.22), residues: 638 sheet: -0.73 (0.19), residues: 710 loop : -1.79 (0.13), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 509 TYR 0.021 0.002 TYR D 904 PHE 0.018 0.002 PHE A 86 TRP 0.043 0.002 TRP A 64 HIS 0.005 0.001 HIS D1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.20 (27258) covalent geometry : angle 0.66547 / 0.34 (37120) SS BOND : bond 0.00495 / 0.34 ( 36) SS BOND : angle 1.43307 / 0.89 ( 72) hydrogen bonds : bond 0.05025 / 3.30 ( 750) hydrogen bonds : angle 5.26197 / 3.61 ( 2073) link_BETA1-4 : bond 0.00397 / 0.27 ( 13) link_BETA1-4 : angle 1.69096 / 1.12 ( 39) link_NAG-ASN : bond 0.00438 / 0.25 ( 41) link_NAG-ASN : angle 2.71757 / 1.80 ( 123) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 180 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 ILE cc_start: 0.7868 (mp) cc_final: 0.7495 (pt) REVERT: A 212 LEU cc_start: 0.7077 (OUTLIER) cc_final: 0.6724 (tp) REVERT: A 858 LEU cc_start: 0.9717 (OUTLIER) cc_final: 0.9460 (mp) REVERT: A 1002 GLN cc_start: 0.9203 (tp40) cc_final: 0.8764 (tp40) REVERT: B 118 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7921 (mp) REVERT: B 152 TRP cc_start: 0.2532 (m-10) cc_final: 0.1437 (m100) REVERT: B 186 PHE cc_start: 0.4689 (OUTLIER) cc_final: 0.4398 (m-10) REVERT: B 191 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7064 (mp0) REVERT: B 371 PHE cc_start: 0.7332 (OUTLIER) cc_final: 0.7053 (t80) REVERT: B 387 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8851 (tt) REVERT: B 394 ASN cc_start: 0.7088 (OUTLIER) cc_final: 0.6867 (p0) REVERT: B 515 PHE cc_start: 0.7362 (m-80) cc_final: 0.6968 (m-80) REVERT: B 565 PHE cc_start: 0.6831 (m-80) cc_final: 0.6296 (m-80) REVERT: B 590 CYS cc_start: 0.8085 (OUTLIER) cc_final: 0.7827 (m) REVERT: B 957 GLN cc_start: 0.7963 (tm-30) cc_final: 0.7650 (tm-30) REVERT: B 985 ASP cc_start: 0.8278 (t70) cc_final: 0.7756 (t0) REVERT: B 1002 GLN cc_start: 0.8820 (tm-30) cc_final: 0.8058 (tm-30) REVERT: D 177 MET cc_start: 0.5913 (tmm) cc_final: 0.4792 (tpt) REVERT: D 186 PHE cc_start: 0.6379 (m-80) cc_final: 0.5991 (m-10) REVERT: D 386 LYS cc_start: 0.7119 (ptpp) cc_final: 0.6895 (tppt) REVERT: D 515 PHE cc_start: 0.6851 (m-80) cc_final: 0.6628 (m-80) REVERT: D 773 GLU cc_start: 0.8595 (tp30) cc_final: 0.8005 (tm-30) REVERT: D 955 ASN cc_start: 0.8819 (m110) cc_final: 0.8498 (t0) REVERT: D 979 ASP cc_start: 0.8447 (t70) cc_final: 0.8226 (t0) outliers start: 86 outliers final: 51 residues processed: 249 average time/residue: 0.1670 time to fit residues: 68.6932 Evaluate side-chains 222 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 163 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 204 TYR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 833 PHE Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 581 THR Chi-restraints excluded: chain D residue 633 TRP Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 752 LEU Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 878 LEU Chi-restraints excluded: chain D residue 882 ILE Chi-restraints excluded: chain D residue 952 VAL Chi-restraints excluded: chain D residue 991 VAL Chi-restraints excluded: chain D residue 1096 VAL Chi-restraints excluded: chain D residue 1104 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 180 optimal weight: 1.9990 chunk 64 optimal weight: 0.0970 chunk 246 optimal weight: 6.9990 chunk 285 optimal weight: 0.5980 chunk 162 optimal weight: 8.9990 chunk 255 optimal weight: 9.9990 chunk 54 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 155 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 ASN ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 ASN B 49 HIS B 148 ASN B 394 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.129392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.086472 restraints weight = 75593.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.089106 restraints weight = 37116.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.090752 restraints weight = 24002.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.091835 restraints weight = 18415.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.092386 restraints weight = 15645.470| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.5193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 27348 Z= 0.116 Angle : 0.612 12.716 37354 Z= 0.303 Chirality : 0.045 0.415 4337 Planarity : 0.004 0.057 4743 Dihedral : 4.281 28.583 3554 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.89 % Favored : 93.65 % Rotamer: Outliers : 2.09 % Allowed : 18.79 % Favored : 79.12 % 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: -1.17 (0.15), residues: 3292 helix: 1.53 (0.22), residues: 638 sheet: -0.65 (0.19), residues: 710 loop : -1.71 (0.13), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 983 TYR 0.020 0.001 TYR A1067 PHE 0.018 0.001 PHE A 374 TRP 0.051 0.001 TRP A 64 HIS 0.003 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (27258) covalent geometry : angle 0.59465 / 0.30 (37120) SS BOND : bond 0.00444 / 0.33 ( 36) SS BOND : angle 1.14359 / 0.71 ( 72) hydrogen bonds : bond 0.03940 / 2.57 ( 750) hydrogen bonds : angle 4.98904 / 3.41 ( 2073) link_BETA1-4 : bond 0.00343 / 0.22 ( 13) link_BETA1-4 : angle 1.21090 / 0.80 ( 39) link_NAG-ASN : bond 0.00337 / 0.17 ( 41) link_NAG-ASN : angle 2.44077 / 1.59 ( 123) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 173 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 ILE cc_start: 0.7929 (mp) cc_final: 0.7601 (pt) REVERT: A 212 LEU cc_start: 0.7168 (OUTLIER) cc_final: 0.6868 (tp) REVERT: A 858 LEU cc_start: 0.9714 (OUTLIER) cc_final: 0.9444 (mp) REVERT: A 990 GLU cc_start: 0.9115 (tm-30) cc_final: 0.8747 (tt0) REVERT: A 1002 GLN cc_start: 0.9192 (tp40) cc_final: 0.8737 (tp40) REVERT: B 118 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7990 (mp) REVERT: B 177 MET cc_start: 0.6529 (mmt) cc_final: 0.6241 (mmp) REVERT: B 186 PHE cc_start: 0.4771 (OUTLIER) cc_final: 0.4375 (m-10) REVERT: B 191 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7062 (mp0) REVERT: B 371 PHE cc_start: 0.7225 (OUTLIER) cc_final: 0.6951 (t80) REVERT: B 394 ASN cc_start: 0.7322 (OUTLIER) cc_final: 0.7050 (p0) REVERT: B 515 PHE cc_start: 0.7204 (m-80) cc_final: 0.6976 (m-80) REVERT: B 565 PHE cc_start: 0.6704 (m-80) cc_final: 0.6202 (m-80) REVERT: B 590 CYS cc_start: 0.8029 (OUTLIER) cc_final: 0.7805 (m) REVERT: B 957 GLN cc_start: 0.7993 (tm-30) cc_final: 0.7594 (tm-30) REVERT: B 985 ASP cc_start: 0.8186 (t70) cc_final: 0.7671 (t0) REVERT: B 1002 GLN cc_start: 0.8804 (tm-30) cc_final: 0.8056 (tm-30) REVERT: D 177 MET cc_start: 0.5795 (tmm) cc_final: 0.4872 (tpt) REVERT: D 386 LYS cc_start: 0.7218 (ptpp) cc_final: 0.6990 (tppt) REVERT: D 754 LEU cc_start: 0.9453 (tt) cc_final: 0.9251 (mt) REVERT: D 869 MET cc_start: 0.8741 (mtt) cc_final: 0.8316 (mtm) REVERT: D 955 ASN cc_start: 0.8731 (m110) cc_final: 0.8425 (t0) REVERT: D 979 ASP cc_start: 0.8450 (t70) cc_final: 0.8195 (t0) outliers start: 60 outliers final: 44 residues processed: 222 average time/residue: 0.1646 time to fit residues: 60.6068 Evaluate side-chains 216 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 165 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 833 PHE Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 633 TRP Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 752 LEU Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 878 LEU Chi-restraints excluded: chain D residue 882 ILE Chi-restraints excluded: chain D residue 959 LEU Chi-restraints excluded: chain D residue 1096 VAL Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain D residue 1145 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 43 optimal weight: 9.9990 chunk 157 optimal weight: 7.9990 chunk 297 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 chunk 124 optimal weight: 10.0000 chunk 302 optimal weight: 0.9980 chunk 42 optimal weight: 9.9990 chunk 111 optimal weight: 2.9990 chunk 189 optimal weight: 3.9990 chunk 22 optimal weight: 0.0980 chunk 264 optimal weight: 9.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 ASN ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 ASN B 148 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.128353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.085600 restraints weight = 75863.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.088221 restraints weight = 36522.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.089906 restraints weight = 23379.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.090988 restraints weight = 17776.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.091636 restraints weight = 15041.933| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.5373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 27348 Z= 0.142 Angle : 0.624 14.297 37354 Z= 0.309 Chirality : 0.045 0.407 4337 Planarity : 0.004 0.059 4743 Dihedral : 4.273 27.896 3554 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.32 % Favored : 92.22 % Rotamer: Outliers : 2.16 % Allowed : 18.89 % Favored : 78.95 % 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: -1.16 (0.15), residues: 3292 helix: 1.55 (0.22), residues: 641 sheet: -0.59 (0.20), residues: 693 loop : -1.73 (0.13), residues: 1958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 44 TYR 0.019 0.001 TYR A1067 PHE 0.031 0.001 PHE D 92 TRP 0.048 0.001 TRP A 64 HIS 0.003 0.001 HIS D1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (27258) covalent geometry : angle 0.60596 / 0.30 (37120) SS BOND : bond 0.00311 / 0.22 ( 36) SS BOND : angle 1.25942 / 0.81 ( 72) hydrogen bonds : bond 0.04083 / 2.65 ( 750) hydrogen bonds : angle 4.95766 / 3.39 ( 2073) link_BETA1-4 : bond 0.00309 / 0.20 ( 13) link_BETA1-4 : angle 1.33609 / 0.88 ( 39) link_NAG-ASN : bond 0.00332 / 0.17 ( 41) link_NAG-ASN : angle 2.46448 / 1.62 ( 123) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 168 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 ILE cc_start: 0.7873 (mp) cc_final: 0.7550 (pt) REVERT: A 212 LEU cc_start: 0.7275 (OUTLIER) cc_final: 0.6910 (tp) REVERT: A 298 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8480 (tm-30) REVERT: A 858 LEU cc_start: 0.9722 (OUTLIER) cc_final: 0.9470 (mp) REVERT: A 983 ARG cc_start: 0.8173 (ttp80) cc_final: 0.7762 (mtm110) REVERT: A 990 GLU cc_start: 0.9130 (tm-30) cc_final: 0.8760 (tt0) REVERT: A 1002 GLN cc_start: 0.9204 (tp40) cc_final: 0.8745 (tp40) REVERT: B 118 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.8014 (mp) REVERT: B 177 MET cc_start: 0.6683 (mmt) cc_final: 0.6358 (mmp) REVERT: B 186 PHE cc_start: 0.4695 (OUTLIER) cc_final: 0.4281 (m-10) REVERT: B 191 GLU cc_start: 0.8144 (mm-30) cc_final: 0.6986 (mp0) REVERT: B 371 PHE cc_start: 0.7388 (OUTLIER) cc_final: 0.7140 (t80) REVERT: B 394 ASN cc_start: 0.7372 (OUTLIER) cc_final: 0.6761 (p0) REVERT: B 515 PHE cc_start: 0.7242 (m-80) cc_final: 0.6978 (m-80) REVERT: B 565 PHE cc_start: 0.6762 (m-80) cc_final: 0.6265 (m-80) REVERT: B 957 GLN cc_start: 0.7997 (tm-30) cc_final: 0.7593 (tm-30) REVERT: B 985 ASP cc_start: 0.8248 (OUTLIER) cc_final: 0.7739 (t0) REVERT: B 1002 GLN cc_start: 0.8822 (tm-30) cc_final: 0.8066 (tm-30) REVERT: D 177 MET cc_start: 0.6119 (tmm) cc_final: 0.5251 (tpt) REVERT: D 386 LYS cc_start: 0.7228 (ptpp) cc_final: 0.6993 (tppt) REVERT: D 754 LEU cc_start: 0.9456 (tt) cc_final: 0.9214 (mt) REVERT: D 955 ASN cc_start: 0.8755 (m110) cc_final: 0.8438 (t0) REVERT: D 979 ASP cc_start: 0.8483 (t70) cc_final: 0.8247 (t0) outliers start: 62 outliers final: 48 residues processed: 216 average time/residue: 0.1639 time to fit residues: 58.6619 Evaluate side-chains 221 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 165 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 633 TRP Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 752 LEU Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 878 LEU Chi-restraints excluded: chain D residue 882 ILE Chi-restraints excluded: chain D residue 906 PHE Chi-restraints excluded: chain D residue 959 LEU Chi-restraints excluded: chain D residue 1096 VAL Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain D residue 1145 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 153 optimal weight: 3.9990 chunk 158 optimal weight: 6.9990 chunk 216 optimal weight: 0.9990 chunk 14 optimal weight: 20.0000 chunk 35 optimal weight: 10.0000 chunk 8 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 55 optimal weight: 7.9990 chunk 311 optimal weight: 0.8980 chunk 7 optimal weight: 0.3980 chunk 67 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 405 ASN B 394 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.129630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.086951 restraints weight = 75262.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.089597 restraints weight = 36609.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.091347 restraints weight = 23790.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.092314 restraints weight = 18153.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.093052 restraints weight = 15511.894| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.5434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 27348 Z= 0.107 Angle : 0.606 13.915 37354 Z= 0.299 Chirality : 0.045 0.405 4337 Planarity : 0.004 0.061 4743 Dihedral : 4.139 26.948 3554 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.43 % Allowed : 5.95 % Favored : 93.62 % Rotamer: Outliers : 2.16 % Allowed : 18.86 % Favored : 78.98 % 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: 3292 helix: 1.69 (0.22), residues: 641 sheet: -0.54 (0.19), residues: 709 loop : -1.68 (0.13), residues: 1942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 44 TYR 0.018 0.001 TYR A1067 PHE 0.031 0.001 PHE D 92 TRP 0.060 0.001 TRP A 64 HIS 0.003 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (27258) covalent geometry : angle 0.58942 / 0.29 (37120) SS BOND : bond 0.00283 / 0.19 ( 36) SS BOND : angle 1.12134 / 0.73 ( 72) hydrogen bonds : bond 0.03617 / 2.34 ( 750) hydrogen bonds : angle 4.78412 / 3.28 ( 2073) link_BETA1-4 : bond 0.00357 / 0.24 ( 13) link_BETA1-4 : angle 1.18985 / 0.78 ( 39) link_NAG-ASN : bond 0.00339 / 0.18 ( 41) link_NAG-ASN : angle 2.36827 / 1.55 ( 123) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 175 time to evaluate : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 ILE cc_start: 0.7973 (mp) cc_final: 0.7664 (pt) REVERT: A 212 LEU cc_start: 0.7286 (OUTLIER) cc_final: 0.6848 (tp) REVERT: A 298 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.8461 (tm-30) REVERT: A 858 LEU cc_start: 0.9703 (OUTLIER) cc_final: 0.9440 (mp) REVERT: A 983 ARG cc_start: 0.8257 (ttp80) cc_final: 0.7875 (mtm110) REVERT: A 990 GLU cc_start: 0.9104 (tm-30) cc_final: 0.8808 (tt0) REVERT: A 1002 GLN cc_start: 0.9166 (tp40) cc_final: 0.8722 (tp40) REVERT: B 118 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7925 (mp) REVERT: B 170 TYR cc_start: 0.8346 (t80) cc_final: 0.8109 (t80) REVERT: B 177 MET cc_start: 0.6531 (mmt) cc_final: 0.6244 (mmp) REVERT: B 186 PHE cc_start: 0.4634 (OUTLIER) cc_final: 0.4244 (m-10) REVERT: B 371 PHE cc_start: 0.7294 (OUTLIER) cc_final: 0.7056 (t80) REVERT: B 398 ASP cc_start: 0.6201 (OUTLIER) cc_final: 0.5454 (p0) REVERT: B 515 PHE cc_start: 0.7058 (m-80) cc_final: 0.6776 (m-80) REVERT: B 565 PHE cc_start: 0.6674 (m-80) cc_final: 0.6170 (m-80) REVERT: B 957 GLN cc_start: 0.7960 (tm-30) cc_final: 0.7556 (tm-30) REVERT: B 985 ASP cc_start: 0.8182 (OUTLIER) cc_final: 0.7627 (t0) REVERT: B 1002 GLN cc_start: 0.8809 (tm-30) cc_final: 0.8035 (tm-30) REVERT: B 1148 PHE cc_start: 0.8329 (t80) cc_final: 0.7967 (t80) REVERT: D 177 MET cc_start: 0.6148 (tmm) cc_final: 0.5297 (tpt) REVERT: D 754 LEU cc_start: 0.9455 (tt) cc_final: 0.9235 (mt) REVERT: D 773 GLU cc_start: 0.8485 (tp30) cc_final: 0.7982 (tm-30) REVERT: D 955 ASN cc_start: 0.8690 (m110) cc_final: 0.8381 (t0) REVERT: D 979 ASP cc_start: 0.8462 (t70) cc_final: 0.8225 (t0) outliers start: 62 outliers final: 46 residues processed: 223 average time/residue: 0.1529 time to fit residues: 56.8529 Evaluate side-chains 217 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 163 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 633 TRP Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 878 LEU Chi-restraints excluded: chain D residue 959 LEU Chi-restraints excluded: chain D residue 991 VAL Chi-restraints excluded: chain D residue 1096 VAL Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain D residue 1145 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 182 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 249 optimal weight: 0.9980 chunk 260 optimal weight: 10.0000 chunk 178 optimal weight: 2.9990 chunk 174 optimal weight: 2.9990 chunk 230 optimal weight: 8.9990 chunk 309 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 216 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 405 ASN A 580 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.128037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.085425 restraints weight = 75323.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.088030 restraints weight = 36314.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.089703 restraints weight = 23313.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.090768 restraints weight = 17719.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.091412 restraints weight = 15040.840| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.5606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27348 Z= 0.149 Angle : 0.624 13.970 37354 Z= 0.308 Chirality : 0.045 0.410 4337 Planarity : 0.004 0.060 4743 Dihedral : 4.205 26.809 3554 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.43 % Allowed : 7.41 % Favored : 92.16 % Rotamer: Outliers : 2.09 % Allowed : 19.14 % Favored : 78.77 % 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: -1.13 (0.15), residues: 3292 helix: 1.60 (0.22), residues: 638 sheet: -0.51 (0.20), residues: 694 loop : -1.74 (0.13), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 577 TYR 0.029 0.001 TYR B 396 PHE 0.032 0.001 PHE D 92 TRP 0.058 0.002 TRP A 64 HIS 0.004 0.001 HIS D1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (27258) covalent geometry : angle 0.60552 / 0.30 (37120) SS BOND : bond 0.00260 / 0.19 ( 36) SS BOND : angle 1.23607 / 0.80 ( 72) hydrogen bonds : bond 0.04027 / 2.62 ( 750) hydrogen bonds : angle 4.85098 / 3.32 ( 2073) link_BETA1-4 : bond 0.00236 / 0.15 ( 13) link_BETA1-4 : angle 1.32942 / 0.87 ( 39) link_NAG-ASN : bond 0.00331 / 0.17 ( 41) link_NAG-ASN : angle 2.44199 / 1.61 ( 123) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5740.41 seconds wall clock time: 114 minutes 47.85 seconds (6887.85 seconds total)