Starting phenix.real_space_refine on Sun May 25 16:08:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y71_33650/05_2025/7y71_33650.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y71_33650/05_2025/7y71_33650.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y71_33650/05_2025/7y71_33650.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y71_33650/05_2025/7y71_33650.map" model { file = "/net/cci-nas-00/data/ceres_data/7y71_33650/05_2025/7y71_33650.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y71_33650/05_2025/7y71_33650.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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 116 5.16 5 C 17251 2.51 5 N 4457 2.21 5 O 5251 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 27075 Number of models: 1 Model: "" Number of chains: 15 Chain: "P" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1679 Classifications: {'peptide': 219} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 205} Chain: "O" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1644 Classifications: {'peptide': 221} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 204} Chain: "A" Number of atoms: 7862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1005, 7862 Classifications: {'peptide': 1005} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 54, 'TRANS': 950} Chain breaks: 10 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 7644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 977, 7644 Classifications: {'peptide': 977} Link IDs: {'PTRANS': 53, 'TRANS': 923} Chain breaks: 12 Chain: "C" Number of atoms: 7854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 7854 Classifications: {'peptide': 1006} Link IDs: {'PTRANS': 54, 'TRANS': 951} Chain breaks: 8 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N GLU O 155 " occ=0.71 ... (7 atoms not shown) pdb=" OE2 GLU O 155 " occ=0.71 residue: pdb=" N VAL O 157 " occ=0.79 ... (5 atoms not shown) pdb=" CG2 VAL O 157 " occ=0.79 residue: pdb=" N SER O 186 " occ=0.78 ... (4 atoms not shown) pdb=" OG SER O 186 " occ=0.78 residue: pdb=" N ARG O 217 " occ=0.78 ... (9 atoms not shown) pdb=" NH2 ARG O 217 " occ=0.78 Time building chain proxies: 15.65, per 1000 atoms: 0.58 Number of scatterers: 27075 At special positions: 0 Unit cell: (138.125, 141.44, 238.68, 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 116 16.00 O 5251 8.00 N 4457 7.00 C 17251 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 93 " distance=2.04 Simple disulfide: pdb=" SG CYS P 139 " - pdb=" SG CYS P 199 " distance=2.04 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 95 " distance=2.03 Simple disulfide: pdb=" SG CYS O 147 " - pdb=" SG CYS O 203 " distance=2.03 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=2.03 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 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.02 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.04 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG 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-ASN " NAG A1301 " - " ASN A 709 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 657 " " NAG B1304 " - " ASN B 709 " " NAG B1305 " - " ASN B 717 " " NAG B1306 " - " ASN B1098 " " NAG B1307 " - " ASN B1134 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 616 " " NAG C1303 " - " ASN C 657 " " NAG C1304 " - " ASN C 709 " " NAG C1305 " - " ASN C1098 " " NAG C1306 " - " ASN C1134 " " NAG D 1 " - " ASN A 331 " " NAG I 1 " - " ASN A1098 " " NAG J 1 " - " ASN B 801 " " NAG K 1 " - " ASN B1074 " " NAG L 1 " - " ASN C 717 " " NAG M 1 " - " ASN C 801 " " NAG N 1 " - " ASN C1074 " Time building additional restraints: 6.85 Conformation dependent library (CDL) restraints added in 3.6 seconds 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6418 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 51 sheets defined 22.2% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.83 Creating SS restraints... Processing helix chain 'P' and resid 126 through 133 removed outlier: 3.654A pdb=" N GLY P 133 " --> pdb=" O GLN P 129 " (cutoff:3.500A) Processing helix chain 'O' and resid 61 through 64 removed outlier: 3.640A pdb=" N LYS O 64 " --> pdb=" O PRO O 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 61 through 64' Processing helix chain 'O' and resid 86 through 90 Processing helix chain 'O' and resid 163 through 165 No H-bonds generated for 'chain 'O' and resid 163 through 165' Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 366 through 371 removed outlier: 3.612A pdb=" N SER A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.838A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.744A pdb=" N GLN A 409 " --> pdb=" O GLU A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.689A pdb=" N ILE A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N CYS A 743 " --> pdb=" O THR A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 removed outlier: 4.019A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 760 through 783 removed outlier: 3.869A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.677A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 965 removed outlier: 4.422A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.700A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.563A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.539A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 4.058A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.541A pdb=" N LYS B 386 " --> pdb=" O SER B 383 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 383 through 387' Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 747 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 758 through 783 removed outlier: 3.589A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA B 766 " --> pdb=" O GLN B 762 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 815 removed outlier: 3.739A pdb=" N LYS B 814 " --> pdb=" O LYS B 811 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ARG B 815 " --> pdb=" O PRO B 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 811 through 815' Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.578A pdb=" N ILE B 870 " --> pdb=" O THR B 866 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.513A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.689A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.273A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 removed outlier: 3.741A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.087A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.702A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.781A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 4.295A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 161 Processing helix chain 'C' and resid 296 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.722A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 383 through 390 removed outlier: 4.345A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 411 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.822A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 4.052A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.697A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.523A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.730A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.223A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 removed outlier: 4.072A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.510A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.587A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'P' and resid 5 through 7 removed outlier: 3.600A pdb=" N SER P 22 " --> pdb=" O SER P 7 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N CYS P 23 " --> pdb=" O PHE P 76 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE P 76 " --> pdb=" O CYS P 23 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N THR P 74 " --> pdb=" O SER P 25 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR P 77 " --> pdb=" O SER P 70 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER P 68 " --> pdb=" O LYS P 79 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'P' and resid 10 through 13 removed outlier: 6.242A pdb=" N LEU P 11 " --> pdb=" O GLU P 110 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE P 53 " --> pdb=" O TRP P 40 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU P 42 " --> pdb=" O LEU P 51 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N LEU P 51 " --> pdb=" O LEU P 42 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'P' and resid 119 through 123 removed outlier: 3.527A pdb=" N SER P 119 " --> pdb=" O ASN P 142 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL P 137 " --> pdb=" O LEU P 184 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N TYR P 178 " --> pdb=" O ASN P 143 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'P' and resid 158 through 160 removed outlier: 4.767A pdb=" N TRP P 153 " --> pdb=" O GLN P 160 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LYS P 150 " --> pdb=" O THR P 202 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N THR P 202 " --> pdb=" O LYS P 150 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA P 198 " --> pdb=" O LYS P 154 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N CYS P 199 " --> pdb=" O LYS P 212 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LYS P 212 " --> pdb=" O CYS P 199 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL P 201 " --> pdb=" O VAL P 210 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL P 210 " --> pdb=" O VAL P 201 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'O' and resid 5 through 7 removed outlier: 3.563A pdb=" N LEU O 80 " --> pdb=" O LEU O 20 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE O 78 " --> pdb=" O CYS O 22 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'O' and resid 11 through 12 removed outlier: 3.994A pdb=" N GLY O 49 " --> pdb=" O TRP O 36 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ARG O 38 " --> pdb=" O TRP O 47 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N TRP O 47 " --> pdb=" O ARG O 38 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR O 50 " --> pdb=" O ASN O 58 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASN O 58 " --> pdb=" O TYR O 50 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'O' and resid 127 through 131 removed outlier: 3.659A pdb=" N GLY O 146 " --> pdb=" O LEU O 131 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA O 143 " --> pdb=" O VAL O 191 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP O 151 " --> pdb=" O TYR O 183 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N TYR O 183 " --> pdb=" O ASP O 151 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'O' and resid 127 through 131 removed outlier: 3.659A pdb=" N GLY O 146 " --> pdb=" O LEU O 131 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA O 143 " --> pdb=" O VAL O 191 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP O 151 " --> pdb=" O TYR O 183 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N TYR O 183 " --> pdb=" O ASP O 151 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'O' and resid 158 through 161 removed outlier: 3.982A pdb=" N THR O 158 " --> pdb=" O ASN O 206 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N TYR O 201 " --> pdb=" O VAL O 218 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N CYS O 203 " --> pdb=" O LYS O 216 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS O 216 " --> pdb=" O CYS O 203 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.699A pdb=" N TYR A 91 " --> pdb=" O GLY A 268 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.422A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.565A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.279A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASN A 122 " --> pdb=" O ASN A 125 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.763A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR A 612 " --> pdb=" O CYS A 649 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 324 through 325 removed outlier: 7.573A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.701A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY A 566 " --> pdb=" O ALA A 575 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 357 through 358 removed outlier: 3.921A pdb=" N ILE A 358 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE A 402 " --> pdb=" O TYR A 508 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB8, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.369A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 9.012A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 713 through 715 Processing sheet with id=AC1, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.645A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 5.973A 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=AC2, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.666A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC4, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC5, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.332A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.726A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.584A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 50 through 55 removed outlier: 4.154A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.010A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE B 106 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.917A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.569A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR B 396 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE B 400 " --> pdb=" O VAL B 510 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AD2, first strand: chain 'B' and resid 538 through 543 removed outlier: 3.596A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL B 576 " --> pdb=" O LEU B 585 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.198A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.884A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 712 Processing sheet with id=AD5, first strand: chain 'B' and resid 717 through 728 removed outlier: 3.710A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD8, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD9, first strand: chain 'C' and resid 28 through 30 removed outlier: 7.685A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR C 95 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR C 208 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER C 205 " --> pdb=" O GLU C 224 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 9.066A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 48 through 51 removed outlier: 3.668A pdb=" N THR C 51 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL C 289 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE4, first strand: chain 'C' and resid 118 through 122 removed outlier: 3.749A pdb=" N ASN C 122 " --> pdb=" O ASN C 125 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.429A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.740A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.703A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLY C 431 " --> pdb=" O TYR C 380 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N TYR C 380 " --> pdb=" O GLY C 431 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE9, first strand: chain 'C' and resid 565 through 568 removed outlier: 6.634A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASP C 574 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.977A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 712 through 713 Processing sheet with id=AF3, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.589A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.621A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF6, first strand: chain 'C' and resid 1094 through 1097 939 hydrogen bonds defined for protein. 2538 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: 11.27 Time building geometry restraints manager: 7.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5457 1.33 - 1.45: 6858 1.45 - 1.58: 15228 1.58 - 1.70: 0 1.70 - 1.82: 143 Bond restraints: 27686 Sorted by residual: bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.472 -0.066 2.00e-02 2.50e+03 1.10e+01 bond pdb=" N SER C 514 " pdb=" CA SER C 514 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.20e-02 6.94e+03 5.87e+00 bond pdb=" CA SER C 514 " pdb=" C SER C 514 " ideal model delta sigma weight residual 1.524 1.553 -0.030 1.23e-02 6.61e+03 5.80e+00 bond pdb=" CA LYS O 124 " pdb=" C LYS O 124 " ideal model delta sigma weight residual 1.522 1.550 -0.028 1.20e-02 6.94e+03 5.42e+00 bond pdb=" N PHE C 515 " pdb=" CA PHE C 515 " ideal model delta sigma weight residual 1.455 1.482 -0.027 1.27e-02 6.20e+03 4.60e+00 ... (remaining 27681 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 37105 2.16 - 4.31: 513 4.31 - 6.47: 52 6.47 - 8.63: 9 8.63 - 10.79: 4 Bond angle restraints: 37683 Sorted by residual: angle pdb=" N CYS C 525 " pdb=" CA CYS C 525 " pdb=" C CYS C 525 " ideal model delta sigma weight residual 110.59 120.92 -10.33 1.45e+00 4.76e-01 5.08e+01 angle pdb=" N THR A 393 " pdb=" CA THR A 393 " pdb=" C THR A 393 " ideal model delta sigma weight residual 111.28 118.86 -7.58 1.09e+00 8.42e-01 4.83e+01 angle pdb=" N SER C 514 " pdb=" CA SER C 514 " pdb=" C SER C 514 " ideal model delta sigma weight residual 108.38 117.49 -9.11 1.35e+00 5.49e-01 4.56e+01 angle pdb=" C CYS C 488 " pdb=" N TYR C 489 " pdb=" CA TYR C 489 " ideal model delta sigma weight residual 122.21 133.00 -10.79 1.62e+00 3.81e-01 4.43e+01 angle pdb=" N PHE C 486 " pdb=" CA PHE C 486 " pdb=" C PHE C 486 " ideal model delta sigma weight residual 111.28 117.32 -6.04 1.09e+00 8.42e-01 3.07e+01 ... (remaining 37678 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.29: 15718 24.29 - 48.59: 1002 48.59 - 72.88: 136 72.88 - 97.17: 33 97.17 - 121.46: 3 Dihedral angle restraints: 16892 sinusoidal: 6930 harmonic: 9962 Sorted by residual: dihedral pdb=" CB CYS B 743 " pdb=" SG CYS B 743 " pdb=" SG CYS B 749 " pdb=" CB CYS B 749 " ideal model delta sinusoidal sigma weight residual -86.00 -170.04 84.04 1 1.00e+01 1.00e-02 8.60e+01 dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual -86.00 -12.16 -73.84 1 1.00e+01 1.00e-02 6.93e+01 dihedral pdb=" CB CYS B 738 " pdb=" SG CYS B 738 " pdb=" SG CYS B 760 " pdb=" CB CYS B 760 " ideal model delta sinusoidal sigma weight residual -86.00 -41.12 -44.88 1 1.00e+01 1.00e-02 2.80e+01 ... (remaining 16889 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 4071 0.093 - 0.186: 298 0.186 - 0.278: 4 0.278 - 0.371: 2 0.371 - 0.464: 1 Chirality restraints: 4376 Sorted by residual: chirality pdb=" CA ASN C 87 " pdb=" N ASN C 87 " pdb=" C ASN C 87 " pdb=" CB ASN C 87 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.39e+00 chirality pdb=" CA LEU C 517 " pdb=" N LEU C 517 " pdb=" C LEU C 517 " pdb=" CB LEU C 517 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" CA ASP C 88 " pdb=" N ASP C 88 " pdb=" C ASP C 88 " pdb=" CB ASP C 88 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 4373 not shown) Planarity restraints: 4858 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B1139 " 0.068 5.00e-02 4.00e+02 1.02e-01 1.67e+01 pdb=" N PRO B1140 " -0.177 5.00e-02 4.00e+02 pdb=" CA PRO B1140 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO B1140 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 512 " 0.018 2.00e-02 2.50e+03 3.66e-02 1.34e+01 pdb=" C VAL C 512 " -0.063 2.00e-02 2.50e+03 pdb=" O VAL C 512 " 0.024 2.00e-02 2.50e+03 pdb=" N LEU C 513 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 111 " -0.013 2.00e-02 2.50e+03 2.59e-02 6.70e+00 pdb=" CG ASP A 111 " 0.045 2.00e-02 2.50e+03 pdb=" OD1 ASP A 111 " -0.016 2.00e-02 2.50e+03 pdb=" OD2 ASP A 111 " -0.016 2.00e-02 2.50e+03 ... (remaining 4855 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 101 2.49 - 3.10: 18061 3.10 - 3.70: 37228 3.70 - 4.30: 51164 4.30 - 4.90: 90156 Nonbonded interactions: 196710 Sorted by model distance: nonbonded pdb=" O THR B 286 " pdb=" OD1 ASP B 287 " model vdw 1.894 3.040 nonbonded pdb=" CD2 PHE A 79 " pdb=" OD1 ASP A 80 " model vdw 2.056 3.340 nonbonded pdb=" OG1 THR B 108 " pdb=" O ASN B 234 " model vdw 2.207 3.040 nonbonded pdb=" OD1 ASP P 75 " pdb=" OE1 GLN C 493 " model vdw 2.208 3.040 nonbonded pdb=" OG SER A 349 " pdb=" O LEU A 452 " model vdw 2.224 3.040 ... (remaining 196705 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 26 through 66 or resid 81 through 140 or resid 157 through \ 209 or resid 217 through 243 or resid 264 through 443 or resid 449 through 454 \ or resid 460 through 473 or resid 487 through 620 or resid 641 through 672 or re \ sid 690 through 1146 or resid 1301)) selection = (chain 'B' and (resid 26 through 95 or resid 99 through 140 or resid 157 through \ 620 or resid 641 through 672 or resid 690 through 1146 or resid 1301)) selection = (chain 'C' and (resid 26 through 66 or resid 81 through 209 or resid 217 through \ 243 or resid 264 through 443 or resid 449 through 454 or resid 460 through 473 \ or resid 487 through 500 or resid 503 through 672 or resid 690 through 1146 or r \ esid 1301)) } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.71 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.770 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: 0.920 Check model and map are aligned: 0.170 Set scattering table: 0.240 Process input model: 60.160 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 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 0.066 27751 Z= 0.165 Angle : 0.617 10.785 37841 Z= 0.337 Chirality : 0.046 0.464 4376 Planarity : 0.005 0.102 4837 Dihedral : 15.547 121.465 10363 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.65 % Favored : 95.29 % Rotamer: Outliers : 0.17 % Allowed : 16.81 % Favored : 83.02 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.14), residues: 3358 helix: 1.52 (0.22), residues: 624 sheet: 0.10 (0.18), residues: 831 loop : -1.63 (0.13), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 353 HIS 0.002 0.000 HIS B1048 PHE 0.019 0.001 PHE C 86 TYR 0.017 0.001 TYR C 451 ARG 0.007 0.000 ARG A 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00215 ( 21) link_NAG-ASN : angle 2.11597 ( 63) link_BETA1-4 : bond 0.00352 ( 7) link_BETA1-4 : angle 1.41807 ( 21) hydrogen bonds : bond 0.23438 ( 927) hydrogen bonds : angle 7.92186 ( 2538) SS BOND : bond 0.00340 ( 37) SS BOND : angle 1.10779 ( 74) covalent geometry : bond 0.00325 (27686) covalent geometry : angle 0.60940 (37683) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 212 time to evaluate : 2.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 513 LEU cc_start: 0.6646 (mp) cc_final: 0.6419 (mt) REVERT: C 409 GLN cc_start: 0.7164 (mt0) cc_final: 0.6879 (mt0) REVERT: C 1050 MET cc_start: 0.8703 (ptm) cc_final: 0.8422 (ptm) outliers start: 5 outliers final: 1 residues processed: 216 average time/residue: 0.3422 time to fit residues: 124.2915 Evaluate side-chains 166 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 165 time to evaluate : 2.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 123 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 287 optimal weight: 4.9990 chunk 257 optimal weight: 20.0000 chunk 142 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 173 optimal weight: 20.0000 chunk 137 optimal weight: 0.7980 chunk 266 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 chunk 162 optimal weight: 0.9990 chunk 198 optimal weight: 2.9990 chunk 308 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 ASN A 360 ASN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 603 ASN B 784 GLN B1010 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.224417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.157971 restraints weight = 32976.646| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 2.77 r_work: 0.3369 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3205 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3205 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 27751 Z= 0.180 Angle : 0.641 9.439 37841 Z= 0.330 Chirality : 0.047 0.261 4376 Planarity : 0.005 0.069 4837 Dihedral : 6.760 108.412 4243 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.60 % Allowed : 17.21 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.14), residues: 3358 helix: 1.21 (0.21), residues: 649 sheet: 0.17 (0.18), residues: 843 loop : -1.56 (0.14), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP P 153 HIS 0.005 0.001 HIS B1048 PHE 0.028 0.002 PHE C 497 TYR 0.023 0.001 TYR A1067 ARG 0.006 0.001 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00222 ( 21) link_NAG-ASN : angle 2.14726 ( 63) link_BETA1-4 : bond 0.00266 ( 7) link_BETA1-4 : angle 1.38520 ( 21) hydrogen bonds : bond 0.07214 ( 927) hydrogen bonds : angle 5.72557 ( 2538) SS BOND : bond 0.00463 ( 37) SS BOND : angle 1.29612 ( 74) covalent geometry : bond 0.00430 (27686) covalent geometry : angle 0.63269 (37683) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 190 time to evaluate : 3.014 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: O 183 TYR cc_start: 0.3652 (m-80) cc_final: 0.3371 (m-80) REVERT: A 200 TYR cc_start: 0.6801 (m-80) cc_final: 0.6446 (m-80) REVERT: A 365 TYR cc_start: 0.6231 (m-80) cc_final: 0.5888 (m-80) REVERT: A 616 ASN cc_start: 0.7881 (t0) cc_final: 0.7434 (t0) REVERT: A 1039 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.7902 (mtp180) REVERT: B 326 ILE cc_start: 0.2158 (OUTLIER) cc_final: 0.1313 (tp) REVERT: B 726 ILE cc_start: 0.9318 (OUTLIER) cc_final: 0.9020 (mp) REVERT: B 1045 LYS cc_start: 0.7892 (OUTLIER) cc_final: 0.7474 (mtpt) REVERT: C 81 ASN cc_start: 0.2741 (OUTLIER) cc_final: 0.2471 (t0) REVERT: C 273 ARG cc_start: 0.7094 (ptm-80) cc_final: 0.5866 (ptm-80) REVERT: C 564 GLN cc_start: 0.7622 (mm110) cc_final: 0.6828 (tt0) REVERT: C 720 ILE cc_start: 0.8750 (OUTLIER) cc_final: 0.8258 (mp) REVERT: C 866 THR cc_start: 0.8314 (OUTLIER) cc_final: 0.8104 (m) outliers start: 78 outliers final: 40 residues processed: 252 average time/residue: 0.3293 time to fit residues: 139.7587 Evaluate side-chains 214 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 167 time to evaluate : 2.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 138 VAL Chi-restraints excluded: chain P residue 168 VAL Chi-restraints excluded: chain O residue 73 MET Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 85 optimal weight: 6.9990 chunk 162 optimal weight: 2.9990 chunk 197 optimal weight: 4.9990 chunk 146 optimal weight: 4.9990 chunk 271 optimal weight: 0.6980 chunk 114 optimal weight: 0.9990 chunk 206 optimal weight: 1.9990 chunk 39 optimal weight: 20.0000 chunk 165 optimal weight: 3.9990 chunk 305 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 6 GLN A 211 ASN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 603 ASN B1010 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.223548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.159624 restraints weight = 32877.781| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 2.71 r_work: 0.3359 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3189 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3189 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 27751 Z= 0.169 Angle : 0.602 9.530 37841 Z= 0.308 Chirality : 0.047 0.264 4376 Planarity : 0.005 0.055 4837 Dihedral : 6.391 111.418 4242 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.86 % Allowed : 17.61 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.14), residues: 3358 helix: 1.17 (0.21), residues: 652 sheet: 0.21 (0.18), residues: 819 loop : -1.57 (0.13), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.006 0.001 HIS C 207 PHE 0.028 0.002 PHE C 497 TYR 0.021 0.001 TYR A1067 ARG 0.004 0.000 ARG C 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00199 ( 21) link_NAG-ASN : angle 2.03574 ( 63) link_BETA1-4 : bond 0.00273 ( 7) link_BETA1-4 : angle 1.52592 ( 21) hydrogen bonds : bond 0.07154 ( 927) hydrogen bonds : angle 5.25604 ( 2538) SS BOND : bond 0.00338 ( 37) SS BOND : angle 1.41237 ( 74) covalent geometry : bond 0.00408 (27686) covalent geometry : angle 0.59318 (37683) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 202 time to evaluate : 2.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 190 THR cc_start: 0.1248 (t) cc_final: 0.1024 (m) REVERT: A 200 TYR cc_start: 0.6978 (m-80) cc_final: 0.6623 (m-80) REVERT: A 237 ARG cc_start: 0.7647 (OUTLIER) cc_final: 0.6663 (ptt180) REVERT: A 365 TYR cc_start: 0.6555 (m-80) cc_final: 0.6303 (m-80) REVERT: A 804 GLN cc_start: 0.9051 (OUTLIER) cc_final: 0.8473 (mm-40) REVERT: A 1039 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.7668 (mtp180) REVERT: B 326 ILE cc_start: 0.2804 (OUTLIER) cc_final: 0.1883 (tp) REVERT: B 726 ILE cc_start: 0.9382 (OUTLIER) cc_final: 0.9067 (mp) REVERT: B 740 MET cc_start: 0.8988 (OUTLIER) cc_final: 0.8420 (tpp) REVERT: B 1045 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7665 (mtpt) REVERT: C 52 GLN cc_start: 0.6589 (tp40) cc_final: 0.5962 (tp40) REVERT: C 81 ASN cc_start: 0.3215 (OUTLIER) cc_final: 0.2912 (t0) REVERT: C 273 ARG cc_start: 0.7388 (ptm-80) cc_final: 0.5853 (ptp-110) REVERT: C 349 SER cc_start: 0.7715 (m) cc_final: 0.7426 (p) REVERT: C 401 VAL cc_start: 0.9237 (OUTLIER) cc_final: 0.8943 (m) REVERT: C 464 PHE cc_start: 0.6083 (m-10) cc_final: 0.5732 (m-10) REVERT: C 720 ILE cc_start: 0.8807 (OUTLIER) cc_final: 0.8382 (mp) REVERT: C 825 LYS cc_start: 0.7588 (OUTLIER) cc_final: 0.7381 (ttmm) outliers start: 116 outliers final: 74 residues processed: 302 average time/residue: 0.3204 time to fit residues: 165.5944 Evaluate side-chains 268 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 183 time to evaluate : 2.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 138 VAL Chi-restraints excluded: chain P residue 168 VAL Chi-restraints excluded: chain O residue 73 MET Chi-restraints excluded: chain O residue 158 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 804 GLN Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 748 GLU Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 825 LYS Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 147 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 228 optimal weight: 0.9980 chunk 133 optimal weight: 1.9990 chunk 243 optimal weight: 6.9990 chunk 165 optimal weight: 1.9990 chunk 213 optimal weight: 1.9990 chunk 220 optimal weight: 2.9990 chunk 324 optimal weight: 0.7980 chunk 41 optimal weight: 50.0000 chunk 229 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 204 GLN ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN B 81 ASN B1010 GLN C 751 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.222394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.156555 restraints weight = 33068.101| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 2.67 r_work: 0.3359 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3201 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3201 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 27751 Z= 0.170 Angle : 0.606 16.333 37841 Z= 0.307 Chirality : 0.046 0.280 4376 Planarity : 0.005 0.052 4837 Dihedral : 6.258 109.529 4242 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.76 % Allowed : 19.41 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.14), residues: 3358 helix: 1.14 (0.21), residues: 660 sheet: 0.13 (0.18), residues: 837 loop : -1.59 (0.13), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.004 0.001 HIS B1048 PHE 0.027 0.002 PHE C 497 TYR 0.022 0.001 TYR A1067 ARG 0.003 0.000 ARG C 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00200 ( 21) link_NAG-ASN : angle 2.22152 ( 63) link_BETA1-4 : bond 0.00260 ( 7) link_BETA1-4 : angle 1.56215 ( 21) hydrogen bonds : bond 0.06970 ( 927) hydrogen bonds : angle 5.08652 ( 2538) SS BOND : bond 0.00322 ( 37) SS BOND : angle 1.25649 ( 74) covalent geometry : bond 0.00411 (27686) covalent geometry : angle 0.59694 (37683) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 192 time to evaluate : 2.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 33 TYR cc_start: 0.5752 (m-80) cc_final: 0.5499 (m-80) REVERT: O 94 TYR cc_start: 0.3430 (m-10) cc_final: 0.3017 (m-80) REVERT: A 200 TYR cc_start: 0.7065 (m-80) cc_final: 0.6714 (m-80) REVERT: A 237 ARG cc_start: 0.7628 (ptm160) cc_final: 0.6715 (ptt180) REVERT: A 1039 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.7905 (mtp180) REVERT: B 226 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8167 (mp) REVERT: B 326 ILE cc_start: 0.2856 (OUTLIER) cc_final: 0.2032 (tp) REVERT: B 726 ILE cc_start: 0.9359 (OUTLIER) cc_final: 0.9045 (mp) REVERT: B 1045 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7692 (mtpt) REVERT: C 52 GLN cc_start: 0.6242 (tp40) cc_final: 0.6014 (tp40) REVERT: C 273 ARG cc_start: 0.7288 (ptm-80) cc_final: 0.5749 (ptp-110) REVERT: C 349 SER cc_start: 0.7423 (m) cc_final: 0.7185 (p) REVERT: C 401 VAL cc_start: 0.9279 (OUTLIER) cc_final: 0.9011 (m) REVERT: C 465 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.6782 (mt-10) REVERT: C 720 ILE cc_start: 0.8806 (OUTLIER) cc_final: 0.8369 (mp) REVERT: C 866 THR cc_start: 0.8272 (OUTLIER) cc_final: 0.8063 (m) outliers start: 113 outliers final: 73 residues processed: 290 average time/residue: 0.3252 time to fit residues: 160.7537 Evaluate side-chains 265 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 183 time to evaluate : 2.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 138 VAL Chi-restraints excluded: chain P residue 168 VAL Chi-restraints excluded: chain O residue 19 SER Chi-restraints excluded: chain O residue 73 MET Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 304 optimal weight: 3.9990 chunk 321 optimal weight: 1.9990 chunk 172 optimal weight: 0.8980 chunk 185 optimal weight: 9.9990 chunk 124 optimal weight: 2.9990 chunk 216 optimal weight: 0.6980 chunk 180 optimal weight: 0.0570 chunk 208 optimal weight: 1.9990 chunk 230 optimal weight: 3.9990 chunk 122 optimal weight: 0.4980 chunk 88 optimal weight: 3.9990 overall best weight: 0.8300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 204 GLN A 544 ASN B 81 ASN B1010 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.224103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.157414 restraints weight = 32971.645| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 2.60 r_work: 0.3392 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3243 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3243 r_free = 0.3243 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3242 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27751 Z= 0.120 Angle : 0.547 13.573 37841 Z= 0.277 Chirality : 0.045 0.263 4376 Planarity : 0.004 0.054 4837 Dihedral : 5.997 109.221 4242 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.56 % Allowed : 20.01 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.14), residues: 3358 helix: 1.37 (0.21), residues: 664 sheet: 0.23 (0.18), residues: 851 loop : -1.52 (0.14), residues: 1843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.003 0.001 HIS B 49 PHE 0.021 0.001 PHE C 497 TYR 0.016 0.001 TYR A1067 ARG 0.004 0.000 ARG C 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00241 ( 21) link_NAG-ASN : angle 1.83246 ( 63) link_BETA1-4 : bond 0.00312 ( 7) link_BETA1-4 : angle 1.46568 ( 21) hydrogen bonds : bond 0.05893 ( 927) hydrogen bonds : angle 4.90100 ( 2538) SS BOND : bond 0.00305 ( 37) SS BOND : angle 0.97618 ( 74) covalent geometry : bond 0.00267 (27686) covalent geometry : angle 0.54030 (37683) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 198 time to evaluate : 2.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 33 TYR cc_start: 0.5678 (m-80) cc_final: 0.5449 (m-80) REVERT: O 94 TYR cc_start: 0.3371 (m-10) cc_final: 0.3027 (m-80) REVERT: A 200 TYR cc_start: 0.6988 (m-80) cc_final: 0.6607 (m-80) REVERT: A 237 ARG cc_start: 0.7550 (ptm160) cc_final: 0.6658 (ptt180) REVERT: A 804 GLN cc_start: 0.9011 (OUTLIER) cc_final: 0.8441 (mm-40) REVERT: A 821 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7763 (tt) REVERT: A 1039 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.7497 (ptm160) REVERT: B 740 MET cc_start: 0.8975 (OUTLIER) cc_final: 0.8339 (tpp) REVERT: B 1045 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7588 (mtpt) REVERT: C 52 GLN cc_start: 0.6277 (tp40) cc_final: 0.5995 (tp40) REVERT: C 273 ARG cc_start: 0.7311 (ptm-80) cc_final: 0.5804 (ptp-110) REVERT: C 349 SER cc_start: 0.7271 (m) cc_final: 0.7046 (p) REVERT: C 401 VAL cc_start: 0.9291 (OUTLIER) cc_final: 0.9012 (m) REVERT: C 465 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.6704 (mt-10) REVERT: C 564 GLN cc_start: 0.7458 (mm110) cc_final: 0.6704 (tt0) REVERT: C 661 GLU cc_start: 0.8402 (mm-30) cc_final: 0.8125 (tp30) outliers start: 107 outliers final: 71 residues processed: 290 average time/residue: 0.3524 time to fit residues: 172.0448 Evaluate side-chains 264 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 186 time to evaluate : 2.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 138 VAL Chi-restraints excluded: chain P residue 168 VAL Chi-restraints excluded: chain O residue 73 MET Chi-restraints excluded: chain O residue 190 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 804 GLN Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 748 GLU Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 74 optimal weight: 20.0000 chunk 163 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 chunk 303 optimal weight: 2.9990 chunk 290 optimal weight: 1.9990 chunk 314 optimal weight: 0.9980 chunk 331 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 83 optimal weight: 30.0000 chunk 7 optimal weight: 10.0000 chunk 281 optimal weight: 0.7980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 204 GLN ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN B 81 ASN B1010 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 ASN C 613 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.221653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.154337 restraints weight = 32863.914| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 2.59 r_work: 0.3343 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3201 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3201 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 27751 Z= 0.183 Angle : 0.598 13.488 37841 Z= 0.304 Chirality : 0.047 0.274 4376 Planarity : 0.005 0.053 4837 Dihedral : 6.093 108.318 4242 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.89 % Allowed : 19.94 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.14), residues: 3358 helix: 1.23 (0.21), residues: 664 sheet: 0.20 (0.18), residues: 843 loop : -1.59 (0.13), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 353 HIS 0.006 0.001 HIS C 207 PHE 0.026 0.002 PHE C 497 TYR 0.024 0.001 TYR A1067 ARG 0.006 0.000 ARG B 646 Details of bonding type rmsd link_NAG-ASN : bond 0.00190 ( 21) link_NAG-ASN : angle 2.04709 ( 63) link_BETA1-4 : bond 0.00351 ( 7) link_BETA1-4 : angle 1.54563 ( 21) hydrogen bonds : bond 0.06995 ( 927) hydrogen bonds : angle 4.94375 ( 2538) SS BOND : bond 0.00326 ( 37) SS BOND : angle 1.17343 ( 74) covalent geometry : bond 0.00446 (27686) covalent geometry : angle 0.58964 (37683) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 188 time to evaluate : 2.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 33 TYR cc_start: 0.5728 (m-80) cc_final: 0.5445 (m-80) REVERT: O 52 TYR cc_start: 0.5051 (t80) cc_final: 0.4848 (t80) REVERT: O 73 MET cc_start: 0.5150 (OUTLIER) cc_final: 0.4609 (ptm) REVERT: O 94 TYR cc_start: 0.3399 (m-10) cc_final: 0.3026 (m-80) REVERT: A 200 TYR cc_start: 0.7037 (m-80) cc_final: 0.6666 (m-80) REVERT: A 237 ARG cc_start: 0.7584 (ptm160) cc_final: 0.7378 (mtp-110) REVERT: A 804 GLN cc_start: 0.8995 (OUTLIER) cc_final: 0.8426 (mm-40) REVERT: A 821 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7838 (tt) REVERT: A 896 ILE cc_start: 0.8626 (OUTLIER) cc_final: 0.8405 (tp) REVERT: A 1039 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8070 (mtp180) REVERT: B 726 ILE cc_start: 0.9345 (OUTLIER) cc_final: 0.9013 (mp) REVERT: B 740 MET cc_start: 0.8998 (OUTLIER) cc_final: 0.8359 (tpp) REVERT: B 1045 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7646 (mtpt) REVERT: C 273 ARG cc_start: 0.7317 (ptm-80) cc_final: 0.5735 (ptp-110) REVERT: C 349 SER cc_start: 0.7579 (m) cc_final: 0.7359 (m) REVERT: C 354 ASN cc_start: 0.7245 (OUTLIER) cc_final: 0.6855 (p0) REVERT: C 401 VAL cc_start: 0.9346 (OUTLIER) cc_final: 0.9063 (m) REVERT: C 465 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.6774 (mt-10) REVERT: C 543 PHE cc_start: 0.6840 (OUTLIER) cc_final: 0.6272 (m-10) REVERT: C 661 GLU cc_start: 0.8368 (mm-30) cc_final: 0.8089 (tp30) REVERT: C 720 ILE cc_start: 0.8791 (OUTLIER) cc_final: 0.8366 (mp) outliers start: 117 outliers final: 88 residues processed: 291 average time/residue: 0.3159 time to fit residues: 155.9342 Evaluate side-chains 281 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 180 time to evaluate : 2.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 168 VAL Chi-restraints excluded: chain O residue 73 MET Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 804 GLN Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 543 PHE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 748 GLU Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 45 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 268 optimal weight: 0.5980 chunk 257 optimal weight: 0.3980 chunk 222 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 chunk 328 optimal weight: 0.9990 chunk 212 optimal weight: 0.6980 chunk 288 optimal weight: 1.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 204 GLN ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN B 81 ASN B1010 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.223983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.159219 restraints weight = 33169.912| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 2.65 r_work: 0.3383 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3227 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3227 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 27751 Z= 0.115 Angle : 0.540 12.850 37841 Z= 0.273 Chirality : 0.044 0.261 4376 Planarity : 0.004 0.055 4837 Dihedral : 5.907 107.981 4242 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.56 % Allowed : 20.14 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.14), residues: 3358 helix: 1.44 (0.21), residues: 666 sheet: 0.31 (0.18), residues: 852 loop : -1.50 (0.14), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 353 HIS 0.005 0.001 HIS C 207 PHE 0.026 0.001 PHE C 497 TYR 0.016 0.001 TYR C 351 ARG 0.006 0.000 ARG C 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00246 ( 21) link_NAG-ASN : angle 1.81062 ( 63) link_BETA1-4 : bond 0.00340 ( 7) link_BETA1-4 : angle 1.46790 ( 21) hydrogen bonds : bond 0.05799 ( 927) hydrogen bonds : angle 4.79519 ( 2538) SS BOND : bond 0.00300 ( 37) SS BOND : angle 0.92689 ( 74) covalent geometry : bond 0.00253 (27686) covalent geometry : angle 0.53303 (37683) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 187 time to evaluate : 2.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 33 TYR cc_start: 0.5718 (m-80) cc_final: 0.5430 (m-80) REVERT: O 52 TYR cc_start: 0.4990 (t80) cc_final: 0.4705 (t80) REVERT: O 94 TYR cc_start: 0.3537 (m-10) cc_final: 0.3161 (m-80) REVERT: A 200 TYR cc_start: 0.6866 (m-80) cc_final: 0.6477 (m-80) REVERT: A 804 GLN cc_start: 0.9020 (OUTLIER) cc_final: 0.8472 (mm-40) REVERT: A 821 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7832 (tt) REVERT: A 913 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.8206 (pt0) REVERT: A 1039 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.7517 (ptm160) REVERT: B 1045 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7589 (mtpt) REVERT: B 1071 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.7815 (mt0) REVERT: C 273 ARG cc_start: 0.7258 (OUTLIER) cc_final: 0.6960 (ptp-170) REVERT: C 349 SER cc_start: 0.7501 (m) cc_final: 0.7285 (m) REVERT: C 354 ASN cc_start: 0.7258 (OUTLIER) cc_final: 0.6931 (p0) REVERT: C 401 VAL cc_start: 0.9354 (OUTLIER) cc_final: 0.9100 (m) REVERT: C 465 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.6935 (mt-10) REVERT: C 506 GLN cc_start: 0.7677 (mt0) cc_final: 0.7310 (mt0) REVERT: C 543 PHE cc_start: 0.6853 (OUTLIER) cc_final: 0.6344 (m-10) REVERT: C 564 GLN cc_start: 0.7475 (mm110) cc_final: 0.6778 (tt0) REVERT: C 661 GLU cc_start: 0.8399 (mm-30) cc_final: 0.8113 (tp30) REVERT: C 720 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8311 (mp) outliers start: 107 outliers final: 78 residues processed: 283 average time/residue: 0.3283 time to fit residues: 156.4264 Evaluate side-chains 269 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 179 time to evaluate : 2.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 168 VAL Chi-restraints excluded: chain O residue 19 SER Chi-restraints excluded: chain O residue 73 MET Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 804 GLN Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1071 GLN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 273 ARG Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 543 PHE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 175 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 268 optimal weight: 0.6980 chunk 168 optimal weight: 10.0000 chunk 304 optimal weight: 4.9990 chunk 191 optimal weight: 1.9990 chunk 201 optimal weight: 0.5980 chunk 225 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 254 optimal weight: 9.9990 chunk 295 optimal weight: 4.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 204 GLN ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN A 755 GLN A 787 GLN A 895 GLN B 81 ASN B1010 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 ASN C 487 ASN C 907 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.221914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.157585 restraints weight = 33021.770| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 2.69 r_work: 0.3343 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3199 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3199 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 27751 Z= 0.172 Angle : 0.584 12.608 37841 Z= 0.296 Chirality : 0.046 0.269 4376 Planarity : 0.005 0.053 4837 Dihedral : 5.993 107.197 4242 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.89 % Allowed : 20.04 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.14), residues: 3358 helix: 1.27 (0.21), residues: 669 sheet: 0.26 (0.18), residues: 839 loop : -1.53 (0.13), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 353 HIS 0.005 0.001 HIS B 49 PHE 0.028 0.002 PHE C 497 TYR 0.023 0.001 TYR A1067 ARG 0.004 0.000 ARG C1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00183 ( 21) link_NAG-ASN : angle 1.98980 ( 63) link_BETA1-4 : bond 0.00261 ( 7) link_BETA1-4 : angle 1.53745 ( 21) hydrogen bonds : bond 0.06807 ( 927) hydrogen bonds : angle 4.84525 ( 2538) SS BOND : bond 0.00315 ( 37) SS BOND : angle 1.13395 ( 74) covalent geometry : bond 0.00421 (27686) covalent geometry : angle 0.57664 (37683) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 184 time to evaluate : 2.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 33 TYR cc_start: 0.5876 (m-80) cc_final: 0.5578 (m-80) REVERT: O 52 TYR cc_start: 0.4973 (t80) cc_final: 0.4650 (t80) REVERT: O 94 TYR cc_start: 0.3681 (m-10) cc_final: 0.3260 (m-80) REVERT: A 200 TYR cc_start: 0.7077 (m-80) cc_final: 0.6690 (m-80) REVERT: A 237 ARG cc_start: 0.7814 (mtp-110) cc_final: 0.7236 (ptt180) REVERT: A 804 GLN cc_start: 0.9005 (OUTLIER) cc_final: 0.8440 (mm-40) REVERT: A 821 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7856 (tt) REVERT: A 913 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.8303 (pt0) REVERT: A 1039 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.7535 (ptm160) REVERT: B 726 ILE cc_start: 0.9345 (OUTLIER) cc_final: 0.9030 (mp) REVERT: B 740 MET cc_start: 0.9007 (OUTLIER) cc_final: 0.8347 (tpp) REVERT: B 1045 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7716 (mtpt) REVERT: C 52 GLN cc_start: 0.6373 (tp40) cc_final: 0.6030 (tp40) REVERT: C 237 ARG cc_start: 0.7927 (mtt180) cc_final: 0.7591 (mmt-90) REVERT: C 273 ARG cc_start: 0.7439 (OUTLIER) cc_final: 0.5926 (ptp-110) REVERT: C 401 VAL cc_start: 0.9345 (OUTLIER) cc_final: 0.9121 (m) REVERT: C 465 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7029 (mt-10) REVERT: C 506 GLN cc_start: 0.7608 (mt0) cc_final: 0.7238 (mt0) REVERT: C 543 PHE cc_start: 0.6914 (OUTLIER) cc_final: 0.6352 (m-10) REVERT: C 661 GLU cc_start: 0.8432 (mm-30) cc_final: 0.8144 (tp30) REVERT: C 720 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.8345 (mp) outliers start: 117 outliers final: 93 residues processed: 283 average time/residue: 0.3336 time to fit residues: 159.6032 Evaluate side-chains 283 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 178 time to evaluate : 2.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 168 VAL Chi-restraints excluded: chain O residue 19 SER Chi-restraints excluded: chain O residue 73 MET Chi-restraints excluded: chain O residue 158 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 804 GLN Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 273 ARG Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 543 PHE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 748 GLU Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 51 optimal weight: 4.9990 chunk 322 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 85 optimal weight: 9.9990 chunk 126 optimal weight: 4.9990 chunk 280 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 121 optimal weight: 0.8980 chunk 185 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 204 GLN ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN B 81 ASN B1010 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.222580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.157438 restraints weight = 33339.885| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 2.74 r_work: 0.3355 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3197 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3197 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 27751 Z= 0.143 Angle : 0.565 12.414 37841 Z= 0.285 Chirality : 0.045 0.266 4376 Planarity : 0.004 0.054 4837 Dihedral : 5.930 107.080 4242 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.73 % Allowed : 20.24 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.14), residues: 3358 helix: 1.35 (0.21), residues: 668 sheet: 0.33 (0.18), residues: 841 loop : -1.50 (0.13), residues: 1849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 64 HIS 0.005 0.001 HIS C 207 PHE 0.026 0.001 PHE C 497 TYR 0.018 0.001 TYR A1067 ARG 0.004 0.000 ARG A1039 Details of bonding type rmsd link_NAG-ASN : bond 0.00201 ( 21) link_NAG-ASN : angle 1.91444 ( 63) link_BETA1-4 : bond 0.00282 ( 7) link_BETA1-4 : angle 1.51142 ( 21) hydrogen bonds : bond 0.06384 ( 927) hydrogen bonds : angle 4.76789 ( 2538) SS BOND : bond 0.00305 ( 37) SS BOND : angle 1.04850 ( 74) covalent geometry : bond 0.00341 (27686) covalent geometry : angle 0.55797 (37683) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 183 time to evaluate : 2.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 33 TYR cc_start: 0.5957 (m-80) cc_final: 0.5667 (m-80) REVERT: O 52 TYR cc_start: 0.5078 (t80) cc_final: 0.4710 (t80) REVERT: O 94 TYR cc_start: 0.3373 (m-10) cc_final: 0.3048 (m-80) REVERT: A 200 TYR cc_start: 0.7002 (m-80) cc_final: 0.6601 (m-80) REVERT: A 237 ARG cc_start: 0.7768 (mtp-110) cc_final: 0.7251 (ptt180) REVERT: A 804 GLN cc_start: 0.9015 (OUTLIER) cc_final: 0.8464 (mm-40) REVERT: A 821 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7852 (tt) REVERT: A 1039 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.7572 (ptm160) REVERT: B 740 MET cc_start: 0.8991 (OUTLIER) cc_final: 0.8329 (tpp) REVERT: B 1045 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7632 (mtpt) REVERT: B 1071 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.7961 (mt0) REVERT: C 52 GLN cc_start: 0.6390 (tp40) cc_final: 0.6051 (tp40) REVERT: C 273 ARG cc_start: 0.7292 (OUTLIER) cc_final: 0.6156 (ptp-110) REVERT: C 465 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7014 (mt-10) REVERT: C 543 PHE cc_start: 0.6830 (OUTLIER) cc_final: 0.6326 (m-10) REVERT: C 564 GLN cc_start: 0.7472 (mm110) cc_final: 0.6774 (tt0) REVERT: C 661 GLU cc_start: 0.8401 (mm-30) cc_final: 0.8112 (tp30) REVERT: C 720 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8335 (mp) outliers start: 112 outliers final: 95 residues processed: 278 average time/residue: 0.3280 time to fit residues: 154.4512 Evaluate side-chains 282 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 177 time to evaluate : 2.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 33 ASN Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 168 VAL Chi-restraints excluded: chain O residue 19 SER Chi-restraints excluded: chain O residue 73 MET Chi-restraints excluded: chain O residue 158 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 804 GLN Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1071 GLN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 273 ARG Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 543 PHE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 748 GLU Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 313 optimal weight: 1.9990 chunk 213 optimal weight: 1.9990 chunk 23 optimal weight: 40.0000 chunk 94 optimal weight: 2.9990 chunk 318 optimal weight: 0.9990 chunk 282 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 268 optimal weight: 9.9990 chunk 75 optimal weight: 9.9990 chunk 195 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 204 GLN ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN A 895 GLN B 81 ASN B1010 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.220956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.155960 restraints weight = 33094.384| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 2.60 r_work: 0.3344 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3194 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3194 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 27751 Z= 0.187 Angle : 0.616 12.395 37841 Z= 0.313 Chirality : 0.047 0.272 4376 Planarity : 0.005 0.053 4837 Dihedral : 6.107 106.651 4242 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.63 % Allowed : 20.44 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.14), residues: 3358 helix: 1.21 (0.21), residues: 662 sheet: 0.25 (0.18), residues: 836 loop : -1.53 (0.13), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 64 HIS 0.005 0.001 HIS B 49 PHE 0.027 0.002 PHE C 497 TYR 0.026 0.001 TYR A1067 ARG 0.005 0.000 ARG A1039 Details of bonding type rmsd link_NAG-ASN : bond 0.00201 ( 21) link_NAG-ASN : angle 2.15394 ( 63) link_BETA1-4 : bond 0.00276 ( 7) link_BETA1-4 : angle 1.64830 ( 21) hydrogen bonds : bond 0.07362 ( 927) hydrogen bonds : angle 4.88495 ( 2538) SS BOND : bond 0.00348 ( 37) SS BOND : angle 1.25686 ( 74) covalent geometry : bond 0.00460 (27686) covalent geometry : angle 0.60727 (37683) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 191 time to evaluate : 2.714 Fit side-chains revert: symmetry clash REVERT: O 94 TYR cc_start: 0.3518 (m-10) cc_final: 0.3148 (m-80) REVERT: O 183 TYR cc_start: 0.4055 (m-80) cc_final: 0.3421 (m-80) REVERT: A 120 VAL cc_start: 0.7157 (p) cc_final: 0.6808 (t) REVERT: A 200 TYR cc_start: 0.7094 (m-80) cc_final: 0.6704 (m-80) REVERT: A 237 ARG cc_start: 0.7869 (mtp-110) cc_final: 0.7326 (ptt180) REVERT: A 804 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.8435 (mm-40) REVERT: A 821 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7857 (tt) REVERT: A 1039 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.7884 (ptm160) REVERT: A 1139 ASP cc_start: 0.8161 (p0) cc_final: 0.7928 (p0) REVERT: B 740 MET cc_start: 0.9012 (OUTLIER) cc_final: 0.8341 (tpp) REVERT: B 1045 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7754 (mtpt) REVERT: B 1071 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.8051 (mt0) REVERT: C 52 GLN cc_start: 0.6455 (tp40) cc_final: 0.6076 (tp40) REVERT: C 273 ARG cc_start: 0.7295 (OUTLIER) cc_final: 0.6077 (ptp-110) REVERT: C 457 ARG cc_start: 0.5704 (mtt90) cc_final: 0.4231 (mmm-85) REVERT: C 465 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7123 (tt0) REVERT: C 543 PHE cc_start: 0.6839 (OUTLIER) cc_final: 0.6380 (m-10) REVERT: C 661 GLU cc_start: 0.8429 (mm-30) cc_final: 0.8136 (tp30) REVERT: C 720 ILE cc_start: 0.8778 (OUTLIER) cc_final: 0.8445 (mp) outliers start: 109 outliers final: 94 residues processed: 285 average time/residue: 0.3446 time to fit residues: 163.9319 Evaluate side-chains 282 residues out of total 3005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 178 time to evaluate : 2.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 33 ASN Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 168 VAL Chi-restraints excluded: chain O residue 19 SER Chi-restraints excluded: chain O residue 73 MET Chi-restraints excluded: chain O residue 158 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 804 GLN Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1071 GLN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 273 ARG Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 543 PHE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 748 GLU Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 195 optimal weight: 0.8980 chunk 162 optimal weight: 2.9990 chunk 184 optimal weight: 0.3980 chunk 141 optimal weight: 3.9990 chunk 326 optimal weight: 0.5980 chunk 54 optimal weight: 9.9990 chunk 289 optimal weight: 0.9980 chunk 227 optimal weight: 2.9990 chunk 4 optimal weight: 20.0000 chunk 15 optimal weight: 1.9990 chunk 146 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 204 GLN ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN A 895 GLN B 81 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.221459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.165571 restraints weight = 33206.169| |-----------------------------------------------------------------------------| r_work (start): 0.3921 rms_B_bonded: 2.84 r_work: 0.3318 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3297 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3297 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.146 27751 Z= 0.182 Angle : 0.845 59.199 37841 Z= 0.477 Chirality : 0.047 0.599 4376 Planarity : 0.005 0.061 4837 Dihedral : 6.116 106.754 4242 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.56 % Allowed : 20.44 % Favored : 76.00 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.14), residues: 3358 helix: 1.21 (0.20), residues: 662 sheet: 0.25 (0.18), residues: 836 loop : -1.54 (0.13), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 64 HIS 0.004 0.001 HIS B 49 PHE 0.024 0.002 PHE C 497 TYR 0.024 0.001 TYR A1067 ARG 0.012 0.000 ARG C 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00210 ( 21) link_NAG-ASN : angle 2.15890 ( 63) link_BETA1-4 : bond 0.00381 ( 7) link_BETA1-4 : angle 1.65323 ( 21) hydrogen bonds : bond 0.07196 ( 927) hydrogen bonds : angle 4.88873 ( 2538) SS BOND : bond 0.00353 ( 37) SS BOND : angle 1.21530 ( 74) covalent geometry : bond 0.00416 (27686) covalent geometry : angle 0.83965 (37683) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20287.38 seconds wall clock time: 350 minutes 6.26 seconds (21006.26 seconds total)