Starting phenix.real_space_refine on Thu May 22 19:02:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8upx_42456/05_2025/8upx_42456.cif Found real_map, /net/cci-nas-00/data/ceres_data/8upx_42456/05_2025/8upx_42456.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8upx_42456/05_2025/8upx_42456.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8upx_42456/05_2025/8upx_42456.map" model { file = "/net/cci-nas-00/data/ceres_data/8upx_42456/05_2025/8upx_42456.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8upx_42456/05_2025/8upx_42456.cif" } resolution = 3.4 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= 0.017 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 105 5.16 5 C 14809 2.51 5 N 3806 2.21 5 O 4512 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 23232 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 7082 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 906, 7066 Classifications: {'peptide': 906} Link IDs: {'PTRANS': 49, 'TRANS': 856} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 906, 7066 Classifications: {'peptide': 906} Link IDs: {'PTRANS': 49, 'TRANS': 856} Chain breaks: 4 bond proxies already assigned to first conformer: 7207 Chain: "B" Number of atoms: 8530 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1092, 8514 Classifications: {'peptide': 1092} Link IDs: {'PTRANS': 62, 'TRANS': 1029} Chain breaks: 6 Conformer: "B" Number of residues, atoms: 1092, 8514 Classifications: {'peptide': 1092} Link IDs: {'PTRANS': 62, 'TRANS': 1029} Chain breaks: 6 bond proxies already assigned to first conformer: 8691 Chain: "C" Number of atoms: 7088 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 906, 7072 Classifications: {'peptide': 906} Link IDs: {'PTRANS': 48, 'TRANS': 857} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 906, 7072 Classifications: {'peptide': 906} Link IDs: {'PTRANS': 48, 'TRANS': 857} Chain breaks: 4 bond proxies already assigned to first conformer: 7213 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" 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 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 23.82, per 1000 atoms: 1.03 Number of scatterers: 23232 At special positions: 0 Unit cell: (143, 160.6, 174.9, 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 105 16.00 O 4512 8.00 N 3806 7.00 C 14809 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 161 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 553 " - pdb=" SG CYS A 605 " distance=2.03 Simple disulfide: pdb=" SG CYS A 632 " - pdb=" SG CYS A 664 " distance=2.03 Simple disulfide: pdb=" SG CYS A 677 " - pdb=" SG CYS A 686 " distance=2.03 Simple disulfide: pdb=" SG CYS A 753 " - pdb=" SG CYS A 775 " distance=2.03 Simple disulfide: pdb=" SG CYS A 758 " - pdb=" SG CYS A 764 " distance=2.03 Simple disulfide: pdb=" SG CYS A1047 " - pdb=" SG CYS A1058 " distance=2.03 Simple disulfide: pdb=" SG CYS A1097 " - pdb=" SG CYS A1141 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 134 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 161 " distance=2.04 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 334 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.03 Simple disulfide: pdb=" SG CYS B 454 " - pdb=" SG CYS B 477 " distance=2.03 Simple disulfide: pdb=" SG CYS B 553 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 632 " - pdb=" SG CYS B 664 " distance=2.03 Simple disulfide: pdb=" SG CYS B 677 " - pdb=" SG CYS B 686 " distance=2.03 Simple disulfide: pdb=" SG CYS B 753 " - pdb=" SG CYS B 775 " distance=2.03 Simple disulfide: pdb=" SG CYS B 758 " - pdb=" SG CYS B 764 " distance=2.03 Simple disulfide: pdb=" SG CYS B1047 " - pdb=" SG CYS B1058 " distance=2.03 Simple disulfide: pdb=" SG CYS B1097 " - pdb=" SG CYS B1141 " distance=2.04 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 134 " distance=2.03 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 161 " distance=2.03 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 298 " distance=2.03 Simple disulfide: pdb=" SG CYS C 553 " - pdb=" SG CYS C 605 " distance=2.03 Simple disulfide: pdb=" SG CYS C 632 " - pdb=" SG CYS C 664 " distance=2.03 Simple disulfide: pdb=" SG CYS C 677 " - pdb=" SG CYS C 686 " distance=2.03 Simple disulfide: pdb=" SG CYS C 753 " - pdb=" SG CYS C 775 " distance=2.03 Simple disulfide: pdb=" SG CYS C 758 " - pdb=" SG CYS C 764 " distance=2.03 Simple disulfide: pdb=" SG CYS C 855 " - pdb=" SG CYS C 866 " distance=2.03 Simple disulfide: pdb=" SG CYS C1047 " - pdb=" SG CYS C1058 " distance=2.03 Simple disulfide: pdb=" SG CYS C1097 " - pdb=" SG CYS C1141 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A1301 " - " ASN A 631 " " NAG A1302 " - " ASN A 672 " " NAG A1303 " - " ASN A 724 " " NAG A1304 " - " ASN A1089 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 631 " " NAG B1303 " - " ASN B 279 " " NAG B1304 " - " ASN B 672 " " NAG B1305 " - " ASN B 724 " " NAG B1306 " - " ASN B1089 " " NAG C1301 " - " ASN C 631 " " NAG C1302 " - " ASN C 279 " " NAG C1303 " - " ASN C 724 " " NAG C1304 " - " ASN C1089 " " NAG D 1 " - " ASN C 732 " " NAG E 1 " - " ASN A 732 " " NAG F 1 " - " ASN A 816 " " NAG G 1 " - " ASN A1113 " " NAG H 1 " - " ASN A1149 " " NAG I 1 " - " ASN B 732 " " NAG J 1 " - " ASN B 816 " " NAG K 1 " - " ASN B1113 " " NAG L 1 " - " ASN B1149 " " NAG M 1 " - " ASN C 816 " " NAG N 1 " - " ASN C1113 " " NAG O 1 " - " ASN C1149 " Time building additional restraints: 5.90 Conformation dependent library (CDL) restraints added in 5.6 seconds 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5464 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 40 sheets defined 24.8% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.87 Creating SS restraints... Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 648 through 653 Processing helix chain 'A' and resid 752 through 757 removed outlier: 3.584A pdb=" N TYR A 756 " --> pdb=" O ASP A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 770 removed outlier: 4.030A pdb=" N GLN A 770 " --> pdb=" O ASN A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 798 removed outlier: 3.507A pdb=" N GLN A 777 " --> pdb=" O SER A 773 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP A 790 " --> pdb=" O ALA A 786 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 840 Processing helix chain 'A' and resid 864 through 870 Processing helix chain 'A' and resid 883 through 899 Processing helix chain 'A' and resid 901 through 905 Processing helix chain 'A' and resid 912 through 924 removed outlier: 3.644A pdb=" N ILE A 924 " --> pdb=" O ARG A 920 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 955 removed outlier: 3.529A pdb=" N TYR A 932 " --> pdb=" O GLN A 928 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LYS A 936 " --> pdb=" O TYR A 932 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU A 937 " --> pdb=" O GLU A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 980 removed outlier: 3.590A pdb=" N GLN A 964 " --> pdb=" O LEU A 960 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL A 966 " --> pdb=" O LYS A 962 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N VAL A 967 " --> pdb=" O LEU A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 999 removed outlier: 4.128A pdb=" N ARG A 998 " --> pdb=" O ASP A 994 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU A 999 " --> pdb=" O ILE A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1000 through 1048 removed outlier: 4.583A pdb=" N VAL A1006 " --> pdb=" O PRO A1002 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN A1007 " --> pdb=" O GLU A1003 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL A1048 " --> pdb=" O MET A1044 " (cutoff:3.500A) Processing helix chain 'A' and resid 1156 through 1161 Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 336 through 341 removed outlier: 3.740A pdb=" N LEU B 340 " --> pdb=" O PHE B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 350 Processing helix chain 'B' and resid 361 through 369 removed outlier: 3.842A pdb=" N LEU B 365 " --> pdb=" O ASN B 361 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU B 368 " --> pdb=" O LYS B 364 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE B 369 " --> pdb=" O LEU B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 385 removed outlier: 3.964A pdb=" N ALA B 385 " --> pdb=" O PRO B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 407 removed outlier: 4.021A pdb=" N MET B 403 " --> pdb=" O PRO B 400 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N SER B 405 " --> pdb=" O SER B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 419 Processing helix chain 'B' and resid 475 through 480 removed outlier: 4.067A pdb=" N SER B 479 " --> pdb=" O PRO B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 561 removed outlier: 3.583A pdb=" N GLY B 560 " --> pdb=" O ASN B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 757 Processing helix chain 'B' and resid 761 through 769 Processing helix chain 'B' and resid 770 through 772 No H-bonds generated for 'chain 'B' and resid 770 through 772' Processing helix chain 'B' and resid 774 through 798 removed outlier: 3.689A pdb=" N ASP B 790 " --> pdb=" O ALA B 786 " (cutoff:3.500A) Processing helix chain 'B' and resid 831 through 841 removed outlier: 3.538A pdb=" N VAL B 841 " --> pdb=" O LEU B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 870 Processing helix chain 'B' and resid 881 through 899 removed outlier: 3.758A pdb=" N ILE B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA B 886 " --> pdb=" O ASP B 882 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLN B 887 " --> pdb=" O GLU B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 905 removed outlier: 3.619A pdb=" N ALA B 905 " --> pdb=" O THR B 902 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 925 removed outlier: 3.634A pdb=" N ALA B 918 " --> pdb=" O PRO B 914 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR B 919 " --> pdb=" O MET B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 928 through 934 removed outlier: 3.624A pdb=" N TYR B 932 " --> pdb=" O GLN B 928 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU B 933 " --> pdb=" O ASN B 929 " (cutoff:3.500A) Processing helix chain 'B' and resid 934 through 955 removed outlier: 4.340A pdb=" N SER B 954 " --> pdb=" O GLN B 950 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER B 955 " --> pdb=" O ASP B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 960 through 980 removed outlier: 4.204A pdb=" N VAL B 966 " --> pdb=" O LYS B 962 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL B 967 " --> pdb=" O LEU B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 981 through 983 No H-bonds generated for 'chain 'B' and resid 981 through 983' Processing helix chain 'B' and resid 991 through 997 Processing helix chain 'B' and resid 1000 through 1047 removed outlier: 4.550A pdb=" N VAL B1006 " --> pdb=" O PRO B1002 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLN B1007 " --> pdb=" O GLU B1003 " (cutoff:3.500A) Processing helix chain 'B' and resid 1156 through 1161 Processing helix chain 'C' and resid 291 through 300 Processing helix chain 'C' and resid 752 through 758 removed outlier: 3.934A pdb=" N CYS C 758 " --> pdb=" O THR C 754 " (cutoff:3.500A) Processing helix chain 'C' and resid 761 through 770 Processing helix chain 'C' and resid 775 through 798 removed outlier: 3.670A pdb=" N ASP C 790 " --> pdb=" O ALA C 786 " (cutoff:3.500A) Processing helix chain 'C' and resid 833 through 840 Processing helix chain 'C' and resid 856 through 860 Processing helix chain 'C' and resid 863 through 870 Processing helix chain 'C' and resid 881 through 899 removed outlier: 3.739A pdb=" N ILE C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA C 886 " --> pdb=" O ASP C 882 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLN C 887 " --> pdb=" O GLU C 883 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 905 removed outlier: 3.762A pdb=" N ALA C 905 " --> pdb=" O THR C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 925 removed outlier: 3.951A pdb=" N ALA C 918 " --> pdb=" O PRO C 914 " (cutoff:3.500A) Processing helix chain 'C' and resid 928 through 934 Processing helix chain 'C' and resid 934 through 953 Processing helix chain 'C' and resid 960 through 980 removed outlier: 4.068A pdb=" N VAL C 966 " --> pdb=" O LYS C 962 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N VAL C 967 " --> pdb=" O LEU C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 981 through 983 No H-bonds generated for 'chain 'C' and resid 981 through 983' Processing helix chain 'C' and resid 991 through 995 Processing helix chain 'C' and resid 1000 through 1048 removed outlier: 4.974A pdb=" N VAL C1006 " --> pdb=" O PRO C1002 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLN C1007 " --> pdb=" O GLU C1003 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL C1048 " --> pdb=" O MET C1044 " (cutoff:3.500A) Processing helix chain 'C' and resid 1156 through 1161 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 30 removed outlier: 8.093A pdb=" N ASN A 61 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N TYR A 266 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN A 183 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N SER A 200 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.623A pdb=" N ALA C 590 " --> pdb=" O GLY C 581 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ASP C 589 " --> pdb=" O ILE C 602 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 53 removed outlier: 3.817A pdb=" N ASP A 53 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 81 through 83 removed outlier: 3.681A pdb=" N LEU A 139 " --> pdb=" O LEU A 239 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG A 153 " --> pdb=" O PHE A 138 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 81 through 83 removed outlier: 6.985A pdb=" N ARG A 234 " --> pdb=" O PHE A 104 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N PHE A 104 " --> pdb=" O ARG A 234 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLN A 236 " --> pdb=" O TRP A 102 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N TRP A 102 " --> pdb=" O GLN A 236 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LEU A 238 " --> pdb=" O ARG A 100 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N ARG A 100 " --> pdb=" O ASN A 119 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N PHE A 163 " --> pdb=" O VAL A 128 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 307 through 313 removed outlier: 5.690A pdb=" N ILE A 309 " --> pdb=" O THR A 614 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N THR A 614 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N GLN A 311 " --> pdb=" O VAL A 612 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL A 612 " --> pdb=" O GLN A 311 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER A 313 " --> pdb=" O VAL A 610 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 322 through 323 removed outlier: 3.789A pdb=" N VAL A 554 " --> pdb=" O GLY A 565 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 669 through 670 removed outlier: 6.146A pdb=" N GLU A 669 " --> pdb=" O ALA A 709 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N THR A 711 " --> pdb=" O GLU A 669 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N SER A 706 " --> pdb=" O GLN A 690 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN A 690 " --> pdb=" O SER A 706 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA A 687 " --> pdb=" O PRO A 680 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 716 through 717 removed outlier: 6.894A pdb=" N ALA A 716 " --> pdb=" O ILE B 803 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 726 through 730 removed outlier: 3.701A pdb=" N ILE A 727 " --> pdb=" O PHE A1090 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA A1093 " --> pdb=" O PHE A1110 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N PHE A1110 " --> pdb=" O ALA A1093 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 733 through 743 removed outlier: 5.951A pdb=" N TYR A1082 " --> pdb=" O HIS A1063 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N HIS A1063 " --> pdb=" O TYR A1082 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 749 through 750 Processing sheet with id=AB4, first strand: chain 'A' and resid 802 through 803 Processing sheet with id=AB5, first strand: chain 'A' and resid 1135 through 1137 Processing sheet with id=AB6, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.802A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N ASN B 61 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N TYR B 266 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N SER B 200 " --> pdb=" O PRO B 222 " (cutoff:3.500A) removed outlier: 9.474A pdb=" N HIS B 202 " --> pdb=" O LEU B 220 " (cutoff:3.500A) removed outlier: 9.858A pdb=" N LEU B 220 " --> pdb=" O HIS B 202 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N VAL B 36 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.725A pdb=" N VAL B 47 " --> pdb=" O TYR B 276 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 82 through 83 Processing sheet with id=AB9, first strand: chain 'B' and resid 131 through 133 removed outlier: 5.017A pdb=" N SER B 157 " --> pdb=" O GLN B 132 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 308 through 316 removed outlier: 4.511A pdb=" N VAL B 610 " --> pdb=" O THR B 312 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ASN B 314 " --> pdb=" O GLY B 608 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N GLY B 608 " --> pdb=" O ASN B 314 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N CYS B 664 " --> pdb=" O TYR B 627 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLY B 663 " --> pdb=" O THR B 660 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 351 through 355 removed outlier: 3.785A pdb=" N LEU B 392 " --> pdb=" O PHE B 355 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N SER B 391 " --> pdb=" O GLN B 527 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU B 518 " --> pdb=" O VAL B 435 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N THR B 428 " --> pdb=" O CYS B 376 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N CYS B 376 " --> pdb=" O THR B 428 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU B 430 " --> pdb=" O PHE B 374 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N PHE B 374 " --> pdb=" O LEU B 430 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU B 432 " --> pdb=" O ASN B 372 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 464 through 466 removed outlier: 5.177A pdb=" N SER B 449 " --> pdb=" O VAL B 512 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL B 512 " --> pdb=" O SER B 449 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ILE B 451 " --> pdb=" O SER B 510 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N SER B 510 " --> pdb=" O ILE B 451 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 554 through 556 removed outlier: 3.638A pdb=" N VAL B 554 " --> pdb=" O GLY B 565 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY B 565 " --> pdb=" O VAL B 554 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 590 through 592 Processing sheet with id=AC6, first strand: chain 'B' and resid 669 through 670 removed outlier: 6.075A pdb=" N GLU B 669 " --> pdb=" O ALA B 709 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N THR B 711 " --> pdb=" O GLU B 669 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ALA B 687 " --> pdb=" O PRO B 680 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 716 through 719 removed outlier: 3.618A pdb=" N LYS C 805 " --> pdb=" O ASN B 718 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 726 through 743 removed outlier: 6.209A pdb=" N GLN B1086 " --> pdb=" O THR B 731 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N PHE B 733 " --> pdb=" O PRO B1084 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ILE B 735 " --> pdb=" O TYR B1082 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N TYR B1082 " --> pdb=" O ILE B 735 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL B 737 " --> pdb=" O VAL B1080 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N VAL B1080 " --> pdb=" O VAL B 737 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N THR B 739 " --> pdb=" O LEU B1078 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU B1078 " --> pdb=" O THR B 739 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ILE B 741 " --> pdb=" O VAL B1076 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL B1076 " --> pdb=" O ILE B 741 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N GLY B1074 " --> pdb=" O PRO B 743 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N TYR B1082 " --> pdb=" O HIS B1063 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N HIS B1063 " --> pdb=" O TYR B1082 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 749 through 751 Processing sheet with id=AD1, first strand: chain 'B' and resid 1135 through 1140 removed outlier: 4.715A pdb=" N ALA B1102 " --> pdb=" O SER B1138 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1109 through 1112 Processing sheet with id=AD3, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.820A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ASN C 61 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N TYR C 266 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N SER C 200 " --> pdb=" O PRO C 222 " (cutoff:3.500A) removed outlier: 9.855A pdb=" N HIS C 202 " --> pdb=" O LEU C 220 " (cutoff:3.500A) removed outlier: 9.955A pdb=" N LEU C 220 " --> pdb=" O HIS C 202 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL C 36 " --> pdb=" O LEU C 220 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.249A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 161 through 166 removed outlier: 4.272A pdb=" N PHE C 163 " --> pdb=" O VAL C 128 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLY C 101 " --> pdb=" O LEU C 238 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 147 through 152 removed outlier: 5.957A pdb=" N GLU C 149 " --> pdb=" O LYS C 142 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LYS C 142 " --> pdb=" O GLU C 149 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU C 151 " --> pdb=" O ASP C 140 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS C 141 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG C 243 " --> pdb=" O HIS C 141 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 308 through 314 removed outlier: 5.460A pdb=" N ILE C 309 " --> pdb=" O THR C 614 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N THR C 614 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N GLN C 311 " --> pdb=" O VAL C 612 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL C 612 " --> pdb=" O GLN C 311 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N SER C 313 " --> pdb=" O VAL C 610 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 669 through 670 removed outlier: 6.086A pdb=" N GLU C 669 " --> pdb=" O ALA C 709 " (cutoff:3.500A) removed outlier: 8.685A pdb=" N THR C 711 " --> pdb=" O GLU C 669 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ALA C 687 " --> pdb=" O PRO C 680 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 726 through 730 Processing sheet with id=AE1, first strand: chain 'C' and resid 733 through 743 removed outlier: 5.976A pdb=" N TYR C1082 " --> pdb=" O HIS C1063 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N HIS C1063 " --> pdb=" O TYR C1082 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 749 through 750 Processing sheet with id=AE3, first strand: chain 'C' and resid 1135 through 1137 Processing sheet with id=AE4, first strand: chain 'C' and resid 1109 through 1112 884 hydrogen bonds defined for protein. 2433 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: 10.84 Time building geometry restraints manager: 6.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7361 1.34 - 1.46: 5469 1.46 - 1.58: 10789 1.58 - 1.70: 0 1.70 - 1.82: 138 Bond restraints: 23757 Sorted by residual: bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.494 -0.088 2.00e-02 2.50e+03 1.95e+01 bond pdb=" C1 NAG L 1 " pdb=" O5 NAG L 1 " ideal model delta sigma weight residual 1.406 1.471 -0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" CA GLU B 278 " pdb=" C GLU B 278 " ideal model delta sigma weight residual 1.524 1.575 -0.051 1.66e-02 3.63e+03 9.36e+00 bond pdb=" C1 NAG M 1 " pdb=" O5 NAG M 1 " ideal model delta sigma weight residual 1.406 1.462 -0.056 2.00e-02 2.50e+03 7.98e+00 bond pdb=" CG PRO B 594 " pdb=" CD PRO B 594 " ideal model delta sigma weight residual 1.503 1.413 0.090 3.40e-02 8.65e+02 6.99e+00 ... (remaining 23752 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 31935 2.57 - 5.15: 359 5.15 - 7.72: 29 7.72 - 10.29: 6 10.29 - 12.87: 4 Bond angle restraints: 32333 Sorted by residual: angle pdb=" N PRO B 594 " pdb=" CD PRO B 594 " pdb=" CG PRO B 594 " ideal model delta sigma weight residual 103.20 94.06 9.14 1.50e+00 4.44e-01 3.71e+01 angle pdb=" C ASN A1089 " pdb=" CA ASN A1089 " pdb=" CB ASN A1089 " ideal model delta sigma weight residual 110.14 118.73 -8.59 1.54e+00 4.22e-01 3.11e+01 angle pdb=" CA CYS B 161 " pdb=" CB CYS B 161 " pdb=" SG CYS B 161 " ideal model delta sigma weight residual 114.40 125.30 -10.90 2.30e+00 1.89e-01 2.24e+01 angle pdb=" CA PRO B 594 " pdb=" CB PRO B 594 " pdb=" CG PRO B 594 " ideal model delta sigma weight residual 104.50 96.56 7.94 1.90e+00 2.77e-01 1.75e+01 angle pdb=" CA PRO B 594 " pdb=" N PRO B 594 " pdb=" CD PRO B 594 " ideal model delta sigma weight residual 112.00 106.49 5.51 1.40e+00 5.10e-01 1.55e+01 ... (remaining 32328 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.08: 13391 23.08 - 46.16: 1066 46.16 - 69.23: 181 69.23 - 92.31: 74 92.31 - 115.39: 40 Dihedral angle restraints: 14752 sinusoidal: 6278 harmonic: 8474 Sorted by residual: dihedral pdb=" CB CYS C 632 " pdb=" SG CYS C 632 " pdb=" SG CYS C 664 " pdb=" CB CYS C 664 " ideal model delta sinusoidal sigma weight residual -86.00 3.39 -89.39 1 1.00e+01 1.00e-02 9.50e+01 dihedral pdb=" CB CYS C1097 " pdb=" SG CYS C1097 " pdb=" SG CYS C1141 " pdb=" CB CYS C1141 " ideal model delta sinusoidal sigma weight residual 93.00 4.42 88.58 1 1.00e+01 1.00e-02 9.36e+01 dihedral pdb=" CB CYS B 334 " pdb=" SG CYS B 334 " pdb=" SG CYS B 358 " pdb=" CB CYS B 358 " ideal model delta sinusoidal sigma weight residual 93.00 28.02 64.98 1 1.00e+01 1.00e-02 5.54e+01 ... (remaining 14749 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.155: 3785 0.155 - 0.310: 21 0.310 - 0.465: 1 0.465 - 0.620: 0 0.620 - 0.775: 2 Chirality restraints: 3809 Sorted by residual: chirality pdb=" C1 NAG A1304 " pdb=" ND2 ASN A1089 " pdb=" C2 NAG A1304 " pdb=" O5 NAG A1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.62 -0.78 2.00e-01 2.50e+01 1.50e+01 chirality pdb=" C1 NAG B1301 " pdb=" ND2 ASN B 61 " pdb=" C2 NAG B1301 " pdb=" O5 NAG B1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.76 -0.64 2.00e-01 2.50e+01 1.01e+01 chirality pdb=" C1 NAG B1305 " pdb=" ND2 ASN B 724 " pdb=" C2 NAG B1305 " pdb=" O5 NAG B1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.19e+00 ... (remaining 3806 not shown) Planarity restraints: 4149 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A1089 " 0.043 2.00e-02 2.50e+03 4.08e-02 2.08e+01 pdb=" CG ASN A1089 " -0.053 2.00e-02 2.50e+03 pdb=" OD1 ASN A1089 " 0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN A1089 " -0.043 2.00e-02 2.50e+03 pdb=" C1 NAG A1304 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 221 " 0.069 5.00e-02 4.00e+02 1.03e-01 1.68e+01 pdb=" N PRO A 222 " -0.177 5.00e-02 4.00e+02 pdb=" CA PRO A 222 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 222 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 816 " 0.038 2.00e-02 2.50e+03 3.44e-02 1.48e+01 pdb=" CG ASN A 816 " -0.034 2.00e-02 2.50e+03 pdb=" OD1 ASN A 816 " -0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN A 816 " -0.041 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " 0.041 2.00e-02 2.50e+03 ... (remaining 4146 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 433 2.67 - 3.23: 21397 3.23 - 3.79: 33690 3.79 - 4.34: 44199 4.34 - 4.90: 76000 Nonbonded interactions: 175719 Sorted by model distance: nonbonded pdb=" OG SER A 302 " pdb=" O THR A 304 " model vdw 2.118 3.040 nonbonded pdb=" O ALA B 894 " pdb=" OG1 THR B 898 " model vdw 2.222 3.040 nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.240 3.040 nonbonded pdb=" NE2 GLN A 819 " pdb=" OE1 GLN A 950 " model vdw 2.246 3.120 nonbonded pdb=" OH TYR B 399 " pdb=" O MET B 403 " model vdw 2.247 3.040 ... (remaining 175714 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 14 through 325 or resid 542 through 637 or resid 648 throu \ gh 837 or resid 839 through 1033 or resid 1035 through 1161 or resid 1301 throug \ h 1304)) selection = (chain 'C' and (resid 14 through 325 or resid 327 through 837 or resid 839 throu \ gh 851 or resid 863 through 1033 or resid 1035 through 1161 or resid 1301 throug \ h 1304)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.840 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: 1.040 Check model and map are aligned: 0.170 Set scattering table: 0.250 Process input model: 69.050 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.620 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:3.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 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 : 0.004 0.090 23828 Z= 0.174 Angle : 0.705 13.328 32513 Z= 0.344 Chirality : 0.051 0.775 3809 Planarity : 0.005 0.103 4123 Dihedral : 18.281 115.389 9189 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.55 % Favored : 93.34 % Rotamer: Outliers : 0.20 % Allowed : 18.12 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.97 (0.16), residues: 2876 helix: 2.24 (0.23), residues: 598 sheet: 0.28 (0.21), residues: 600 loop : -2.24 (0.14), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 102 HIS 0.005 0.001 HIS C 202 PHE 0.019 0.001 PHE B 870 TYR 0.020 0.001 TYR C1082 ARG 0.004 0.000 ARG C 44 Details of bonding type rmsd link_NAG-ASN : bond 0.01067 ( 26) link_NAG-ASN : angle 4.92049 ( 78) link_BETA1-4 : bond 0.00648 ( 12) link_BETA1-4 : angle 1.70719 ( 36) hydrogen bonds : bond 0.13798 ( 882) hydrogen bonds : angle 6.08061 ( 2433) SS BOND : bond 0.00241 ( 33) SS BOND : angle 1.34924 ( 66) covalent geometry : bond 0.00375 (23757) covalent geometry : angle 0.65897 (32333) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 107 time to evaluate : 2.466 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 111 average time/residue: 0.3289 time to fit residues: 60.2341 Evaluate side-chains 91 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 90 time to evaluate : 2.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 589 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 244 optimal weight: 4.9990 chunk 219 optimal weight: 0.0370 chunk 121 optimal weight: 0.4980 chunk 74 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 226 optimal weight: 0.0670 chunk 87 optimal weight: 0.9980 chunk 137 optimal weight: 8.9990 chunk 168 optimal weight: 0.1980 chunk 262 optimal weight: 1.9990 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 HIS ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.112465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.065482 restraints weight = 125676.590| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 5.67 r_work: 0.2917 rms_B_bonded: 5.00 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2867 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2866 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.0733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 23828 Z= 0.122 Angle : 0.684 10.982 32513 Z= 0.326 Chirality : 0.048 0.515 3809 Planarity : 0.005 0.074 4123 Dihedral : 11.464 92.055 3902 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.78 % Favored : 94.11 % Rotamer: Outliers : 0.98 % Allowed : 18.04 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.16), residues: 2876 helix: 2.57 (0.22), residues: 608 sheet: 0.33 (0.21), residues: 594 loop : -2.19 (0.14), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP B 102 HIS 0.004 0.001 HIS C 202 PHE 0.024 0.001 PHE B 580 TYR 0.017 0.001 TYR C1082 ARG 0.004 0.000 ARG A 243 Details of bonding type rmsd link_NAG-ASN : bond 0.00863 ( 26) link_NAG-ASN : angle 3.71923 ( 78) link_BETA1-4 : bond 0.00641 ( 12) link_BETA1-4 : angle 1.46040 ( 36) hydrogen bonds : bond 0.04844 ( 882) hydrogen bonds : angle 5.01974 ( 2433) SS BOND : bond 0.00248 ( 33) SS BOND : angle 1.14010 ( 66) covalent geometry : bond 0.00262 (23757) covalent geometry : angle 0.65762 (32333) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 2.527 Fit side-chains revert: symmetry clash REVERT: B 172 MET cc_start: 0.3987 (ppp) cc_final: 0.3771 (pmm) REVERT: B 514 MET cc_start: 0.7172 (OUTLIER) cc_final: 0.6811 (mmm) outliers start: 24 outliers final: 8 residues processed: 124 average time/residue: 0.2946 time to fit residues: 62.8274 Evaluate side-chains 104 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 2.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 1107 GLU Chi-restraints excluded: chain A residue 1115 THR Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain B residue 587 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 202 optimal weight: 3.9990 chunk 213 optimal weight: 0.9980 chunk 176 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 126 optimal weight: 10.0000 chunk 183 optimal weight: 0.9980 chunk 216 optimal weight: 0.6980 chunk 148 optimal weight: 0.0870 chunk 256 optimal weight: 1.9990 chunk 200 optimal weight: 4.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 HIS ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 595 GLN ** C 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.112197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.064458 restraints weight = 107722.867| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 5.26 r_work: 0.2941 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2889 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2889 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.0960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 23828 Z= 0.125 Angle : 0.657 10.934 32513 Z= 0.313 Chirality : 0.047 0.476 3809 Planarity : 0.004 0.066 4123 Dihedral : 8.881 84.972 3900 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.92 % Favored : 94.01 % Rotamer: Outliers : 1.52 % Allowed : 17.61 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.68 (0.16), residues: 2876 helix: 2.75 (0.22), residues: 610 sheet: 0.25 (0.21), residues: 620 loop : -2.15 (0.14), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 102 HIS 0.004 0.001 HIS C 202 PHE 0.024 0.001 PHE C 996 TYR 0.019 0.001 TYR C1082 ARG 0.004 0.000 ARG A 243 Details of bonding type rmsd link_NAG-ASN : bond 0.00723 ( 26) link_NAG-ASN : angle 3.62190 ( 78) link_BETA1-4 : bond 0.00453 ( 12) link_BETA1-4 : angle 1.52944 ( 36) hydrogen bonds : bond 0.04678 ( 882) hydrogen bonds : angle 4.83348 ( 2433) SS BOND : bond 0.00241 ( 33) SS BOND : angle 1.27427 ( 66) covalent geometry : bond 0.00283 (23757) covalent geometry : angle 0.62919 (32333) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 102 time to evaluate : 2.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 TRP cc_start: 0.8026 (m-10) cc_final: 0.7116 (m-10) REVERT: B 514 MET cc_start: 0.7242 (OUTLIER) cc_final: 0.6877 (mmm) REVERT: C 1115 THR cc_start: 0.9120 (OUTLIER) cc_final: 0.8825 (p) REVERT: C 1153 TYR cc_start: 0.8095 (t80) cc_final: 0.7854 (t80) outliers start: 38 outliers final: 17 residues processed: 135 average time/residue: 0.3128 time to fit residues: 72.4034 Evaluate side-chains 113 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 2.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 141 HIS Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 866 CYS Chi-restraints excluded: chain A residue 1107 GLU Chi-restraints excluded: chain A residue 1115 THR Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 242 HIS Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 949 ILE Chi-restraints excluded: chain B residue 1160 LEU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1119 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 155 optimal weight: 4.9990 chunk 65 optimal weight: 0.4980 chunk 150 optimal weight: 0.0980 chunk 59 optimal weight: 2.9990 chunk 137 optimal weight: 30.0000 chunk 165 optimal weight: 0.4980 chunk 117 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 95 optimal weight: 8.9990 chunk 98 optimal weight: 4.9990 chunk 217 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 HIS A1069 GLN ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.111237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.063258 restraints weight = 132485.400| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 5.97 r_work: 0.2867 rms_B_bonded: 5.16 restraints_weight: 2.0000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2823 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2823 r_free = 0.2823 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2823 r_free = 0.2823 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2823 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23828 Z= 0.140 Angle : 0.650 11.007 32513 Z= 0.313 Chirality : 0.047 0.461 3809 Planarity : 0.004 0.061 4123 Dihedral : 7.755 79.595 3900 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.13 % Favored : 93.80 % Rotamer: Outliers : 1.76 % Allowed : 17.73 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.16), residues: 2876 helix: 2.79 (0.22), residues: 608 sheet: 0.22 (0.21), residues: 625 loop : -2.13 (0.14), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 504 HIS 0.003 0.001 HIS C 202 PHE 0.024 0.001 PHE B 336 TYR 0.021 0.001 TYR C1082 ARG 0.004 0.000 ARG A 243 Details of bonding type rmsd link_NAG-ASN : bond 0.00669 ( 26) link_NAG-ASN : angle 3.56709 ( 78) link_BETA1-4 : bond 0.00483 ( 12) link_BETA1-4 : angle 1.35385 ( 36) hydrogen bonds : bond 0.04799 ( 882) hydrogen bonds : angle 4.79985 ( 2433) SS BOND : bond 0.00287 ( 33) SS BOND : angle 1.22271 ( 66) covalent geometry : bond 0.00329 (23757) covalent geometry : angle 0.62323 (32333) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 99 time to evaluate : 2.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.8070 (mm110) REVERT: B 102 TRP cc_start: 0.8202 (m-10) cc_final: 0.7371 (m-10) REVERT: B 186 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.6986 (mp0) REVERT: C 1115 THR cc_start: 0.9143 (OUTLIER) cc_final: 0.8837 (p) REVERT: C 1153 TYR cc_start: 0.8158 (t80) cc_final: 0.7891 (t80) outliers start: 44 outliers final: 23 residues processed: 137 average time/residue: 0.2925 time to fit residues: 68.1236 Evaluate side-chains 116 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 90 time to evaluate : 2.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 141 HIS Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 664 CYS Chi-restraints excluded: chain A residue 866 CYS Chi-restraints excluded: chain A residue 976 THR Chi-restraints excluded: chain A residue 1107 GLU Chi-restraints excluded: chain A residue 1115 THR Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 242 HIS Chi-restraints excluded: chain B residue 558 PHE Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 664 CYS Chi-restraints excluded: chain B residue 1151 THR Chi-restraints excluded: chain B residue 1160 LEU Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1119 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 65 optimal weight: 0.2980 chunk 198 optimal weight: 0.9980 chunk 13 optimal weight: 6.9990 chunk 110 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 32 optimal weight: 0.8980 chunk 233 optimal weight: 5.9990 chunk 166 optimal weight: 0.9990 chunk 273 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 HIS ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 ASN ** C 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.109782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.061888 restraints weight = 104567.756| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 5.17 r_work: 0.2834 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2835 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2835 r_free = 0.2835 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2835 r_free = 0.2835 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2835 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23828 Z= 0.173 Angle : 0.666 10.968 32513 Z= 0.323 Chirality : 0.047 0.476 3809 Planarity : 0.004 0.057 4123 Dihedral : 7.384 76.424 3900 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.55 % Favored : 93.38 % Rotamer: Outliers : 1.76 % Allowed : 18.20 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.16), residues: 2876 helix: 2.71 (0.22), residues: 605 sheet: 0.18 (0.20), residues: 641 loop : -2.17 (0.14), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 102 HIS 0.004 0.001 HIS B1103 PHE 0.032 0.002 PHE B 326 TYR 0.022 0.001 TYR C1082 ARG 0.007 0.000 ARG B 325 Details of bonding type rmsd link_NAG-ASN : bond 0.00564 ( 26) link_NAG-ASN : angle 3.60888 ( 78) link_BETA1-4 : bond 0.00409 ( 12) link_BETA1-4 : angle 1.37184 ( 36) hydrogen bonds : bond 0.05358 ( 882) hydrogen bonds : angle 4.85061 ( 2433) SS BOND : bond 0.00274 ( 33) SS BOND : angle 1.31779 ( 66) covalent geometry : bond 0.00414 (23757) covalent geometry : angle 0.63976 (32333) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 94 time to evaluate : 2.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.8112 (mm110) REVERT: A 116 LEU cc_start: 0.7067 (OUTLIER) cc_final: 0.6366 (mp) REVERT: A 133 PHE cc_start: 0.6999 (m-80) cc_final: 0.6474 (m-80) REVERT: A 628 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.7738 (mp10) REVERT: B 102 TRP cc_start: 0.8135 (m-10) cc_final: 0.7305 (m-10) REVERT: B 172 MET cc_start: 0.4684 (ptt) cc_final: 0.3108 (pmm) REVERT: C 223 LEU cc_start: 0.6983 (OUTLIER) cc_final: 0.6776 (mp) REVERT: C 1115 THR cc_start: 0.9128 (OUTLIER) cc_final: 0.8822 (p) REVERT: C 1153 TYR cc_start: 0.8165 (t80) cc_final: 0.7820 (t80) outliers start: 44 outliers final: 27 residues processed: 134 average time/residue: 0.3086 time to fit residues: 69.7599 Evaluate side-chains 121 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 89 time to evaluate : 2.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 141 HIS Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 628 GLN Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 664 CYS Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 866 CYS Chi-restraints excluded: chain A residue 949 ILE Chi-restraints excluded: chain A residue 976 THR Chi-restraints excluded: chain A residue 1107 GLU Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 242 HIS Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 614 THR Chi-restraints excluded: chain B residue 664 CYS Chi-restraints excluded: chain B residue 1151 THR Chi-restraints excluded: chain B residue 1160 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 760 ASP Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1119 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 202 optimal weight: 2.9990 chunk 224 optimal weight: 0.8980 chunk 173 optimal weight: 0.0010 chunk 14 optimal weight: 8.9990 chunk 249 optimal weight: 0.0370 chunk 13 optimal weight: 0.9980 chunk 207 optimal weight: 0.0670 chunk 22 optimal weight: 0.0040 chunk 65 optimal weight: 0.0670 chunk 102 optimal weight: 0.0470 chunk 117 optimal weight: 0.6980 overall best weight: 0.0312 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 HIS ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 372 ASN B 934 ASN B 972 GLN C 113 GLN ** C 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.113116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.065894 restraints weight = 132047.003| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 6.04 r_work: 0.2929 rms_B_bonded: 5.17 restraints_weight: 2.0000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2909 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2909 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 23828 Z= 0.110 Angle : 0.617 11.613 32513 Z= 0.295 Chirality : 0.046 0.394 3809 Planarity : 0.004 0.056 4123 Dihedral : 6.688 66.066 3900 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.44 % Favored : 94.53 % Rotamer: Outliers : 0.86 % Allowed : 19.37 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.49 (0.16), residues: 2876 helix: 2.95 (0.22), residues: 600 sheet: 0.36 (0.21), residues: 610 loop : -1.99 (0.14), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 102 HIS 0.005 0.001 HIS C 202 PHE 0.022 0.001 PHE B 336 TYR 0.017 0.001 TYR A1082 ARG 0.006 0.000 ARG C1106 Details of bonding type rmsd link_NAG-ASN : bond 0.00804 ( 26) link_NAG-ASN : angle 3.37657 ( 78) link_BETA1-4 : bond 0.00557 ( 12) link_BETA1-4 : angle 1.60076 ( 36) hydrogen bonds : bond 0.03832 ( 882) hydrogen bonds : angle 4.58842 ( 2433) SS BOND : bond 0.00207 ( 33) SS BOND : angle 0.79903 ( 66) covalent geometry : bond 0.00230 (23757) covalent geometry : angle 0.59308 (32333) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 2.611 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 ASN cc_start: 0.8251 (OUTLIER) cc_final: 0.6785 (t0) REVERT: A 116 LEU cc_start: 0.7064 (OUTLIER) cc_final: 0.6359 (mp) REVERT: A 131 PHE cc_start: 0.8402 (m-80) cc_final: 0.6745 (m-80) REVERT: A 133 PHE cc_start: 0.6998 (m-80) cc_final: 0.6470 (m-80) REVERT: B 102 TRP cc_start: 0.8118 (m-10) cc_final: 0.7138 (m-10) REVERT: B 172 MET cc_start: 0.4829 (ptt) cc_final: 0.3250 (pmm) REVERT: B 801 LYS cc_start: 0.8716 (mmtt) cc_final: 0.8489 (mmmt) REVERT: C 1153 TYR cc_start: 0.8216 (t80) cc_final: 0.7835 (t80) outliers start: 21 outliers final: 13 residues processed: 117 average time/residue: 0.3126 time to fit residues: 62.2325 Evaluate side-chains 109 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 2.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 664 CYS Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 866 CYS Chi-restraints excluded: chain B residue 242 HIS Chi-restraints excluded: chain B residue 558 PHE Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1119 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 255 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 165 optimal weight: 1.9990 chunk 154 optimal weight: 4.9990 chunk 169 optimal weight: 10.0000 chunk 282 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 chunk 265 optimal weight: 1.9990 chunk 210 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 244 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 640 HIS ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.110696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.062848 restraints weight = 130678.834| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 5.95 r_work: 0.2865 rms_B_bonded: 5.13 restraints_weight: 2.0000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2842 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2842 r_free = 0.2842 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2842 r_free = 0.2842 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2842 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23828 Z= 0.148 Angle : 0.635 11.138 32513 Z= 0.304 Chirality : 0.046 0.441 3809 Planarity : 0.004 0.055 4123 Dihedral : 6.616 60.681 3900 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.41 % Favored : 93.52 % Rotamer: Outliers : 1.17 % Allowed : 19.21 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.55 (0.16), residues: 2876 helix: 2.90 (0.22), residues: 601 sheet: 0.25 (0.20), residues: 640 loop : -2.03 (0.15), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 102 HIS 0.007 0.001 HIS A 141 PHE 0.018 0.001 PHE B 870 TYR 0.020 0.001 TYR C1082 ARG 0.003 0.000 ARG C 185 Details of bonding type rmsd link_NAG-ASN : bond 0.00542 ( 26) link_NAG-ASN : angle 3.43095 ( 78) link_BETA1-4 : bond 0.00458 ( 12) link_BETA1-4 : angle 1.44521 ( 36) hydrogen bonds : bond 0.04682 ( 882) hydrogen bonds : angle 4.64267 ( 2433) SS BOND : bond 0.00243 ( 33) SS BOND : angle 1.15502 ( 66) covalent geometry : bond 0.00354 (23757) covalent geometry : angle 0.60983 (32333) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 2.761 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 LEU cc_start: 0.7298 (OUTLIER) cc_final: 0.6580 (mp) REVERT: A 131 PHE cc_start: 0.8390 (m-80) cc_final: 0.6620 (m-80) REVERT: A 133 PHE cc_start: 0.6951 (m-80) cc_final: 0.6407 (m-80) REVERT: B 102 TRP cc_start: 0.8203 (m-10) cc_final: 0.7311 (m-10) REVERT: B 172 MET cc_start: 0.4812 (OUTLIER) cc_final: 0.3219 (pmm) REVERT: B 186 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7042 (mp0) REVERT: B 384 ILE cc_start: 0.8656 (tp) cc_final: 0.8338 (mm) REVERT: C 1153 TYR cc_start: 0.8282 (t80) cc_final: 0.7905 (t80) outliers start: 29 outliers final: 21 residues processed: 126 average time/residue: 0.3170 time to fit residues: 68.2323 Evaluate side-chains 120 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 2.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 664 CYS Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 866 CYS Chi-restraints excluded: chain A residue 1107 GLU Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 242 HIS Chi-restraints excluded: chain B residue 558 PHE Chi-restraints excluded: chain B residue 614 THR Chi-restraints excluded: chain B residue 664 CYS Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1119 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 262 optimal weight: 1.9990 chunk 160 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 105 optimal weight: 0.0370 chunk 263 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 181 optimal weight: 0.2980 chunk 202 optimal weight: 5.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 640 HIS ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.111823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.064300 restraints weight = 111904.603| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 5.37 r_work: 0.2913 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2924 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2924 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 23828 Z= 0.109 Angle : 0.613 11.479 32513 Z= 0.293 Chirality : 0.046 0.399 3809 Planarity : 0.004 0.054 4123 Dihedral : 6.348 59.502 3900 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.89 % Favored : 94.04 % Rotamer: Outliers : 1.09 % Allowed : 19.29 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.47 (0.16), residues: 2876 helix: 2.96 (0.22), residues: 604 sheet: 0.37 (0.21), residues: 613 loop : -1.99 (0.14), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP B 504 HIS 0.008 0.001 HIS A 141 PHE 0.030 0.001 PHE B 181 TYR 0.019 0.001 TYR C1082 ARG 0.004 0.000 ARG C 185 Details of bonding type rmsd link_NAG-ASN : bond 0.00639 ( 26) link_NAG-ASN : angle 3.34541 ( 78) link_BETA1-4 : bond 0.00506 ( 12) link_BETA1-4 : angle 1.50979 ( 36) hydrogen bonds : bond 0.04129 ( 882) hydrogen bonds : angle 4.59334 ( 2433) SS BOND : bond 0.00204 ( 33) SS BOND : angle 0.92910 ( 66) covalent geometry : bond 0.00245 (23757) covalent geometry : angle 0.58901 (32333) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 100 time to evaluate : 2.630 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 LEU cc_start: 0.7251 (OUTLIER) cc_final: 0.6547 (mp) REVERT: A 131 PHE cc_start: 0.8366 (m-80) cc_final: 0.6594 (m-80) REVERT: A 133 PHE cc_start: 0.6951 (m-80) cc_final: 0.6429 (m-80) REVERT: B 102 TRP cc_start: 0.8096 (m-10) cc_final: 0.7200 (m-10) REVERT: B 172 MET cc_start: 0.4759 (OUTLIER) cc_final: 0.3082 (pmm) REVERT: B 186 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7080 (mp0) REVERT: B 801 LYS cc_start: 0.8728 (mmtt) cc_final: 0.8499 (mmmt) REVERT: C 1153 TYR cc_start: 0.8271 (t80) cc_final: 0.7906 (t80) outliers start: 27 outliers final: 22 residues processed: 124 average time/residue: 0.3081 time to fit residues: 64.6654 Evaluate side-chains 120 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 95 time to evaluate : 2.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 664 CYS Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 866 CYS Chi-restraints excluded: chain A residue 976 THR Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 242 HIS Chi-restraints excluded: chain B residue 558 PHE Chi-restraints excluded: chain B residue 614 THR Chi-restraints excluded: chain B residue 664 CYS Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1119 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 170 optimal weight: 1.9990 chunk 34 optimal weight: 0.3980 chunk 241 optimal weight: 1.9990 chunk 227 optimal weight: 4.9990 chunk 138 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 21 optimal weight: 8.9990 chunk 107 optimal weight: 0.5980 chunk 171 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 259 optimal weight: 6.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 640 HIS ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.109813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.062902 restraints weight = 118022.505| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 5.45 r_work: 0.2891 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2865 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2865 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 23828 Z= 0.153 Angle : 0.644 11.175 32513 Z= 0.310 Chirality : 0.047 0.428 3809 Planarity : 0.004 0.055 4123 Dihedral : 6.298 58.621 3900 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.52 % Favored : 93.41 % Rotamer: Outliers : 1.13 % Allowed : 19.33 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.51 (0.16), residues: 2876 helix: 2.96 (0.22), residues: 598 sheet: 0.26 (0.21), residues: 640 loop : -2.00 (0.15), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP B 504 HIS 0.007 0.001 HIS A 141 PHE 0.026 0.002 PHE B 181 TYR 0.021 0.001 TYR C1082 ARG 0.003 0.000 ARG C 185 Details of bonding type rmsd link_NAG-ASN : bond 0.00511 ( 26) link_NAG-ASN : angle 3.38450 ( 78) link_BETA1-4 : bond 0.00465 ( 12) link_BETA1-4 : angle 1.46164 ( 36) hydrogen bonds : bond 0.04837 ( 882) hydrogen bonds : angle 4.69546 ( 2433) SS BOND : bond 0.00243 ( 33) SS BOND : angle 1.17529 ( 66) covalent geometry : bond 0.00365 (23757) covalent geometry : angle 0.61982 (32333) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 98 time to evaluate : 2.557 Fit side-chains revert: symmetry clash REVERT: A 116 LEU cc_start: 0.7279 (OUTLIER) cc_final: 0.6552 (mp) REVERT: A 131 PHE cc_start: 0.8424 (m-80) cc_final: 0.6756 (m-80) REVERT: A 133 PHE cc_start: 0.6952 (m-80) cc_final: 0.6418 (m-80) REVERT: A 138 PHE cc_start: 0.7354 (p90) cc_final: 0.6799 (p90) REVERT: A 628 GLN cc_start: 0.8065 (OUTLIER) cc_final: 0.7743 (mp10) REVERT: B 172 MET cc_start: 0.4765 (OUTLIER) cc_final: 0.3092 (pmm) REVERT: B 186 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7077 (mp0) REVERT: C 1153 TYR cc_start: 0.8294 (t80) cc_final: 0.7909 (t80) outliers start: 29 outliers final: 21 residues processed: 124 average time/residue: 0.2982 time to fit residues: 63.7755 Evaluate side-chains 120 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 95 time to evaluate : 2.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 628 GLN Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 664 CYS Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 866 CYS Chi-restraints excluded: chain A residue 976 THR Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 242 HIS Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 614 THR Chi-restraints excluded: chain B residue 664 CYS Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1119 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 74 optimal weight: 0.6980 chunk 142 optimal weight: 3.9990 chunk 248 optimal weight: 0.0470 chunk 99 optimal weight: 8.9990 chunk 95 optimal weight: 9.9990 chunk 159 optimal weight: 3.9990 chunk 185 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 70 optimal weight: 0.0030 chunk 2 optimal weight: 0.0370 chunk 163 optimal weight: 0.9980 overall best weight: 0.3566 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 640 HIS ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.111934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.064415 restraints weight = 126535.923| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 5.90 r_work: 0.2901 rms_B_bonded: 5.11 restraints_weight: 2.0000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2854 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2854 r_free = 0.2854 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2854 r_free = 0.2854 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2854 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 23828 Z= 0.105 Angle : 0.613 11.520 32513 Z= 0.292 Chirality : 0.046 0.385 3809 Planarity : 0.004 0.054 4123 Dihedral : 6.082 59.533 3900 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.47 % Favored : 94.46 % Rotamer: Outliers : 0.90 % Allowed : 19.68 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.40 (0.16), residues: 2876 helix: 2.98 (0.22), residues: 600 sheet: 0.42 (0.21), residues: 611 loop : -1.91 (0.14), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP B 504 HIS 0.008 0.001 HIS A 141 PHE 0.018 0.001 PHE B 235 TYR 0.018 0.001 TYR C1082 ARG 0.003 0.000 ARG C 185 Details of bonding type rmsd link_NAG-ASN : bond 0.00651 ( 26) link_NAG-ASN : angle 3.30288 ( 78) link_BETA1-4 : bond 0.00503 ( 12) link_BETA1-4 : angle 1.49024 ( 36) hydrogen bonds : bond 0.04089 ( 882) hydrogen bonds : angle 4.58299 ( 2433) SS BOND : bond 0.00198 ( 33) SS BOND : angle 0.91946 ( 66) covalent geometry : bond 0.00230 (23757) covalent geometry : angle 0.58913 (32333) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 98 time to evaluate : 2.806 Fit side-chains revert: symmetry clash REVERT: A 85 ASN cc_start: 0.8144 (OUTLIER) cc_final: 0.6765 (t0) REVERT: A 116 LEU cc_start: 0.7268 (OUTLIER) cc_final: 0.6580 (mp) REVERT: A 131 PHE cc_start: 0.8366 (m-80) cc_final: 0.6673 (m-80) REVERT: A 133 PHE cc_start: 0.6960 (m-80) cc_final: 0.6446 (m-80) REVERT: B 172 MET cc_start: 0.4772 (OUTLIER) cc_final: 0.2926 (pmm) REVERT: B 186 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7059 (mp0) REVERT: B 801 LYS cc_start: 0.8717 (mmtt) cc_final: 0.8479 (mmmt) REVERT: C 1153 TYR cc_start: 0.8279 (t80) cc_final: 0.7924 (t80) outliers start: 23 outliers final: 19 residues processed: 118 average time/residue: 0.3364 time to fit residues: 69.7972 Evaluate side-chains 119 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 2.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 664 CYS Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 866 CYS Chi-restraints excluded: chain A residue 1107 GLU Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 242 HIS Chi-restraints excluded: chain B residue 558 PHE Chi-restraints excluded: chain B residue 664 CYS Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 1119 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 62 optimal weight: 0.6980 chunk 105 optimal weight: 10.0000 chunk 101 optimal weight: 9.9990 chunk 251 optimal weight: 0.8980 chunk 126 optimal weight: 20.0000 chunk 78 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 210 optimal weight: 7.9990 chunk 134 optimal weight: 0.9980 chunk 15 optimal weight: 0.4980 chunk 267 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 640 HIS ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.111019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.063371 restraints weight = 107350.530| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 5.32 r_work: 0.2895 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2850 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2850 r_free = 0.2850 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2850 r_free = 0.2850 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2850 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23828 Z= 0.122 Angle : 0.618 11.428 32513 Z= 0.296 Chirality : 0.046 0.398 3809 Planarity : 0.004 0.054 4123 Dihedral : 6.010 59.904 3900 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.03 % Favored : 93.90 % Rotamer: Outliers : 1.13 % Allowed : 19.48 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.40 (0.16), residues: 2876 helix: 3.03 (0.22), residues: 597 sheet: 0.37 (0.21), residues: 627 loop : -1.92 (0.15), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP B 504 HIS 0.007 0.001 HIS A 141 PHE 0.030 0.001 PHE B 181 TYR 0.019 0.001 TYR C1082 ARG 0.003 0.000 ARG C 185 Details of bonding type rmsd link_NAG-ASN : bond 0.00557 ( 26) link_NAG-ASN : angle 3.29955 ( 78) link_BETA1-4 : bond 0.00459 ( 12) link_BETA1-4 : angle 1.44124 ( 36) hydrogen bonds : bond 0.04362 ( 882) hydrogen bonds : angle 4.59719 ( 2433) SS BOND : bond 0.00234 ( 33) SS BOND : angle 1.14797 ( 66) covalent geometry : bond 0.00285 (23757) covalent geometry : angle 0.59362 (32333) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14044.85 seconds wall clock time: 243 minutes 6.81 seconds (14586.81 seconds total)