Starting phenix.real_space_refine on Mon Jun 23 04:37:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tgw_25887/06_2025/7tgw_25887.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tgw_25887/06_2025/7tgw_25887.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tgw_25887/06_2025/7tgw_25887.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tgw_25887/06_2025/7tgw_25887.map" model { file = "/net/cci-nas-00/data/ceres_data/7tgw_25887/06_2025/7tgw_25887.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tgw_25887/06_2025/7tgw_25887.cif" } resolution = 3.0 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= -0.001 sd= 0.033 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 119 5.16 5 C 16993 2.51 5 N 4383 2.21 5 O 5122 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 26617 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 8741 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1113, 8725 Classifications: {'peptide': 1113} Link IDs: {'PTRANS': 61, 'TRANS': 1051} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 1113, 8725 Classifications: {'peptide': 1113} Link IDs: {'PTRANS': 61, 'TRANS': 1051} Chain breaks: 2 bond proxies already assigned to first conformer: 8918 Chain: "B" Number of atoms: 8579 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1091, 8563 Classifications: {'peptide': 1091} Link IDs: {'PTRANS': 60, 'TRANS': 1030} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 1091, 8563 Classifications: {'peptide': 1091} Link IDs: {'PTRANS': 60, 'TRANS': 1030} Chain breaks: 4 bond proxies already assigned to first conformer: 8751 Chain: "C" Number of atoms: 8667 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1103, 8651 Classifications: {'peptide': 1103} Link IDs: {'PTRANS': 60, 'TRANS': 1042} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 1103, 8651 Classifications: {'peptide': 1103} Link IDs: {'PTRANS': 60, 'TRANS': 1042} Chain breaks: 3 bond proxies already assigned to first conformer: 8841 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: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 29.03, per 1000 atoms: 1.09 Number of scatterers: 26617 At special positions: 0 Unit cell: (152.19, 150.41, 201.14, 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 119 16.00 O 5122 8.00 N 4383 7.00 C 16993 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 134 " distance=2.03 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 161 " distance=2.04 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.04 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 587 " distance=2.04 Simple disulfide: pdb=" SG CYS A 614 " - pdb=" SG CYS A 646 " distance=2.04 Simple disulfide: pdb=" SG CYS A 659 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS A 837 " - pdb=" SG CYS A 848 " distance=2.04 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=2.05 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 333 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.00 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 485 " distance=2.03 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 587 " distance=2.02 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 646 " distance=2.03 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.04 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.04 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.04 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " distance=2.05 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 333 " - pdb=" SG CYS C 358 " distance=2.03 Simple disulfide: pdb=" SG CYS C 376 " - pdb=" SG CYS C 429 " distance=2.03 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 522 " distance=2.04 Simple disulfide: pdb=" SG CYS C 477 " - pdb=" SG CYS C 485 " distance=2.04 Simple disulfide: pdb=" SG CYS C 535 " - pdb=" SG CYS C 587 " distance=2.05 Simple disulfide: pdb=" SG CYS C 614 " - pdb=" SG CYS C 646 " distance=2.05 Simple disulfide: pdb=" SG CYS C 659 " - pdb=" SG CYS C 668 " distance=2.03 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 757 " distance=2.03 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.03 Simple disulfide: pdb=" SG CYS C 837 " - pdb=" SG CYS C 848 " distance=2.03 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.03 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " distance=2.05 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 Atom "HETATM26027 O5 NAG E 1 .*. O " rejected from bonding due to valence issues. 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 160 " " NAG A1302 " - " ASN A 231 " " NAG A1303 " - " ASN A 613 " " NAG A1304 " - " ASN A 279 " " NAG A1305 " - " ASN A 654 " " NAG A1306 " - " ASN A 706 " " NAG A1307 " - " ASN A1071 " " NAG A1308 " - " ASN A 61 " " NAG B1301 " - " ASN B 61 " " NAG B1305 " - " ASN B 654 " " NAG B1307 " - " ASN B1071 " " NAG C1301 " - " ASN C 613 " " NAG C1302 " - " ASN C 714 " " NAG C1304 " - " ASN C 279 " " NAG C1305 " - " ASN C 706 " " NAG D 1 " - " ASN A 120 " " NAG E 1 " - " ASN A 714 " " NAG F 1 " - " ASN A 798 " " NAG G 1 " - " ASN A1095 " " NAG H 1 " - " ASN A1131 " " NAG I 1 " - " ASN B 714 " " NAG J 1 " - " ASN B 798 " " NAG K 1 " - " ASN B1095 " " NAG L 1 " - " ASN B1131 " " NAG M 1 " - " ASN C 798 " " NAG N 1 " - " ASN C1095 " " NAG O 1 " - " ASN C1131 " Time building additional restraints: 6.80 Conformation dependent library (CDL) restraints added in 6.3 seconds 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6210 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 50 sheets defined 23.0% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.65 Creating SS restraints... Processing helix chain 'A' and resid 291 through 301 removed outlier: 3.646A pdb=" N GLU A 295 " --> pdb=" O ASP A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 348 through 350 No H-bonds generated for 'chain 'A' and resid 348 through 350' Processing helix chain 'A' and resid 402 through 408 removed outlier: 4.944A pdb=" N ARG A 405 " --> pdb=" O ASP A 402 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA A 408 " --> pdb=" O ARG A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 440 Processing helix chain 'A' and resid 622 through 626 removed outlier: 3.726A pdb=" N LEU A 626 " --> pdb=" O ALA A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 634 Processing helix chain 'A' and resid 734 through 740 Processing helix chain 'A' and resid 744 through 751 removed outlier: 3.803A pdb=" N ASN A 748 " --> pdb=" O THR A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 754 No H-bonds generated for 'chain 'A' and resid 752 through 754' Processing helix chain 'A' and resid 755 through 780 removed outlier: 3.783A pdb=" N ASP A 772 " --> pdb=" O ALA A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 822 removed outlier: 3.853A pdb=" N LEU A 818 " --> pdb=" O PRO A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 852 Processing helix chain 'A' and resid 863 through 882 removed outlier: 3.591A pdb=" N ILE A 867 " --> pdb=" O THR A 863 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA A 868 " --> pdb=" O ASP A 864 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN A 869 " --> pdb=" O GLU A 865 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 887 removed outlier: 3.501A pdb=" N GLY A 886 " --> pdb=" O TRP A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 906 removed outlier: 3.943A pdb=" N TYR A 901 " --> pdb=" O MET A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 916 removed outlier: 3.687A pdb=" N TYR A 914 " --> pdb=" O GLN A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 937 removed outlier: 3.584A pdb=" N ALA A 921 " --> pdb=" O GLN A 917 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN A 922 " --> pdb=" O LYS A 918 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER A 937 " --> pdb=" O ASP A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 962 removed outlier: 3.691A pdb=" N GLN A 946 " --> pdb=" O LEU A 942 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP A 947 " --> pdb=" O GLY A 943 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N VAL A 948 " --> pdb=" O LYS A 944 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N VAL A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 979 Processing helix chain 'A' and resid 982 through 1030 removed outlier: 5.248A pdb=" N VAL A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLN A 989 " --> pdb=" O GLU A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1143 Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 335 through 340 Processing helix chain 'B' and resid 380 through 386 removed outlier: 4.304A pdb=" N ASN B 385 " --> pdb=" O THR B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 406 Processing helix chain 'B' and resid 499 through 502 removed outlier: 3.588A pdb=" N HIS B 502 " --> pdb=" O GLY B 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 499 through 502' Processing helix chain 'B' and resid 734 through 739 Processing helix chain 'B' and resid 744 through 751 removed outlier: 3.662A pdb=" N ASN B 748 " --> pdb=" O THR B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 780 removed outlier: 3.793A pdb=" N ASP B 772 " --> pdb=" O ALA B 768 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 823 removed outlier: 3.840A pdb=" N LEU B 818 " --> pdb=" O PRO B 814 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL B 823 " --> pdb=" O LEU B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 847 through 853 removed outlier: 3.670A pdb=" N LYS B 851 " --> pdb=" O ILE B 847 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 882 removed outlier: 3.571A pdb=" N ILE B 867 " --> pdb=" O THR B 863 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA B 868 " --> pdb=" O ASP B 864 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN B 869 " --> pdb=" O GLU B 865 " (cutoff:3.500A) Processing helix chain 'B' and resid 883 through 887 removed outlier: 3.542A pdb=" N GLY B 886 " --> pdb=" O TRP B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 907 removed outlier: 3.716A pdb=" N ALA B 900 " --> pdb=" O PRO B 896 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TYR B 901 " --> pdb=" O MET B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 910 through 916 removed outlier: 3.822A pdb=" N TYR B 914 " --> pdb=" O GLN B 910 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU B 915 " --> pdb=" O ASN B 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 937 removed outlier: 3.590A pdb=" N LEU B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER B 936 " --> pdb=" O GLN B 932 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER B 937 " --> pdb=" O ASP B 933 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 962 removed outlier: 3.942A pdb=" N VAL B 948 " --> pdb=" O LYS B 944 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 965 No H-bonds generated for 'chain 'B' and resid 963 through 965' Processing helix chain 'B' and resid 973 through 979 Processing helix chain 'B' and resid 982 through 1030 removed outlier: 4.730A pdb=" N VAL B 988 " --> pdb=" O PRO B 984 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLN B 989 " --> pdb=" O GLU B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 1138 through 1143 Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 334 through 340 removed outlier: 4.026A pdb=" N VAL C 338 " --> pdb=" O PRO C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 350 removed outlier: 3.762A pdb=" N TRP C 350 " --> pdb=" O VAL C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 368 removed outlier: 3.975A pdb=" N TYR C 366 " --> pdb=" O TYR C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 386 removed outlier: 3.614A pdb=" N LEU C 384 " --> pdb=" O PRO C 381 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASN C 385 " --> pdb=" O THR C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 407 removed outlier: 4.180A pdb=" N ARG C 405 " --> pdb=" O ASP C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 419 Processing helix chain 'C' and resid 499 through 502 Processing helix chain 'C' and resid 734 through 740 Processing helix chain 'C' and resid 743 through 751 removed outlier: 4.000A pdb=" N SER C 747 " --> pdb=" O SER C 743 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASN C 748 " --> pdb=" O THR C 744 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU C 749 " --> pdb=" O GLU C 745 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 780 removed outlier: 3.854A pdb=" N ASP C 772 " --> pdb=" O ALA C 768 " (cutoff:3.500A) Processing helix chain 'C' and resid 815 through 822 Processing helix chain 'C' and resid 838 through 842 Processing helix chain 'C' and resid 847 through 852 Processing helix chain 'C' and resid 863 through 882 removed outlier: 3.591A pdb=" N ILE C 867 " --> pdb=" O THR C 863 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA C 868 " --> pdb=" O ASP C 864 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN C 869 " --> pdb=" O GLU C 865 " (cutoff:3.500A) Processing helix chain 'C' and resid 883 through 887 removed outlier: 3.600A pdb=" N GLY C 886 " --> pdb=" O TRP C 883 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 896 No H-bonds generated for 'chain 'C' and resid 894 through 896' Processing helix chain 'C' and resid 897 through 907 removed outlier: 3.949A pdb=" N TYR C 901 " --> pdb=" O MET C 897 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 916 removed outlier: 3.708A pdb=" N TYR C 914 " --> pdb=" O GLN C 910 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 937 removed outlier: 3.849A pdb=" N SER C 936 " --> pdb=" O GLN C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 962 removed outlier: 4.213A pdb=" N VAL C 948 " --> pdb=" O LYS C 944 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 963 through 965 No H-bonds generated for 'chain 'C' and resid 963 through 965' Processing helix chain 'C' and resid 973 through 979 Processing helix chain 'C' and resid 982 through 1030 removed outlier: 5.390A pdb=" N VAL C 988 " --> pdb=" O PRO C 984 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLN C 989 " --> pdb=" O GLU C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 1138 through 1143 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.226A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN A 183 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL A 224 " --> pdb=" O ILE A 198 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N SER A 200 " --> pdb=" O PRO A 222 " (cutoff:3.500A) removed outlier: 9.380A pdb=" N HIS A 202 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 8.804A pdb=" N LEU A 220 " --> pdb=" O HIS A 202 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N VAL A 36 " --> pdb=" O LEU A 220 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.076A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 82 through 83 removed outlier: 6.940A pdb=" N ARG A 234 " --> pdb=" O PHE A 104 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N PHE A 104 " --> pdb=" O ARG A 234 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLN A 236 " --> pdb=" O TRP A 102 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N TRP A 102 " --> pdb=" O GLN A 236 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU A 238 " --> pdb=" O ARG A 100 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ARG A 100 " --> pdb=" O ASN A 119 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASN A 119 " --> pdb=" O ARG A 100 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N VAL A 124 " --> pdb=" O SER A 167 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL A 128 " --> pdb=" O PHE A 163 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N PHE A 163 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N GLU A 130 " --> pdb=" O CYS A 161 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N CYS A 161 " --> pdb=" O GLU A 130 " (cutoff:3.500A) removed outlier: 10.154A pdb=" N GLN A 132 " --> pdb=" O ASN A 159 " (cutoff:3.500A) removed outlier: 9.276A pdb=" N ASN A 159 " --> pdb=" O GLN A 132 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N CYS A 134 " --> pdb=" O SER A 157 " (cutoff:3.500A) removed outlier: 10.349A pdb=" N SER A 157 " --> pdb=" O CYS A 134 " (cutoff:3.500A) removed outlier: 9.999A pdb=" N ASP A 136 " --> pdb=" O TYR A 155 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N TYR A 155 " --> pdb=" O ASP A 136 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 82 through 83 removed outlier: 12.452A pdb=" N PHE A 235 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 12.858A pdb=" N ASN A 135 " --> pdb=" O PHE A 235 " (cutoff:3.500A) removed outlier: 9.925A pdb=" N THR A 237 " --> pdb=" O ASN A 135 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N LEU A 239 " --> pdb=" O PRO A 137 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N VAL A 124 " --> pdb=" O SER A 167 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL A 128 " --> pdb=" O PHE A 163 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N PHE A 163 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N GLU A 130 " --> pdb=" O CYS A 161 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N CYS A 161 " --> pdb=" O GLU A 130 " (cutoff:3.500A) removed outlier: 10.154A pdb=" N GLN A 132 " --> pdb=" O ASN A 159 " (cutoff:3.500A) removed outlier: 9.276A pdb=" N ASN A 159 " --> pdb=" O GLN A 132 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N CYS A 134 " --> pdb=" O SER A 157 " (cutoff:3.500A) removed outlier: 10.349A pdb=" N SER A 157 " --> pdb=" O CYS A 134 " (cutoff:3.500A) removed outlier: 9.999A pdb=" N ASP A 136 " --> pdb=" O TYR A 155 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N TYR A 155 " --> pdb=" O ASP A 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 308 through 311 Processing sheet with id=AA6, first strand: chain 'A' and resid 345 through 346 removed outlier: 7.261A pdb=" N ALA A 345 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 9.208A pdb=" N ARG A 400 " --> pdb=" O ALA A 345 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER A 396 " --> pdb=" O ASN A 351 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ASN A 351 " --> pdb=" O SER A 396 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 345 through 346 removed outlier: 7.261A pdb=" N ALA A 345 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 9.208A pdb=" N ARG A 400 " --> pdb=" O ALA A 345 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TYR A 393 " --> pdb=" O SER A 511 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG A 506 " --> pdb=" O TRP A 433 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TRP A 433 " --> pdb=" O ARG A 506 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL A 430 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS A 375 " --> pdb=" O VAL A 430 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 449 through 451 removed outlier: 3.626A pdb=" N ARG A 490 " --> pdb=" O TYR A 450 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 470 through 471 Processing sheet with id=AB1, first strand: chain 'A' and resid 536 through 540 removed outlier: 6.001A pdb=" N ASP A 571 " --> pdb=" O ILE A 584 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLY A 563 " --> pdb=" O ASP A 571 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N PHE A 562 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 651 through 652 removed outlier: 6.211A pdb=" N GLU A 651 " --> pdb=" O ALA A 691 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N THR A 693 " --> pdb=" O GLU A 651 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SER A 688 " --> pdb=" O GLN A 672 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN A 672 " --> pdb=" O SER A 688 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ALA A 669 " --> pdb=" O PRO A 662 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 698 through 699 removed outlier: 7.124A pdb=" N ALA A 698 " --> pdb=" O ILE B 785 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 708 through 709 removed outlier: 3.662A pdb=" N THR A1073 " --> pdb=" O SER A1094 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ALA A1075 " --> pdb=" O PHE A1092 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N PHE A1092 " --> pdb=" O ALA A1075 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 715 through 725 removed outlier: 6.068A pdb=" N TYR A1064 " --> pdb=" O HIS A1045 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N HIS A1045 " --> pdb=" O TYR A1064 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 731 through 733 Processing sheet with id=AB7, first strand: chain 'A' and resid 784 through 785 Processing sheet with id=AB8, first strand: chain 'A' and resid 1117 through 1119 Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 30 removed outlier: 4.280A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N ASN B 61 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N TYR B 266 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL B 264 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N SER B 200 " --> pdb=" O PRO B 222 " (cutoff:3.500A) removed outlier: 9.409A pdb=" N HIS B 202 " --> pdb=" O LEU B 220 " (cutoff:3.500A) removed outlier: 9.509A pdb=" N LEU B 220 " --> pdb=" O HIS B 202 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N VAL B 36 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.984A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 82 through 83 removed outlier: 3.820A pdb=" N GLY B 101 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE B 163 " --> pdb=" O VAL B 128 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 131 through 133 removed outlier: 4.919A pdb=" N SER B 157 " --> pdb=" O GLN B 132 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 308 through 312 removed outlier: 4.391A pdb=" N VAL B 592 " --> pdb=" O THR B 312 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 351 through 355 removed outlier: 3.658A pdb=" N ASN B 351 " --> pdb=" O SER B 396 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL B 392 " --> pdb=" O ILE B 355 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ASN B 391 " --> pdb=" O GLU B 513 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLU B 513 " --> pdb=" O ASN B 391 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 358 through 359 removed outlier: 6.930A pdb=" N CYS B 358 " --> pdb=" O CYS B 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AC8, first strand: chain 'B' and resid 539 through 540 Processing sheet with id=AC9, first strand: chain 'B' and resid 548 through 551 removed outlier: 3.715A pdb=" N THR B 550 " --> pdb=" O ASP B 583 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 562 through 563 removed outlier: 7.463A pdb=" N PHE B 562 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 651 through 652 removed outlier: 6.278A pdb=" N GLU B 651 " --> pdb=" O ALA B 691 " (cutoff:3.500A) removed outlier: 8.732A pdb=" N THR B 693 " --> pdb=" O GLU B 651 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ALA B 669 " --> pdb=" O PRO B 662 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 698 through 699 removed outlier: 7.000A pdb=" N ALA B 698 " --> pdb=" O ILE C 785 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 708 through 712 Processing sheet with id=AD5, first strand: chain 'B' and resid 715 through 725 removed outlier: 6.022A pdb=" N TYR B1064 " --> pdb=" O HIS B1045 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N HIS B1045 " --> pdb=" O TYR B1064 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 731 through 733 Processing sheet with id=AD7, first strand: chain 'B' and resid 1117 through 1122 removed outlier: 4.649A pdb=" N ALA B1084 " --> pdb=" O SER B1120 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1091 through 1094 Processing sheet with id=AD9, first strand: chain 'C' and resid 27 through 30 removed outlier: 4.081A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ASN C 61 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N TYR C 266 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA C 261 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N PHE C 196 " --> pdb=" O ASP C 225 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ASP C 225 " --> pdb=" O PHE C 196 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ILE C 198 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N HIS C 202 " --> pdb=" O ALA C 219 " (cutoff:3.500A) removed outlier: 9.212A pdb=" N ALA C 219 " --> pdb=" O HIS C 202 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N VAL C 36 " --> pdb=" O LEU C 220 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.053A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 82 through 83 removed outlier: 3.743A pdb=" N GLN C 236 " --> pdb=" O ILE C 103 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL C 128 " --> pdb=" O PHE C 163 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N PHE C 163 " --> pdb=" O VAL C 128 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 147 through 152 removed outlier: 5.422A pdb=" N GLU C 149 " --> pdb=" O LYS C 142 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N LYS C 142 " --> pdb=" O GLU C 149 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU C 151 " --> pdb=" O ASP C 140 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU C 241 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N HIS C 141 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ARG C 243 " --> pdb=" O HIS C 141 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 308 through 313 removed outlier: 7.099A pdb=" N VAL C 592 " --> pdb=" O THR C 312 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 353 through 355 removed outlier: 3.860A pdb=" N VAL C 392 " --> pdb=" O ILE C 355 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ASN C 391 " --> pdb=" O GLU C 513 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLU C 513 " --> pdb=" O ASN C 391 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 353 through 355 removed outlier: 3.860A pdb=" N VAL C 392 " --> pdb=" O ILE C 355 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL C 521 " --> pdb=" O PHE C 389 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 449 through 451 Processing sheet with id=AE8, first strand: chain 'C' and resid 536 through 540 removed outlier: 3.537A pdb=" N PHE C 540 " --> pdb=" O LEU C 543 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE C 584 " --> pdb=" O ASP C 571 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N ASP C 571 " --> pdb=" O ILE C 584 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N GLY C 563 " --> pdb=" O ASP C 571 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 651 through 652 removed outlier: 6.142A pdb=" N GLU C 651 " --> pdb=" O ALA C 691 " (cutoff:3.500A) removed outlier: 8.771A pdb=" N THR C 693 " --> pdb=" O GLU C 651 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ALA C 669 " --> pdb=" O PRO C 662 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 708 through 709 Processing sheet with id=AF2, first strand: chain 'C' and resid 715 through 725 removed outlier: 5.945A pdb=" N TYR C1064 " --> pdb=" O HIS C1045 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N HIS C1045 " --> pdb=" O TYR C1064 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 731 through 733 Processing sheet with id=AF4, first strand: chain 'C' and resid 1117 through 1119 Processing sheet with id=AF5, first strand: chain 'C' and resid 1091 through 1094 915 hydrogen bonds defined for protein. 2481 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.35 Time building geometry restraints manager: 8.07 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: 8444 1.34 - 1.47: 6923 1.47 - 1.59: 11738 1.59 - 1.72: 1 1.72 - 1.84: 148 Bond restraints: 27254 Sorted by residual: bond pdb=" C1 NAG A1306 " pdb=" O5 NAG A1306 " ideal model delta sigma weight residual 1.406 1.564 -0.158 2.00e-02 2.50e+03 6.28e+01 bond pdb=" N THR A 320 " pdb=" CA THR A 320 " ideal model delta sigma weight residual 1.457 1.511 -0.054 1.29e-02 6.01e+03 1.76e+01 bond pdb=" C1 NAG I 1 " pdb=" O5 NAG I 1 " ideal model delta sigma weight residual 1.406 1.478 -0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" N VAL B 632 " pdb=" CA VAL B 632 " ideal model delta sigma weight residual 1.462 1.496 -0.033 1.06e-02 8.90e+03 9.99e+00 bond pdb=" N GLN A 318 " pdb=" CA GLN A 318 " ideal model delta sigma weight residual 1.457 1.501 -0.044 1.41e-02 5.03e+03 9.90e+00 ... (remaining 27249 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.19: 37043 5.19 - 10.37: 55 10.37 - 15.56: 0 15.56 - 20.75: 0 20.75 - 25.93: 1 Bond angle restraints: 37099 Sorted by residual: angle pdb=" CA CYS C 522 " pdb=" CB CYS C 522 " pdb=" SG CYS C 522 " ideal model delta sigma weight residual 114.40 140.33 -25.93 2.30e+00 1.89e-01 1.27e+02 angle pdb=" N PRO A 319 " pdb=" CA PRO A 319 " pdb=" C PRO A 319 " ideal model delta sigma weight residual 113.47 122.80 -9.33 1.43e+00 4.89e-01 4.26e+01 angle pdb=" C TYR B 633 " pdb=" N SER B 634 " pdb=" CA SER B 634 " ideal model delta sigma weight residual 122.67 132.73 -10.06 1.73e+00 3.34e-01 3.38e+01 angle pdb=" C THR A 713 " pdb=" N ASN A 714 " pdb=" CA ASN A 714 " ideal model delta sigma weight residual 122.11 130.98 -8.87 1.59e+00 3.96e-01 3.11e+01 angle pdb=" N ASP B 140 " pdb=" CA ASP B 140 " pdb=" CB ASP B 140 " ideal model delta sigma weight residual 110.49 101.51 8.98 1.69e+00 3.50e-01 2.82e+01 ... (remaining 37094 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.67: 15910 23.67 - 47.33: 709 47.33 - 71.00: 176 71.00 - 94.66: 56 94.66 - 118.33: 33 Dihedral angle restraints: 16884 sinusoidal: 7221 harmonic: 9663 Sorted by residual: dihedral pdb=" CA CYS A 614 " pdb=" C CYS A 614 " pdb=" N THR A 615 " pdb=" CA THR A 615 " ideal model delta harmonic sigma weight residual 180.00 127.75 52.25 0 5.00e+00 4.00e-02 1.09e+02 dihedral pdb=" CB CYS C 614 " pdb=" SG CYS C 614 " pdb=" SG CYS C 646 " pdb=" CB CYS C 646 " ideal model delta sinusoidal sigma weight residual 93.00 7.50 85.50 1 1.00e+01 1.00e-02 8.85e+01 dihedral pdb=" CB CYS A 614 " pdb=" SG CYS A 614 " pdb=" SG CYS A 646 " pdb=" CB CYS A 646 " ideal model delta sinusoidal sigma weight residual 93.00 169.93 -76.93 1 1.00e+01 1.00e-02 7.43e+01 ... (remaining 16881 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.085: 4297 1.085 - 2.170: 0 2.170 - 3.254: 0 3.254 - 4.339: 0 4.339 - 5.424: 1 Chirality restraints: 4298 Sorted by residual: chirality pdb=" C1 NAG A1308 " pdb=" ND2 ASN A 61 " pdb=" C2 NAG A1308 " pdb=" O5 NAG A1308 " both_signs ideal model delta sigma weight residual False -2.40 3.02 -5.42 2.00e-01 2.50e+01 7.35e+02 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.46 0.06 2.00e-02 2.50e+03 8.61e+00 chirality pdb=" C1 NAG A1306 " pdb=" ND2 ASN A 706 " pdb=" C2 NAG A1306 " pdb=" O5 NAG A1306 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.06e+00 ... (remaining 4295 not shown) Planarity restraints: 4776 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 714 " 0.066 2.00e-02 2.50e+03 6.61e-02 5.47e+01 pdb=" CG ASN A 714 " -0.084 2.00e-02 2.50e+03 pdb=" OD1 ASN A 714 " 0.028 2.00e-02 2.50e+03 pdb=" ND2 ASN A 714 " -0.074 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " 0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 61 " 0.001 2.00e-02 2.50e+03 6.38e-02 5.08e+01 pdb=" CG ASN A 61 " -0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN A 61 " 0.064 2.00e-02 2.50e+03 pdb=" ND2 ASN A 61 " -0.109 2.00e-02 2.50e+03 pdb=" C1 NAG A1308 " 0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 140 " 0.021 2.00e-02 2.50e+03 4.31e-02 1.86e+01 pdb=" C ASP A 140 " -0.074 2.00e-02 2.50e+03 pdb=" O ASP A 140 " 0.029 2.00e-02 2.50e+03 pdb=" N HIS A 141 " 0.024 2.00e-02 2.50e+03 ... (remaining 4773 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 251 2.57 - 3.15: 21691 3.15 - 3.73: 35894 3.73 - 4.32: 52169 4.32 - 4.90: 89627 Nonbonded interactions: 199632 Sorted by model distance: nonbonded pdb=" O3 NAG I 2 " pdb=" O7 NAG I 2 " model vdw 1.983 3.040 nonbonded pdb=" NZ LYS B 808 " pdb=" OD2 ASP B 817 " model vdw 2.007 3.120 nonbonded pdb=" O3 NAG K 2 " pdb=" O7 NAG K 2 " model vdw 2.021 3.040 nonbonded pdb=" OD2 ASP C 840 " pdb=" NH1 ARG C 844 " model vdw 2.029 3.120 nonbonded pdb=" NH1 ARG B 208 " pdb=" O GLU B 209 " model vdw 2.092 3.120 ... (remaining 199627 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 618 or resid 630 through 819 or resid 821 throu \ gh 832 or resid 845 through 1015 or resid 1017 through 1143 or resid 1301 throug \ h 1306)) selection = (chain 'B' and (resid 14 through 618 or resid 630 through 819 or resid 821 throu \ gh 1015 or resid 1017 through 1143 or resid 1301 through 1306)) selection = (chain 'C' and (resid 14 through 618 or resid 630 through 819 or resid 821 throu \ gh 832 or resid 845 through 1015 or resid 1017 through 1143 or resid 1301 throug \ h 1306)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.290 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: 1.080 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 79.420 Find NCS groups from input model: 1.760 Set up NCS constraints: 0.180 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:12.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 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 : 0.008 0.450 27337 Z= 0.346 Angle : 0.928 27.402 37304 Z= 0.487 Chirality : 0.098 5.424 4298 Planarity : 0.006 0.069 4749 Dihedral : 15.753 118.331 10542 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.34 % Favored : 92.63 % Rotamer: Outliers : 0.24 % Allowed : 0.41 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.46 (0.13), residues: 3289 helix: -0.09 (0.20), residues: 653 sheet: -0.51 (0.20), residues: 617 loop : -2.71 (0.11), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP B 883 HIS 0.014 0.002 HIS C 951 PHE 0.026 0.002 PHE B 640 TYR 0.033 0.002 TYR B 753 ARG 0.012 0.001 ARG B 153 Details of bonding type rmsd link_NAG-ASN : bond 0.08683 ( 27) link_NAG-ASN : angle 6.97465 ( 81) link_BETA1-4 : bond 0.00887 ( 12) link_BETA1-4 : angle 2.28527 ( 36) hydrogen bonds : bond 0.16240 ( 905) hydrogen bonds : angle 7.09118 ( 2481) SS BOND : bond 0.00834 ( 44) SS BOND : angle 3.11473 ( 88) covalent geometry : bond 0.00725 (27254) covalent geometry : angle 0.85537 (37099) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 194 time to evaluate : 3.202 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 165 TYR cc_start: 0.7724 (t80) cc_final: 0.7377 (t80) REVERT: A 529 ASN cc_start: 0.7947 (m-40) cc_final: 0.7651 (m-40) REVERT: A 755 SER cc_start: 0.8529 (m) cc_final: 0.8219 (p) REVERT: B 172 MET cc_start: 0.3347 (mtt) cc_final: 0.2910 (mtt) REVERT: B 516 HIS cc_start: 0.8252 (m90) cc_final: 0.7890 (m90) REVERT: B 633 TYR cc_start: 0.5127 (m-10) cc_final: 0.4231 (m-10) REVERT: C 172 MET cc_start: 0.4331 (mtt) cc_final: 0.3922 (mtp) outliers start: 6 outliers final: 0 residues processed: 199 average time/residue: 1.4641 time to fit residues: 340.5032 Evaluate side-chains 101 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 3.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 278 optimal weight: 0.9990 chunk 250 optimal weight: 3.9990 chunk 138 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 168 optimal weight: 0.9980 chunk 133 optimal weight: 6.9990 chunk 258 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 192 optimal weight: 1.9990 chunk 299 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN ** A 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 502 HIS A 503 GLN A1116 ASN B 14 GLN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN B 434 ASN B 436 ASN B 503 GLN C 14 GLN C 119 ASN C 141 HIS C 391 ASN C 951 HIS C 999 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.124398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.067799 restraints weight = 84998.462| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 4.68 r_work: 0.2838 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2833 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2833 r_free = 0.2833 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2833 r_free = 0.2833 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2833 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 27337 Z= 0.165 Angle : 0.822 21.628 37304 Z= 0.398 Chirality : 0.054 1.324 4298 Planarity : 0.005 0.053 4749 Dihedral : 11.011 103.365 4520 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.39 % Favored : 94.55 % Rotamer: Outliers : 0.76 % Allowed : 5.38 % Favored : 93.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.74 (0.14), residues: 3289 helix: 0.87 (0.21), residues: 652 sheet: 0.03 (0.21), residues: 626 loop : -2.40 (0.12), residues: 2011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 147 HIS 0.013 0.001 HIS B 242 PHE 0.016 0.001 PHE A 77 TYR 0.026 0.001 TYR B 492 ARG 0.012 0.001 ARG B 153 Details of bonding type rmsd link_NAG-ASN : bond 0.00480 ( 27) link_NAG-ASN : angle 5.37258 ( 81) link_BETA1-4 : bond 0.00618 ( 12) link_BETA1-4 : angle 1.44528 ( 36) hydrogen bonds : bond 0.06957 ( 905) hydrogen bonds : angle 5.82433 ( 2481) SS BOND : bond 0.00496 ( 44) SS BOND : angle 2.16402 ( 88) covalent geometry : bond 0.00374 (27254) covalent geometry : angle 0.77694 (37099) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 4.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 TYR cc_start: 0.7467 (t80) cc_final: 0.6897 (t80) REVERT: A 999 GLN cc_start: 0.8823 (tp40) cc_final: 0.8604 (mt0) REVERT: B 454 ARG cc_start: 0.7140 (OUTLIER) cc_final: 0.6861 (mmm-85) REVERT: B 513 GLU cc_start: 0.8549 (tp30) cc_final: 0.7848 (tp30) REVERT: B 516 HIS cc_start: 0.8705 (m90) cc_final: 0.8086 (m90) REVERT: B 616 GLU cc_start: 0.8428 (tt0) cc_final: 0.8197 (tm-30) REVERT: C 116 LEU cc_start: 0.7368 (mp) cc_final: 0.6932 (pt) REVERT: C 195 TYR cc_start: 0.8030 (m-80) cc_final: 0.7620 (m-80) REVERT: C 498 TYR cc_start: 0.8550 (m-80) cc_final: 0.8240 (m-80) REVERT: C 999 GLN cc_start: 0.8803 (tp40) cc_final: 0.8587 (tp-100) outliers start: 21 outliers final: 5 residues processed: 139 average time/residue: 1.8818 time to fit residues: 317.0505 Evaluate side-chains 109 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 103 time to evaluate : 3.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 454 ARG Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain C residue 938 THR Chi-restraints excluded: chain C residue 1089 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 258 optimal weight: 2.9990 chunk 323 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 232 optimal weight: 0.9990 chunk 318 optimal weight: 3.9990 chunk 260 optimal weight: 6.9990 chunk 118 optimal weight: 9.9990 chunk 297 optimal weight: 4.9990 chunk 95 optimal weight: 0.0970 chunk 81 optimal weight: 0.7980 chunk 168 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN ** A 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 ASN A 923 GLN B 14 GLN B 66 HIS B 279 ASN B 436 ASN ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.124399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.070891 restraints weight = 88894.304| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 4.42 r_work: 0.2868 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2846 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2846 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27337 Z= 0.136 Angle : 0.705 20.206 37304 Z= 0.343 Chirality : 0.048 0.664 4298 Planarity : 0.004 0.046 4749 Dihedral : 8.336 95.560 4520 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.79 % Favored : 94.18 % Rotamer: Outliers : 0.79 % Allowed : 6.58 % Favored : 92.62 % 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: -1.38 (0.14), residues: 3289 helix: 1.41 (0.22), residues: 656 sheet: 0.18 (0.21), residues: 630 loop : -2.25 (0.12), residues: 2003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 433 HIS 0.005 0.001 HIS A 66 PHE 0.024 0.001 PHE A 77 TYR 0.023 0.001 TYR B 492 ARG 0.007 0.001 ARG B 343 Details of bonding type rmsd link_NAG-ASN : bond 0.00621 ( 27) link_NAG-ASN : angle 4.14965 ( 81) link_BETA1-4 : bond 0.00361 ( 12) link_BETA1-4 : angle 1.16545 ( 36) hydrogen bonds : bond 0.05976 ( 905) hydrogen bonds : angle 5.39073 ( 2481) SS BOND : bond 0.00431 ( 44) SS BOND : angle 1.62313 ( 88) covalent geometry : bond 0.00303 (27254) covalent geometry : angle 0.67424 (37099) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 2.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 172 MET cc_start: 0.3709 (mtt) cc_final: 0.3280 (mtt) REVERT: B 348 TYR cc_start: 0.4554 (p90) cc_final: 0.4348 (p90) REVERT: B 513 GLU cc_start: 0.8591 (tp30) cc_final: 0.7918 (tp30) REVERT: B 516 HIS cc_start: 0.8639 (m90) cc_final: 0.8186 (m90) REVERT: B 866 MET cc_start: 0.8970 (mtt) cc_final: 0.8702 (mtt) REVERT: C 116 LEU cc_start: 0.7486 (mp) cc_final: 0.7195 (OUTLIER) REVERT: C 195 TYR cc_start: 0.8301 (m-80) cc_final: 0.7909 (m-80) REVERT: C 632 VAL cc_start: 0.8042 (m) cc_final: 0.7734 (p) REVERT: C 938 THR cc_start: 0.7703 (OUTLIER) cc_final: 0.7459 (t) outliers start: 22 outliers final: 12 residues processed: 146 average time/residue: 1.1519 time to fit residues: 203.0901 Evaluate side-chains 122 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 2.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 614 CYS Chi-restraints excluded: chain A residue 714 ASN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 397 PHE Chi-restraints excluded: chain B residue 454 ARG Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 777 GLU Chi-restraints excluded: chain C residue 77 PHE Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 938 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 245 optimal weight: 5.9990 chunk 53 optimal weight: 0.1980 chunk 45 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 117 optimal weight: 8.9990 chunk 283 optimal weight: 0.5980 chunk 251 optimal weight: 8.9990 chunk 221 optimal weight: 6.9990 chunk 252 optimal weight: 5.9990 chunk 299 optimal weight: 10.0000 chunk 243 optimal weight: 50.0000 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN B 14 GLN ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 HIS C 502 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.118948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.065463 restraints weight = 102845.819| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 5.32 r_work: 0.2664 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2669 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2669 r_free = 0.2669 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2669 r_free = 0.2669 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2669 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.075 27337 Z= 0.307 Angle : 0.826 16.525 37304 Z= 0.413 Chirality : 0.053 0.616 4298 Planarity : 0.005 0.051 4749 Dihedral : 8.103 90.399 4520 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.67 % Favored : 93.30 % Rotamer: Outliers : 0.90 % Allowed : 7.76 % Favored : 91.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.55 (0.14), residues: 3289 helix: 1.11 (0.21), residues: 652 sheet: 0.27 (0.21), residues: 602 loop : -2.34 (0.12), residues: 2035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP B 883 HIS 0.005 0.001 HIS B 242 PHE 0.035 0.002 PHE A 152 TYR 0.032 0.002 TYR B 753 ARG 0.009 0.001 ARG C 631 Details of bonding type rmsd link_NAG-ASN : bond 0.00443 ( 27) link_NAG-ASN : angle 4.27976 ( 81) link_BETA1-4 : bond 0.00290 ( 12) link_BETA1-4 : angle 1.12959 ( 36) hydrogen bonds : bond 0.08998 ( 905) hydrogen bonds : angle 5.69440 ( 2481) SS BOND : bond 0.00618 ( 44) SS BOND : angle 2.71383 ( 88) covalent geometry : bond 0.00769 (27254) covalent geometry : angle 0.79174 (37099) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 2.847 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 985 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8060 (mp0) REVERT: B 172 MET cc_start: 0.4326 (mtt) cc_final: 0.3655 (mtt) REVERT: B 348 TYR cc_start: 0.4814 (p90) cc_final: 0.4578 (p90) REVERT: B 454 ARG cc_start: 0.7601 (OUTLIER) cc_final: 0.7271 (mmm160) REVERT: B 513 GLU cc_start: 0.8636 (tp30) cc_final: 0.8026 (tp30) REVERT: B 516 HIS cc_start: 0.8747 (m90) cc_final: 0.8197 (m90) REVERT: B 866 MET cc_start: 0.9198 (mtt) cc_final: 0.8967 (mtt) REVERT: C 100 ARG cc_start: 0.7089 (mtt180) cc_final: 0.5733 (mtt180) REVERT: C 195 TYR cc_start: 0.8336 (m-80) cc_final: 0.7915 (m-80) REVERT: C 498 TYR cc_start: 0.8511 (m-80) cc_final: 0.8266 (m-80) REVERT: C 938 THR cc_start: 0.8002 (OUTLIER) cc_final: 0.7720 (t) outliers start: 25 outliers final: 19 residues processed: 132 average time/residue: 1.2934 time to fit residues: 203.9800 Evaluate side-chains 122 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 3.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 614 CYS Chi-restraints excluded: chain A residue 714 ASN Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 397 PHE Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 454 ARG Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 753 TYR Chi-restraints excluded: chain B residue 777 GLU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 938 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 76 optimal weight: 0.9980 chunk 228 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 281 optimal weight: 2.9990 chunk 272 optimal weight: 3.9990 chunk 206 optimal weight: 1.9990 chunk 329 optimal weight: 4.9990 chunk 127 optimal weight: 9.9990 chunk 307 optimal weight: 0.6980 chunk 108 optimal weight: 0.9990 chunk 232 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN B 14 GLN B 30 ASN ** B 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.124361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.069663 restraints weight = 106670.943| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 5.20 r_work: 0.2734 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2743 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2743 r_free = 0.2743 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2743 r_free = 0.2743 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2743 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 27337 Z= 0.141 Angle : 0.691 16.507 37304 Z= 0.339 Chirality : 0.048 0.540 4298 Planarity : 0.004 0.050 4749 Dihedral : 7.484 88.044 4520 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.48 % Favored : 94.49 % Rotamer: Outliers : 0.86 % Allowed : 8.48 % Favored : 90.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.31 (0.14), residues: 3289 helix: 1.50 (0.22), residues: 650 sheet: 0.27 (0.21), residues: 622 loop : -2.22 (0.12), residues: 2017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 433 HIS 0.008 0.001 HIS B 242 PHE 0.032 0.001 PHE A 152 TYR 0.020 0.001 TYR A 165 ARG 0.009 0.001 ARG C 631 Details of bonding type rmsd link_NAG-ASN : bond 0.00468 ( 27) link_NAG-ASN : angle 3.88687 ( 81) link_BETA1-4 : bond 0.00364 ( 12) link_BETA1-4 : angle 0.94277 ( 36) hydrogen bonds : bond 0.06630 ( 905) hydrogen bonds : angle 5.35537 ( 2481) SS BOND : bond 0.00391 ( 44) SS BOND : angle 1.68566 ( 88) covalent geometry : bond 0.00322 (27254) covalent geometry : angle 0.66292 (37099) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 2.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 172 MET cc_start: 0.4027 (mtt) cc_final: 0.3546 (mtt) REVERT: B 418 TYR cc_start: 0.8720 (m-80) cc_final: 0.8485 (m-80) REVERT: B 513 GLU cc_start: 0.8630 (tp30) cc_final: 0.8026 (tp30) REVERT: B 516 HIS cc_start: 0.8731 (m90) cc_final: 0.8204 (m90) REVERT: B 866 MET cc_start: 0.9036 (mtt) cc_final: 0.8721 (mtt) REVERT: C 195 TYR cc_start: 0.8303 (m-80) cc_final: 0.7914 (m-80) REVERT: C 498 TYR cc_start: 0.8479 (m-80) cc_final: 0.8222 (m-80) REVERT: C 632 VAL cc_start: 0.8246 (OUTLIER) cc_final: 0.7888 (p) REVERT: C 938 THR cc_start: 0.8011 (OUTLIER) cc_final: 0.7771 (t) outliers start: 24 outliers final: 15 residues processed: 132 average time/residue: 1.0994 time to fit residues: 176.2908 Evaluate side-chains 125 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 2.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 614 CYS Chi-restraints excluded: chain A residue 714 ASN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 77 PHE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 397 PHE Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 777 GLU Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 938 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 200 optimal weight: 1.9990 chunk 223 optimal weight: 0.7980 chunk 126 optimal weight: 9.9990 chunk 153 optimal weight: 20.0000 chunk 214 optimal weight: 0.7980 chunk 171 optimal weight: 0.4980 chunk 19 optimal weight: 0.0270 chunk 34 optimal weight: 20.0000 chunk 0 optimal weight: 40.0000 chunk 321 optimal weight: 0.0980 chunk 162 optimal weight: 0.0570 overall best weight: 0.2956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 923 GLN B 14 GLN ** C 14 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 = 0.3980 r_free = 0.3980 target = 0.128369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.073536 restraints weight = 103791.711| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 5.39 r_work: 0.2827 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2834 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2834 r_free = 0.2834 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2834 r_free = 0.2834 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2834 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 27337 Z= 0.112 Angle : 0.633 14.950 37304 Z= 0.310 Chirality : 0.046 0.491 4298 Planarity : 0.004 0.044 4749 Dihedral : 6.803 82.019 4520 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.12 % Favored : 94.85 % Rotamer: Outliers : 0.76 % Allowed : 8.93 % Favored : 90.31 % 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: -1.01 (0.14), residues: 3289 helix: 1.95 (0.22), residues: 642 sheet: 0.32 (0.21), residues: 647 loop : -2.05 (0.13), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 255 HIS 0.005 0.001 HIS B 242 PHE 0.031 0.001 PHE A 152 TYR 0.022 0.001 TYR A 165 ARG 0.006 0.000 ARG B 631 Details of bonding type rmsd link_NAG-ASN : bond 0.00559 ( 27) link_NAG-ASN : angle 3.39051 ( 81) link_BETA1-4 : bond 0.00423 ( 12) link_BETA1-4 : angle 0.88808 ( 36) hydrogen bonds : bond 0.04684 ( 905) hydrogen bonds : angle 4.96180 ( 2481) SS BOND : bond 0.00296 ( 44) SS BOND : angle 1.12040 ( 88) covalent geometry : bond 0.00235 (27254) covalent geometry : angle 0.61117 (37099) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 2.832 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 PHE cc_start: 0.8041 (m-10) cc_final: 0.7832 (m-10) REVERT: B 172 MET cc_start: 0.3620 (mtt) cc_final: 0.3087 (mtt) REVERT: B 418 TYR cc_start: 0.8648 (m-80) cc_final: 0.8410 (m-80) REVERT: B 492 TYR cc_start: 0.7336 (m-10) cc_final: 0.5982 (m-10) REVERT: B 513 GLU cc_start: 0.8667 (tp30) cc_final: 0.7994 (tp30) REVERT: B 516 HIS cc_start: 0.8721 (m90) cc_final: 0.8121 (m90) REVERT: B 866 MET cc_start: 0.8864 (mtt) cc_final: 0.8643 (mtt) REVERT: C 195 TYR cc_start: 0.8203 (m-80) cc_final: 0.7897 (m-80) REVERT: C 498 TYR cc_start: 0.8435 (m-80) cc_final: 0.8233 (m-80) REVERT: C 632 VAL cc_start: 0.8208 (m) cc_final: 0.7829 (p) REVERT: C 1135 TYR cc_start: 0.8810 (t80) cc_final: 0.8571 (t80) outliers start: 21 outliers final: 13 residues processed: 138 average time/residue: 1.0643 time to fit residues: 179.6418 Evaluate side-chains 128 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 2.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 614 CYS Chi-restraints excluded: chain A residue 714 ASN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 1089 GLU Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 931 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 295 optimal weight: 0.4980 chunk 242 optimal weight: 8.9990 chunk 50 optimal weight: 10.0000 chunk 45 optimal weight: 0.0770 chunk 113 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 185 optimal weight: 8.9990 chunk 177 optimal weight: 0.8980 chunk 26 optimal weight: 8.9990 chunk 208 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 overall best weight: 0.8940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 923 GLN B 14 GLN ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.126928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.072116 restraints weight = 93225.906| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 4.57 r_work: 0.2852 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2857 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2857 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27337 Z= 0.121 Angle : 0.632 14.724 37304 Z= 0.310 Chirality : 0.046 0.489 4298 Planarity : 0.004 0.046 4749 Dihedral : 6.606 78.399 4520 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.18 % Favored : 94.79 % Rotamer: Outliers : 0.83 % Allowed : 9.38 % Favored : 89.80 % 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: -0.95 (0.15), residues: 3289 helix: 1.99 (0.22), residues: 646 sheet: 0.43 (0.21), residues: 633 loop : -2.03 (0.13), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 102 HIS 0.006 0.001 HIS B 242 PHE 0.054 0.001 PHE B 77 TYR 0.017 0.001 TYR B1064 ARG 0.008 0.000 ARG C 631 Details of bonding type rmsd link_NAG-ASN : bond 0.00488 ( 27) link_NAG-ASN : angle 3.39540 ( 81) link_BETA1-4 : bond 0.00345 ( 12) link_BETA1-4 : angle 0.91320 ( 36) hydrogen bonds : bond 0.05251 ( 905) hydrogen bonds : angle 4.90619 ( 2481) SS BOND : bond 0.00314 ( 44) SS BOND : angle 1.34699 ( 88) covalent geometry : bond 0.00275 (27254) covalent geometry : angle 0.60953 (37099) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 113 time to evaluate : 3.042 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 985 GLU cc_start: 0.8504 (mm-30) cc_final: 0.7990 (mp0) REVERT: B 172 MET cc_start: 0.3415 (mtt) cc_final: 0.2924 (mtt) REVERT: B 418 TYR cc_start: 0.8561 (m-80) cc_final: 0.8314 (m-80) REVERT: B 513 GLU cc_start: 0.8570 (tp30) cc_final: 0.7939 (tp30) REVERT: B 516 HIS cc_start: 0.8668 (m90) cc_final: 0.8122 (m90) REVERT: B 866 MET cc_start: 0.8945 (mtt) cc_final: 0.8658 (mtt) REVERT: C 100 ARG cc_start: 0.7027 (mtt180) cc_final: 0.6703 (mtm180) REVERT: C 116 LEU cc_start: 0.6806 (pt) cc_final: 0.6587 (pt) REVERT: C 195 TYR cc_start: 0.8144 (m-80) cc_final: 0.7859 (m-80) REVERT: C 498 TYR cc_start: 0.8485 (m-80) cc_final: 0.8274 (m-80) REVERT: C 632 VAL cc_start: 0.8099 (OUTLIER) cc_final: 0.7755 (p) REVERT: C 1135 TYR cc_start: 0.8760 (t80) cc_final: 0.8535 (t80) outliers start: 24 outliers final: 13 residues processed: 131 average time/residue: 1.5368 time to fit residues: 243.2156 Evaluate side-chains 121 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 3.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 614 CYS Chi-restraints excluded: chain A residue 714 ASN Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 1089 GLU Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 1089 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 259 optimal weight: 0.6980 chunk 228 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 5 optimal weight: 9.9990 chunk 125 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 225 optimal weight: 3.9990 chunk 204 optimal weight: 0.4980 chunk 309 optimal weight: 0.9980 chunk 77 optimal weight: 0.0670 chunk 15 optimal weight: 10.0000 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 GLN ** C 14 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 = 0.3966 r_free = 0.3966 target = 0.126687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.070917 restraints weight = 123624.811| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 6.22 r_work: 0.2787 rms_B_bonded: 5.07 restraints_weight: 2.0000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2808 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2808 r_free = 0.2808 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2808 r_free = 0.2808 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2808 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 27337 Z= 0.111 Angle : 0.623 14.219 37304 Z= 0.304 Chirality : 0.046 0.477 4298 Planarity : 0.004 0.047 4749 Dihedral : 6.415 74.432 4520 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.84 % Favored : 95.13 % Rotamer: Outliers : 0.79 % Allowed : 9.51 % Favored : 89.69 % 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: -0.87 (0.15), residues: 3289 helix: 2.01 (0.22), residues: 653 sheet: 0.41 (0.21), residues: 642 loop : -1.95 (0.13), residues: 1994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 102 HIS 0.006 0.001 HIS B 242 PHE 0.044 0.001 PHE B 77 TYR 0.021 0.001 TYR B 492 ARG 0.009 0.000 ARG B 631 Details of bonding type rmsd link_NAG-ASN : bond 0.00506 ( 27) link_NAG-ASN : angle 3.29645 ( 81) link_BETA1-4 : bond 0.00427 ( 12) link_BETA1-4 : angle 0.90785 ( 36) hydrogen bonds : bond 0.04815 ( 905) hydrogen bonds : angle 4.81641 ( 2481) SS BOND : bond 0.00284 ( 44) SS BOND : angle 1.17765 ( 88) covalent geometry : bond 0.00242 (27254) covalent geometry : angle 0.60177 (37099) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 2.868 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 172 MET cc_start: 0.3843 (mtt) cc_final: 0.3284 (mtt) REVERT: B 418 TYR cc_start: 0.8681 (m-80) cc_final: 0.8452 (m-80) REVERT: B 513 GLU cc_start: 0.8633 (tp30) cc_final: 0.8063 (tp30) REVERT: B 516 HIS cc_start: 0.8712 (m90) cc_final: 0.8093 (m90) REVERT: B 866 MET cc_start: 0.8966 (mtt) cc_final: 0.8702 (mtt) REVERT: C 116 LEU cc_start: 0.6701 (pt) cc_final: 0.6488 (pt) REVERT: C 195 TYR cc_start: 0.8021 (m-80) cc_final: 0.7731 (m-80) REVERT: C 498 TYR cc_start: 0.8533 (m-80) cc_final: 0.8294 (m-80) REVERT: C 617 VAL cc_start: 0.7796 (t) cc_final: 0.7498 (p) REVERT: C 632 VAL cc_start: 0.8157 (OUTLIER) cc_final: 0.7783 (p) REVERT: C 1135 TYR cc_start: 0.8840 (t80) cc_final: 0.8563 (t80) outliers start: 23 outliers final: 15 residues processed: 132 average time/residue: 1.1674 time to fit residues: 187.2201 Evaluate side-chains 127 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 3.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 714 ASN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1089 GLU Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 1089 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 303 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 256 optimal weight: 4.9990 chunk 268 optimal weight: 9.9990 chunk 320 optimal weight: 3.9990 chunk 295 optimal weight: 0.6980 chunk 329 optimal weight: 0.7980 chunk 297 optimal weight: 0.9980 chunk 149 optimal weight: 20.0000 chunk 275 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 GLN ** C 14 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 = 0.3944 r_free = 0.3944 target = 0.125005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.069300 restraints weight = 88621.649| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 4.51 r_work: 0.2803 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2794 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2794 r_free = 0.2794 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2794 r_free = 0.2794 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2794 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 27337 Z= 0.149 Angle : 0.651 13.910 37304 Z= 0.322 Chirality : 0.047 0.477 4298 Planarity : 0.004 0.046 4749 Dihedral : 6.443 70.614 4520 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.51 % Favored : 94.46 % Rotamer: Outliers : 0.72 % Allowed : 9.79 % Favored : 89.49 % 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: -0.90 (0.15), residues: 3289 helix: 1.91 (0.22), residues: 653 sheet: 0.41 (0.21), residues: 635 loop : -1.94 (0.13), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP C 102 HIS 0.006 0.001 HIS B 242 PHE 0.024 0.001 PHE A 152 TYR 0.018 0.001 TYR B1064 ARG 0.010 0.000 ARG B 631 Details of bonding type rmsd link_NAG-ASN : bond 0.00433 ( 27) link_NAG-ASN : angle 3.36955 ( 81) link_BETA1-4 : bond 0.00302 ( 12) link_BETA1-4 : angle 0.93845 ( 36) hydrogen bonds : bond 0.06060 ( 905) hydrogen bonds : angle 4.91430 ( 2481) SS BOND : bond 0.00344 ( 44) SS BOND : angle 1.55059 ( 88) covalent geometry : bond 0.00356 (27254) covalent geometry : angle 0.62862 (37099) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 3.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 PHE cc_start: 0.7872 (m-10) cc_final: 0.7597 (m-10) REVERT: A 985 GLU cc_start: 0.8463 (mm-30) cc_final: 0.7961 (mp0) REVERT: B 172 MET cc_start: 0.3419 (mtt) cc_final: 0.2935 (mtt) REVERT: B 513 GLU cc_start: 0.8569 (tp30) cc_final: 0.7883 (tp30) REVERT: B 516 HIS cc_start: 0.8641 (m90) cc_final: 0.8055 (m90) REVERT: B 866 MET cc_start: 0.9012 (mtt) cc_final: 0.8706 (mtt) REVERT: C 195 TYR cc_start: 0.8278 (m-80) cc_final: 0.7937 (m-80) REVERT: C 617 VAL cc_start: 0.7847 (t) cc_final: 0.7618 (p) REVERT: C 632 VAL cc_start: 0.8109 (OUTLIER) cc_final: 0.7748 (p) REVERT: C 1135 TYR cc_start: 0.8727 (t80) cc_final: 0.8524 (t80) outliers start: 21 outliers final: 14 residues processed: 121 average time/residue: 1.3692 time to fit residues: 200.3238 Evaluate side-chains 118 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 3.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 614 CYS Chi-restraints excluded: chain A residue 714 ASN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 1089 GLU Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 632 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 108 optimal weight: 0.0980 chunk 48 optimal weight: 2.9990 chunk 303 optimal weight: 0.4980 chunk 276 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 315 optimal weight: 2.9990 chunk 221 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 287 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 GLN B 66 HIS ** C 14 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 = 0.3967 r_free = 0.3967 target = 0.125784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.071869 restraints weight = 110262.392| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 5.59 r_work: 0.2923 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2862 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2862 r_free = 0.2862 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2862 r_free = 0.2862 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2862 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27337 Z= 0.119 Angle : 0.628 13.607 37304 Z= 0.308 Chirality : 0.046 0.466 4298 Planarity : 0.004 0.045 4749 Dihedral : 6.319 67.563 4520 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.12 % Favored : 94.85 % Rotamer: Outliers : 0.62 % Allowed : 10.03 % Favored : 89.35 % 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: -0.82 (0.15), residues: 3289 helix: 2.06 (0.22), residues: 648 sheet: 0.46 (0.21), residues: 635 loop : -1.91 (0.13), residues: 2006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP C 102 HIS 0.007 0.001 HIS B 242 PHE 0.059 0.001 PHE B 77 TYR 0.018 0.001 TYR A 165 ARG 0.008 0.000 ARG B 631 Details of bonding type rmsd link_NAG-ASN : bond 0.00472 ( 27) link_NAG-ASN : angle 3.26121 ( 81) link_BETA1-4 : bond 0.00373 ( 12) link_BETA1-4 : angle 0.91636 ( 36) hydrogen bonds : bond 0.05342 ( 905) hydrogen bonds : angle 4.83767 ( 2481) SS BOND : bond 0.00300 ( 44) SS BOND : angle 1.29757 ( 88) covalent geometry : bond 0.00268 (27254) covalent geometry : angle 0.60665 (37099) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 3.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 148 MET cc_start: 0.8136 (mpp) cc_final: 0.7785 (pmm) REVERT: B 172 MET cc_start: 0.3757 (mtt) cc_final: 0.3193 (mtt) REVERT: B 513 GLU cc_start: 0.8555 (tp30) cc_final: 0.7973 (tp30) REVERT: B 516 HIS cc_start: 0.8739 (m90) cc_final: 0.8118 (m90) REVERT: B 866 MET cc_start: 0.8935 (mtt) cc_final: 0.8629 (mtt) REVERT: C 100 ARG cc_start: 0.7016 (mtt180) cc_final: 0.5666 (mtt180) REVERT: C 172 MET cc_start: 0.2380 (ptt) cc_final: 0.1907 (mtt) REVERT: C 195 TYR cc_start: 0.8068 (m-80) cc_final: 0.7821 (m-80) REVERT: C 498 TYR cc_start: 0.8436 (m-80) cc_final: 0.8100 (m-80) REVERT: C 617 VAL cc_start: 0.7808 (t) cc_final: 0.7538 (p) REVERT: C 632 VAL cc_start: 0.8200 (OUTLIER) cc_final: 0.7893 (p) REVERT: C 1135 TYR cc_start: 0.8780 (t80) cc_final: 0.8554 (t80) outliers start: 18 outliers final: 15 residues processed: 129 average time/residue: 1.2162 time to fit residues: 188.3308 Evaluate side-chains 127 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 2.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 614 CYS Chi-restraints excluded: chain A residue 714 ASN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1089 GLU Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 632 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 298 optimal weight: 6.9990 chunk 148 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 271 optimal weight: 0.0980 chunk 52 optimal weight: 8.9990 chunk 214 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 193 optimal weight: 3.9990 chunk 196 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 238 optimal weight: 5.9990 overall best weight: 2.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 GLN B 113 GLN ** B 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN ** B 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.120798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.064660 restraints weight = 69676.578| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 4.29 r_work: 0.2771 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2892 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2892 r_free = 0.2892 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2892 r_free = 0.2892 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2892 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 27337 Z= 0.241 Angle : 0.730 13.613 37304 Z= 0.366 Chirality : 0.050 0.485 4298 Planarity : 0.005 0.073 4749 Dihedral : 6.654 63.897 4520 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.67 % Favored : 93.30 % Rotamer: Outliers : 0.76 % Allowed : 10.00 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.07 (0.14), residues: 3289 helix: 1.72 (0.21), residues: 639 sheet: 0.35 (0.21), residues: 635 loop : -2.03 (0.13), residues: 2015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.003 TRP C 102 HIS 0.008 0.001 HIS B 242 PHE 0.030 0.002 PHE A 77 TYR 0.025 0.002 TYR B 753 ARG 0.012 0.001 ARG B 631 Details of bonding type rmsd link_NAG-ASN : bond 0.00461 ( 27) link_NAG-ASN : angle 3.57949 ( 81) link_BETA1-4 : bond 0.00353 ( 12) link_BETA1-4 : angle 1.08718 ( 36) hydrogen bonds : bond 0.07942 ( 905) hydrogen bonds : angle 5.20597 ( 2481) SS BOND : bond 0.00454 ( 44) SS BOND : angle 2.03705 ( 88) covalent geometry : bond 0.00592 (27254) covalent geometry : angle 0.70529 (37099) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23261.44 seconds wall clock time: 407 minutes 45.72 seconds (24465.72 seconds total)