Starting phenix.real_space_refine on Fri Mar 6 00:59:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tgw_25887/03_2026/7tgw_25887.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tgw_25887/03_2026/7tgw_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_25887/03_2026/7tgw_25887.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tgw_25887/03_2026/7tgw_25887.map" model { file = "/net/cci-nas-00/data/ceres_data/7tgw_25887/03_2026/7tgw_25887.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tgw_25887/03_2026/7tgw_25887.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.033 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 10.02, per 1000 atoms: 0.38 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: 2.46 Conformation dependent library (CDL) restraints added in 2.5 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: 1.19 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: 6.56 Time building geometry restraints manager: 3.32 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 1306)) selection = (chain 'B' and (resid 14 through 618 or resid 630 through 819 or resid 821 throu \ gh 1015 or resid 1017 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 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: 5.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.530 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 33.320 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.100 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:6.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.940 ------------------------------------------------------------------------------- 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 : 10.36 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.012 0.001 ARG B 153 TYR 0.033 0.002 TYR B 753 PHE 0.026 0.002 PHE B 640 TRP 0.033 0.003 TRP B 883 HIS 0.014 0.002 HIS C 951 Details of bonding type rmsd covalent geometry : bond 0.00725 (27254) covalent geometry : angle 0.85537 (37099) SS BOND : bond 0.00834 ( 44) SS BOND : angle 3.11473 ( 88) hydrogen bonds : bond 0.16240 ( 905) hydrogen bonds : angle 7.09118 ( 2481) link_BETA1-4 : bond 0.00887 ( 12) link_BETA1-4 : angle 2.28527 ( 36) link_NAG-ASN : bond 0.08683 ( 27) link_NAG-ASN : angle 6.97465 ( 81) *********************** 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 : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash 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 230 ILE cc_start: 0.8572 (pt) cc_final: 0.8361 (pp) 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: 1 residues processed: 199 average time/residue: 0.6696 time to fit residues: 153.2072 Evaluate side-chains 100 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 99 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 931 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 144 ASN B 434 ASN B 436 ASN B 503 GLN ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 119 ASN C 141 HIS C 391 ASN ** C 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 951 HIS C 999 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.124353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.069264 restraints weight = 113831.168| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 5.89 r_work: 0.2892 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2921 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2921 r_free = 0.2921 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2921 r_free = 0.2921 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2921 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 27337 Z= 0.163 Angle : 0.817 21.954 37304 Z= 0.396 Chirality : 0.055 1.414 4298 Planarity : 0.005 0.067 4749 Dihedral : 11.101 103.568 4522 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.39 % Favored : 94.58 % Rotamer: Outliers : 0.76 % Allowed : 5.34 % Favored : 93.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.14), residues: 3289 helix: 0.84 (0.21), residues: 653 sheet: 0.03 (0.21), residues: 626 loop : -2.43 (0.12), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 153 TYR 0.022 0.001 TYR B 492 PHE 0.018 0.002 PHE C 77 TRP 0.022 0.003 TRP B 147 HIS 0.016 0.001 HIS B 242 Details of bonding type rmsd covalent geometry : bond 0.00367 (27254) covalent geometry : angle 0.77043 (37099) SS BOND : bond 0.00537 ( 44) SS BOND : angle 2.19495 ( 88) hydrogen bonds : bond 0.07014 ( 905) hydrogen bonds : angle 5.84829 ( 2481) link_BETA1-4 : bond 0.00589 ( 12) link_BETA1-4 : angle 1.43391 ( 36) link_NAG-ASN : bond 0.00475 ( 27) link_NAG-ASN : angle 5.45242 ( 81) *********************** 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 : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 MET cc_start: -0.1814 (mmt) cc_final: -0.2117 (mtp) REVERT: A 991 ASP cc_start: 0.8608 (t70) cc_final: 0.8382 (t0) REVERT: A 999 GLN cc_start: 0.8905 (tp40) cc_final: 0.8694 (mt0) REVERT: B 138 PHE cc_start: 0.4903 (m-10) cc_final: 0.3623 (m-10) REVERT: B 139 LEU cc_start: 0.7968 (mm) cc_final: 0.7716 (pt) REVERT: B 513 GLU cc_start: 0.8612 (tp30) cc_final: 0.7921 (tp30) REVERT: B 516 HIS cc_start: 0.8755 (m90) cc_final: 0.8157 (m90) REVERT: B 616 GLU cc_start: 0.8459 (tt0) cc_final: 0.8239 (tm-30) REVERT: C 116 LEU cc_start: 0.7430 (mp) cc_final: 0.7015 (pt) REVERT: C 195 TYR cc_start: 0.8108 (m-80) cc_final: 0.7763 (m-80) REVERT: C 498 TYR cc_start: 0.8525 (m-80) cc_final: 0.8210 (m-80) REVERT: C 999 GLN cc_start: 0.8925 (tp40) cc_final: 0.8716 (tp-100) outliers start: 21 outliers final: 6 residues processed: 138 average time/residue: 0.5746 time to fit residues: 93.8313 Evaluate side-chains 110 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 104 time to evaluate : 1.033 ------------------------------------------------------------------------------- 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 535 CYS Chi-restraints excluded: chain C residue 931 ILE 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 227 optimal weight: 5.9990 chunk 208 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 234 optimal weight: 6.9990 chunk 173 optimal weight: 2.9990 chunk 249 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 204 optimal weight: 4.9990 chunk 213 optimal weight: 1.9990 chunk 321 optimal weight: 0.0040 overall best weight: 2.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 HIS A 144 ASN A 923 GLN B 14 GLN B 66 HIS B 279 ASN B 436 ASN B 600 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.124788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.069045 restraints weight = 102835.608| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 5.40 r_work: 0.2725 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2725 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2725 r_free = 0.2725 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2725 r_free = 0.2725 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2725 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 27337 Z= 0.193 Angle : 0.759 20.471 37304 Z= 0.374 Chirality : 0.050 0.711 4298 Planarity : 0.005 0.086 4749 Dihedral : 8.870 96.711 4522 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.37 % Favored : 93.60 % Rotamer: Outliers : 0.86 % Allowed : 6.76 % Favored : 92.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.14), residues: 3289 helix: 1.18 (0.22), residues: 653 sheet: 0.16 (0.21), residues: 623 loop : -2.37 (0.12), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 153 TYR 0.023 0.001 TYR B 492 PHE 0.016 0.002 PHE B 494 TRP 0.022 0.002 TRP B 883 HIS 0.005 0.001 HIS B 242 Details of bonding type rmsd covalent geometry : bond 0.00464 (27254) covalent geometry : angle 0.72573 (37099) SS BOND : bond 0.00494 ( 44) SS BOND : angle 2.03480 ( 88) hydrogen bonds : bond 0.07481 ( 905) hydrogen bonds : angle 5.60552 ( 2481) link_BETA1-4 : bond 0.00318 ( 12) link_BETA1-4 : angle 1.14667 ( 36) link_NAG-ASN : bond 0.00478 ( 27) link_NAG-ASN : angle 4.36927 ( 81) *********************** 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 142 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 172 MET cc_start: -0.1556 (mmt) cc_final: -0.1830 (mtt) REVERT: A 991 ASP cc_start: 0.8617 (t70) cc_final: 0.8381 (t0) REVERT: B 172 MET cc_start: 0.4324 (mtt) cc_final: 0.3667 (mtt) REVERT: B 362 TYR cc_start: 0.8976 (m-80) cc_final: 0.8765 (m-80) REVERT: B 492 TYR cc_start: 0.6872 (m-10) cc_final: 0.6672 (m-10) REVERT: B 513 GLU cc_start: 0.8627 (tp30) cc_final: 0.7923 (tp30) REVERT: B 514 LEU cc_start: 0.7936 (mt) cc_final: 0.7734 (mm) REVERT: B 516 HIS cc_start: 0.8785 (m90) cc_final: 0.8222 (m90) REVERT: B 866 MET cc_start: 0.9123 (mtt) cc_final: 0.8823 (mtt) REVERT: C 100 ARG cc_start: 0.7006 (mtt180) cc_final: 0.5641 (mtt180) REVERT: C 116 LEU cc_start: 0.7443 (mp) cc_final: 0.7130 (OUTLIER) REVERT: C 148 MET cc_start: 0.7683 (mpt) cc_final: 0.7481 (mpm) REVERT: C 195 TYR cc_start: 0.8232 (m-80) cc_final: 0.7789 (m-80) REVERT: C 498 TYR cc_start: 0.8533 (m-80) cc_final: 0.8274 (m-80) REVERT: C 632 VAL cc_start: 0.8196 (m) cc_final: 0.7881 (p) REVERT: C 938 THR cc_start: 0.7867 (OUTLIER) cc_final: 0.7585 (t) outliers start: 24 outliers final: 16 residues processed: 138 average time/residue: 0.5353 time to fit residues: 88.6186 Evaluate side-chains 123 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 614 CYS Chi-restraints excluded: chain A residue 626 LEU 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 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 B residue 990 ILE Chi-restraints excluded: chain B residue 1089 GLU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 938 THR Chi-restraints excluded: chain C residue 1089 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 43 optimal weight: 7.9990 chunk 291 optimal weight: 2.9990 chunk 181 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 227 optimal weight: 7.9990 chunk 34 optimal weight: 20.0000 chunk 220 optimal weight: 50.0000 chunk 180 optimal weight: 1.9990 chunk 149 optimal weight: 20.0000 chunk 66 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 999 GLN B 14 GLN B 30 ASN C 242 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.123502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.067493 restraints weight = 101050.606| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 5.17 r_work: 0.2702 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2704 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2704 r_free = 0.2704 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2704 r_free = 0.2704 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2704 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 27337 Z= 0.225 Angle : 0.763 16.553 37304 Z= 0.378 Chirality : 0.051 0.606 4298 Planarity : 0.005 0.076 4749 Dihedral : 8.199 91.313 4522 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.15 % Favored : 93.82 % Rotamer: Outliers : 0.97 % Allowed : 7.31 % Favored : 91.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.14), residues: 3289 helix: 1.27 (0.22), residues: 651 sheet: 0.28 (0.21), residues: 608 loop : -2.33 (0.12), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 631 TYR 0.023 0.001 TYR B 753 PHE 0.037 0.002 PHE A 152 TRP 0.026 0.002 TRP B 883 HIS 0.007 0.001 HIS B 242 Details of bonding type rmsd covalent geometry : bond 0.00551 (27254) covalent geometry : angle 0.73041 (37099) SS BOND : bond 0.00574 ( 44) SS BOND : angle 2.44356 ( 88) hydrogen bonds : bond 0.07796 ( 905) hydrogen bonds : angle 5.54729 ( 2481) link_BETA1-4 : bond 0.00391 ( 12) link_BETA1-4 : angle 1.06439 ( 36) link_NAG-ASN : bond 0.00360 ( 27) link_NAG-ASN : angle 4.12353 ( 81) *********************** 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 135 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 108 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 172 MET cc_start: -0.1428 (mmt) cc_final: -0.1746 (mtt) REVERT: A 985 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8085 (mp0) REVERT: B 172 MET cc_start: 0.4281 (mtt) cc_final: 0.3658 (mtt) REVERT: B 513 GLU cc_start: 0.8653 (tp30) cc_final: 0.8086 (tp30) REVERT: B 516 HIS cc_start: 0.8769 (m90) cc_final: 0.8243 (m90) REVERT: B 866 MET cc_start: 0.9131 (mtt) cc_final: 0.8835 (mtt) REVERT: C 148 MET cc_start: 0.7593 (mpt) cc_final: 0.7384 (mpm) REVERT: C 195 TYR cc_start: 0.8344 (m-80) cc_final: 0.7907 (m-80) REVERT: C 498 TYR cc_start: 0.8544 (m-80) cc_final: 0.8332 (m-80) REVERT: C 938 THR cc_start: 0.8025 (OUTLIER) cc_final: 0.7768 (t) outliers start: 27 outliers final: 20 residues processed: 128 average time/residue: 0.5767 time to fit residues: 87.3634 Evaluate side-chains 120 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.692 ------------------------------------------------------------------------------- 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 626 LEU 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 213 LEU Chi-restraints excluded: chain B residue 397 PHE Chi-restraints excluded: chain B residue 446 TYR 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 B residue 897 MET Chi-restraints excluded: chain B residue 1089 GLU Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 938 THR Chi-restraints excluded: chain C residue 1089 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 234 optimal weight: 10.0000 chunk 267 optimal weight: 10.0000 chunk 122 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 261 optimal weight: 0.9990 chunk 220 optimal weight: 50.0000 chunk 248 optimal weight: 1.9990 chunk 45 optimal weight: 0.0970 chunk 62 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 GLN ** B 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3862 r_free = 0.3862 target = 0.121597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.066742 restraints weight = 89981.600| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 5.40 r_work: 0.2667 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2675 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2675 r_free = 0.2675 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2675 r_free = 0.2675 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2675 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2206 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= 0.138 Angle : 0.675 16.432 37304 Z= 0.332 Chirality : 0.048 0.528 4298 Planarity : 0.005 0.065 4749 Dihedral : 7.406 87.641 4522 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.97 % Favored : 94.00 % Rotamer: Outliers : 0.93 % Allowed : 8.03 % Favored : 91.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.14), residues: 3289 helix: 1.58 (0.22), residues: 651 sheet: 0.28 (0.21), residues: 641 loop : -2.21 (0.12), residues: 1997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 631 TYR 0.031 0.001 TYR B 492 PHE 0.031 0.001 PHE A 152 TRP 0.019 0.002 TRP B 433 HIS 0.006 0.001 HIS B 242 Details of bonding type rmsd covalent geometry : bond 0.00315 (27254) covalent geometry : angle 0.64725 (37099) SS BOND : bond 0.00388 ( 44) SS BOND : angle 1.62588 ( 88) hydrogen bonds : bond 0.06300 ( 905) hydrogen bonds : angle 5.23760 ( 2481) link_BETA1-4 : bond 0.00330 ( 12) link_BETA1-4 : angle 0.94209 ( 36) link_NAG-ASN : bond 0.00461 ( 27) link_NAG-ASN : angle 3.80720 ( 81) *********************** 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 146 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 120 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 770 GLU cc_start: 0.8648 (tt0) cc_final: 0.8330 (tt0) REVERT: A 985 GLU cc_start: 0.8641 (mm-30) cc_final: 0.8067 (mp0) REVERT: B 172 MET cc_start: 0.4290 (mtt) cc_final: 0.3676 (mtt) REVERT: B 380 SER cc_start: 0.8100 (m) cc_final: 0.7866 (t) REVERT: B 492 TYR cc_start: 0.6766 (m-10) cc_final: 0.6319 (m-10) REVERT: B 513 GLU cc_start: 0.8569 (tp30) cc_final: 0.8053 (tp30) REVERT: B 516 HIS cc_start: 0.8751 (m90) cc_final: 0.8169 (m90) REVERT: B 694 MET cc_start: 0.9345 (ptm) cc_final: 0.9092 (ptm) REVERT: B 866 MET cc_start: 0.8908 (mtt) cc_final: 0.8554 (mtt) REVERT: C 116 LEU cc_start: 0.7430 (mp) cc_final: 0.7171 (mm) REVERT: C 148 MET cc_start: 0.7645 (mpt) cc_final: 0.7431 (mpm) REVERT: C 195 TYR cc_start: 0.7968 (m-80) cc_final: 0.7547 (m-80) REVERT: C 498 TYR cc_start: 0.8513 (m-80) cc_final: 0.8190 (m-80) REVERT: C 632 VAL cc_start: 0.8224 (OUTLIER) cc_final: 0.7867 (p) REVERT: C 938 THR cc_start: 0.7867 (OUTLIER) cc_final: 0.7591 (t) outliers start: 26 outliers final: 17 residues processed: 138 average time/residue: 0.5431 time to fit residues: 90.0987 Evaluate side-chains 130 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 1.028 ------------------------------------------------------------------------------- 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 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 213 LEU Chi-restraints excluded: chain B residue 397 PHE Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 777 GLU Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 938 THR Chi-restraints excluded: chain C residue 1089 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 94 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 176 optimal weight: 4.9990 chunk 316 optimal weight: 2.9990 chunk 294 optimal weight: 0.7980 chunk 194 optimal weight: 0.9990 chunk 144 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 159 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 chunk 253 optimal weight: 7.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 ** 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 = 0.3841 r_free = 0.3841 target = 0.120176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.065184 restraints weight = 92156.607| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 5.28 r_work: 0.2638 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2646 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2646 r_free = 0.2646 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2646 r_free = 0.2646 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2646 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 27337 Z= 0.182 Angle : 0.696 15.578 37304 Z= 0.345 Chirality : 0.048 0.522 4298 Planarity : 0.005 0.054 4749 Dihedral : 7.163 83.505 4520 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.97 % Favored : 94.00 % Rotamer: Outliers : 0.79 % Allowed : 8.93 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.14), residues: 3289 helix: 1.63 (0.22), residues: 646 sheet: 0.34 (0.21), residues: 622 loop : -2.21 (0.12), residues: 2021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 631 TYR 0.025 0.001 TYR B 492 PHE 0.029 0.001 PHE A 152 TRP 0.021 0.002 TRP C 883 HIS 0.006 0.001 HIS B 242 Details of bonding type rmsd covalent geometry : bond 0.00444 (27254) covalent geometry : angle 0.66895 (37099) SS BOND : bond 0.00423 ( 44) SS BOND : angle 1.81971 ( 88) hydrogen bonds : bond 0.07021 ( 905) hydrogen bonds : angle 5.22730 ( 2481) link_BETA1-4 : bond 0.00304 ( 12) link_BETA1-4 : angle 0.96068 ( 36) link_NAG-ASN : bond 0.00425 ( 27) link_NAG-ASN : angle 3.74263 ( 81) *********************** 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 133 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 985 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8450 (mm-30) REVERT: B 77 PHE cc_start: 0.8276 (OUTLIER) cc_final: 0.8058 (m-80) REVERT: B 172 MET cc_start: 0.4316 (mtt) cc_final: 0.3716 (mtt) REVERT: B 380 SER cc_start: 0.8148 (m) cc_final: 0.7908 (t) REVERT: B 513 GLU cc_start: 0.8561 (tp30) cc_final: 0.7908 (tp30) REVERT: B 516 HIS cc_start: 0.8740 (m90) cc_final: 0.8102 (m90) REVERT: B 866 MET cc_start: 0.8976 (mtt) cc_final: 0.8627 (mtt) REVERT: C 100 ARG cc_start: 0.7108 (mtt180) cc_final: 0.6893 (mtm180) REVERT: C 116 LEU cc_start: 0.7376 (mp) cc_final: 0.7129 (mp) REVERT: C 195 TYR cc_start: 0.8002 (m-80) cc_final: 0.7612 (m-80) REVERT: C 498 TYR cc_start: 0.8535 (m-80) cc_final: 0.8239 (m-80) REVERT: C 632 VAL cc_start: 0.8304 (OUTLIER) cc_final: 0.7910 (p) REVERT: C 938 THR cc_start: 0.7829 (OUTLIER) cc_final: 0.7592 (t) outliers start: 23 outliers final: 17 residues processed: 128 average time/residue: 0.5532 time to fit residues: 85.3449 Evaluate side-chains 124 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.968 ------------------------------------------------------------------------------- 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 568 ASP Chi-restraints excluded: chain A residue 614 CYS Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 714 ASN Chi-restraints excluded: chain A residue 931 ILE 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 148 MET Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 397 PHE Chi-restraints excluded: chain B residue 512 PHE 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 Chi-restraints excluded: chain C residue 1089 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 69 optimal weight: 1.9990 chunk 216 optimal weight: 0.6980 chunk 17 optimal weight: 6.9990 chunk 288 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 22 optimal weight: 8.9990 chunk 188 optimal weight: 2.9990 chunk 318 optimal weight: 1.9990 chunk 249 optimal weight: 0.4980 chunk 59 optimal weight: 4.9990 chunk 202 optimal weight: 4.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3853 r_free = 0.3853 target = 0.120985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.066369 restraints weight = 85019.139| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 5.15 r_work: 0.2671 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2673 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2673 r_free = 0.2673 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2673 r_free = 0.2673 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2673 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 27337 Z= 0.159 Angle : 0.671 15.045 37304 Z= 0.332 Chirality : 0.048 0.499 4298 Planarity : 0.004 0.047 4749 Dihedral : 6.904 79.523 4520 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.94 % Favored : 94.03 % Rotamer: Outliers : 0.93 % Allowed : 9.10 % Favored : 89.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.14), residues: 3289 helix: 1.71 (0.22), residues: 644 sheet: 0.39 (0.21), residues: 620 loop : -2.15 (0.12), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 631 TYR 0.020 0.001 TYR B 492 PHE 0.034 0.001 PHE A 152 TRP 0.025 0.002 TRP C 102 HIS 0.005 0.001 HIS B 242 Details of bonding type rmsd covalent geometry : bond 0.00380 (27254) covalent geometry : angle 0.64625 (37099) SS BOND : bond 0.00386 ( 44) SS BOND : angle 1.62812 ( 88) hydrogen bonds : bond 0.06521 ( 905) hydrogen bonds : angle 5.12701 ( 2481) link_BETA1-4 : bond 0.00315 ( 12) link_BETA1-4 : angle 0.93231 ( 36) link_NAG-ASN : bond 0.00455 ( 27) link_NAG-ASN : angle 3.60184 ( 81) *********************** 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: 27 poor density : 110 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 985 GLU cc_start: 0.8683 (mm-30) cc_final: 0.8444 (mm-30) REVERT: B 77 PHE cc_start: 0.8296 (OUTLIER) cc_final: 0.8080 (m-80) REVERT: B 139 LEU cc_start: 0.7726 (mm) cc_final: 0.7359 (mm) REVERT: B 172 MET cc_start: 0.4013 (mtt) cc_final: 0.3352 (mtt) REVERT: B 380 SER cc_start: 0.8129 (m) cc_final: 0.7872 (t) REVERT: B 513 GLU cc_start: 0.8529 (tp30) cc_final: 0.7958 (tp30) REVERT: B 516 HIS cc_start: 0.8714 (m90) cc_final: 0.8127 (m90) REVERT: B 866 MET cc_start: 0.8893 (mtt) cc_final: 0.8577 (mtt) REVERT: C 100 ARG cc_start: 0.7261 (mtt180) cc_final: 0.6988 (mtm180) REVERT: C 195 TYR cc_start: 0.7956 (m-80) cc_final: 0.7623 (m-80) REVERT: C 498 TYR cc_start: 0.8560 (m-80) cc_final: 0.8285 (m-80) REVERT: C 632 VAL cc_start: 0.8259 (OUTLIER) cc_final: 0.7885 (p) REVERT: C 1135 TYR cc_start: 0.8803 (t80) cc_final: 0.8486 (t80) outliers start: 27 outliers final: 17 residues processed: 128 average time/residue: 0.5461 time to fit residues: 83.5489 Evaluate side-chains 125 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.957 ------------------------------------------------------------------------------- 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 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 148 MET Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 397 PHE Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 777 GLU 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 1047 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 243 optimal weight: 30.0000 chunk 36 optimal weight: 0.6980 chunk 249 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 125 optimal weight: 6.9990 chunk 311 optimal weight: 3.9990 chunk 158 optimal weight: 6.9990 chunk 43 optimal weight: 50.0000 chunk 179 optimal weight: 1.9990 chunk 303 optimal weight: 0.8980 chunk 255 optimal weight: 7.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 999 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 = 0.3855 r_free = 0.3855 target = 0.121454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.066199 restraints weight = 103287.249| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 5.69 r_work: 0.2644 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2650 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2650 r_free = 0.2650 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2650 r_free = 0.2650 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2650 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 27337 Z= 0.152 Angle : 0.666 14.496 37304 Z= 0.329 Chirality : 0.047 0.488 4298 Planarity : 0.004 0.049 4749 Dihedral : 6.729 75.855 4520 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.79 % Favored : 94.18 % Rotamer: Outliers : 0.93 % Allowed : 9.17 % Favored : 89.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.14), residues: 3289 helix: 1.75 (0.22), residues: 647 sheet: 0.39 (0.21), residues: 621 loop : -2.12 (0.12), residues: 2021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 631 TYR 0.018 0.001 TYR B 492 PHE 0.029 0.001 PHE A 152 TRP 0.028 0.002 TRP C 102 HIS 0.006 0.001 HIS B 242 Details of bonding type rmsd covalent geometry : bond 0.00360 (27254) covalent geometry : angle 0.64209 (37099) SS BOND : bond 0.00375 ( 44) SS BOND : angle 1.60121 ( 88) hydrogen bonds : bond 0.06415 ( 905) hydrogen bonds : angle 5.06091 ( 2481) link_BETA1-4 : bond 0.00314 ( 12) link_BETA1-4 : angle 0.95582 ( 36) link_NAG-ASN : bond 0.00444 ( 27) link_NAG-ASN : angle 3.50674 ( 81) *********************** 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 137 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 PHE cc_start: 0.8044 (m-10) cc_final: 0.7305 (m-10) REVERT: A 985 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8459 (mm-30) REVERT: B 77 PHE cc_start: 0.8353 (OUTLIER) cc_final: 0.8085 (m-80) REVERT: B 139 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7407 (mm) REVERT: B 172 MET cc_start: 0.4090 (mtt) cc_final: 0.3400 (mtt) REVERT: B 513 GLU cc_start: 0.8488 (tp30) cc_final: 0.7724 (tp30) REVERT: B 516 HIS cc_start: 0.8751 (m90) cc_final: 0.8110 (m90) REVERT: B 866 MET cc_start: 0.8898 (mtt) cc_final: 0.8587 (mtt) REVERT: C 195 TYR cc_start: 0.7963 (m-80) cc_final: 0.7601 (m-80) REVERT: C 498 TYR cc_start: 0.8579 (m-80) cc_final: 0.8323 (m-80) REVERT: C 632 VAL cc_start: 0.8322 (OUTLIER) cc_final: 0.7930 (p) REVERT: C 1135 TYR cc_start: 0.8826 (t80) cc_final: 0.8468 (t80) outliers start: 27 outliers final: 20 residues processed: 131 average time/residue: 0.5779 time to fit residues: 90.3037 Evaluate side-chains 131 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 1.035 ------------------------------------------------------------------------------- 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 568 ASP 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 77 PHE 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 397 PHE Chi-restraints excluded: chain B residue 448 TYR Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 777 GLU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 990 ILE Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 1047 MET 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 161 optimal weight: 5.9990 chunk 236 optimal weight: 7.9990 chunk 251 optimal weight: 5.9990 chunk 132 optimal weight: 0.9990 chunk 312 optimal weight: 4.9990 chunk 185 optimal weight: 0.9980 chunk 37 optimal weight: 40.0000 chunk 304 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 43 optimal weight: 8.9990 chunk 5 optimal weight: 9.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3916 r_free = 0.3916 target = 0.123142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.068171 restraints weight = 75307.753| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 4.24 r_work: 0.2783 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2786 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2786 r_free = 0.2786 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2786 r_free = 0.2786 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2786 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 27337 Z= 0.176 Angle : 0.677 14.229 37304 Z= 0.337 Chirality : 0.048 0.484 4298 Planarity : 0.004 0.045 4749 Dihedral : 6.715 72.697 4520 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.06 % Favored : 93.88 % Rotamer: Outliers : 1.00 % Allowed : 9.27 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.14), residues: 3289 helix: 1.74 (0.22), residues: 642 sheet: 0.39 (0.21), residues: 624 loop : -2.09 (0.13), residues: 2023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 631 TYR 0.019 0.001 TYR B1064 PHE 0.033 0.001 PHE C 453 TRP 0.036 0.002 TRP C 102 HIS 0.005 0.001 HIS B 242 Details of bonding type rmsd covalent geometry : bond 0.00427 (27254) covalent geometry : angle 0.65292 (37099) SS BOND : bond 0.00406 ( 44) SS BOND : angle 1.72721 ( 88) hydrogen bonds : bond 0.06867 ( 905) hydrogen bonds : angle 5.09426 ( 2481) link_BETA1-4 : bond 0.00318 ( 12) link_BETA1-4 : angle 0.97429 ( 36) link_NAG-ASN : bond 0.00431 ( 27) link_NAG-ASN : angle 3.52238 ( 81) *********************** 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 136 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 107 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 985 GLU cc_start: 0.8641 (mm-30) cc_final: 0.8431 (mm-30) REVERT: B 77 PHE cc_start: 0.8300 (OUTLIER) cc_final: 0.8070 (m-10) REVERT: B 139 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7383 (mm) REVERT: B 172 MET cc_start: 0.3695 (mtt) cc_final: 0.3083 (mtt) REVERT: B 513 GLU cc_start: 0.8508 (tp30) cc_final: 0.7981 (tp30) REVERT: B 516 HIS cc_start: 0.8663 (m90) cc_final: 0.8155 (m90) REVERT: B 866 MET cc_start: 0.9029 (mtt) cc_final: 0.8732 (mtt) REVERT: C 195 TYR cc_start: 0.8276 (m-80) cc_final: 0.7933 (m-80) REVERT: C 632 VAL cc_start: 0.8165 (OUTLIER) cc_final: 0.7813 (p) outliers start: 29 outliers final: 21 residues processed: 127 average time/residue: 0.5774 time to fit residues: 87.8836 Evaluate side-chains 125 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.947 ------------------------------------------------------------------------------- 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 568 ASP 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 139 LEU Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 397 PHE Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 777 GLU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 990 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 1047 MET Chi-restraints excluded: chain C residue 1089 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 170 optimal weight: 0.7980 chunk 256 optimal weight: 0.0970 chunk 39 optimal weight: 7.9990 chunk 197 optimal weight: 0.7980 chunk 303 optimal weight: 0.9990 chunk 311 optimal weight: 0.9980 chunk 152 optimal weight: 0.6980 chunk 106 optimal weight: 3.9990 chunk 148 optimal weight: 0.9990 chunk 222 optimal weight: 0.6980 chunk 255 optimal weight: 0.0870 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 923 GLN A 999 GLN B 14 GLN B 999 GLN ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 999 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.128412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.075313 restraints weight = 88863.134| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 5.15 r_work: 0.2966 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2990 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 27337 Z= 0.113 Angle : 0.630 13.629 37304 Z= 0.310 Chirality : 0.046 0.458 4298 Planarity : 0.004 0.044 4749 Dihedral : 6.406 68.634 4520 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.03 % Favored : 94.94 % Rotamer: Outliers : 0.59 % Allowed : 9.69 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.15), residues: 3289 helix: 1.99 (0.22), residues: 645 sheet: 0.40 (0.21), residues: 597 loop : -1.97 (0.13), residues: 2047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 631 TYR 0.023 0.001 TYR C1135 PHE 0.030 0.001 PHE C 453 TRP 0.037 0.002 TRP C 102 HIS 0.005 0.001 HIS B 242 Details of bonding type rmsd covalent geometry : bond 0.00241 (27254) covalent geometry : angle 0.60974 (37099) SS BOND : bond 0.00303 ( 44) SS BOND : angle 1.12262 ( 88) hydrogen bonds : bond 0.05000 ( 905) hydrogen bonds : angle 4.86922 ( 2481) link_BETA1-4 : bond 0.00415 ( 12) link_BETA1-4 : angle 0.89619 ( 36) link_NAG-ASN : bond 0.00519 ( 27) link_NAG-ASN : angle 3.25505 ( 81) ********************** 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 141 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 1.043 Fit side-chains revert: symmetry clash REVERT: A 159 ASN cc_start: 0.8141 (t0) cc_final: 0.7865 (t0) REVERT: A 324 VAL cc_start: 0.8552 (t) cc_final: 0.8225 (p) REVERT: A 770 GLU cc_start: 0.8621 (tt0) cc_final: 0.8303 (tt0) REVERT: A 985 GLU cc_start: 0.8741 (mm-30) cc_final: 0.8527 (mm-30) REVERT: B 77 PHE cc_start: 0.8356 (OUTLIER) cc_final: 0.8115 (m-10) REVERT: B 172 MET cc_start: 0.3707 (mtt) cc_final: 0.3043 (mtt) REVERT: B 449 LEU cc_start: 0.7350 (mm) cc_final: 0.6854 (pt) REVERT: B 513 GLU cc_start: 0.8472 (tp30) cc_final: 0.7777 (tp30) REVERT: B 516 HIS cc_start: 0.8698 (m90) cc_final: 0.8062 (m90) REVERT: B 566 ILE cc_start: 0.9151 (pt) cc_final: 0.8878 (mp) REVERT: B 866 MET cc_start: 0.8821 (mtt) cc_final: 0.8536 (mtt) REVERT: C 172 MET cc_start: 0.2184 (ptt) cc_final: 0.1804 (mtt) REVERT: C 498 TYR cc_start: 0.8406 (m-80) cc_final: 0.8125 (m-80) REVERT: C 632 VAL cc_start: 0.8246 (OUTLIER) cc_final: 0.7852 (p) outliers start: 17 outliers final: 13 residues processed: 135 average time/residue: 0.5542 time to fit residues: 89.6110 Evaluate side-chains 128 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.752 ------------------------------------------------------------------------------- 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 714 ASN Chi-restraints excluded: chain A residue 875 LEU 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 148 MET Chi-restraints excluded: chain B residue 213 LEU 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 180 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 212 optimal weight: 0.6980 chunk 302 optimal weight: 0.0980 chunk 124 optimal weight: 0.0370 chunk 41 optimal weight: 9.9990 chunk 267 optimal weight: 1.9990 chunk 328 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 158 optimal weight: 9.9990 chunk 0 optimal weight: 40.0000 overall best weight: 0.5660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 923 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 = 0.4029 r_free = 0.4029 target = 0.128939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.077168 restraints weight = 107725.218| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 5.85 r_work: 0.2803 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2966 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2966 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27337 Z= 0.114 Angle : 0.629 13.252 37304 Z= 0.310 Chirality : 0.046 0.454 4298 Planarity : 0.004 0.041 4749 Dihedral : 6.268 64.890 4520 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.60 % Favored : 94.36 % Rotamer: Outliers : 0.55 % Allowed : 10.27 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.15), residues: 3289 helix: 2.08 (0.22), residues: 647 sheet: 0.35 (0.21), residues: 617 loop : -1.90 (0.13), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 631 TYR 0.018 0.001 TYR C1135 PHE 0.063 0.001 PHE C 77 TRP 0.048 0.002 TRP C 102 HIS 0.006 0.001 HIS B 242 Details of bonding type rmsd covalent geometry : bond 0.00252 (27254) covalent geometry : angle 0.60935 (37099) SS BOND : bond 0.00304 ( 44) SS BOND : angle 1.18555 ( 88) hydrogen bonds : bond 0.04971 ( 905) hydrogen bonds : angle 4.79068 ( 2481) link_BETA1-4 : bond 0.00385 ( 12) link_BETA1-4 : angle 0.91036 ( 36) link_NAG-ASN : bond 0.00472 ( 27) link_NAG-ASN : angle 3.21836 ( 81) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9442.73 seconds wall clock time: 161 minutes 1.39 seconds (9661.39 seconds total)