Starting phenix.real_space_refine on Sun Jul 5 08:42:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tgw_25887/07_2026/7tgw_25887.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tgw_25887/07_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_25887/07_2026/7tgw_25887.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tgw_25887/07_2026/7tgw_25887.map" model { file = "/net/cci-nas-00/data/ceres_data/7tgw_25887/07_2026/7tgw_25887.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tgw_25887/07_2026/7tgw_25887.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7tgw_25887/07_2026/7tgw_25887.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tgw_25887/07_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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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 chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 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 chiralities: 6 Time building chain proxies: 10.77, per 1000 atoms: 0.40 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: 1.86 Conformation dependent library (CDL) restraints added in 1.9 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: 5.99 Time building geometry restraints manager: 2.65 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 - 17.91: 14666 17.91 - 35.82: 1006 35.82 - 53.73: 190 53.73 - 71.64: 56 71.64 - 89.55: 21 Dihedral angle restraints: 15939 sinusoidal: 6276 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 15936 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: 5.760 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: 0.590 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 31.320 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.070 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:6.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 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 : 13.008 89.550 9597 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/Z covalent geometry : bond 0.00725 / 0.32 (27254) covalent geometry : angle 0.85537 / 0.47 (37099) SS BOND : bond 0.00834 / 0.49 ( 44) SS BOND : angle 3.11473 / 2.11 ( 88) hydrogen bonds : bond 0.16240 / 10.81 ( 905) hydrogen bonds : angle 7.09118 / 4.80 ( 2481) link_BETA1-4 : bond 0.00887 / 0.41 ( 12) link_BETA1-4 : angle 2.28527 / 1.40 ( 36) link_NAG-ASN : bond 0.08683 / 4.58 ( 27) link_NAG-ASN : angle 6.97465 / 5.31 ( 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 : 1.016 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: 0.6723 time to fit residues: 154.7530 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 : 1.258 ------------------------------------------------------------------------------- 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... A 119 ASN ** A 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 502 HIS A 503 GLN A1116 ASN B 14 GLN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN ** B 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3925 r_free = 0.3925 target = 0.124361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.068918 restraints weight = 113873.001| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 5.66 r_work: 0.2904 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2933 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.2933 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8939 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 27337 Z= 0.162 Angle : 0.805 21.866 37304 Z= 0.394 Chirality : 0.055 1.297 4298 Planarity : 0.005 0.067 4749 Dihedral : 5.482 34.438 3577 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.36 % Favored : 94.58 % Rotamer: Outliers : 0.76 % Allowed : 5.38 % Favored : 93.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z 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: -1.75 (0.14), residues: 3289 helix: 0.86 (0.21), residues: 652 sheet: 0.03 (0.21), residues: 626 loop : -2.43 (0.12), residues: 2011 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 0.016 0.002 PHE A 77 TRP 0.023 0.002 TRP B 147 HIS 0.016 0.001 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (27254) covalent geometry : angle 0.76061 / 0.38 (37099) SS BOND : bond 0.00498 / 0.31 ( 44) SS BOND : angle 2.18376 / 1.50 ( 88) hydrogen bonds : bond 0.06936 / 4.72 ( 905) hydrogen bonds : angle 5.83263 / 3.93 ( 2481) link_BETA1-4 : bond 0.00569 / 0.30 ( 12) link_BETA1-4 : angle 1.55036 / 0.96 ( 36) link_NAG-ASN : bond 0.00426 / 0.26 ( 27) link_NAG-ASN : angle 5.18665 / 4.06 ( 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 144 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 MET cc_start: -0.1715 (mmt) cc_final: -0.2069 (mtp) REVERT: A 991 ASP cc_start: 0.8592 (t70) cc_final: 0.8363 (t0) REVERT: A 999 GLN cc_start: 0.8887 (tp40) cc_final: 0.8676 (mt0) REVERT: B 138 PHE cc_start: 0.4920 (m-10) cc_final: 0.3673 (m-10) REVERT: B 139 LEU cc_start: 0.7945 (mm) cc_final: 0.7719 (pt) REVERT: B 513 GLU cc_start: 0.8620 (tp30) cc_final: 0.7929 (tp30) REVERT: B 516 HIS cc_start: 0.8750 (m90) cc_final: 0.8152 (m90) REVERT: B 616 GLU cc_start: 0.8441 (tt0) cc_final: 0.8231 (tm-30) REVERT: C 116 LEU cc_start: 0.7433 (mp) cc_final: 0.7021 (pt) REVERT: C 195 TYR cc_start: 0.8131 (m-80) cc_final: 0.7726 (m-80) REVERT: C 498 TYR cc_start: 0.8536 (m-80) cc_final: 0.8240 (m-80) REVERT: C 999 GLN cc_start: 0.8891 (tp40) cc_final: 0.8689 (tp-100) outliers start: 21 outliers final: 6 residues processed: 139 average time/residue: 0.5859 time to fit residues: 97.2631 Evaluate side-chains 108 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 102 time to evaluate : 1.038 ------------------------------------------------------------------------------- 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: 4.9990 chunk 20 optimal weight: 2.9990 chunk 234 optimal weight: 5.9990 chunk 173 optimal weight: 2.9990 chunk 249 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 204 optimal weight: 4.9990 chunk 213 optimal weight: 1.9990 chunk 321 optimal weight: 0.6980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 ASN A 923 GLN B 14 GLN B 66 HIS B 436 ASN B 600 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.125000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.069069 restraints weight = 104963.648| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 5.70 r_work: 0.2711 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2713 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2713 r_free = 0.2713 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2713 r_free = 0.2713 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2713 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9007 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 27337 Z= 0.185 Angle : 0.747 19.598 37304 Z= 0.369 Chirality : 0.051 0.631 4298 Planarity : 0.005 0.085 4749 Dihedral : 5.178 31.317 3577 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.40 % Favored : 93.57 % Rotamer: Outliers : 0.86 % Allowed : 6.79 % Favored : 92.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z 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: -1.54 (0.14), residues: 3289 helix: 1.21 (0.22), residues: 653 sheet: 0.18 (0.21), residues: 618 loop : -2.36 (0.12), residues: 2018 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 0.017 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/Z covalent geometry : bond 0.00442 / 0.18 (27254) covalent geometry : angle 0.71703 / 0.36 (37099) SS BOND : bond 0.00508 / 0.31 ( 44) SS BOND : angle 2.00869 / 1.33 ( 88) hydrogen bonds : bond 0.07327 / 4.95 ( 905) hydrogen bonds : angle 5.58041 / 3.77 ( 2481) link_BETA1-4 : bond 0.00285 / 0.17 ( 12) link_BETA1-4 : angle 1.36249 / 0.85 ( 36) link_NAG-ASN : bond 0.00468 / 0.25 ( 27) link_NAG-ASN : angle 4.02442 / 2.98 ( 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 144 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 172 MET cc_start: -0.1538 (mmt) cc_final: -0.1897 (mtt) REVERT: A 991 ASP cc_start: 0.8618 (t70) cc_final: 0.8385 (t0) REVERT: B 172 MET cc_start: 0.4327 (mtt) cc_final: 0.3673 (mtt) REVERT: B 348 TYR cc_start: 0.4735 (p90) cc_final: 0.4529 (p90) REVERT: B 513 GLU cc_start: 0.8648 (tp30) cc_final: 0.7998 (tp30) REVERT: B 516 HIS cc_start: 0.8776 (m90) cc_final: 0.8263 (m90) REVERT: B 866 MET cc_start: 0.9130 (mtt) cc_final: 0.8835 (mtt) REVERT: C 100 ARG cc_start: 0.7027 (mtt180) cc_final: 0.5650 (mtt180) REVERT: C 116 LEU cc_start: 0.7441 (mp) cc_final: 0.7138 (OUTLIER) REVERT: C 195 TYR cc_start: 0.8258 (m-80) cc_final: 0.7826 (m-80) REVERT: C 498 TYR cc_start: 0.8541 (m-80) cc_final: 0.8295 (m-80) REVERT: C 632 VAL cc_start: 0.8189 (m) cc_final: 0.7866 (p) REVERT: C 938 THR cc_start: 0.7855 (OUTLIER) cc_final: 0.7570 (t) outliers start: 24 outliers final: 16 residues processed: 139 average time/residue: 0.5035 time to fit residues: 84.3509 Evaluate side-chains 124 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.975 ------------------------------------------------------------------------------- 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: 9.9990 chunk 291 optimal weight: 2.9990 chunk 181 optimal weight: 0.2980 chunk 84 optimal weight: 3.9990 chunk 227 optimal weight: 7.9990 chunk 34 optimal weight: 20.0000 chunk 220 optimal weight: 50.0000 chunk 180 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 183 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 999 GLN B 14 GLN B 30 ASN C 30 ASN C 242 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.124169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.070704 restraints weight = 102064.826| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 5.26 r_work: 0.2750 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2756 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2756 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8990 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 27337 Z= 0.162 Angle : 0.725 16.309 37304 Z= 0.354 Chirality : 0.050 0.560 4298 Planarity : 0.005 0.075 4749 Dihedral : 5.015 30.529 3577 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.60 % Favored : 94.36 % Rotamer: Outliers : 0.86 % Allowed : 7.58 % Favored : 91.55 % 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: -1.35 (0.14), residues: 3289 helix: 1.45 (0.22), residues: 652 sheet: 0.26 (0.21), residues: 630 loop : -2.26 (0.12), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 631 TYR 0.028 0.001 TYR B 492 PHE 0.035 0.001 PHE A 152 TRP 0.019 0.002 TRP C 147 HIS 0.007 0.001 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 (27254) covalent geometry : angle 0.69650 / 0.35 (37099) SS BOND : bond 0.00505 / 0.32 ( 44) SS BOND : angle 2.17426 / 1.42 ( 88) hydrogen bonds : bond 0.06731 / 4.57 ( 905) hydrogen bonds : angle 5.39632 / 3.64 ( 2481) link_BETA1-4 : bond 0.00418 / 0.23 ( 12) link_BETA1-4 : angle 1.25970 / 0.79 ( 36) link_NAG-ASN : bond 0.00375 / 0.20 ( 27) link_NAG-ASN : angle 3.78100 / 2.76 ( 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 141 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 172 MET cc_start: -0.1541 (mmt) cc_final: -0.1828 (mtt) REVERT: A 770 GLU cc_start: 0.8733 (tt0) cc_final: 0.8492 (tt0) REVERT: A 985 GLU cc_start: 0.8586 (mm-30) cc_final: 0.7961 (mp0) REVERT: A 991 ASP cc_start: 0.8541 (t70) cc_final: 0.8319 (t0) REVERT: B 172 MET cc_start: 0.4156 (mtt) cc_final: 0.3622 (mtt) REVERT: B 513 GLU cc_start: 0.8659 (tp30) cc_final: 0.8046 (tp30) REVERT: B 516 HIS cc_start: 0.8738 (m90) cc_final: 0.8186 (m90) REVERT: B 866 MET cc_start: 0.9066 (mtt) cc_final: 0.8783 (mtt) REVERT: C 116 LEU cc_start: 0.7443 (mp) cc_final: 0.7121 (OUTLIER) REVERT: C 195 TYR cc_start: 0.8286 (m-80) cc_final: 0.7840 (m-80) REVERT: C 498 TYR cc_start: 0.8507 (m-80) cc_final: 0.8289 (m-80) REVERT: C 632 VAL cc_start: 0.8232 (m) cc_final: 0.7879 (p) REVERT: C 938 THR cc_start: 0.7907 (OUTLIER) cc_final: 0.7662 (t) outliers start: 24 outliers final: 15 residues processed: 134 average time/residue: 0.5868 time to fit residues: 93.8108 Evaluate side-chains 122 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 777 GLU 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: 3.9990 chunk 267 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 261 optimal weight: 1.9990 chunk 220 optimal weight: 50.0000 chunk 248 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 105 optimal weight: 7.9990 chunk 69 optimal weight: 0.6980 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 GLN ** B 419 ASN ** 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 = 0.3918 r_free = 0.3918 target = 0.123588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.067968 restraints weight = 89856.169| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 4.51 r_work: 0.2746 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2752 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2752 r_free = 0.2752 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2752 r_free = 0.2752 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2752 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8999 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 27337 Z= 0.182 Angle : 0.706 16.255 37304 Z= 0.348 Chirality : 0.050 0.527 4298 Planarity : 0.005 0.068 4749 Dihedral : 4.940 30.710 3575 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.34 % Favored : 93.63 % Rotamer: Outliers : 1.00 % Allowed : 8.03 % Favored : 90.97 % 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: -1.31 (0.14), residues: 3289 helix: 1.48 (0.22), residues: 653 sheet: 0.34 (0.21), residues: 617 loop : -2.23 (0.12), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 631 TYR 0.020 0.001 TYR B 492 PHE 0.031 0.001 PHE A 152 TRP 0.020 0.002 TRP B 883 HIS 0.007 0.001 HIS A 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.18 (27254) covalent geometry : angle 0.67997 / 0.34 (37099) SS BOND : bond 0.00408 / 0.24 ( 44) SS BOND : angle 1.86960 / 1.25 ( 88) hydrogen bonds : bond 0.07030 / 4.76 ( 905) hydrogen bonds : angle 5.31866 / 3.58 ( 2481) link_BETA1-4 : bond 0.00381 / 0.21 ( 12) link_BETA1-4 : angle 1.17590 / 0.74 ( 36) link_NAG-ASN : bond 0.00388 / 0.21 ( 27) link_NAG-ASN : angle 3.61673 / 2.63 ( 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 140 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 991 ASP cc_start: 0.8524 (t70) cc_final: 0.8304 (t0) REVERT: B 172 MET cc_start: 0.4120 (mtt) cc_final: 0.3562 (mtt) REVERT: B 513 GLU cc_start: 0.8590 (tp30) cc_final: 0.7950 (tp30) REVERT: B 516 HIS cc_start: 0.8723 (m90) cc_final: 0.8139 (m90) REVERT: B 866 MET cc_start: 0.9069 (mtt) cc_final: 0.8764 (mtt) REVERT: C 116 LEU cc_start: 0.7432 (mp) cc_final: 0.7152 (mm) REVERT: C 195 TYR cc_start: 0.8227 (m-80) cc_final: 0.7813 (m-80) REVERT: C 498 TYR cc_start: 0.8549 (m-80) cc_final: 0.8328 (m-80) REVERT: C 632 VAL cc_start: 0.8269 (m) cc_final: 0.7930 (p) REVERT: C 938 THR cc_start: 0.7929 (OUTLIER) cc_final: 0.7663 (t) outliers start: 28 outliers final: 17 residues processed: 134 average time/residue: 0.5532 time to fit residues: 89.5598 Evaluate side-chains 124 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 1.055 ------------------------------------------------------------------------------- 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 613 ASN 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 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 512 PHE Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 753 TYR Chi-restraints excluded: chain B residue 777 GLU Chi-restraints excluded: chain C residue 522 CYS 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: 0.9990 chunk 176 optimal weight: 4.9990 chunk 316 optimal weight: 0.7980 chunk 294 optimal weight: 0.9980 chunk 194 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 159 optimal weight: 9.9990 chunk 57 optimal weight: 0.9990 chunk 253 optimal weight: 6.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 119 ASN ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.124903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.069655 restraints weight = 93223.008| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 4.56 r_work: 0.2784 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2785 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2785 r_free = 0.2785 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2785 r_free = 0.2785 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2785 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9008 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27337 Z= 0.137 Angle : 0.670 15.573 37304 Z= 0.328 Chirality : 0.048 0.509 4298 Planarity : 0.004 0.058 4749 Dihedral : 4.738 29.456 3575 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.48 % Favored : 94.49 % Rotamer: Outliers : 0.86 % Allowed : 8.69 % Favored : 90.45 % 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: -1.19 (0.14), residues: 3289 helix: 1.66 (0.22), residues: 651 sheet: 0.36 (0.21), residues: 634 loop : -2.17 (0.12), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 631 TYR 0.018 0.001 TYR A1064 PHE 0.028 0.001 PHE A 152 TRP 0.019 0.002 TRP B 255 HIS 0.006 0.001 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (27254) covalent geometry : angle 0.64742 / 0.32 (37099) SS BOND : bond 0.00365 / 0.22 ( 44) SS BOND : angle 1.55183 / 1.04 ( 88) hydrogen bonds : bond 0.06152 / 4.18 ( 905) hydrogen bonds : angle 5.15047 / 3.47 ( 2481) link_BETA1-4 : bond 0.00442 / 0.24 ( 12) link_BETA1-4 : angle 1.09442 / 0.69 ( 36) link_NAG-ASN : bond 0.00430 / 0.23 ( 27) link_NAG-ASN : angle 3.43959 / 2.49 ( 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 143 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 770 GLU cc_start: 0.8622 (tt0) cc_final: 0.8401 (tt0) REVERT: A 985 GLU cc_start: 0.8506 (mm-30) cc_final: 0.7954 (mp0) REVERT: B 172 MET cc_start: 0.3764 (mtt) cc_final: 0.3264 (mtt) REVERT: B 492 TYR cc_start: 0.7110 (m-10) cc_final: 0.5628 (m-10) REVERT: B 513 GLU cc_start: 0.8620 (tp30) cc_final: 0.8000 (tp30) REVERT: B 516 HIS cc_start: 0.8686 (m90) cc_final: 0.8145 (m90) REVERT: B 866 MET cc_start: 0.8997 (mtt) cc_final: 0.8678 (mtt) REVERT: C 116 LEU cc_start: 0.7462 (mp) cc_final: 0.7208 (mm) REVERT: C 195 TYR cc_start: 0.8240 (m-80) cc_final: 0.7851 (m-80) REVERT: C 516 HIS cc_start: 0.7885 (m-70) cc_final: 0.7684 (m-70) REVERT: C 632 VAL cc_start: 0.8225 (OUTLIER) cc_final: 0.7853 (p) REVERT: C 938 THR cc_start: 0.7917 (OUTLIER) cc_final: 0.7716 (t) REVERT: C 1135 TYR cc_start: 0.8779 (t80) cc_final: 0.8566 (t80) outliers start: 24 outliers final: 17 residues processed: 136 average time/residue: 0.5538 time to fit residues: 90.9301 Evaluate side-chains 129 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 614 CYS Chi-restraints excluded: chain A residue 714 ASN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 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 B residue 1089 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 69 optimal weight: 1.9990 chunk 216 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 288 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 188 optimal weight: 1.9990 chunk 318 optimal weight: 1.9990 chunk 249 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 202 optimal weight: 4.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 GLN ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.123601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.068049 restraints weight = 85203.807| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 4.43 r_work: 0.2798 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2788 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2788 r_free = 0.2788 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2788 r_free = 0.2788 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2788 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9007 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27337 Z= 0.148 Angle : 0.671 15.133 37304 Z= 0.329 Chirality : 0.048 0.500 4298 Planarity : 0.004 0.050 4749 Dihedral : 4.692 29.505 3575 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.88 % Favored : 94.09 % Rotamer: Outliers : 1.07 % Allowed : 8.96 % 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: -1.15 (0.14), residues: 3289 helix: 1.68 (0.22), residues: 652 sheet: 0.34 (0.21), residues: 631 loop : -2.13 (0.12), residues: 2006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 631 TYR 0.018 0.001 TYR B1064 PHE 0.057 0.001 PHE B 77 TRP 0.026 0.002 TRP C 102 HIS 0.005 0.001 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (27254) covalent geometry : angle 0.64850 / 0.32 (37099) SS BOND : bond 0.00370 / 0.23 ( 44) SS BOND : angle 1.58345 / 1.07 ( 88) hydrogen bonds : bond 0.06268 / 4.25 ( 905) hydrogen bonds : angle 5.06581 / 3.41 ( 2481) link_BETA1-4 : bond 0.00445 / 0.23 ( 12) link_BETA1-4 : angle 1.04470 / 0.66 ( 36) link_NAG-ASN : bond 0.00419 / 0.22 ( 27) link_NAG-ASN : angle 3.36102 / 2.43 ( 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 143 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 113 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 985 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8024 (mp0) REVERT: B 172 MET cc_start: 0.3687 (mtt) cc_final: 0.3114 (mtt) REVERT: B 513 GLU cc_start: 0.8591 (tp30) cc_final: 0.7966 (tp30) REVERT: B 516 HIS cc_start: 0.8686 (m90) cc_final: 0.8143 (m90) REVERT: B 866 MET cc_start: 0.9013 (mtt) cc_final: 0.8685 (mtt) REVERT: C 100 ARG cc_start: 0.6761 (mtm180) cc_final: 0.5895 (mpp-170) REVERT: C 195 TYR cc_start: 0.8228 (m-80) cc_final: 0.7881 (m-80) REVERT: C 498 TYR cc_start: 0.8424 (m-80) cc_final: 0.8186 (m-80) REVERT: C 632 VAL cc_start: 0.8244 (OUTLIER) cc_final: 0.7897 (p) REVERT: C 1135 TYR cc_start: 0.8771 (t80) cc_final: 0.8562 (t80) outliers start: 30 outliers final: 19 residues processed: 135 average time/residue: 0.5623 time to fit residues: 91.3422 Evaluate side-chains 128 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 614 CYS Chi-restraints excluded: chain A residue 714 ASN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 397 PHE Chi-restraints excluded: chain B residue 494 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 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 568 ASP Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 1089 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 243 optimal weight: 40.0000 chunk 36 optimal weight: 1.9990 chunk 249 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 125 optimal weight: 6.9990 chunk 311 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 43 optimal weight: 50.0000 chunk 179 optimal weight: 1.9990 chunk 303 optimal weight: 4.9990 chunk 255 optimal weight: 8.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3899 r_free = 0.3899 target = 0.122343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.067381 restraints weight = 104218.648| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 5.15 r_work: 0.2696 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2700 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2700 r_free = 0.2700 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2700 r_free = 0.2700 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2700 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9028 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 27337 Z= 0.221 Angle : 0.723 14.843 37304 Z= 0.361 Chirality : 0.050 0.502 4298 Planarity : 0.005 0.049 4749 Dihedral : 4.881 30.612 3575 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.21 % Favored : 93.76 % Rotamer: Outliers : 0.93 % Allowed : 9.34 % Favored : 89.73 % 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: -1.25 (0.14), residues: 3289 helix: 1.55 (0.22), residues: 649 sheet: 0.33 (0.21), residues: 636 loop : -2.19 (0.12), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 631 TYR 0.023 0.001 TYR B 753 PHE 0.035 0.002 PHE B 77 TRP 0.031 0.002 TRP C 102 HIS 0.007 0.001 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.22 (27254) covalent geometry : angle 0.69988 / 0.35 (37099) SS BOND : bond 0.00463 / 0.28 ( 44) SS BOND : angle 1.95954 / 1.30 ( 88) hydrogen bonds : bond 0.07663 / 5.16 ( 905) hydrogen bonds : angle 5.25047 / 3.54 ( 2481) link_BETA1-4 : bond 0.00456 / 0.23 ( 12) link_BETA1-4 : angle 1.08013 / 0.69 ( 36) link_NAG-ASN : bond 0.00396 / 0.21 ( 27) link_NAG-ASN : angle 3.45094 / 2.48 ( 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 130 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 103 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 172 MET cc_start: 0.4078 (mtt) cc_final: 0.3389 (mtt) REVERT: B 446 TYR cc_start: 0.5424 (OUTLIER) cc_final: 0.4895 (m-80) REVERT: B 492 TYR cc_start: 0.7415 (m-10) cc_final: 0.6699 (m-10) REVERT: B 513 GLU cc_start: 0.8602 (tp30) cc_final: 0.7946 (tp30) REVERT: B 516 HIS cc_start: 0.8733 (m90) cc_final: 0.8162 (m90) REVERT: B 866 MET cc_start: 0.9125 (mtt) cc_final: 0.8842 (mtt) REVERT: C 195 TYR cc_start: 0.8221 (m-80) cc_final: 0.7840 (m-80) REVERT: C 498 TYR cc_start: 0.8497 (m-80) cc_final: 0.8276 (m-80) REVERT: C 632 VAL cc_start: 0.8338 (OUTLIER) cc_final: 0.7937 (p) outliers start: 27 outliers final: 21 residues processed: 123 average time/residue: 0.5948 time to fit residues: 87.5251 Evaluate side-chains 124 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 1.045 ------------------------------------------------------------------------------- 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 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 446 TYR Chi-restraints excluded: chain B residue 494 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 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 1089 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 161 optimal weight: 10.0000 chunk 236 optimal weight: 6.9990 chunk 251 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 312 optimal weight: 1.9990 chunk 185 optimal weight: 2.9990 chunk 37 optimal weight: 40.0000 chunk 304 optimal weight: 0.6980 chunk 70 optimal weight: 0.5980 chunk 43 optimal weight: 8.9990 chunk 5 optimal weight: 9.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 GLN ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.122963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.068035 restraints weight = 74982.502| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 4.12 r_work: 0.2763 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2779 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2779 r_free = 0.2779 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2779 r_free = 0.2779 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2779 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9016 moved from start: 0.2549 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= 0.184 Angle : 0.694 14.445 37304 Z= 0.344 Chirality : 0.049 0.483 4298 Planarity : 0.004 0.046 4749 Dihedral : 4.818 30.159 3575 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.03 % Favored : 93.91 % Rotamer: Outliers : 0.76 % Allowed : 9.58 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.18 (0.14), residues: 3289 helix: 1.65 (0.22), residues: 648 sheet: 0.28 (0.21), residues: 633 loop : -2.12 (0.13), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 631 TYR 0.019 0.001 TYR B1064 PHE 0.027 0.001 PHE A 152 TRP 0.035 0.002 TRP C 102 HIS 0.007 0.001 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.18 (27254) covalent geometry : angle 0.67228 / 0.34 (37099) SS BOND : bond 0.00416 / 0.25 ( 44) SS BOND : angle 1.75143 / 1.17 ( 88) hydrogen bonds : bond 0.06983 / 4.72 ( 905) hydrogen bonds : angle 5.16019 / 3.47 ( 2481) link_BETA1-4 : bond 0.00445 / 0.23 ( 12) link_BETA1-4 : angle 1.03954 / 0.66 ( 36) link_NAG-ASN : bond 0.00396 / 0.21 ( 27) link_NAG-ASN : angle 3.33812 / 2.39 ( 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 127 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 PHE cc_start: 0.8221 (m-10) cc_final: 0.7842 (m-10) REVERT: A 985 GLU cc_start: 0.8470 (mm-30) cc_final: 0.7927 (mp0) REVERT: B 172 MET cc_start: 0.3711 (mtt) cc_final: 0.3089 (mtt) REVERT: B 513 GLU cc_start: 0.8549 (tp30) cc_final: 0.8014 (tp30) REVERT: B 516 HIS cc_start: 0.8696 (m90) cc_final: 0.8160 (m90) REVERT: B 866 MET cc_start: 0.9026 (mtt) cc_final: 0.8719 (mtt) REVERT: C 195 TYR cc_start: 0.8226 (m-80) cc_final: 0.7874 (m-80) REVERT: C 498 TYR cc_start: 0.8510 (m-80) cc_final: 0.8289 (m-80) REVERT: C 632 VAL cc_start: 0.8292 (OUTLIER) cc_final: 0.7926 (p) outliers start: 22 outliers final: 21 residues processed: 122 average time/residue: 0.5856 time to fit residues: 85.8526 Evaluate side-chains 125 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 1.057 ------------------------------------------------------------------------------- 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 875 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 397 PHE Chi-restraints excluded: chain B residue 494 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 170 optimal weight: 0.0570 chunk 256 optimal weight: 2.9990 chunk 39 optimal weight: 20.0000 chunk 197 optimal weight: 0.9990 chunk 303 optimal weight: 0.6980 chunk 311 optimal weight: 0.8980 chunk 152 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 148 optimal weight: 10.0000 chunk 222 optimal weight: 3.9990 chunk 255 optimal weight: 0.9990 overall best weight: 0.7302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 999 GLN B 66 HIS B 242 HIS 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 = 0.4017 r_free = 0.4017 target = 0.127717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.074118 restraints weight = 87775.602| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 5.13 r_work: 0.2940 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2969 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2969 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27337 Z= 0.120 Angle : 0.650 13.751 37304 Z= 0.318 Chirality : 0.047 0.452 4298 Planarity : 0.004 0.044 4749 Dihedral : 4.555 28.372 3575 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.27 % Favored : 94.70 % Rotamer: Outliers : 0.55 % Allowed : 9.79 % Favored : 89.66 % 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: -0.98 (0.15), residues: 3289 helix: 1.91 (0.22), residues: 647 sheet: 0.36 (0.21), residues: 635 loop : -2.01 (0.13), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 631 TYR 0.017 0.001 TYR A1064 PHE 0.066 0.001 PHE B 77 TRP 0.034 0.002 TRP C 102 HIS 0.007 0.001 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (27254) covalent geometry : angle 0.63238 / 0.31 (37099) SS BOND : bond 0.00327 / 0.20 ( 44) SS BOND : angle 1.24172 / 0.84 ( 88) hydrogen bonds : bond 0.05372 / 3.66 ( 905) hydrogen bonds : angle 4.92316 / 3.31 ( 2481) link_BETA1-4 : bond 0.00487 / 0.26 ( 12) link_BETA1-4 : angle 0.95310 / 0.62 ( 36) link_NAG-ASN : bond 0.00487 / 0.26 ( 27) link_NAG-ASN : angle 3.09562 / 2.22 ( 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 131 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 770 GLU cc_start: 0.8640 (tt0) cc_final: 0.8321 (tt0) REVERT: A 985 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8044 (mp0) REVERT: B 172 MET cc_start: 0.3703 (mtt) cc_final: 0.3018 (mtt) REVERT: B 513 GLU cc_start: 0.8510 (tp30) cc_final: 0.7949 (tp30) REVERT: B 516 HIS cc_start: 0.8722 (m90) cc_final: 0.8148 (m90) REVERT: B 866 MET cc_start: 0.8860 (mtt) cc_final: 0.8550 (mtt) REVERT: C 172 MET cc_start: 0.2479 (ptt) cc_final: 0.2105 (mtt) REVERT: C 195 TYR cc_start: 0.8079 (m-80) cc_final: 0.7821 (m-80) REVERT: C 498 TYR cc_start: 0.8509 (m-80) cc_final: 0.8223 (m-80) REVERT: C 632 VAL cc_start: 0.8331 (OUTLIER) cc_final: 0.7936 (p) REVERT: C 1135 TYR cc_start: 0.8791 (t80) cc_final: 0.8530 (t80) outliers start: 16 outliers final: 14 residues processed: 127 average time/residue: 0.5717 time to fit residues: 87.6961 Evaluate side-chains 124 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 1.066 ------------------------------------------------------------------------------- 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 875 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 180 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 212 optimal weight: 0.7980 chunk 302 optimal weight: 2.9990 chunk 124 optimal weight: 20.0000 chunk 41 optimal weight: 8.9990 chunk 267 optimal weight: 0.3980 chunk 328 optimal weight: 0.0370 chunk 103 optimal weight: 0.9980 chunk 158 optimal weight: 7.9990 chunk 0 optimal weight: 40.0000 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 119 ASN ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 GLN B 242 HIS ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.129205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.077769 restraints weight = 104842.036| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 5.16 r_work: 0.2810 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2881 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2881 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27337 Z= 0.116 Angle : 0.638 13.363 37304 Z= 0.312 Chirality : 0.047 0.447 4298 Planarity : 0.004 0.040 4749 Dihedral : 4.420 27.807 3575 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.57 % Favored : 94.40 % Rotamer: Outliers : 0.52 % Allowed : 10.17 % Favored : 89.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.89 (0.15), residues: 3289 helix: 2.11 (0.22), residues: 640 sheet: 0.32 (0.21), residues: 617 loop : -1.93 (0.13), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 76 TYR 0.017 0.001 TYR A1064 PHE 0.066 0.001 PHE C 77 TRP 0.047 0.002 TRP C 102 HIS 0.006 0.001 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (27254) covalent geometry : angle 0.62024 / 0.31 (37099) SS BOND : bond 0.00318 / 0.20 ( 44) SS BOND : angle 1.23052 / 0.83 ( 88) hydrogen bonds : bond 0.05109 / 3.47 ( 905) hydrogen bonds : angle 4.82105 / 3.25 ( 2481) link_BETA1-4 : bond 0.00484 / 0.26 ( 12) link_BETA1-4 : angle 0.92051 / 0.61 ( 36) link_NAG-ASN : bond 0.00472 / 0.26 ( 27) link_NAG-ASN : angle 3.02457 / 2.16 ( 81) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9333.20 seconds wall clock time: 170 minutes 33.56 seconds (10233.56 seconds total)