Read libraries from system resource. Wattos started at: January 19, 2007 10:19:51 AM CST Program arguments [1] :[-at] SubMenus:----------------------------------------------------- File Edit View Options Prop - Attr Calc Help - Commands:----------------------------------------------------- - Read libraries from system resource. SubMenus:----------------------------------------------------- File Edit View Options Prop - Attr Calc Help - Commands:----------------------------------------------------- - SubMenus:----------------------------------------------------- File Edit View Options Prop - Attr Calc Help - Commands:----------------------------------------------------- - Enter property name: Enter property value (watch value type) for interactiveSession: Enter property name: Enter property value (watch value type) for verbosity: Enter property name: Enter property value (watch value type) for writeSessionOnExit: Enter property name: Enter property value (watch value type) for stopOnError: Enter url to (gzipped) PDB formatted coordinate file: Doing ReadEntryPDB with arguments: [file:/dumpzone/pdb/nozip/data/structures/all/pdb/pdb1tjz.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 14280 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 917 Found number of new bond candidates: 770 Hydrogen bond distance between proton and acceptor cutoff (2.7 Angstroms suggested) Hydrogen bond distance between donor and acceptor cutoff (3.35 Angstroms suggested) Hydrogen bond angle (D-H-A) cutoff (90 degrees suggested) Doing CalcHydrogenBond with arguments: [2.7, 3.35, 90.0] Found number of new hydrogen bond candidates: 29 Found number of new hydrogen bonds: 29 Atom Res#(Nam) Mol# Atom Res#(Nam) Mol# Model# Entry# Value_1 Value_2 RefValue RefSD Type Minimum Average Maximum Under cutoff N1 1(G ) 1 N3 22(C ) 1 1 1 2.945 164.957 5 N2 1(G ) 1 O2 22(C ) 1 1 1 2.865 154.943 5 N1 2(G ) 1 N3 21(C ) 1 1 1 2.948 165.610 5 N2 2(G ) 1 O2 21(C ) 1 1 1 2.870 155.632 5 N3 3(U ) 1 O6 20(G ) 1 1 1 3.032 168.030 5 N2 4(G ) 1 N7 19(A ) 1 1 1 2.827 142.067 5 N6 5(A ) 1 N3 18(C ) 1 1 1 2.745 148.283 5 N4 6(C ) 1 O6 17(G ) 1 1 1 2.921 179.288 5 N1 7(G ) 1 N3 16(C ) 1 1 1 2.867 163.622 5 N2 7(G ) 1 O2 16(C ) 1 1 1 2.951 170.057 5 N4 8(C ) 1 O6 15(G ) 1 1 1 2.888 160.749 5 N4 9(C ) 1 O6 14(G ) 1 1 1 2.906 165.005 5 N1 10(G ) 1 O1P 13(A ) 1 1 1 3.073 126.705 5 N2 10(G ) 1 O1P 13(A ) 1 1 1 2.884 124.316 5 N2 10(G ) 1 N7 13(A ) 1 1 1 2.595 129.696 5 N6 13(A ) 1 O2* 10(G ) 1 1 1 2.339 95.740 5 N6 13(A ) 1 N3 10(G ) 1 1 1 3.212 169.261 5 N1 14(G ) 1 N3 9(C ) 1 1 1 2.954 164.244 5 N2 14(G ) 1 O2 9(C ) 1 1 1 2.904 170.835 5 N1 15(G ) 1 N3 8(C ) 1 1 1 2.947 164.984 5 N2 15(G ) 1 O2 8(C ) 1 1 1 2.879 155.138 5 N2 15(G ) 1 N3 8(C ) 1 1 1 3.267 142.907 5 N4 16(C ) 1 O6 7(G ) 1 1 1 2.870 150.425 5 N1 17(G ) 1 N3 6(C ) 1 1 1 2.977 178.304 5 N2 17(G ) 1 O2 6(C ) 1 1 1 2.920 173.260 5 N6 19(A ) 1 N3 4(G ) 1 1 1 2.755 133.651 5 N1 20(G ) 1 O2 3(U ) 1 1 1 2.891 172.897 5 N4 21(C ) 1 O6 2(G ) 1 1 1 2.900 162.321 5 N4 22(C ) 1 O6 1(G ) 1 1 1 2.900 161.807 5 Angle cutoff (40.0 degrees suggested) Use only Watson Crick basepairing (false suggested) (y/n): Enter cvs file name (with path) for output of CalcCoPlanarBasesSet.: Doing CalcCoPlanarBasesSet with arguments: [45.0, true, 1tjz_wc.csv] Trying to match bases to eachother for number of bases: 22 Considering number of hydrogen bonds: 29 Results contains number of sets of co-planar bases: 6 Results: Residue: 1( G) Mol: 1 Model: 1 Entry: 1 Residue: 22( C) Mol: 1 Model: 1 Entry: 1 Residue: 2( G) Mol: 1 Model: 1 Entry: 1 Residue: 21( C) Mol: 1 Model: 1 Entry: 1 Residue: 6( C) Mol: 1 Model: 1 Entry: 1 Residue: 17( G) Mol: 1 Model: 1 Entry: 1 Residue: 7( G) Mol: 1 Model: 1 Entry: 1 Residue: 16( C) Mol: 1 Model: 1 Entry: 1 Residue: 8( C) Mol: 1 Model: 1 Entry: 1 Residue: 15( G) Mol: 1 Model: 1 Entry: 1 Residue: 9( C) Mol: 1 Model: 1 Entry: 1 Residue: 14( G) Mol: 1 Model: 1 Entry: 1 Writing results to file: 1tjz_wc.csv Wattos started at: January 19, 2007 10:19:51 AM CST Wattos stopped at: January 19, 2007 10:19:56 AM CST Wattos took (#ms): 5189