Read libraries from system resource. Wattos started at: January 19, 2007 10:17:20 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/pdb1l1w.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 941 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 1200 Found number of new bond candidates: 1015 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: 52 WARNING: Got more than two hydrogen bond for this donor (N6). Hydrogen bonds (3) read: WARNING: Atom Res#(Nam) Mol# Atom Res#(Nam) Mol# Model# Entry# Value_1 Value_2 RefValue RefSD Type Minimum Average Maximum Under cutoff N6 26(A ) 1 O6 2(G ) 1 1 1 108.926 5 N6 26(A ) 1 N3 3(U ) 1 1 1 138.696 5 N6 26(A ) 1 O4 3(U ) 1 1 1 149.306 5 Found number of new hydrogen bonds: 52 Atom Res#(Nam) Mol# Atom Res#(Nam) Mol# Model# Entry# Value_1 Value_2 RefValue RefSD Type Minimum Average Maximum Under cutoff O2* 1(G ) 1 O5* 2(G ) 1 1 1 2.817 142.809 5 N1 1(G ) 1 O2 28(C ) 1 1 1 3.173 141.833 5 N1 1(G ) 1 N3 28(C ) 1 1 1 2.930 155.564 5 N2 1(G ) 1 O2 28(C ) 1 1 1 2.920 157.666 5 N1 2(G ) 1 O2 27(C ) 1 1 1 3.196 142.097 5 N1 2(G ) 1 N3 27(C ) 1 1 1 2.949 155.706 5 N2 2(G ) 1 O2 27(C ) 1 1 1 2.950 157.606 5 N3 3(U ) 1 N6 26(A ) 1 1 1 3.319 129.315 5 N3 3(U ) 1 N1 26(A ) 1 1 1 2.935 160.878 5 N1 4(G ) 1 O2 25(C ) 1 1 1 3.109 142.398 5 N1 4(G ) 1 N3 25(C ) 1 1 1 2.904 153.473 5 N2 4(G ) 1 O2 25(C ) 1 1 1 2.905 154.528 5 N6 5(A ) 1 N3 24(C ) 1 1 1 3.045 159.793 5 N4 7(C ) 1 O6 22(G ) 1 1 1 2.952 159.831 5 N3 8(U ) 1 O6 21(G ) 1 1 1 2.990 164.849 5 N3 8(U ) 1 N1 21(G ) 1 1 1 3.309 136.280 5 N4 9(C ) 1 O4 8(U ) 1 1 1 2.995 101.183 5 N4 9(C ) 1 O6 20(G ) 1 1 1 2.940 165.727 5 N4 10(C ) 1 O6 19(G ) 1 1 1 2.945 165.128 5 N4 11(C ) 1 O6 12(G ) 1 1 1 3.019 102.524 5 N4 11(C ) 1 O6 18(G ) 1 1 1 2.973 159.003 5 N1 12(G ) 1 O6 16(G ) 1 1 1 2.926 94.122 5 N1 12(G ) 1 N3 17(C ) 1 1 1 3.011 174.639 5 N2 12(G ) 1 O2 17(C ) 1 1 1 3.011 170.674 5 N2 13(G ) 1 N7 16(G ) 1 1 1 2.866 148.750 5 O2* 14(G ) 1 O5* 15(A ) 1 1 1 2.680 132.304 5 O2* 14(G ) 1 O4* 15(A ) 1 1 1 2.873 124.797 5 O2* 15(A ) 1 O2P 16(G ) 1 1 1 2.674 136.636 5 N6 15(A ) 1 O2* 13(G ) 1 1 1 3.008 113.597 5 O2* 17(C ) 1 O4* 18(G ) 1 1 1 2.925 123.289 5 N4 17(C ) 1 O6 12(G ) 1 1 1 2.884 147.450 5 N1 18(G ) 1 O2 11(C ) 1 1 1 3.169 137.888 5 N1 18(G ) 1 N3 11(C ) 1 1 1 2.948 157.818 5 N2 18(G ) 1 O2 11(C ) 1 1 1 2.888 152.113 5 N1 19(G ) 1 N3 10(C ) 1 1 1 2.984 166.205 5 N2 19(G ) 1 O2 10(C ) 1 1 1 2.948 168.479 5 N1 20(G ) 1 N3 9(C ) 1 1 1 2.974 167.877 5 N2 20(G ) 1 O2 9(C ) 1 1 1 2.943 169.736 5 N1 21(G ) 1 O2 8(U ) 1 1 1 2.904 158.123 5 N1 21(G ) 1 N3 8(U ) 1 1 1 3.309 140.900 5 N2 21(G ) 1 O2 8(U ) 1 1 1 3.128 144.169 5 N1 22(G ) 1 N3 7(C ) 1 1 1 2.957 162.570 5 N2 22(G ) 1 O2 7(C ) 1 1 1 2.955 164.649 5 N6 23(A ) 1 N3 6(C ) 1 1 1 2.939 170.592 5 O2* 24(C ) 1 O4* 25(C ) 1 1 1 3.072 104.601 5 N4 25(C ) 1 O6 4(G ) 1 1 1 2.955 155.497 5 N6 26(A ) 1 O6 2(G ) 1 1 1 3.082 108.926 5 N6 26(A ) 1 N3 3(U ) 1 1 1 3.319 138.696 5 N6 26(A ) 1 O4 3(U ) 1 1 1 2.899 149.306 5 N4 27(C ) 1 O6 2(G ) 1 1 1 2.962 155.574 5 O2* 28(C ) 1 O5* 29(A ) 1 1 1 2.920 139.050 5 N4 28(C ) 1 O6 1(G ) 1 1 1 2.944 153.830 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, 1l1w_wc.csv] Trying to match bases to eachother for number of bases: 29 Considering number of hydrogen bonds: 52 Results contains number of sets of co-planar bases: 9 Results: Residue: 1( G) Mol: 1 Model: 1 Entry: 1 Residue: 28( C) Mol: 1 Model: 1 Entry: 1 Residue: 2( G) Mol: 1 Model: 1 Entry: 1 Residue: 27( C) Mol: 1 Model: 1 Entry: 1 Residue: 3( U) Mol: 1 Model: 1 Entry: 1 Residue: 26( A) Mol: 1 Model: 1 Entry: 1 Residue: 4( G) Mol: 1 Model: 1 Entry: 1 Residue: 25( C) Mol: 1 Model: 1 Entry: 1 Residue: 7( C) Mol: 1 Model: 1 Entry: 1 Residue: 22( G) Mol: 1 Model: 1 Entry: 1 Residue: 9( C) Mol: 1 Model: 1 Entry: 1 Residue: 20( G) Mol: 1 Model: 1 Entry: 1 Residue: 10( C) Mol: 1 Model: 1 Entry: 1 Residue: 19( G) Mol: 1 Model: 1 Entry: 1 Residue: 11( C) Mol: 1 Model: 1 Entry: 1 Residue: 18( G) Mol: 1 Model: 1 Entry: 1 Residue: 12( G) Mol: 1 Model: 1 Entry: 1 Residue: 17( C) Mol: 1 Model: 1 Entry: 1 Writing results to file: 1l1w_wc.csv Wattos started at: January 19, 2007 10:17:20 AM CST Wattos stopped at: January 19, 2007 10:17:23 AM CST Wattos took (#ms): 2629