Read libraries from system resource. Wattos started at: January 19, 2007 10:21:02 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/pdb28sr.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 913 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 1144 Found number of new bond candidates: 986 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: 59 WARNING: Got more than two hydrogen bond for this donor (N2). 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 N2 21(G ) 1 O2* 6(C ) 1 1 1 110.572 5 N2 21(G ) 1 O2P 7(A ) 1 1 1 151.640 5 N2 21(G ) 1 N7 7(A ) 1 1 1 124.117 5 Found number of new hydrogen bonds: 59 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 28(C ) 1 1 1 2.849 167.837 5 N2 1(G ) 1 O2 28(C ) 1 1 1 2.747 174.774 5 O2* 2(G ) 1 O5* 3(C ) 1 1 1 2.664 158.476 5 O2* 2(G ) 1 O4* 3(C ) 1 1 1 3.101 109.358 5 N1 2(G ) 1 O2 27(C ) 1 1 1 3.254 135.048 5 N1 2(G ) 1 N3 27(C ) 1 1 1 2.858 163.073 5 N2 2(G ) 1 O2 27(C ) 1 1 1 2.752 166.440 5 N4 3(C ) 1 O6 2(G ) 1 1 1 2.829 124.165 5 N4 3(C ) 1 O6 26(G ) 1 1 1 2.761 169.712 5 N1 4(G ) 1 N3 25(C ) 1 1 1 2.872 167.124 5 N2 4(G ) 1 O2 25(C ) 1 1 1 2.752 176.543 5 O2* 5(U ) 1 O1P 6(C ) 1 1 1 2.383 172.495 5 N3 5(U ) 1 O6 24(G ) 1 1 1 2.813 166.058 5 O2* 6(C ) 1 N2 21(G ) 1 1 1 3.033 103.927 5 O2* 6(C ) 1 N7 23(A ) 1 1 1 3.011 117.396 5 N4 6(C ) 1 N7 21(G ) 1 1 1 2.881 160.048 5 N1 8(G ) 1 O1P 22(C ) 1 1 1 2.759 147.127 5 O2* 9(G ) 1 O5* 10(U ) 1 1 1 2.612 160.692 5 O2* 9(G ) 1 O4* 10(U ) 1 1 1 2.928 99.497 5 N1 9(G ) 1 N1 20(A ) 1 1 1 2.837 167.448 5 N2 9(G ) 1 O2* 21(G ) 1 1 1 2.983 159.095 5 N3 10(U ) 1 N1 19(A ) 1 1 1 2.945 166.873 5 N4 11(C ) 1 O6 18(G ) 1 1 1 2.807 173.960 5 N4 12(C ) 1 O6 13(G ) 1 1 1 3.079 110.788 5 N4 12(C ) 1 O6 17(G ) 1 1 1 2.783 173.215 5 O2* 13(G ) 1 N7 15(A ) 1 1 1 2.631 177.609 5 N2 13(G ) 1 N7 16(A ) 1 1 1 2.795 158.742 5 O2* 15(A ) 1 O5* 16(A ) 1 1 1 2.683 165.216 5 O2* 15(A ) 1 O4* 16(A ) 1 1 1 2.816 102.458 5 N6 15(A ) 1 O2* 13(G ) 1 1 1 3.133 151.313 5 N6 15(A ) 1 N7 14(G ) 1 1 1 2.984 100.921 5 N1 17(G ) 1 O2 12(C ) 1 1 1 3.336 132.316 5 N1 17(G ) 1 N3 12(C ) 1 1 1 2.846 169.373 5 N2 17(G ) 1 O2 12(C ) 1 1 1 2.758 170.377 5 N1 18(G ) 1 N3 11(C ) 1 1 1 2.833 174.452 5 N2 18(G ) 1 O2 11(C ) 1 1 1 2.754 174.624 5 O2* 19(A ) 1 O4* 20(A ) 1 1 1 2.980 110.772 5 N6 19(A ) 1 O4 10(U ) 1 1 1 2.729 168.889 5 O2* 20(A ) 1 O5* 21(G ) 1 1 1 3.107 135.983 5 N6 20(A ) 1 O6 9(G ) 1 1 1 2.797 170.229 5 O2* 21(G ) 1 O6 8(G ) 1 1 1 2.879 94.805 5 O2* 21(G ) 1 O1P 22(C ) 1 1 1 2.458 172.761 5 N1 21(G ) 1 O2P 7(A ) 1 1 1 2.683 159.365 5 N2 21(G ) 1 O2* 6(C ) 1 1 1 3.033 110.572 5 N2 21(G ) 1 O2P 7(A ) 1 1 1 2.700 151.640 5 N2 21(G ) 1 N7 7(A ) 1 1 1 3.232 124.117 5 O2* 22(C ) 1 N7 24(G ) 1 1 1 2.965 123.165 5 N4 22(C ) 1 O2P 21(G ) 1 1 1 2.758 166.119 5 N6 23(A ) 1 O2* 6(C ) 1 1 1 2.662 158.630 5 N1 24(G ) 1 O2 5(U ) 1 1 1 2.659 168.565 5 O2* 25(C ) 1 O5* 26(G ) 1 1 1 3.267 134.417 5 O2* 25(C ) 1 O4* 26(G ) 1 1 1 3.059 141.464 5 N4 25(C ) 1 O6 4(G ) 1 1 1 2.795 179.786 5 N1 26(G ) 1 N3 3(C ) 1 1 1 2.835 167.955 5 N2 26(G ) 1 O2 3(C ) 1 1 1 2.797 176.747 5 N4 27(C ) 1 O6 2(G ) 1 1 1 2.791 159.889 5 N4 27(C ) 1 O6 26(G ) 1 1 1 2.985 98.706 5 N4 28(C ) 1 O6 1(G ) 1 1 1 2.819 175.261 5 N4 28(C ) 1 N4 27(C ) 1 1 1 2.900 145.869 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, 28sr_wc.csv] Trying to match bases to eachother for number of bases: 28 Considering number of hydrogen bonds: 59 Results contains number of sets of co-planar bases: 7 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( C) Mol: 1 Model: 1 Entry: 1 Residue: 26( G) 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: 10( U) Mol: 1 Model: 1 Entry: 1 Residue: 19( A) 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( C) Mol: 1 Model: 1 Entry: 1 Residue: 17( G) Mol: 1 Model: 1 Entry: 1 Writing results to file: 28sr_wc.csv Wattos started at: January 19, 2007 10:21:02 AM CST Wattos stopped at: January 19, 2007 10:21:05 AM CST Wattos took (#ms): 3041