Read libraries from system resource. Wattos started at: January 19, 2007 10:21:07 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/pdb2au4.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 1376 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 1737 Found number of new bond candidates: 1483 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: 89 Found number of new hydrogen bonds: 89 Atom Res#(Nam) Mol# Atom Res#(Nam) Mol# Model# Entry# Value_1 Value_2 RefValue RefSD Type Minimum Average Maximum Under cutoff O3P 1(G ) 1 N7 2(G ) 1 1 1 2.663 125.541 5 N1 1(G ) 1 N3 41(C ) 1 1 1 2.898 177.886 5 N2 1(G ) 1 O2 41(C ) 1 1 1 2.923 160.310 5 O2* 2(G ) 1 O4* 3(G ) 1 1 1 2.763 137.403 5 N1 2(G ) 1 N3 40(C ) 1 1 1 2.886 179.162 5 N2 2(G ) 1 O2 40(C ) 1 1 1 2.899 163.426 5 O2* 3(G ) 1 O5* 4(A ) 1 1 1 2.731 119.399 5 O2* 3(G ) 1 O4* 4(A ) 1 1 1 2.811 143.002 5 N1 3(G ) 1 N3 39(C ) 1 1 1 2.912 172.346 5 N2 3(G ) 1 O2 39(C ) 1 1 1 2.833 173.966 5 O2* 4(A ) 1 O4* 5(C ) 1 1 1 3.122 122.654 5 N6 4(A ) 1 N3 38(U ) 1 1 1 3.324 128.463 5 N6 4(A ) 1 O4 38(U ) 1 1 1 2.961 158.562 5 O2* 5(C ) 1 O5* 6(G ) 1 1 1 2.574 120.460 5 O2* 5(C ) 1 O4* 6(G ) 1 1 1 2.964 140.552 5 N4 5(C ) 1 O6 37(G ) 1 1 1 2.955 154.827 5 N1 6(G ) 1 N3 36(C ) 1 1 1 2.914 172.025 5 N2 6(G ) 1 O2 36(C ) 1 1 1 2.849 164.938 5 O2* 8(A ) 1 O5* 9(G ) 1 1 1 3.128 162.914 5 O2* 8(A ) 1 O4* 9(G ) 1 1 1 2.997 115.870 5 N1 9(G ) 1 O6 16(G ) 1 1 1 2.528 145.538 5 N1 9(G ) 1 O6 17(G ) 1 1 1 3.002 100.087 5 N2 9(G ) 1 O6 16(G ) 1 1 1 2.906 129.374 5 N2 9(G ) 1 O2B 1(GTP) 2 1 1 2.970 164.876 5 N2 11(G ) 1 N3 8(A ) 1 1 1 2.513 161.719 5 O2* 12(G ) 1 O3* 13(U ) 1 1 1 2.723 107.091 5 N1 12(G ) 1 O4 14(U ) 1 1 1 2.790 100.328 5 N2 12(G ) 1 O2* 34(A ) 1 1 1 2.723 170.130 5 N2 12(G ) 1 O4* 35(A ) 1 1 1 2.826 131.658 5 O2* 13(U ) 1 O5* 14(U ) 1 1 1 2.511 152.105 5 O2* 13(U ) 1 O4* 14(U ) 1 1 1 3.123 118.180 5 O2* 14(U ) 1 O5* 15(G ) 1 1 1 2.825 90.622 5 O2* 14(U ) 1 O4* 15(G ) 1 1 1 2.657 162.752 5 N3 14(U ) 1 N1 33(A ) 1 1 1 2.585 165.998 5 N1 15(G ) 1 N3 32(A ) 1 1 1 3.344 139.524 5 N1 16(G ) 1 O6 29(G ) 1 1 1 2.520 146.197 5 O2* 17(G ) 1 O4* 18(C ) 1 1 1 3.190 117.462 5 N1 17(G ) 1 O2 28(U ) 1 1 1 2.517 170.193 5 N2 17(G ) 1 O2 28(U ) 1 1 1 3.309 127.527 5 O2* 18(C ) 1 O5* 19(G ) 1 1 1 2.611 157.604 5 N4 18(C ) 1 O6 27(G ) 1 1 1 3.101 153.607 5 N1 19(G ) 1 N3 26(C ) 1 1 1 2.917 167.857 5 N2 19(G ) 1 O2 26(C ) 1 1 1 2.844 161.196 5 O2* 20(C ) 1 O5* 21(U ) 1 1 1 3.032 105.432 5 N4 20(C ) 1 O6 19(G ) 1 1 1 3.039 111.537 5 N4 20(C ) 1 O6 25(G ) 1 1 1 2.864 142.145 5 O2* 21(U ) 1 O6 24(G ) 1 1 1 2.584 149.021 5 N3 21(U ) 1 O2 23(C ) 1 1 1 2.685 126.544 5 O2* 22(U ) 1 N7 24(G ) 1 1 1 2.530 159.174 5 N4 23(C ) 1 O2P 22(U ) 1 1 1 2.750 140.552 5 O2* 24(G ) 1 O5* 25(G ) 1 1 1 2.396 160.816 5 N1 24(G ) 1 O2 21(U ) 1 1 1 2.652 164.000 5 N2 24(G ) 1 O2 21(U ) 1 1 1 3.277 131.541 5 N1 25(G ) 1 N3 20(C ) 1 1 1 2.917 178.357 5 N2 25(G ) 1 O2 20(C ) 1 1 1 2.885 167.366 5 O2* 26(C ) 1 O5* 27(G ) 1 1 1 2.907 104.954 5 O2* 26(C ) 1 O4* 27(G ) 1 1 1 2.816 148.696 5 N4 26(C ) 1 O6 19(G ) 1 1 1 2.874 169.880 5 N1 27(G ) 1 O2 18(C ) 1 1 1 3.266 126.164 5 N1 27(G ) 1 N3 18(C ) 1 1 1 2.710 171.741 5 N2 27(G ) 1 O2 18(C ) 1 1 1 2.581 151.283 5 O2* 28(U ) 1 N3 29(G ) 1 1 1 2.842 99.429 5 N3 28(U ) 1 O6 17(G ) 1 1 1 3.196 155.879 5 N1 29(G ) 1 O6 9(G ) 1 1 1 2.876 165.555 5 N2 31(G ) 1 O6 1(GTP) 2 1 1 2.438 172.911 5 N6 32(A ) 1 O6 31(G ) 1 1 1 2.879 92.103 5 O2* 33(A ) 1 O1P 34(A ) 1 1 1 3.143 113.252 5 N6 33(A ) 1 N1 8(A ) 1 1 1 2.977 135.079 5 N6 33(A ) 1 O6 15(G ) 1 1 1 3.104 112.568 5 O2* 36(C ) 1 O5* 37(G ) 1 1 1 2.824 171.638 5 O2* 36(C ) 1 O4* 37(G ) 1 1 1 2.988 100.688 5 N4 36(C ) 1 O6 6(G ) 1 1 1 2.858 169.956 5 N1 37(G ) 1 N3 5(C ) 1 1 1 2.889 168.063 5 N2 37(G ) 1 O2 5(C ) 1 1 1 2.828 171.120 5 O2* 38(U ) 1 O5* 39(C ) 1 1 1 3.012 157.600 5 O2* 38(U ) 1 O4* 39(C ) 1 1 1 2.790 105.229 5 N3 38(U ) 1 N6 4(A ) 1 1 1 3.324 138.808 5 N3 38(U ) 1 N1 4(A ) 1 1 1 2.835 159.166 5 O2* 39(C ) 1 O5* 40(C ) 1 1 1 2.645 167.172 5 O2* 39(C ) 1 O4* 40(C ) 1 1 1 2.952 106.935 5 N4 39(C ) 1 O6 3(G ) 1 1 1 2.887 153.765 5 O2* 40(C ) 1 O1P 41(C ) 1 1 1 2.878 104.091 5 N4 40(C ) 1 O6 1(G ) 1 1 1 2.971 108.248 5 N4 40(C ) 1 O6 2(G ) 1 1 1 2.858 167.706 5 N4 41(C ) 1 O6 1(G ) 1 1 1 2.923 159.271 5 O3G 1(GTP) 2 O2* 9(G ) 1 1 1 2.447 119.880 5 O3G 1(GTP) 2 N3 9(G ) 1 1 1 2.850 95.301 5 O2* 1(GTP) 2 O2* 8(A ) 1 1 1 2.417 166.854 5 N1 1(GTP) 2 N7 16(G ) 1 1 1 2.739 154.288 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, 2au4_wc.csv] Trying to match bases to eachother for number of bases: 41 Considering number of hydrogen bonds: 89 Results contains number of sets of co-planar bases: 9 Results: Residue: 1( G) Mol: 1 Model: 1 Entry: 1 Residue: 41( C) Mol: 1 Model: 1 Entry: 1 Residue: 2( G) Mol: 1 Model: 1 Entry: 1 Residue: 40( C) Mol: 1 Model: 1 Entry: 1 Residue: 3( G) Mol: 1 Model: 1 Entry: 1 Residue: 39( C) Mol: 1 Model: 1 Entry: 1 Residue: 4( A) Mol: 1 Model: 1 Entry: 1 Residue: 38( U) Mol: 1 Model: 1 Entry: 1 Residue: 5( C) Mol: 1 Model: 1 Entry: 1 Residue: 37( G) Mol: 1 Model: 1 Entry: 1 Residue: 6( G) Mol: 1 Model: 1 Entry: 1 Residue: 36( C) Mol: 1 Model: 1 Entry: 1 Residue: 18( C) Mol: 1 Model: 1 Entry: 1 Residue: 27( G) Mol: 1 Model: 1 Entry: 1 Residue: 19( G) Mol: 1 Model: 1 Entry: 1 Residue: 26( C) Mol: 1 Model: 1 Entry: 1 Residue: 20( C) Mol: 1 Model: 1 Entry: 1 Residue: 25( G) Mol: 1 Model: 1 Entry: 1 Writing results to file: 2au4_wc.csv Wattos started at: January 19, 2007 10:21:07 AM CST Wattos stopped at: January 19, 2007 10:21:10 AM CST Wattos took (#ms): 2812