Read libraries from system resource. Wattos started at: January 19, 2007 10:22:31 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/pdb2ldz.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 977 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 1244 Found number of new bond candidates: 1055 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: 58 WARNING: Got more than two hydrogen bond for this donor (N6). Hydrogen bonds (4) 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 4(A ) 1 N4 5(C ) 1 1 1 97.331 5 N6 4(A ) 1 O6 26(G ) 1 1 1 110.577 5 N6 4(A ) 1 N3 27(U ) 1 1 1 132.397 5 N6 4(A ) 1 O4 27(U ) 1 1 1 158.002 5 WARNING: Got more than two hydrogen bond for this donor (N4). 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 N4 28(C ) 1 O6 3(G ) 1 1 1 125.630 5 N4 28(C ) 1 O4 27(U ) 1 1 1 99.112 5 N4 28(C ) 1 O6 29(G ) 1 1 1 148.585 5 Found number of new hydrogen bonds: 58 Atom Res#(Nam) Mol# Atom Res#(Nam) Mol# Model# Entry# Value_1 Value_2 RefValue RefSD Type Minimum Average Maximum Under cutoff N2 1(G ) 1 O2 30(C ) 1 1 1 2.816 117.884 5 N1 1(G ) 1 N3 30(C ) 1 1 1 2.819 133.371 5 N4 2(C ) 1 O6 29(G ) 1 1 1 2.735 160.445 5 N4 2(C ) 1 N1 29(G ) 1 1 1 3.277 136.443 5 N2 3(G ) 1 O2 28(C ) 1 1 1 2.763 130.358 5 N1 3(G ) 1 N1 4(A ) 1 1 1 3.122 107.430 5 N1 3(G ) 1 N3 28(C ) 1 1 1 2.867 139.716 5 N6 4(A ) 1 N4 5(C ) 1 1 1 2.990 97.331 5 N6 4(A ) 1 O6 26(G ) 1 1 1 2.785 110.577 5 N6 4(A ) 1 N3 27(U ) 1 1 1 3.347 132.397 5 N6 4(A ) 1 O4 27(U ) 1 1 1 3.083 158.002 5 O2* 4(A ) 1 O4* 5(C ) 1 1 1 2.938 131.371 5 N4 5(C ) 1 N6 25(A ) 1 1 1 2.802 107.394 5 N4 5(C ) 1 O6 26(G ) 1 1 1 2.847 149.045 5 O2* 7(G ) 1 N7 8(A ) 1 1 1 2.607 137.125 5 N4 10(C ) 1 O6 23(G ) 1 1 1 2.873 167.928 5 N4 11(C ) 1 N4 10(C ) 1 1 1 2.960 109.702 5 N4 11(C ) 1 O6 22(G ) 1 1 1 3.080 170.018 5 N6 12(A ) 1 O4 21(U ) 1 1 1 3.074 168.419 5 O2* 12(A ) 1 O5* 13(G ) 1 1 1 2.939 154.445 5 N1 13(G ) 1 O2 20(U ) 1 1 1 2.727 144.759 5 N4 14(C ) 1 O6 19(G ) 1 1 1 2.904 136.919 5 N2 15(G ) 1 O1P 18(A ) 1 1 1 3.268 132.682 5 N2 15(G ) 1 N7 18(A ) 1 1 1 2.919 98.527 5 O2* 15(G ) 1 N7 16(A ) 1 1 1 3.253 120.618 5 N6 17(A ) 1 O2* 15(G ) 1 1 1 2.875 120.081 5 O2* 17(A ) 1 O4* 18(A ) 1 1 1 2.797 112.508 5 N6 18(A ) 1 N3 19(G ) 1 1 1 2.985 97.421 5 N2 19(G ) 1 O2 14(C ) 1 1 1 2.964 143.998 5 N1 19(G ) 1 O2 14(C ) 1 1 1 3.297 133.116 5 N1 19(G ) 1 N3 14(C ) 1 1 1 2.950 151.381 5 O2* 20(U ) 1 O5* 21(U ) 1 1 1 2.927 157.878 5 O2* 20(U ) 1 O4* 21(U ) 1 1 1 3.299 128.896 5 N3 20(U ) 1 O6 13(G ) 1 1 1 3.056 147.778 5 N3 21(U ) 1 N1 12(A ) 1 1 1 2.754 151.256 5 N2 22(G ) 1 O2 11(C ) 1 1 1 2.726 149.494 5 N1 22(G ) 1 N3 11(C ) 1 1 1 2.921 166.611 5 N2 23(G ) 1 O2 10(C ) 1 1 1 3.032 164.755 5 N1 23(G ) 1 N3 10(C ) 1 1 1 2.915 173.573 5 O2* 24(G ) 1 O4* 25(A ) 1 1 1 3.087 134.140 5 N6 25(A ) 1 N4 5(C ) 1 1 1 2.802 117.633 5 N6 25(A ) 1 N3 6(C ) 1 1 1 3.163 157.411 5 N1 25(A ) 1 O2 6(C ) 1 1 1 3.106 158.726 5 N2 26(G ) 1 O2 5(C ) 1 1 1 2.880 162.968 5 N2 26(G ) 1 N3 5(C ) 1 1 1 3.301 133.868 5 N1 26(G ) 1 N3 5(C ) 1 1 1 2.751 161.479 5 N3 27(U ) 1 N6 4(A ) 1 1 1 3.347 137.229 5 N3 27(U ) 1 N1 4(A ) 1 1 1 2.796 161.245 5 N4 28(C ) 1 O6 3(G ) 1 1 1 2.904 125.630 5 N4 28(C ) 1 O4 27(U ) 1 1 1 2.864 99.112 5 N4 28(C ) 1 O6 29(G ) 1 1 1 3.032 148.585 5 O2* 28(C ) 1 O5* 29(G ) 1 1 1 3.129 143.762 5 N2 29(G ) 1 O2 2(C ) 1 1 1 2.902 140.914 5 N2 29(G ) 1 N3 2(C ) 1 1 1 3.265 129.184 5 O2* 29(G ) 1 O4* 30(C ) 1 1 1 3.235 127.396 5 N1 29(G ) 1 N3 2(C ) 1 1 1 2.872 140.160 5 N1 29(G ) 1 N4 2(C ) 1 1 1 3.277 122.363 5 N4 30(C ) 1 O6 1(G ) 1 1 1 2.833 125.391 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, 2ldz_wc.csv] Trying to match bases to eachother for number of bases: 30 Considering number of hydrogen bonds: 58 Results contains number of sets of co-planar bases: 9 Results: Residue: 1( G) Mol: 1 Model: 1 Entry: 1 Residue: 30( C) Mol: 1 Model: 1 Entry: 1 Residue: 2( C) Mol: 1 Model: 1 Entry: 1 Residue: 29( G) Mol: 1 Model: 1 Entry: 1 Residue: 3( G) Mol: 1 Model: 1 Entry: 1 Residue: 28( C) Mol: 1 Model: 1 Entry: 1 Residue: 4( A) Mol: 1 Model: 1 Entry: 1 Residue: 27( U) Mol: 1 Model: 1 Entry: 1 Residue: 5( C) Mol: 1 Model: 1 Entry: 1 Residue: 26( G) Mol: 1 Model: 1 Entry: 1 Residue: 10( C) Mol: 1 Model: 1 Entry: 1 Residue: 23( G) Mol: 1 Model: 1 Entry: 1 Residue: 11( C) Mol: 1 Model: 1 Entry: 1 Residue: 22( G) Mol: 1 Model: 1 Entry: 1 Residue: 12( A) Mol: 1 Model: 1 Entry: 1 Residue: 21( U) Mol: 1 Model: 1 Entry: 1 Residue: 14( C) Mol: 1 Model: 1 Entry: 1 Residue: 19( G) Mol: 1 Model: 1 Entry: 1 Writing results to file: 2ldz_wc.csv Wattos started at: January 19, 2007 10:22:31 AM CST Wattos stopped at: January 19, 2007 10:22:34 AM CST Wattos took (#ms): 3146