Read libraries from system resource. Wattos started at: April 20, 2007 11:49:58 AM CDT 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/pdb1ldz.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 24425 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 1263 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: 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 N2 1(G ) 1 O2 30(C ) 1 1 1 2.815 136.157 5 N1 1(G ) 1 N3 30(C ) 1 1 1 2.816 132.751 5 N4 2(C ) 1 O6 29(G ) 1 1 1 2.814 162.717 5 N2 3(G ) 1 O2 28(C ) 1 1 1 2.774 143.661 5 N1 3(G ) 1 N3 28(C ) 1 1 1 2.885 157.943 5 N6 4(A ) 1 O4 27(U ) 1 1 1 3.081 175.060 5 N4 5(C ) 1 O6 26(G ) 1 1 1 2.771 161.171 5 N4 10(C ) 1 O6 23(G ) 1 1 1 2.911 171.531 5 N4 11(C ) 1 O6 22(G ) 1 1 1 2.805 155.768 5 N6 12(A ) 1 O4 21(U ) 1 1 1 3.065 173.764 5 N1 13(G ) 1 O2 20(U ) 1 1 1 2.763 145.719 5 N4 14(C ) 1 O6 19(G ) 1 1 1 2.846 131.699 5 N2 19(G ) 1 O2 14(C ) 1 1 1 2.981 151.710 5 N1 19(G ) 1 N3 14(C ) 1 1 1 2.954 150.949 5 N3 20(U ) 1 O6 13(G ) 1 1 1 3.073 143.186 5 N3 21(U ) 1 N1 12(A ) 1 1 1 2.749 148.290 5 N2 22(G ) 1 O2 11(C ) 1 1 1 2.904 152.036 5 N1 22(G ) 1 N3 11(C ) 1 1 1 2.904 149.148 5 N2 23(G ) 1 O2 10(C ) 1 1 1 3.009 154.758 5 N1 23(G ) 1 N3 10(C ) 1 1 1 2.924 171.167 5 N6 25(A ) 1 N3 6(C ) 1 1 1 3.161 156.517 5 N1 25(A ) 1 O2 6(C ) 1 1 1 2.883 161.668 5 N2 26(G ) 1 O2 5(C ) 1 1 1 3.081 144.969 5 N1 26(G ) 1 N3 5(C ) 1 1 1 2.749 175.284 5 N3 27(U ) 1 N1 4(A ) 1 1 1 2.936 159.170 5 N4 28(C ) 1 O6 3(G ) 1 1 1 2.929 153.902 5 N2 29(G ) 1 O2 2(C ) 1 1 1 2.961 152.930 5 N1 29(G ) 1 N3 2(C ) 1 1 1 2.889 141.962 5 N4 30(C ) 1 O6 1(G ) 1 1 1 2.734 111.266 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, 1ldz_wc.csv] Trying to match bases to eachother for number of bases: 30 Considering number of hydrogen bonds: 29 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: 1ldz_wc.csv Wattos started at: April 20, 2007 11:49:58 AM CDT Wattos stopped at: April 20, 2007 11:50:06 AM CDT Wattos took (#ms): 7727