Read libraries from system resource. Wattos started at: April 20, 2007 11:46:10 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/pdb1c11.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 4818 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 804 Found number of new bond candidates: 730 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: 20 Found number of new hydrogen bonds: 20 Atom Res#(Nam) Mol# Atom Res#(Nam) Mol# Model# Entry# Value_1 Value_2 RefValue RefSD Type Minimum Average Maximum Under cutoff N4 2(C ) 1 O2 2(C ) 2 1 1 2.895 171.073 5 N4 3(C ) 1 O2 3(C ) 2 1 1 2.867 169.525 5 N4 4(C ) 1 O2 4(C ) 2 1 1 2.910 169.100 5 N4 4(C ) 1 O2 8(T ) 2 1 1 2.759 134.079 5 N1 5(G ) 1 O2 8(T ) 2 1 1 2.852 153.120 5 N2 5(G ) 1 O4* 5(G ) 2 1 1 3.023 101.123 5 N2 5(G ) 1 N3 5(G ) 2 1 1 3.055 163.079 5 N3 8(T ) 1 O6 5(G ) 2 1 1 2.910 164.298 5 N4 9(C ) 1 O2 9(C ) 2 1 1 2.926 172.036 5 N4 10(C ) 1 O2 10(C ) 2 1 1 2.910 170.987 5 N4 2(C ) 2 O2 2(C ) 1 1 1 2.916 171.123 5 N4 3(C ) 2 O2 3(C ) 1 1 1 2.905 169.871 5 N4 4(C ) 2 O2 4(C ) 1 1 1 2.933 169.090 5 N4 4(C ) 2 O2 8(T ) 1 1 1 2.778 131.565 5 N1 5(G ) 2 O2 8(T ) 1 1 1 2.851 155.058 5 N2 5(G ) 2 O4* 5(G ) 1 1 1 3.060 102.474 5 N2 5(G ) 2 N3 5(G ) 1 1 1 3.066 162.961 5 N3 8(T ) 2 O6 5(G ) 1 1 1 2.902 161.504 5 N4 9(C ) 2 O2 9(C ) 1 1 1 2.932 172.173 5 N4 10(C ) 2 O2 10(C ) 1 1 1 2.923 171.138 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, 1c11_wc.csv] Trying to match bases to eachother for number of bases: 22 Considering number of hydrogen bonds: 20 WARNING: requested less than 1 new rows in getNewRowIdList: 0 Results contains number of sets of co-planar bases: 0 Results: Writing results to file: 1c11_wc.csv Wattos started at: April 20, 2007 11:46:10 AM CDT Wattos stopped at: April 20, 2007 11:46:11 AM CDT Wattos took (#ms): 1397