Read libraries from system resource. Wattos started at: April 20, 2007 11:46:52 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/pdb1evm.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 5184 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 783 Found number of new bond candidates: 700 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: 39 WARNING: Got more than two hydrogen bond for this donor (N6). 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 N6 1(A ) 4 N6 1(A ) 1 1 1 130.623 5 N6 1(A ) 4 N6 1(A ) 3 1 1 107.121 5 N6 1(A ) 4 N1 1(A ) 3 1 1 166.044 5 Found number of new hydrogen bonds: 39 Atom Res#(Nam) Mol# Atom Res#(Nam) Mol# Model# Entry# Value_1 Value_2 RefValue RefSD Type Minimum Average Maximum Under cutoff N1 2(G ) 1 O6 2(G ) 4 1 1 2.812 168.718 5 N2 2(G ) 1 N7 2(G ) 4 1 1 2.783 163.727 5 N1 3(G ) 1 O6 3(G ) 4 1 1 2.802 160.194 5 N2 3(G ) 1 N7 3(G ) 4 1 1 2.729 171.750 5 N1 4(G ) 1 O6 4(G ) 4 1 1 2.791 161.300 5 N2 4(G ) 1 O4* 5(T ) 1 1 1 3.102 141.886 5 N2 4(G ) 1 N7 4(G ) 4 1 1 2.728 173.584 5 O3* 5(T ) 1 O2P 4(G ) 4 1 1 2.657 161.753 5 N3 5(T ) 1 O4 5(T ) 4 1 1 2.829 166.383 5 N1 2(G ) 2 O6 2(G ) 1 1 1 2.789 167.538 5 N2 2(G ) 2 N7 2(G ) 1 1 1 2.801 162.620 5 N1 3(G ) 2 O6 3(G ) 1 1 1 2.811 161.315 5 N2 3(G ) 2 N7 3(G ) 1 1 1 2.721 169.334 5 N1 4(G ) 2 O6 4(G ) 1 1 1 2.783 158.857 5 N2 4(G ) 2 N7 4(G ) 1 1 1 2.738 171.977 5 N2 4(G ) 2 O4* 5(T ) 2 1 1 3.279 136.161 5 O3* 5(T ) 2 O2P 4(G ) 1 1 1 2.643 161.562 5 N3 5(T ) 2 O4 5(T ) 1 1 1 2.788 156.374 5 N1 2(G ) 3 O6 2(G ) 2 1 1 2.806 167.456 5 N2 2(G ) 3 N7 2(G ) 2 1 1 2.788 163.618 5 N1 3(G ) 3 O6 3(G ) 2 1 1 2.803 160.212 5 N2 3(G ) 3 N7 3(G ) 2 1 1 2.728 172.016 5 N1 4(G ) 3 O6 4(G ) 2 1 1 2.804 160.049 5 N2 4(G ) 3 N7 4(G ) 2 1 1 2.728 175.583 5 N2 4(G ) 3 O4* 5(T ) 3 1 1 3.156 142.553 5 O3* 5(T ) 3 O2P 4(G ) 2 1 1 2.649 161.032 5 N3 5(T ) 3 O4 5(T ) 2 1 1 2.781 165.154 5 N6 1(A ) 4 N6 1(A ) 1 1 1 2.995 130.623 5 N6 1(A ) 4 N6 1(A ) 3 1 1 2.992 107.121 5 N6 1(A ) 4 N1 1(A ) 3 1 1 2.719 166.044 5 N1 2(G ) 4 O6 2(G ) 3 1 1 2.788 165.970 5 N2 2(G ) 4 N7 2(G ) 3 1 1 2.802 162.634 5 N1 3(G ) 4 O6 3(G ) 3 1 1 2.802 160.130 5 N2 3(G ) 4 N7 3(G ) 3 1 1 2.724 169.253 5 N1 4(G ) 4 O6 4(G ) 3 1 1 2.783 159.023 5 N2 4(G ) 4 N7 4(G ) 3 1 1 2.729 173.879 5 N2 4(G ) 4 O4* 5(T ) 4 1 1 3.182 141.084 5 O3* 5(T ) 4 O2P 4(G ) 3 1 1 2.645 161.346 5 N3 5(T ) 4 O4 5(T ) 3 1 1 2.810 163.545 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, 1evm_wc.csv] Trying to match bases to eachother for number of bases: 20 Considering number of hydrogen bonds: 39 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: 1evm_wc.csv Wattos started at: April 20, 2007 11:46:52 AM CDT Wattos stopped at: April 20, 2007 11:46:53 AM CDT Wattos took (#ms): 983