Read libraries from system resource. Wattos started at: April 20, 2007 11:46:49 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/pdb1emq.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 900 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 1078 Found number of new bond candidates: 968 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: 55 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 7(C ) 2 N4 7(C ) 1 1 1 136.085 5 N4 7(C ) 2 O6 6(G ) 2 1 1 109.197 5 N4 7(C ) 2 N3 7(C ) 4 1 1 155.697 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 7(C ) 3 N3 7(C ) 1 1 1 159.931 5 N4 7(C ) 3 O6 6(G ) 4 1 1 157.611 5 N4 7(C ) 3 N4 7(C ) 4 1 1 109.641 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 7(C ) 4 N4 7(C ) 2 1 1 141.675 5 N4 7(C ) 4 N3 7(C ) 3 1 1 162.528 5 N4 7(C ) 4 N4 7(C ) 3 1 1 108.147 5 Found number of new hydrogen bonds: 55 Atom Res#(Nam) Mol# Atom Res#(Nam) Mol# Model# Entry# Value_1 Value_2 RefValue RefSD Type Minimum Average Maximum Under cutoff N3 1(T ) 1 O4 1(T ) 3 1 1 2.848 164.166 5 N1 2(G ) 1 O6 2(G ) 3 1 1 2.791 163.142 5 N2 2(G ) 1 N7 2(G ) 3 1 1 2.763 170.444 5 N1 3(G ) 1 O6 3(G ) 3 1 1 2.783 162.041 5 N2 3(G ) 1 N7 3(G ) 3 1 1 2.751 168.515 5 N3 4(T ) 1 O4 4(T ) 3 1 1 3.014 169.663 5 N1 5(G ) 1 O6 5(G ) 3 1 1 2.818 166.052 5 N2 5(G ) 1 N7 5(G ) 3 1 1 2.763 166.446 5 N1 6(G ) 1 O6 6(G ) 3 1 1 2.853 153.262 5 N2 6(G ) 1 O4* 7(C ) 1 1 1 3.064 130.544 5 N2 6(G ) 1 N7 6(G ) 3 1 1 2.701 176.016 5 N4 7(C ) 1 N3 7(C ) 2 1 1 2.704 158.490 5 N4 7(C ) 1 N4 7(C ) 3 1 1 3.182 146.063 5 N3 1(T ) 2 O4 1(T ) 1 1 1 2.844 163.120 5 N1 2(G ) 2 O6 2(G ) 1 1 1 2.781 165.860 5 N2 2(G ) 2 N7 2(G ) 1 1 1 2.751 166.901 5 N1 3(G ) 2 O6 3(G ) 1 1 1 2.785 165.300 5 N2 3(G ) 2 N7 3(G ) 1 1 1 2.754 166.623 5 N3 4(T ) 2 O4 4(T ) 1 1 1 3.012 170.423 5 N1 5(G ) 2 O6 5(G ) 1 1 1 2.811 166.941 5 N2 5(G ) 2 N7 5(G ) 1 1 1 2.772 166.796 5 N1 6(G ) 2 O6 6(G ) 1 1 1 2.784 151.230 5 N2 6(G ) 2 N7 6(G ) 1 1 1 2.708 178.211 5 N4 7(C ) 2 N4 7(C ) 1 1 1 3.208 136.085 5 N4 7(C ) 2 O6 6(G ) 2 1 1 3.033 109.197 5 N4 7(C ) 2 N3 7(C ) 4 1 1 2.689 155.697 5 O5* 1(T ) 3 O1P 2(G ) 3 1 1 2.649 168.938 5 N3 1(T ) 3 O4 1(T ) 4 1 1 2.974 169.258 5 N1 2(G ) 3 O6 2(G ) 4 1 1 2.772 162.831 5 N2 2(G ) 3 N7 2(G ) 4 1 1 2.768 167.585 5 N1 3(G ) 3 O6 3(G ) 4 1 1 2.775 165.463 5 N2 3(G ) 3 N7 3(G ) 4 1 1 2.766 166.459 5 N3 4(T ) 3 O4 4(T ) 4 1 1 3.016 169.494 5 N1 5(G ) 3 O6 5(G ) 4 1 1 2.800 162.499 5 N2 5(G ) 3 N7 5(G ) 4 1 1 2.761 166.674 5 N1 6(G ) 3 O6 6(G ) 4 1 1 2.823 144.377 5 N2 6(G ) 3 O4* 7(C ) 3 1 1 2.914 141.093 5 N2 6(G ) 3 N7 6(G ) 4 1 1 2.709 176.296 5 N4 7(C ) 3 N3 7(C ) 1 1 1 2.756 159.931 5 N4 7(C ) 3 O6 6(G ) 4 1 1 2.911 157.611 5 N4 7(C ) 3 N4 7(C ) 4 1 1 3.154 109.641 5 N3 1(T ) 4 O4 1(T ) 2 1 1 2.857 170.147 5 N1 2(G ) 4 O6 2(G ) 2 1 1 2.776 161.840 5 N2 2(G ) 4 N7 2(G ) 2 1 1 2.763 169.322 5 N1 3(G ) 4 O6 3(G ) 2 1 1 2.783 163.898 5 N2 3(G ) 4 N7 3(G ) 2 1 1 2.753 168.052 5 N3 4(T ) 4 O4 4(T ) 2 1 1 3.012 169.152 5 N1 5(G ) 4 O6 5(G ) 2 1 1 2.807 165.518 5 N2 5(G ) 4 N7 5(G ) 2 1 1 2.763 167.692 5 N1 6(G ) 4 O6 6(G ) 2 1 1 2.777 156.336 5 N2 6(G ) 4 N7 6(G ) 2 1 1 2.712 175.499 5 N2 6(G ) 4 O4* 7(C ) 4 1 1 3.242 127.679 5 N4 7(C ) 4 N4 7(C ) 2 1 1 3.192 141.675 5 N4 7(C ) 4 N3 7(C ) 3 1 1 2.767 162.528 5 N4 7(C ) 4 N4 7(C ) 3 1 1 3.154 108.147 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, 1emq_wc.csv] Trying to match bases to eachother for number of bases: 28 Considering number of hydrogen bonds: 55 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: 1emq_wc.csv Wattos started at: April 20, 2007 11:46:49 AM CDT Wattos stopped at: April 20, 2007 11:46:50 AM CDT Wattos took (#ms): 1092