Read libraries from system resource. Wattos started at: April 20, 2007 11:47:36 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/pdb1i4c.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 415 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 514 Found number of new bond candidates: 434 WARNING: Got no bonds for atoms: WARNING: Atom: O2* Res: 1( G) Mol: 1 Model: 1 Entry: 1 Atom: HO*2 Res: 1( G) Mol: 1 Model: 1 Entry: 1 Atom: H5*2 Res: 2( G) Mol: 1 Model: 1 Entry: 1 Atom: O2P Res: 10( C) Mol: 1 Model: 1 Entry: 1 Atom: O2* Res: 13( C) Mol: 1 Model: 1 Entry: 1 Atom: H2* Res: 13( C) Mol: 1 Model: 1 Entry: 1 Atom: HO*2 Res: 13( C) Mol: 1 Model: 1 Entry: 1 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: 24 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 11(A ) 1 O6 2(G ) 1 1 1 101.859 5 N6 11(A ) 1 O4 3(U ) 1 1 1 147.222 5 N6 11(A ) 1 N4 10(C ) 1 1 1 107.065 5 Found number of new hydrogen bonds: 24 Atom Res#(Nam) Mol# Atom Res#(Nam) Mol# Model# Entry# Value_1 Value_2 RefValue RefSD Type Minimum Average Maximum Under cutoff N1 1(G ) 1 N3 13(C ) 1 1 1 2.856 171.505 5 N2 1(G ) 1 O2 13(C ) 1 1 1 2.899 176.455 5 O2* 2(G ) 1 O5* 3(U ) 1 1 1 3.058 104.115 5 O2* 2(G ) 1 O4* 3(U ) 1 1 1 2.901 151.323 5 N1 2(G ) 1 N3 12(C ) 1 1 1 2.871 170.355 5 N2 2(G ) 1 O2 12(C ) 1 1 1 3.082 159.944 5 N3 3(U ) 1 N1 11(A ) 1 1 1 2.749 148.500 5 N1 4(G ) 1 N3 10(C ) 1 1 1 2.780 174.394 5 N2 4(G ) 1 O2 10(C ) 1 1 1 3.060 152.396 5 N4 5(C ) 1 O6 9(G ) 1 1 1 2.807 172.914 5 O2* 8(A ) 1 N7 9(G ) 1 1 1 2.424 93.231 5 O2* 9(G ) 1 O1P 10(C ) 1 1 1 2.389 138.269 5 N1 9(G ) 1 N3 5(C ) 1 1 1 2.727 156.360 5 N2 9(G ) 1 O2 5(C ) 1 1 1 2.667 129.595 5 N2 9(G ) 1 O2* 6(U ) 1 1 1 2.421 107.295 5 N4 10(C ) 1 O6 4(G ) 1 1 1 2.814 166.167 5 N4 10(C ) 1 N6 11(A ) 1 1 1 2.535 92.559 5 O2* 11(A ) 1 O4* 12(C ) 1 1 1 2.464 165.668 5 N6 11(A ) 1 O6 2(G ) 1 1 1 2.958 101.859 5 N6 11(A ) 1 O4 3(U ) 1 1 1 2.587 147.222 5 N6 11(A ) 1 N4 10(C ) 1 1 1 2.535 107.065 5 N4 12(C ) 1 O6 2(G ) 1 1 1 2.765 173.180 5 N4 12(C ) 1 N4 13(C ) 1 1 1 2.699 91.320 5 N4 13(C ) 1 O6 1(G ) 1 1 1 2.702 154.688 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, 1i4c_wc.csv] Trying to match bases to eachother for number of bases: 13 Considering number of hydrogen bonds: 24 Results contains number of sets of co-planar bases: 5 Results: Residue: 1( G) Mol: 1 Model: 1 Entry: 1 Residue: 13( C) Mol: 1 Model: 1 Entry: 1 Residue: 2( G) Mol: 1 Model: 1 Entry: 1 Residue: 12( C) Mol: 1 Model: 1 Entry: 1 Residue: 3( U) Mol: 1 Model: 1 Entry: 1 Residue: 11( A) Mol: 1 Model: 1 Entry: 1 Residue: 4( G) Mol: 1 Model: 1 Entry: 1 Residue: 10( C) Mol: 1 Model: 1 Entry: 1 Residue: 5( C) Mol: 1 Model: 1 Entry: 1 Residue: 9( G) Mol: 1 Model: 1 Entry: 1 Writing results to file: 1i4c_wc.csv Wattos started at: April 20, 2007 11:47:36 AM CDT Wattos stopped at: April 20, 2007 11:47:38 AM CDT Wattos took (#ms): 1943