Read libraries from system resource. Wattos started at: January 19, 2007 10:16:05 AM CST 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/pdb1c4l.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 575 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 709 Found number of new bond candidates: 617 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: 31 Found number of new hydrogen bonds: 31 Atom Res#(Nam) Mol# Atom Res#(Nam) Mol# Model# Entry# Value_1 Value_2 RefValue RefSD Type Minimum Average Maximum Under cutoff O2* 1(C ) 1 O4* 2(G ) 1 1 1 2.707 156.156 5 N4 1(C ) 1 O6 9(G ) 2 1 1 2.984 177.717 5 N1 2(G ) 1 N3 8(C ) 2 1 1 2.971 172.256 5 N2 2(G ) 1 O2 8(C ) 2 1 1 2.990 161.318 5 N6 3(A ) 1 O4 7(U ) 2 1 1 3.069 173.540 5 N4 4(C ) 1 O6 6(G ) 2 1 1 2.931 177.112 5 O2* 6(C ) 1 O4* 7(A ) 1 1 1 2.905 93.272 5 N4 6(C ) 1 O6 4(G ) 2 1 1 2.976 160.297 5 O2* 7(A ) 1 O4* 8(G ) 1 1 1 2.659 159.677 5 N6 7(A ) 1 O4 3(U ) 2 1 1 3.045 177.965 5 N1 8(G ) 1 N3 2(C ) 2 1 1 3.037 172.969 5 N2 8(G ) 1 O2 2(C ) 2 1 1 3.008 168.565 5 N1 9(G ) 1 N3 1(C ) 2 1 1 3.028 175.516 5 N2 9(G ) 1 O2 1(C ) 2 1 1 2.971 171.402 5 O2* 1(C ) 2 O4* 2(C ) 2 1 1 2.719 142.952 5 N4 1(C ) 2 O6 9(G ) 1 1 1 2.978 172.805 5 O2* 2(C ) 2 O4* 3(U ) 2 1 1 2.816 125.591 5 N4 2(C ) 2 O6 8(G ) 1 1 1 2.957 175.506 5 N3 3(U ) 2 N1 7(A ) 1 1 1 2.985 161.215 5 N1 4(G ) 2 N3 6(C ) 1 1 1 2.982 159.113 5 N2 4(G ) 2 O2 6(C ) 1 1 1 2.974 146.383 5 N4 5(C ) 2 O4 5(U ) 1 1 1 2.956 156.378 5 N1 6(G ) 2 N3 4(C ) 1 1 1 3.019 164.455 5 N2 6(G ) 2 O2 4(C ) 1 1 1 3.002 167.167 5 O2* 7(U ) 2 O5* 8(C ) 2 1 1 2.882 97.390 5 N3 7(U ) 2 N1 3(A ) 1 1 1 2.999 171.839 5 O2* 8(C ) 2 O4* 9(G ) 2 1 1 2.492 112.659 5 N4 8(C ) 2 O6 2(G ) 1 1 1 2.955 171.770 5 N4 8(C ) 2 O4 7(U ) 2 1 1 3.269 123.767 5 N1 9(G ) 2 N3 1(C ) 1 1 1 3.026 173.595 5 N2 9(G ) 2 O2 1(C ) 1 1 1 2.977 165.510 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, 1c4l_wc.csv] Trying to match bases to eachother for number of bases: 18 Considering number of hydrogen bonds: 31 Results contains number of sets of co-planar bases: 8 Results: Residue: 1( C) Mol: 1 Model: 1 Entry: 1 Residue: 9( G) Mol: 2 Model: 1 Entry: 1 Residue: 2( G) Mol: 1 Model: 1 Entry: 1 Residue: 8( C) Mol: 2 Model: 1 Entry: 1 Residue: 3( A) Mol: 1 Model: 1 Entry: 1 Residue: 7( U) Mol: 2 Model: 1 Entry: 1 Residue: 4( C) Mol: 1 Model: 1 Entry: 1 Residue: 6( G) Mol: 2 Model: 1 Entry: 1 Residue: 6( C) Mol: 1 Model: 1 Entry: 1 Residue: 4( G) Mol: 2 Model: 1 Entry: 1 Residue: 7( A) Mol: 1 Model: 1 Entry: 1 Residue: 3( U) Mol: 2 Model: 1 Entry: 1 Residue: 8( G) Mol: 1 Model: 1 Entry: 1 Residue: 2( C) Mol: 2 Model: 1 Entry: 1 Residue: 9( G) Mol: 1 Model: 1 Entry: 1 Residue: 1( C) Mol: 2 Model: 1 Entry: 1 Writing results to file: 1c4l_wc.csv Wattos started at: January 19, 2007 10:16:05 AM CST Wattos stopped at: January 19, 2007 10:16:07 AM CST Wattos took (#ms): 2316