Read libraries from system resource. Wattos started at: April 20, 2007 11:51:45 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/pdb1naj.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 3790 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 928 Found number of new bond candidates: 816 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: 36 Found number of new hydrogen bonds: 36 Atom Res#(Nam) Mol# Atom Res#(Nam) Mol# Model# Entry# Value_1 Value_2 RefValue RefSD Type Minimum Average Maximum Under cutoff N4 1(C ) 1 O6 12(G ) 2 1 1 2.670 162.506 5 N1 2(G ) 1 N3 11(C ) 2 1 1 2.670 163.948 5 N2 2(G ) 1 O2 11(C ) 2 1 1 2.561 171.632 5 N4 3(C ) 1 O6 10(G ) 2 1 1 2.705 161.392 5 N1 4(G ) 1 N3 9(C ) 2 1 1 2.676 172.811 5 N2 4(G ) 1 O2 9(C ) 2 1 1 2.631 155.546 5 N6 5(A ) 1 O4 8(T ) 2 1 1 2.816 161.791 5 N6 6(A ) 1 N6 6(A ) 2 1 1 2.968 97.199 5 N6 6(A ) 1 O4 7(T ) 2 1 1 2.737 161.337 5 N3 7(T ) 1 N1 6(A ) 2 1 1 2.709 157.819 5 N3 8(T ) 1 N1 5(A ) 2 1 1 2.690 157.297 5 N4 9(C ) 1 O6 4(G ) 2 1 1 2.725 164.794 5 N1 10(G ) 1 O2 3(C ) 2 1 1 3.197 126.495 5 N1 10(G ) 1 N3 3(C ) 2 1 1 2.632 165.029 5 N2 10(G ) 1 O2 3(C ) 2 1 1 2.613 142.674 5 N4 11(C ) 1 O6 2(G ) 2 1 1 2.815 158.778 5 N1 12(G ) 1 N3 1(C ) 2 1 1 2.648 150.108 5 N2 12(G ) 1 O2 1(C ) 2 1 1 2.748 128.558 5 N4 1(C ) 2 O6 12(G ) 1 1 1 2.668 164.038 5 N1 2(G ) 2 N3 11(C ) 1 1 1 2.680 165.494 5 N2 2(G ) 2 O2 11(C ) 1 1 1 2.568 169.231 5 N4 3(C ) 2 O6 10(G ) 1 1 1 2.711 161.249 5 N1 4(G ) 2 N3 9(C ) 1 1 1 2.675 173.864 5 N2 4(G ) 2 O2 9(C ) 1 1 1 2.632 156.249 5 N6 5(A ) 2 O4 8(T ) 1 1 1 2.813 162.746 5 N6 6(A ) 2 N6 6(A ) 1 1 1 2.968 96.424 5 N6 6(A ) 2 O4 7(T ) 1 1 1 2.728 161.631 5 N3 7(T ) 2 N1 6(A ) 1 1 1 2.720 158.280 5 N3 8(T ) 2 N1 5(A ) 1 1 1 2.707 158.392 5 N4 9(C ) 2 O6 4(G ) 1 1 1 2.730 164.624 5 N1 10(G ) 2 O2 3(C ) 1 1 1 3.183 125.561 5 N1 10(G ) 2 N3 3(C ) 1 1 1 2.630 162.824 5 N2 10(G ) 2 O2 3(C ) 1 1 1 2.614 139.287 5 N4 11(C ) 2 O6 2(G ) 1 1 1 2.807 157.811 5 N1 12(G ) 2 N3 1(C ) 1 1 1 2.631 150.159 5 N2 12(G ) 2 O2 1(C ) 1 1 1 2.713 128.055 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, 1naj_wc.csv] Trying to match bases to eachother for number of bases: 24 Considering number of hydrogen bonds: 36 Results contains number of sets of co-planar bases: 12 Results: Residue: 1( C) Mol: 1 Model: 1 Entry: 1 Residue: 12( G) Mol: 2 Model: 1 Entry: 1 Residue: 2( G) Mol: 1 Model: 1 Entry: 1 Residue: 11( C) Mol: 2 Model: 1 Entry: 1 Residue: 3( C) Mol: 1 Model: 1 Entry: 1 Residue: 10( G) Mol: 2 Model: 1 Entry: 1 Residue: 4( G) Mol: 1 Model: 1 Entry: 1 Residue: 9( C) Mol: 2 Model: 1 Entry: 1 Residue: 5( A) Mol: 1 Model: 1 Entry: 1 Residue: 8( T) Mol: 2 Model: 1 Entry: 1 Residue: 6( A) Mol: 1 Model: 1 Entry: 1 Residue: 7( T) Mol: 2 Model: 1 Entry: 1 Residue: 7( T) Mol: 1 Model: 1 Entry: 1 Residue: 6( A) Mol: 2 Model: 1 Entry: 1 Residue: 8( T) Mol: 1 Model: 1 Entry: 1 Residue: 5( A) Mol: 2 Model: 1 Entry: 1 Residue: 9( C) Mol: 1 Model: 1 Entry: 1 Residue: 4( G) Mol: 2 Model: 1 Entry: 1 Residue: 10( G) Mol: 1 Model: 1 Entry: 1 Residue: 3( C) Mol: 2 Model: 1 Entry: 1 Residue: 11( C) Mol: 1 Model: 1 Entry: 1 Residue: 2( G) Mol: 2 Model: 1 Entry: 1 Residue: 12( G) Mol: 1 Model: 1 Entry: 1 Residue: 1( C) Mol: 2 Model: 1 Entry: 1 Writing results to file: 1naj_wc.csv Wattos started at: April 20, 2007 11:51:45 AM CDT Wattos stopped at: April 20, 2007 11:51:49 AM CDT Wattos took (#ms): 3874