Read libraries from system resource. Wattos started at: January 19, 2007 10:16:59 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/pdb1k8s.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 807 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 990 Found number of new bond candidates: 868 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: 56 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 6(A ) 1 O6 5(G ) 1 1 1 112.138 5 N6 6(A ) 1 N4 7(C ) 2 1 1 113.291 5 N6 6(A ) 1 N3 8(C ) 2 1 1 111.468 5 Found number of new hydrogen bonds: 56 Atom Res#(Nam) Mol# Atom Res#(Nam) Mol# Model# Entry# Value_1 Value_2 RefValue RefSD Type Minimum Average Maximum Under cutoff O2* 1(G ) 1 O5* 2(G ) 1 1 1 2.770 149.507 5 N1 1(G ) 1 N3 12(C ) 2 1 1 2.836 170.921 5 N2 1(G ) 1 O2 12(C ) 2 1 1 2.739 170.959 5 N1 2(G ) 1 N3 11(C ) 2 1 1 2.857 176.233 5 N2 2(G ) 1 O2 11(C ) 2 1 1 2.738 175.922 5 N4 3(C ) 1 O6 10(G ) 2 1 1 2.792 173.781 5 N6 4(A ) 1 N4 3(C ) 1 1 1 3.167 109.908 5 N6 4(A ) 1 O4 9(U ) 2 1 1 2.853 170.957 5 O2* 5(G ) 1 O5* 6(A ) 1 1 1 2.667 161.995 5 O2* 5(G ) 1 O4* 6(A ) 1 1 1 3.073 107.032 5 N1 5(G ) 1 N3 8(C ) 2 1 1 2.844 170.852 5 N2 5(G ) 1 O2 8(C ) 2 1 1 2.767 176.018 5 O2* 6(A ) 1 O5* 7(G ) 1 1 1 2.776 155.434 5 N6 6(A ) 1 O6 5(G ) 1 1 1 3.192 112.138 5 N6 6(A ) 1 N4 7(C ) 2 1 1 3.041 113.291 5 N6 6(A ) 1 N3 8(C ) 2 1 1 3.179 111.468 5 N1 7(G ) 1 N3 7(C ) 2 1 1 2.827 162.590 5 N2 7(G ) 1 O2 7(C ) 2 1 1 2.727 173.371 5 O2* 8(U ) 1 O4* 9(G ) 1 1 1 2.685 170.686 5 N3 8(U ) 1 N1 6(A ) 2 1 1 2.805 157.910 5 N1 9(G ) 1 O2 5(C ) 2 1 1 3.313 131.931 5 N1 9(G ) 1 N3 5(C ) 2 1 1 2.821 169.940 5 N2 9(G ) 1 O2 5(C ) 2 1 1 2.745 170.011 5 N4 10(C ) 1 O6 4(G ) 2 1 1 2.815 174.870 5 O2* 11(C ) 1 O5* 12(G ) 1 1 1 3.244 116.724 5 O2* 11(C ) 1 O4* 12(G ) 1 1 1 2.683 166.732 5 N4 11(C ) 1 O6 3(G ) 2 1 1 2.802 172.649 5 N1 12(G ) 1 O2 2(C ) 2 1 1 3.341 130.581 5 N1 12(G ) 1 N3 2(C ) 2 1 1 2.824 171.466 5 N2 12(G ) 1 O2 2(C ) 2 1 1 2.736 169.601 5 N4 13(C ) 1 O6 1(G ) 2 1 1 2.825 175.818 5 O2* 1(G ) 2 O5* 2(C ) 2 1 1 2.591 158.186 5 O2* 1(G ) 2 O4* 2(C ) 2 1 1 2.743 97.771 5 N1 1(G ) 2 N3 13(C ) 1 1 1 2.847 167.687 5 N2 1(G ) 2 O2 13(C ) 1 1 1 2.717 172.481 5 N4 2(C ) 2 O6 12(G ) 1 1 1 2.846 170.154 5 O2* 3(G ) 2 O5* 4(G ) 2 1 1 3.114 126.708 5 O2* 3(G ) 2 O4* 4(G ) 2 1 1 2.797 152.572 5 N1 3(G ) 2 N3 11(C ) 1 1 1 2.815 173.948 5 N2 3(G ) 2 O2 11(C ) 1 1 1 2.768 173.391 5 N1 4(G ) 2 N3 10(C ) 1 1 1 2.843 171.473 5 N2 4(G ) 2 O2 10(C ) 1 1 1 2.744 173.190 5 N4 5(C ) 2 O6 9(G ) 1 1 1 2.802 175.859 5 O2* 6(A ) 2 O4* 7(C ) 2 1 1 2.606 167.135 5 N6 6(A ) 2 O6 7(G ) 1 1 1 3.097 104.614 5 N6 6(A ) 2 O4 8(U ) 1 1 1 2.961 169.023 5 N4 7(C ) 2 O6 7(G ) 1 1 1 2.836 178.011 5 N4 8(C ) 2 O6 5(G ) 1 1 1 2.792 178.567 5 O2* 9(U ) 2 O5* 10(G ) 2 1 1 2.651 158.511 5 O2* 9(U ) 2 O4* 10(G ) 2 1 1 2.818 106.170 5 N3 9(U ) 2 N1 4(A ) 1 1 1 2.814 172.216 5 N1 10(G ) 2 O2 3(C ) 1 1 1 3.296 132.599 5 N1 10(G ) 2 N3 3(C ) 1 1 1 2.828 168.569 5 N2 10(G ) 2 O2 3(C ) 1 1 1 2.738 169.558 5 N4 11(C ) 2 O6 2(G ) 1 1 1 2.816 178.346 5 N4 12(C ) 2 O6 1(G ) 1 1 1 2.766 170.938 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, 1k8s_wc.csv] Trying to match bases to eachother for number of bases: 25 Considering number of hydrogen bonds: 56 Results contains number of sets of co-planar bases: 12 Results: Residue: 1( G) Mol: 1 Model: 1 Entry: 1 Residue: 12( C) 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( A) Mol: 1 Model: 1 Entry: 1 Residue: 9( U) Mol: 2 Model: 1 Entry: 1 Residue: 5( G) Mol: 1 Model: 1 Entry: 1 Residue: 8( C) Mol: 2 Model: 1 Entry: 1 Residue: 7( G) Mol: 1 Model: 1 Entry: 1 Residue: 7( C) Mol: 2 Model: 1 Entry: 1 Residue: 8( U) Mol: 1 Model: 1 Entry: 1 Residue: 6( A) Mol: 2 Model: 1 Entry: 1 Residue: 9( G) Mol: 1 Model: 1 Entry: 1 Residue: 5( C) Mol: 2 Model: 1 Entry: 1 Residue: 10( C) Mol: 1 Model: 1 Entry: 1 Residue: 4( G) Mol: 2 Model: 1 Entry: 1 Residue: 11( C) Mol: 1 Model: 1 Entry: 1 Residue: 3( G) Mol: 2 Model: 1 Entry: 1 Residue: 12( G) Mol: 1 Model: 1 Entry: 1 Residue: 2( C) Mol: 2 Model: 1 Entry: 1 Residue: 13( C) Mol: 1 Model: 1 Entry: 1 Residue: 1( G) Mol: 2 Model: 1 Entry: 1 Writing results to file: 1k8s_wc.csv Wattos started at: January 19, 2007 10:16:59 AM CST Wattos stopped at: January 19, 2007 10:17:03 AM CST Wattos took (#ms): 3573