Read libraries from system resource. Wattos started at: January 19, 2007 10:22:36 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/pdb2tpk.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 1155 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 1431 Found number of new bond candidates: 1244 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: 64 WARNING: Got more than two hydrogen bond for this donor (N2). 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 N2 17(G ) 1 O2 6(C ) 1 1 1 167.482 5 N2 17(G ) 1 O4 25(U ) 1 1 1 92.340 5 N2 17(G ) 1 N3 26(C ) 1 1 1 90.045 5 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 24(A ) 1 O2* 18(U ) 1 1 1 128.544 5 N6 24(A ) 1 O2 18(U ) 1 1 1 159.801 5 N6 24(A ) 1 O4 25(U ) 1 1 1 104.181 5 WARNING: Got more than two hydrogen bond for this donor (N4). Hydrogen bonds (4) 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 26(C ) 1 O4* 7(C ) 1 1 1 117.084 5 N4 26(C ) 1 N1 7(C ) 1 1 1 143.931 5 N4 26(C ) 1 O2 7(C ) 1 1 1 95.163 5 N4 26(C ) 1 N2 17(G ) 1 1 1 116.801 5 Found number of new hydrogen bonds: 64 Atom Res#(Nam) Mol# Atom Res#(Nam) Mol# Model# Entry# Value_1 Value_2 RefValue RefSD Type Minimum Average Maximum Under cutoff O3P 1(G ) 1 O1P 2(C ) 1 1 1 2.943 107.049 5 O2* 1(G ) 1 O4* 2(C ) 1 1 1 2.785 141.018 5 N4 2(C ) 1 O2* 21(U ) 1 1 1 2.748 133.341 5 N3 3(U ) 1 N1 20(A ) 1 1 1 2.941 177.461 5 O2* 4(G ) 1 O4* 5(A ) 1 1 1 3.162 151.724 5 O2* 4(G ) 1 O2P 24(A ) 1 1 1 3.257 118.032 5 N1 4(G ) 1 N3 19(C ) 1 1 1 2.880 172.981 5 N2 4(G ) 1 O2 19(C ) 1 1 1 2.988 171.409 5 N6 5(A ) 1 O4 18(U ) 1 1 1 2.816 165.183 5 N4 6(C ) 1 O6 17(G ) 1 1 1 2.671 162.944 5 O2* 7(C ) 1 O2P 28(U ) 1 1 1 2.657 123.779 5 N4 7(C ) 1 O6 16(G ) 1 1 1 2.853 159.081 5 N6 8(A ) 1 O4 11(U ) 1 1 1 2.774 141.251 5 O2* 9(G ) 1 O5* 10(C ) 1 1 1 3.066 126.082 5 O2* 9(G ) 1 O4* 10(C ) 1 1 1 3.098 156.129 5 N1 9(G ) 1 N3 34(C ) 1 1 1 2.873 161.172 5 N2 9(G ) 1 O2 34(C ) 1 1 1 2.799 163.497 5 N4 10(C ) 1 O6 33(G ) 1 1 1 2.690 161.459 5 N3 11(U ) 1 N1 32(A ) 1 1 1 2.941 178.622 5 N6 12(A ) 1 O4 31(U ) 1 1 1 2.821 166.154 5 N3 13(U ) 1 N1 30(A ) 1 1 1 2.944 178.451 5 O2* 14(G ) 1 O5* 15(A ) 1 1 1 3.034 146.968 5 N1 14(G ) 1 N3 29(C ) 1 1 1 2.881 170.848 5 N2 14(G ) 1 O2 29(C ) 1 1 1 3.016 171.192 5 N6 15(A ) 1 O6 16(G ) 1 1 1 3.058 101.298 5 N6 15(A ) 1 O4 28(U ) 1 1 1 2.909 163.221 5 N1 16(G ) 1 N3 7(C ) 1 1 1 2.927 162.984 5 N2 16(G ) 1 O2 7(C ) 1 1 1 2.872 162.161 5 N1 17(G ) 1 N3 6(C ) 1 1 1 2.884 170.404 5 N2 17(G ) 1 O2 6(C ) 1 1 1 3.043 167.482 5 N2 17(G ) 1 O4 25(U ) 1 1 1 2.601 92.340 5 N2 17(G ) 1 N3 26(C ) 1 1 1 2.690 90.045 5 O2* 18(U ) 1 O5* 19(C ) 1 1 1 3.336 126.526 5 O2* 18(U ) 1 O4* 19(C ) 1 1 1 3.092 140.440 5 N3 18(U ) 1 N1 5(A ) 1 1 1 2.942 179.542 5 O2* 19(C ) 1 O4* 20(A ) 1 1 1 3.105 147.414 5 N4 19(C ) 1 O6 4(G ) 1 1 1 2.677 167.194 5 O2* 20(A ) 1 O1P 23(C ) 1 1 1 3.040 114.540 5 N6 20(A ) 1 O4 3(U ) 1 1 1 2.839 162.813 5 O2* 22(A ) 1 O5* 23(C ) 1 1 1 2.282 154.227 5 N6 22(A ) 1 O2* 3(U ) 1 1 1 2.645 98.432 5 N4 23(C ) 1 O2* 19(C ) 1 1 1 2.730 134.838 5 N6 24(A ) 1 O2* 18(U ) 1 1 1 2.834 128.544 5 N6 24(A ) 1 O2 18(U ) 1 1 1 2.628 159.801 5 N6 24(A ) 1 O4 25(U ) 1 1 1 3.018 104.181 5 N4 26(C ) 1 O4* 7(C ) 1 1 1 2.998 117.084 5 N4 26(C ) 1 N1 7(C ) 1 1 1 2.994 143.931 5 N4 26(C ) 1 O2 7(C ) 1 1 1 2.963 95.163 5 N4 26(C ) 1 N2 17(G ) 1 1 1 3.263 116.801 5 O2* 27(G ) 1 O4* 28(U ) 1 1 1 2.816 130.510 5 N2 27(G ) 1 O4* 28(U ) 1 1 1 3.201 117.534 5 O2* 28(U ) 1 O4* 29(C ) 1 1 1 3.053 126.215 5 N3 28(U ) 1 N1 15(A ) 1 1 1 2.804 155.643 5 N4 29(C ) 1 O6 14(G ) 1 1 1 2.696 162.190 5 N6 30(A ) 1 O4 13(U ) 1 1 1 2.831 163.956 5 N3 31(U ) 1 N1 12(A ) 1 1 1 2.948 179.681 5 O2* 32(A ) 1 O5* 33(G ) 1 1 1 3.350 130.936 5 O2* 32(A ) 1 O4* 33(G ) 1 1 1 3.065 132.293 5 N6 32(A ) 1 O4 11(U ) 1 1 1 2.826 165.010 5 O2* 33(G ) 1 O5* 34(C ) 1 1 1 3.052 144.377 5 N1 33(G ) 1 N3 10(C ) 1 1 1 2.869 168.003 5 N2 33(G ) 1 O2 10(C ) 1 1 1 2.997 172.743 5 O2* 34(C ) 1 O5* 35(A ) 1 1 1 3.205 114.454 5 N4 34(C ) 1 O6 9(G ) 1 1 1 2.840 164.325 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, 2tpk_wc.csv] Trying to match bases to eachother for number of bases: 36 Considering number of hydrogen bonds: 64 Results contains number of sets of co-planar bases: 12 Results: Residue: 3( U) Mol: 1 Model: 1 Entry: 1 Residue: 20( A) Mol: 1 Model: 1 Entry: 1 Residue: 4( G) Mol: 1 Model: 1 Entry: 1 Residue: 19( C) Mol: 1 Model: 1 Entry: 1 Residue: 5( A) Mol: 1 Model: 1 Entry: 1 Residue: 18( U) Mol: 1 Model: 1 Entry: 1 Residue: 6( C) Mol: 1 Model: 1 Entry: 1 Residue: 17( G) Mol: 1 Model: 1 Entry: 1 Residue: 7( C) Mol: 1 Model: 1 Entry: 1 Residue: 16( G) Mol: 1 Model: 1 Entry: 1 Residue: 9( G) Mol: 1 Model: 1 Entry: 1 Residue: 34( C) Mol: 1 Model: 1 Entry: 1 Residue: 10( C) Mol: 1 Model: 1 Entry: 1 Residue: 33( G) Mol: 1 Model: 1 Entry: 1 Residue: 11( U) Mol: 1 Model: 1 Entry: 1 Residue: 32( A) Mol: 1 Model: 1 Entry: 1 Residue: 12( A) Mol: 1 Model: 1 Entry: 1 Residue: 31( U) Mol: 1 Model: 1 Entry: 1 Residue: 13( U) Mol: 1 Model: 1 Entry: 1 Residue: 30( A) Mol: 1 Model: 1 Entry: 1 Residue: 14( G) Mol: 1 Model: 1 Entry: 1 Residue: 29( C) Mol: 1 Model: 1 Entry: 1 Residue: 15( A) Mol: 1 Model: 1 Entry: 1 Residue: 28( U) Mol: 1 Model: 1 Entry: 1 Writing results to file: 2tpk_wc.csv Wattos started at: January 19, 2007 10:22:36 AM CST Wattos stopped at: January 19, 2007 10:22:40 AM CST Wattos took (#ms): 3327