Read libraries from system resource. Wattos started at: January 19, 2007 10:20:34 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/pdb1z2j.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 29020 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 1833 Found number of new bond candidates: 1565 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: 61 WARNING: Got more than two hydrogen bond for this donor (N4). 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 N4 19(C ) 1 N4 18(C ) 1 1 1 103.835 5 N4 19(C ) 1 N6 20(A ) 1 1 1 99.629 5 N4 19(C ) 1 O6 24(G ) 1 1 1 154.004 5 WARNING: Got more than two hydrogen bond for this donor (N6). 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 N6 28(A ) 1 N3 15(U ) 1 1 1 131.509 5 N6 28(A ) 1 O4 15(U ) 1 1 1 120.128 5 N6 28(A ) 1 O4 16(U ) 1 1 1 111.283 5 N6 28(A ) 1 N6 27(A ) 1 1 1 123.597 5 Found number of new hydrogen bonds: 61 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 45(C ) 1 1 1 2.941 163.167 5 N2 1(G ) 1 O2 45(C ) 1 1 1 2.895 163.104 5 N1 2(G ) 1 N3 44(C ) 1 1 1 2.944 176.383 5 N2 2(G ) 1 O2 44(C ) 1 1 1 2.923 168.949 5 N1 3(G ) 1 N3 43(C ) 1 1 1 2.951 170.371 5 N2 3(G ) 1 O2 43(C ) 1 1 1 2.916 168.817 5 N6 4(A ) 1 O4 42(U ) 1 1 1 2.943 164.573 5 N6 5(A ) 1 O4 41(U ) 1 1 1 2.942 160.910 5 N1 6(G ) 1 N3 40(C ) 1 1 1 2.957 175.355 5 N2 6(G ) 1 O2 40(C ) 1 1 1 2.909 166.180 5 N6 7(A ) 1 O4 39(U ) 1 1 1 2.919 160.372 5 N3 8(U ) 1 N1 38(A ) 1 1 1 2.949 171.185 5 N4 9(C ) 1 O6 34(G ) 1 1 1 2.894 162.759 5 N3 10(U ) 1 N1 33(A ) 1 1 1 2.951 162.299 5 N1 11(G ) 1 O2 32(C ) 1 1 1 3.071 145.846 5 N1 11(G ) 1 N3 32(C ) 1 1 1 2.905 148.828 5 N2 11(G ) 1 O2 32(C ) 1 1 1 2.918 155.052 5 N1 12(G ) 1 N3 31(C ) 1 1 1 2.921 154.922 5 N1 12(G ) 1 N4 31(C ) 1 1 1 3.252 140.313 5 N2 12(G ) 1 O2 31(C ) 1 1 1 2.805 147.876 5 N2 12(G ) 1 N3 31(C ) 1 1 1 3.101 144.565 5 N4 13(C ) 1 O6 30(G ) 1 1 1 2.905 165.529 5 N4 14(C ) 1 O6 29(G ) 1 1 1 2.902 163.826 5 N3 15(U ) 1 N6 28(A ) 1 1 1 3.128 126.060 5 N3 15(U ) 1 N1 28(A ) 1 1 1 2.962 156.375 5 N3 16(U ) 1 N1 27(A ) 1 1 1 2.984 167.378 5 N4 17(C ) 1 O6 26(G ) 1 1 1 2.915 170.489 5 N4 18(C ) 1 O6 25(G ) 1 1 1 2.895 160.410 5 N4 19(C ) 1 N4 18(C ) 1 1 1 2.821 103.835 5 N4 19(C ) 1 N6 20(A ) 1 1 1 2.617 99.629 5 N4 19(C ) 1 O6 24(G ) 1 1 1 2.894 154.004 5 N6 23(A ) 1 N3 20(A ) 1 1 1 2.908 155.090 5 N1 24(G ) 1 N3 19(C ) 1 1 1 2.904 167.333 5 N2 24(G ) 1 O2 19(C ) 1 1 1 2.914 159.750 5 N1 25(G ) 1 N3 18(C ) 1 1 1 2.954 165.141 5 N2 25(G ) 1 O2 18(C ) 1 1 1 2.894 161.867 5 N1 26(G ) 1 N3 17(C ) 1 1 1 2.975 176.449 5 N2 26(G ) 1 O2 17(C ) 1 1 1 2.906 171.812 5 N6 27(A ) 1 O4 16(U ) 1 1 1 2.965 167.222 5 N6 28(A ) 1 N3 15(U ) 1 1 1 3.128 131.509 5 N6 28(A ) 1 O4 15(U ) 1 1 1 2.709 120.128 5 N6 28(A ) 1 O4 16(U ) 1 1 1 2.702 111.283 5 N6 28(A ) 1 N6 27(A ) 1 1 1 3.111 123.597 5 N1 29(G ) 1 N3 14(C ) 1 1 1 2.939 167.442 5 N2 29(G ) 1 O2 14(C ) 1 1 1 2.886 154.474 5 N1 30(G ) 1 N3 13(C ) 1 1 1 2.954 169.643 5 N2 30(G ) 1 O2 13(C ) 1 1 1 2.909 163.336 5 N4 31(C ) 1 O6 12(G ) 1 1 1 2.897 159.026 5 N4 31(C ) 1 N1 12(G ) 1 1 1 3.252 139.281 5 N4 32(C ) 1 O6 11(G ) 1 1 1 2.803 147.584 5 N6 33(A ) 1 O4 10(U ) 1 1 1 2.937 160.516 5 N1 34(G ) 1 N3 9(C ) 1 1 1 2.947 166.119 5 N2 34(G ) 1 O2 9(C ) 1 1 1 2.919 163.734 5 N6 38(A ) 1 O4 8(U ) 1 1 1 2.992 176.632 5 N3 39(U ) 1 N1 7(A ) 1 1 1 2.959 159.930 5 N4 40(C ) 1 O6 6(G ) 1 1 1 2.923 170.909 5 N3 41(U ) 1 N1 5(A ) 1 1 1 2.954 162.440 5 N3 42(U ) 1 N1 4(A ) 1 1 1 2.985 165.253 5 N4 43(C ) 1 O6 3(G ) 1 1 1 2.906 163.673 5 N4 44(C ) 1 O6 2(G ) 1 1 1 2.907 163.409 5 N4 45(C ) 1 O6 1(G ) 1 1 1 2.900 161.047 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, 1z2j_wc.csv] Trying to match bases to eachother for number of bases: 45 Considering number of hydrogen bonds: 61 Results contains number of sets of co-planar bases: 19 Results: Residue: 1( G) Mol: 1 Model: 1 Entry: 1 Residue: 45( C) Mol: 1 Model: 1 Entry: 1 Residue: 2( G) Mol: 1 Model: 1 Entry: 1 Residue: 44( C) Mol: 1 Model: 1 Entry: 1 Residue: 3( G) Mol: 1 Model: 1 Entry: 1 Residue: 43( C) Mol: 1 Model: 1 Entry: 1 Residue: 4( A) Mol: 1 Model: 1 Entry: 1 Residue: 42( U) Mol: 1 Model: 1 Entry: 1 Residue: 5( A) Mol: 1 Model: 1 Entry: 1 Residue: 41( U) Mol: 1 Model: 1 Entry: 1 Residue: 6( G) Mol: 1 Model: 1 Entry: 1 Residue: 40( C) Mol: 1 Model: 1 Entry: 1 Residue: 7( A) Mol: 1 Model: 1 Entry: 1 Residue: 39( U) Mol: 1 Model: 1 Entry: 1 Residue: 8( U) Mol: 1 Model: 1 Entry: 1 Residue: 38( A) Mol: 1 Model: 1 Entry: 1 Residue: 9( C) Mol: 1 Model: 1 Entry: 1 Residue: 34( G) Mol: 1 Model: 1 Entry: 1 Residue: 10( U) Mol: 1 Model: 1 Entry: 1 Residue: 33( A) Mol: 1 Model: 1 Entry: 1 Residue: 11( G) Mol: 1 Model: 1 Entry: 1 Residue: 32( C) Mol: 1 Model: 1 Entry: 1 Residue: 12( G) Mol: 1 Model: 1 Entry: 1 Residue: 31( C) Mol: 1 Model: 1 Entry: 1 Residue: 13( C) Mol: 1 Model: 1 Entry: 1 Residue: 30( G) Mol: 1 Model: 1 Entry: 1 Residue: 14( C) Mol: 1 Model: 1 Entry: 1 Residue: 29( G) Mol: 1 Model: 1 Entry: 1 Residue: 15( U) Mol: 1 Model: 1 Entry: 1 Residue: 28( A) Mol: 1 Model: 1 Entry: 1 Residue: 16( U) Mol: 1 Model: 1 Entry: 1 Residue: 27( A) Mol: 1 Model: 1 Entry: 1 Residue: 17( C) Mol: 1 Model: 1 Entry: 1 Residue: 26( G) Mol: 1 Model: 1 Entry: 1 Residue: 18( C) Mol: 1 Model: 1 Entry: 1 Residue: 25( G) Mol: 1 Model: 1 Entry: 1 Residue: 19( C) Mol: 1 Model: 1 Entry: 1 Residue: 24( G) Mol: 1 Model: 1 Entry: 1 Writing results to file: 1z2j_wc.csv Wattos started at: January 19, 2007 10:20:34 AM CST Wattos stopped at: January 19, 2007 10:20:43 AM CST Wattos took (#ms): 8795