Read libraries from system resource. Wattos started at: January 19, 2007 10:17:15 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/pdb1kpz.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 904 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 1191 Found number of new bond candidates: 975 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: 80 WARNING: Got more than two hydrogen bond for this donor (N2). 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 N2 4(G ) 1 O2 13(C ) 1 1 1 155.084 5 N2 4(G ) 1 N3 13(C ) 1 1 1 142.434 5 N2 4(G ) 1 N6 20(A ) 1 1 1 117.719 5 N2 4(G ) 1 N6 22(A ) 1 1 1 102.765 5 WARNING: Got more than two hydrogen bond for this donor (N2). 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 N2 5(G ) 1 O2 12(C ) 1 1 1 162.606 5 N2 5(G ) 1 N6 23(A ) 1 1 1 132.106 5 N2 5(G ) 1 N1 23(A ) 1 1 1 154.906 5 N2 5(G ) 1 N6 24(A ) 1 1 1 98.060 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 9(A ) 1 O2 7(CH ) 1 1 1 119.189 5 N6 9(A ) 1 O6 25(G ) 1 1 1 127.355 5 N6 9(A ) 1 O4 26(U ) 1 1 1 133.188 5 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 13(C ) 1 O6 4(G ) 1 1 1 155.415 5 N4 13(C ) 1 N1 4(G ) 1 1 1 139.352 5 N4 13(C ) 1 O6 14(G ) 1 1 1 108.729 5 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 14(G ) 1 O2 3(C ) 1 1 1 151.306 5 N2 14(G ) 1 N3 3(C ) 1 1 1 147.115 5 N2 14(G ) 1 N7 20(A ) 1 1 1 147.039 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 20(A ) 1 N2 4(G ) 1 1 1 97.672 5 N6 20(A ) 1 N3 4(G ) 1 1 1 151.611 5 N6 20(A ) 1 O2* 14(G ) 1 1 1 123.226 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 23(A ) 1 N2 5(G ) 1 1 1 135.031 5 N6 23(A ) 1 N3 5(G ) 1 1 1 119.554 5 N6 23(A ) 1 N1 6(U ) 1 1 1 131.226 5 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 25(G ) 1 O2 10(C ) 1 1 1 147.897 5 N2 25(G ) 1 N3 10(C ) 1 1 1 144.412 5 N2 25(G ) 1 O4* 12(C ) 1 1 1 99.211 5 Found number of new hydrogen bonds: 80 Atom Res#(Nam) Mol# Atom Res#(Nam) Mol# Model# Entry# Value_1 Value_2 RefValue RefSD Type Minimum Average Maximum Under cutoff N3 1(U ) 1 N1 16(A ) 1 1 1 3.106 127.678 5 N4 2(C ) 1 O6 15(G ) 1 1 1 2.731 174.341 5 N4 2(C ) 1 N6 16(A ) 1 1 1 3.305 121.780 5 O2* 3(C ) 1 O3* 19(A ) 1 1 1 2.327 95.709 5 N4 3(C ) 1 O6 14(G ) 1 1 1 2.803 156.653 5 N4 3(C ) 1 N1 14(G ) 1 1 1 3.234 140.452 5 N1 4(G ) 1 N3 13(C ) 1 1 1 2.895 161.809 5 N1 4(G ) 1 N4 13(C ) 1 1 1 3.205 135.348 5 N2 4(G ) 1 O2 13(C ) 1 1 1 2.852 155.084 5 N2 4(G ) 1 N3 13(C ) 1 1 1 3.210 142.434 5 N2 4(G ) 1 N6 20(A ) 1 1 1 2.889 117.719 5 N2 4(G ) 1 N6 22(A ) 1 1 1 2.763 102.765 5 N1 5(G ) 1 O2 12(C ) 1 1 1 3.202 148.942 5 N1 5(G ) 1 N3 12(C ) 1 1 1 2.966 148.509 5 N2 5(G ) 1 O2 12(C ) 1 1 1 2.964 162.606 5 N2 5(G ) 1 N6 23(A ) 1 1 1 2.859 132.106 5 N2 5(G ) 1 N1 23(A ) 1 1 1 2.684 154.906 5 N2 5(G ) 1 N6 24(A ) 1 1 1 2.964 98.060 5 N3 6(U ) 1 N7 24(A ) 1 1 1 2.845 166.669 5 N3 7(CH ) 1 O6 25(G ) 1 1 1 3.031 140.307 5 N4 7(CH ) 1 N7 25(G ) 1 1 1 2.909 168.217 5 N1 8(G ) 1 N3 27(C ) 1 1 1 2.975 164.290 5 N2 8(G ) 1 O2 27(C ) 1 1 1 3.009 173.053 5 N2 8(G ) 1 N3 28(A ) 1 1 1 3.070 103.606 5 O2* 9(A ) 1 O3* 28(A ) 1 1 1 3.027 103.771 5 O2* 9(A ) 1 O2* 28(A ) 1 1 1 3.224 161.507 5 N6 9(A ) 1 O2 7(CH ) 1 1 1 2.787 119.189 5 N6 9(A ) 1 O6 25(G ) 1 1 1 3.117 127.355 5 N6 9(A ) 1 O4 26(U ) 1 1 1 2.632 133.188 5 N4 10(C ) 1 O6 25(G ) 1 1 1 2.900 130.377 5 N4 10(C ) 1 N1 25(G ) 1 1 1 3.175 135.460 5 O2* 12(C ) 1 N1 24(A ) 1 1 1 2.731 127.908 5 N4 12(C ) 1 O6 5(G ) 1 1 1 2.770 155.912 5 O2* 13(C ) 1 N1 22(A ) 1 1 1 2.738 118.889 5 N4 13(C ) 1 O6 4(G ) 1 1 1 2.748 155.415 5 N4 13(C ) 1 N1 4(G ) 1 1 1 3.205 139.352 5 N4 13(C ) 1 O6 14(G ) 1 1 1 3.082 108.729 5 N1 14(G ) 1 N3 3(C ) 1 1 1 3.015 159.657 5 N1 14(G ) 1 N4 3(C ) 1 1 1 3.234 138.295 5 N2 14(G ) 1 O2 3(C ) 1 1 1 3.020 151.306 5 N2 14(G ) 1 N3 3(C ) 1 1 1 3.203 147.115 5 N2 14(G ) 1 N7 20(A ) 1 1 1 3.089 147.039 5 O2* 15(G ) 1 N1 19(A ) 1 1 1 2.276 118.516 5 O2* 15(G ) 1 N3 20(A ) 1 1 1 2.620 104.861 5 N1 15(G ) 1 N3 2(C ) 1 1 1 2.993 167.110 5 N2 15(G ) 1 O2 2(C ) 1 1 1 3.169 171.962 5 N2 15(G ) 1 N3 19(A ) 1 1 1 2.716 149.984 5 O2* 16(A ) 1 O4* 17(G ) 1 1 1 2.681 100.835 5 N6 16(A ) 1 O4 1(U ) 1 1 1 2.537 134.654 5 O2* 17(G ) 1 N3 18(A ) 1 1 1 2.747 137.080 5 O2* 18(A ) 1 O2* 19(A ) 1 1 1 2.842 140.657 5 N6 18(A ) 1 O2 1(U ) 1 1 1 3.087 104.017 5 N6 18(A ) 1 N3 17(G ) 1 1 1 2.595 98.260 5 O2* 19(A ) 1 N3 18(A ) 1 1 1 2.798 159.730 5 N6 19(A ) 1 O2* 15(G ) 1 1 1 3.251 118.028 5 O2* 20(A ) 1 O5* 21(C ) 1 1 1 2.826 170.415 5 O2* 20(A ) 1 O4* 21(C ) 1 1 1 2.892 107.256 5 N6 20(A ) 1 N2 4(G ) 1 1 1 2.889 97.672 5 N6 20(A ) 1 N3 4(G ) 1 1 1 2.907 151.611 5 N6 20(A ) 1 O2* 14(G ) 1 1 1 3.109 123.226 5 O2* 21(C ) 1 O5* 22(A ) 1 1 1 2.286 102.636 5 O2* 21(C ) 1 O4* 22(A ) 1 1 1 3.324 170.751 5 N6 22(A ) 1 N2 4(G ) 1 1 1 2.763 104.556 5 N6 22(A ) 1 O2 13(C ) 1 1 1 2.379 155.119 5 O2* 23(A ) 1 O2P 24(A ) 1 1 1 3.108 121.779 5 O2* 23(A ) 1 O5* 24(A ) 1 1 1 2.651 164.632 5 N6 23(A ) 1 N2 5(G ) 1 1 1 2.859 135.031 5 N6 23(A ) 1 N3 5(G ) 1 1 1 2.760 119.554 5 N6 23(A ) 1 N1 6(U ) 1 1 1 2.707 131.226 5 O2* 24(A ) 1 O4* 25(G ) 1 1 1 2.403 148.262 5 N6 24(A ) 1 O4 6(U ) 1 1 1 2.351 99.360 5 N6 24(A ) 1 N1 23(A ) 1 1 1 2.707 108.540 5 N1 25(G ) 1 N3 10(C ) 1 1 1 2.876 155.882 5 N1 25(G ) 1 N4 10(C ) 1 1 1 3.175 138.910 5 N2 25(G ) 1 O2 10(C ) 1 1 1 2.921 147.897 5 N2 25(G ) 1 N3 10(C ) 1 1 1 3.061 144.412 5 N2 25(G ) 1 O4* 12(C ) 1 1 1 2.565 99.211 5 N3 26(U ) 1 N1 9(A ) 1 1 1 3.074 125.547 5 N4 27(C ) 1 O6 8(G ) 1 1 1 2.784 167.506 5 O2* 28(A ) 1 O2* 9(A ) 1 1 1 3.224 176.353 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, 1kpz_wc.csv] Trying to match bases to eachother for number of bases: 27 Considering number of hydrogen bonds: 80 Results contains number of sets of co-planar bases: 8 Results: Residue: 1( U) Mol: 1 Model: 1 Entry: 1 Residue: 16( A) Mol: 1 Model: 1 Entry: 1 Residue: 2( C) Mol: 1 Model: 1 Entry: 1 Residue: 15( G) Mol: 1 Model: 1 Entry: 1 Residue: 3( C) Mol: 1 Model: 1 Entry: 1 Residue: 14( G) Mol: 1 Model: 1 Entry: 1 Residue: 4( G) Mol: 1 Model: 1 Entry: 1 Residue: 13( C) Mol: 1 Model: 1 Entry: 1 Residue: 5( G) Mol: 1 Model: 1 Entry: 1 Residue: 12( C) Mol: 1 Model: 1 Entry: 1 Residue: 8( G) Mol: 1 Model: 1 Entry: 1 Residue: 27( C) Mol: 1 Model: 1 Entry: 1 Residue: 9( A) Mol: 1 Model: 1 Entry: 1 Residue: 26( U) Mol: 1 Model: 1 Entry: 1 Residue: 10( C) Mol: 1 Model: 1 Entry: 1 Residue: 25( G) Mol: 1 Model: 1 Entry: 1 Writing results to file: 1kpz_wc.csv Wattos started at: January 19, 2007 10:17:15 AM CST Wattos stopped at: January 19, 2007 10:17:18 AM CST Wattos took (#ms): 2713