Read libraries from system resource. Wattos started at: January 19, 2007 10:21:41 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/pdb2ese.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 42000 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 2462 Found number of new bond candidates: 2169 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: 124 WARNING: Got more than two hydrogen bond for this donor (N). 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 N 37(GLU) 1 O 34(PRO) 1 1 1 158.121 5 N 37(GLU) 1 O 35(TRP) 1 1 1 98.240 5 N 37(GLU) 1 N 36(ILE) 1 1 1 103.412 5 WARNING: Got more than two hydrogen bond for this donor (N). 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 N 38(LEU) 1 O 34(PRO) 1 1 1 170.928 5 N 38(LEU) 1 O 35(TRP) 1 1 1 102.169 5 N 38(LEU) 1 N 37(GLU) 1 1 1 97.183 5 WARNING: Got more than two hydrogen bond for this donor (N). 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 N 49(LYS) 1 O 45(THR) 1 1 1 125.618 5 N 49(LYS) 1 O 46(LEU) 1 1 1 131.061 5 N 49(LYS) 1 N 48(LYS) 1 1 1 102.251 5 WARNING: Got more than two hydrogen bond for this donor (N). 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 N 59(LYS) 1 O 55(GLY) 1 1 1 149.263 5 N 59(LYS) 1 O 56(ALA) 1 1 1 124.674 5 N 59(LYS) 1 N 58(ARG) 1 1 1 98.954 5 WARNING: Got more than two hydrogen bond for this donor (N). 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 N 60(LEU) 1 O 56(ALA) 1 1 1 138.551 5 N 60(LEU) 1 O 57(ARG) 1 1 1 127.985 5 N 60(LEU) 1 N 59(LYS) 1 1 1 99.211 5 WARNING: Got more than two hydrogen bond for this donor (N). 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 N 69(ASP) 1 O 65(GLY) 1 1 1 132.527 5 N 69(ASP) 1 O 66(ILE) 1 1 1 124.321 5 N 69(ASP) 1 N 68(ILE) 1 1 1 99.109 5 WARNING: Got more than two hydrogen bond for this donor (N). 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 N 71(LYS) 1 O 67(VAL) 1 1 1 141.157 5 N 71(LYS) 1 O 68(ILE) 1 1 1 118.946 5 N 71(LYS) 1 N 70(TYR) 1 1 1 100.797 5 Found number of new hydrogen bonds: 124 Atom Res#(Nam) Mol# Atom Res#(Nam) Mol# Model# Entry# Value_1 Value_2 RefValue RefSD Type Minimum Average Maximum Under cutoff N 7(ASP) 1 O 5(LEU) 1 1 1 2.936 152.989 5 N 9(LYS) 1 OD1 7(ASP) 1 1 1 2.973 132.444 5 N 9(LYS) 1 N 8(PRO) 1 1 1 2.752 103.683 5 N 10(LEU) 1 OD1 7(ASP) 1 1 1 3.058 158.557 5 N 10(LEU) 1 N 9(LYS) 1 1 1 2.765 96.265 5 N 11(LEU) 1 O 7(ASP) 1 1 1 2.818 170.940 5 N 11(LEU) 1 N 10(LEU) 1 1 1 2.889 93.573 5 N 12(LYS) 1 O 8(PRO) 1 1 1 2.878 163.752 5 N 13(ASN) 1 O 9(LYS) 1 1 1 3.049 134.651 5 N 16(MET) 1 O 13(ASN) 1 1 1 2.830 143.016 5 N 16(MET) 1 N 15(PRO) 1 1 1 2.922 98.779 5 N 17(TRP) 1 O 13(ASN) 1 1 1 3.204 154.631 5 N 17(TRP) 1 N 16(MET) 1 1 1 2.783 98.778 5 N 18(LEU) 1 O 14(ILE) 1 1 1 3.092 171.267 5 N 19(LYS) 1 O 15(PRO) 1 1 1 2.901 141.367 5 N 19(LYS) 1 N 18(LEU) 1 1 1 2.839 96.777 5 N 21(LEU) 1 O 18(LEU) 1 1 1 3.034 148.804 5 N 21(LEU) 1 N 20(SER) 1 1 1 2.827 108.015 5 N 22(ARG) 1 N 21(LEU) 1 1 1 2.766 104.863 5 N 23(LEU) 1 N 22(ARG) 1 1 1 2.774 106.086 5 N 24(HIS) 1 N 23(LEU) 1 1 1 2.717 105.373 5 N 25(LYS) 1 O 23(LEU) 1 1 1 2.762 118.097 5 N 25(LYS) 1 N 24(HIS) 1 1 1 2.848 104.891 5 N 26(TYR) 1 N 25(LYS) 1 1 1 2.666 103.047 5 N 29(ALA) 1 N 28(ASP) 1 1 1 2.749 103.611 5 N 30(LEU) 1 N 29(ALA) 1 1 1 2.711 101.959 5 N 31(SER) 1 O 27(SER) 1 1 1 2.816 125.407 5 N 31(SER) 1 N 30(LEU) 1 1 1 2.722 102.949 5 N 33(THR) 1 N 32(GLY) 1 1 1 2.735 105.639 5 NE1 35(TRP) 1 O 80(ALA) 1 1 1 2.869 142.831 5 N 37(GLU) 1 O 34(PRO) 1 1 1 3.122 158.121 5 N 37(GLU) 1 O 35(TRP) 1 1 1 2.744 98.240 5 N 37(GLU) 1 N 36(ILE) 1 1 1 2.911 103.412 5 N 38(LEU) 1 O 34(PRO) 1 1 1 2.857 170.928 5 N 38(LEU) 1 O 35(TRP) 1 1 1 3.065 102.169 5 N 38(LEU) 1 N 37(GLU) 1 1 1 2.825 97.183 5 N 39(ILE) 1 O 35(TRP) 1 1 1 3.117 170.620 5 N 39(ILE) 1 N 38(LEU) 1 1 1 2.937 95.578 5 N 40(TYR) 1 O 37(GLU) 1 1 1 2.864 133.584 5 N 40(TYR) 1 N 39(ILE) 1 1 1 2.927 98.727 5 N 41(LEU) 1 O 38(LEU) 1 1 1 2.786 158.946 5 N 41(LEU) 1 N 40(TYR) 1 1 1 2.796 103.151 5 N 44(GLU) 1 N 43(ASP) 1 1 1 2.824 98.118 5 N 45(THR) 1 N 44(GLU) 1 1 1 2.865 96.683 5 N 46(LEU) 1 O 42(ASP) 1 1 1 2.848 159.003 5 N 46(LEU) 1 N 45(THR) 1 1 1 2.853 94.983 5 N 47(GLU) 1 O 43(ASP) 1 1 1 3.222 162.171 5 N 48(LYS) 1 O 44(GLU) 1 1 1 3.175 155.843 5 N 48(LYS) 1 N 47(GLU) 1 1 1 2.812 97.214 5 N 49(LYS) 1 O 45(THR) 1 1 1 2.776 125.618 5 N 49(LYS) 1 O 46(LEU) 1 1 1 2.981 131.061 5 N 49(LYS) 1 N 48(LYS) 1 1 1 2.815 102.251 5 N 50(GLY) 1 N 49(LYS) 1 1 1 2.751 102.254 5 N 51(VAL) 1 O 46(LEU) 1 1 1 2.842 158.502 5 N 51(VAL) 1 N 50(GLY) 1 1 1 2.758 104.626 5 N 53(ALA) 1 N 52(LEU) 1 1 1 2.849 100.651 5 N 54(LEU) 1 O2P 11(U ) 2 1 1 2.814 158.856 5 N 55(GLY) 1 N 54(LEU) 1 1 1 2.846 96.526 5 N 57(ARG) 1 O 53(ALA) 1 1 1 3.211 170.651 5 N 58(ARG) 1 O 54(LEU) 1 1 1 3.104 168.291 5 N 59(LYS) 1 O 55(GLY) 1 1 1 3.060 149.263 5 N 59(LYS) 1 O 56(ALA) 1 1 1 2.941 124.674 5 N 59(LYS) 1 N 58(ARG) 1 1 1 2.815 98.954 5 N 60(LEU) 1 O 56(ALA) 1 1 1 3.027 138.551 5 N 60(LEU) 1 O 57(ARG) 1 1 1 3.065 127.985 5 N 60(LEU) 1 N 59(LYS) 1 1 1 2.811 99.211 5 N 61(LEU) 1 O 57(ARG) 1 1 1 3.151 160.921 5 N 61(LEU) 1 N 60(LEU) 1 1 1 2.864 94.226 5 N 62(LYS) 1 O 58(ARG) 1 1 1 3.199 156.441 5 N 62(LYS) 1 N 61(LEU) 1 1 1 2.811 97.504 5 N 63(ALA) 1 O 59(LYS) 1 1 1 3.017 172.132 5 N 64(PHE) 1 O 60(LEU) 1 1 1 2.810 171.594 5 N 64(PHE) 1 N 63(ALA) 1 1 1 2.853 98.700 5 N 65(GLY) 1 O 61(LEU) 1 1 1 2.953 136.363 5 N 65(GLY) 1 O 62(LYS) 1 1 1 3.007 126.173 5 N 66(ILE) 1 O 62(LYS) 1 1 1 3.223 145.327 5 N 66(ILE) 1 N 65(GLY) 1 1 1 2.739 102.428 5 N 67(VAL) 1 O 63(ALA) 1 1 1 3.265 166.728 5 N 68(ILE) 1 O 64(PHE) 1 1 1 3.030 165.824 5 N 69(ASP) 1 O 65(GLY) 1 1 1 3.129 132.527 5 N 69(ASP) 1 O 66(ILE) 1 1 1 2.843 124.321 5 N 69(ASP) 1 N 68(ILE) 1 1 1 2.873 99.109 5 N 70(TYR) 1 O 66(ILE) 1 1 1 3.165 160.968 5 N 70(TYR) 1 N 69(ASP) 1 1 1 2.858 92.209 5 N 71(LYS) 1 O 67(VAL) 1 1 1 2.823 141.157 5 N 71(LYS) 1 O 68(ILE) 1 1 1 3.103 118.946 5 N 71(LYS) 1 N 70(TYR) 1 1 1 2.847 100.797 5 N 72(GLU) 1 O 68(ILE) 1 1 1 2.795 156.172 5 N 72(GLU) 1 N 71(LYS) 1 1 1 2.783 97.509 5 N 73(ARG) 1 N 72(GLU) 1 1 1 2.726 104.013 5 N 74(ASP) 1 O 70(TYR) 1 1 1 2.778 132.417 5 N 74(ASP) 1 N 73(ARG) 1 1 1 2.736 100.983 5 N 75(LEU) 1 O 70(TYR) 1 1 1 3.156 144.764 5 N 75(LEU) 1 N 74(ASP) 1 1 1 2.785 102.573 5 N 76(ILE) 1 N 75(LEU) 1 1 1 2.694 107.297 5 N 79(SER) 1 N 78(ARG) 1 1 1 2.758 104.307 5 N 80(ALA) 1 N 79(SER) 1 1 1 2.819 102.088 5 N 81(TYR) 1 N 80(ALA) 1 1 1 2.767 101.940 5 N1 1(G ) 2 N3 23(C ) 2 1 1 2.941 166.646 5 N2 1(G ) 2 O2 23(C ) 2 1 1 2.819 167.413 5 N1 2(G ) 2 N3 22(C ) 2 1 1 2.927 174.849 5 N2 2(G ) 2 O2 22(C ) 2 1 1 2.856 177.532 5 N6 3(A ) 2 O4 21(U ) 2 1 1 2.874 168.824 5 N1 4(G ) 2 O2 20(U ) 2 1 1 2.849 177.401 5 N6 5(A ) 2 O4 19(U ) 2 1 1 2.851 164.219 5 N1 6(G ) 2 O2 18(U ) 2 1 1 2.794 178.669 5 N1 7(G ) 2 N3 17(C ) 2 1 1 2.893 167.418 5 N2 7(G ) 2 O2 17(C ) 2 1 1 2.888 173.936 5 N4 8(C ) 2 O6 16(G ) 2 1 1 2.850 170.829 5 N3 9(U ) 2 N1 15(A ) 2 1 1 2.932 173.857 5 N4 10(C ) 2 O4 9(U ) 2 1 1 3.039 135.774 5 N4 10(C ) 2 O6 13(G ) 2 1 1 2.927 171.430 5 N1 13(G ) 2 N3 10(C ) 2 1 1 2.928 160.717 5 N2 13(G ) 2 O2 10(C ) 2 1 1 2.815 170.926 5 N6 15(A ) 2 O4 9(U ) 2 1 1 2.830 167.338 5 N1 16(G ) 2 N3 8(C ) 2 1 1 2.878 169.108 5 N2 16(G ) 2 O2 8(C ) 2 1 1 2.842 173.955 5 N4 17(C ) 2 O6 7(G ) 2 1 1 2.847 171.006 5 N3 18(U ) 2 O6 6(G ) 2 1 1 2.784 164.736 5 N3 19(U ) 2 N1 5(A ) 2 1 1 2.907 170.599 5 N3 20(U ) 2 O6 4(G ) 2 1 1 2.809 170.849 5 N3 21(U ) 2 N1 3(A ) 2 1 1 2.859 168.848 5 N4 22(C ) 2 O6 2(G ) 2 1 1 2.848 175.119 5 N4 23(C ) 2 O6 1(G ) 2 1 1 2.931 173.890 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, 2ese_wc.csv] Trying to match bases to eachother for number of bases: 23 Considering number of hydrogen bonds: 124 Results contains number of sets of co-planar bases: 8 Results: Residue: 1( G) Mol: 2 Model: 1 Entry: 1 Residue: 23( C) Mol: 2 Model: 1 Entry: 1 Residue: 2( G) Mol: 2 Model: 1 Entry: 1 Residue: 22( C) Mol: 2 Model: 1 Entry: 1 Residue: 3( A) Mol: 2 Model: 1 Entry: 1 Residue: 21( U) Mol: 2 Model: 1 Entry: 1 Residue: 5( A) Mol: 2 Model: 1 Entry: 1 Residue: 19( U) Mol: 2 Model: 1 Entry: 1 Residue: 7( G) Mol: 2 Model: 1 Entry: 1 Residue: 17( C) Mol: 2 Model: 1 Entry: 1 Residue: 8( C) Mol: 2 Model: 1 Entry: 1 Residue: 16( G) Mol: 2 Model: 1 Entry: 1 Residue: 9( U) Mol: 2 Model: 1 Entry: 1 Residue: 15( A) Mol: 2 Model: 1 Entry: 1 Residue: 10( C) Mol: 2 Model: 1 Entry: 1 Residue: 13( G) Mol: 2 Model: 1 Entry: 1 Writing results to file: 2ese_wc.csv Wattos started at: January 19, 2007 10:21:41 AM CST Wattos stopped at: January 19, 2007 10:21:51 AM CST Wattos took (#ms): 9822