Read libraries from system resource. Wattos started at: January 19, 2007 10:22:17 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/pdb2hgh.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 63320 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 3829 Found number of new bond candidates: 3332 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: 188 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 22(HIS) 1 O 18(GLN) 1 1 1 151.052 5 N 22(HIS) 1 O 19(LEU) 1 1 1 113.166 5 N 22(HIS) 1 N 21(VAL) 1 1 1 96.327 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 52(HIS) 1 O 48(ARG) 1 1 1 153.747 5 N 52(HIS) 1 O 49(LEU) 1 1 1 105.545 5 N 52(HIS) 1 N 51(ARG) 1 1 1 96.275 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 76(LEU) 1 O 73(THR) 1 1 1 111.140 5 N 76(LEU) 1 N 75(THR) 1 1 1 94.571 5 N 76(LEU) 1 OG1 75(THR) 1 1 1 110.935 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 77(TYR) 1 O 73(THR) 1 1 1 145.237 5 N 77(TYR) 1 O 74(TRP) 1 1 1 127.758 5 N 77(TYR) 1 N 76(LEU) 1 1 1 100.734 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 80(HIS) 1 O 76(LEU) 1 1 1 147.584 5 N 80(HIS) 1 O 77(TYR) 1 1 1 108.437 5 N 80(HIS) 1 N 79(LYS) 1 1 1 97.456 5 Found number of new hydrogen bonds: 188 Atom Res#(Nam) Mol# Atom Res#(Nam) Mol# Model# Entry# Value_1 Value_2 RefValue RefSD Type Minimum Average Maximum Under cutoff N 2(TYR) 1 O 13(PHE) 1 1 1 2.907 162.231 5 N 4(CYS) 1 O 11(LYS) 1 1 1 2.764 171.246 5 N 6(PHE) 1 N 5(HIS) 1 1 1 2.723 103.041 5 N 9(CYS) 1 O 6(PHE) 1 1 1 2.976 163.572 5 N 9(CYS) 1 N 8(ASN) 1 1 1 2.748 105.162 5 N 10(GLY) 1 O 4(CYS) 1 1 1 3.264 121.615 5 N 11(LYS) 1 N 10(GLY) 1 1 1 2.790 103.957 5 N 13(PHE) 1 O 2(TYR) 1 1 1 2.772 170.444 5 N 15(LYS) 1 N 14(LYS) 1 1 1 2.815 97.885 5 N 16(HIS) 1 N7 26(G ) 2 1 1 3.087 162.053 5 NE2 16(HIS) 1 N7 41(G ) 2 1 1 2.722 137.841 5 N 17(ASN) 1 N 16(HIS) 1 1 1 2.790 101.026 5 N 18(GLN) 1 O 15(LYS) 1 1 1 3.032 138.486 5 N 18(GLN) 1 N 17(ASN) 1 1 1 2.774 101.815 5 N 19(LEU) 1 O 15(LYS) 1 1 1 3.254 155.023 5 N 19(LEU) 1 N 18(GLN) 1 1 1 2.803 95.836 5 N 20(LYS) 1 O 16(HIS) 1 1 1 2.831 176.544 5 N 20(LYS) 1 N 19(LEU) 1 1 1 2.852 90.715 5 N 21(VAL) 1 O 17(ASN) 1 1 1 2.947 148.517 5 N 21(VAL) 1 N 20(LYS) 1 1 1 2.806 96.882 5 N 22(HIS) 1 O 18(GLN) 1 1 1 2.923 151.052 5 N 22(HIS) 1 O 19(LEU) 1 1 1 3.061 113.166 5 N 22(HIS) 1 N 21(VAL) 1 1 1 2.816 96.327 5 N 23(GLN) 1 O 19(LEU) 1 1 1 2.970 165.397 5 N 23(GLN) 1 N 22(HIS) 1 1 1 2.851 95.343 5 N 24(PHE) 1 O 20(LYS) 1 1 1 3.063 152.543 5 N 24(PHE) 1 N 23(GLN) 1 1 1 2.773 99.776 5 N 25(SER) 1 O 22(HIS) 1 1 1 3.033 144.896 5 N 25(SER) 1 N 24(PHE) 1 1 1 2.766 101.672 5 N 26(HIS) 1 O 23(GLN) 1 1 1 2.947 114.037 5 N 26(HIS) 1 N 25(SER) 1 1 1 2.884 95.451 5 N 27(THR) 1 O 23(GLN) 1 1 1 2.975 163.115 5 N 27(THR) 1 N 26(HIS) 1 1 1 2.792 98.906 5 OG1 27(THR) 1 O 24(PHE) 1 1 1 2.982 123.058 5 N 28(GLN) 1 O 24(PHE) 1 1 1 2.738 119.337 5 N 28(GLN) 1 N 27(THR) 1 1 1 2.699 105.567 5 NE2 28(GLN) 1 O 25(SER) 1 1 1 2.945 129.043 5 N 29(GLN) 1 N 28(GLN) 1 1 1 2.804 102.003 5 NE2 29(GLN) 1 OG1 27(THR) 1 1 1 2.896 170.383 5 N 32(TYR) 1 N 31(PRO) 1 1 1 2.846 100.469 5 N 34(CYS) 1 O 41(LYS) 1 1 1 2.871 174.125 5 N 36(HIS) 1 N 35(PRO) 1 1 1 2.742 105.237 5 N 39(CYS) 1 O 36(HIS) 1 1 1 3.128 158.433 5 N 39(CYS) 1 N 38(GLY) 1 1 1 2.723 106.276 5 N 41(LYS) 1 N 40(ASP) 1 1 1 2.712 105.113 5 N 43(PHE) 1 O 32(TYR) 1 1 1 2.723 159.295 5 N 45(LEU) 1 N 44(SER) 1 1 1 2.742 101.682 5 N 47(SER) 1 N 46(PRO) 1 1 1 2.804 97.189 5 N 48(ARG) 1 O 45(LEU) 1 1 1 3.183 126.275 5 N 48(ARG) 1 N 47(SER) 1 1 1 2.768 101.014 5 N 49(LEU) 1 O 45(LEU) 1 1 1 3.122 151.229 5 N 49(LEU) 1 N 48(ARG) 1 1 1 2.805 97.909 5 N 50(LYS) 1 O 46(PRO) 1 1 1 2.800 166.519 5 N 50(LYS) 1 N 49(LEU) 1 1 1 2.841 94.466 5 N 51(ARG) 1 O 47(SER) 1 1 1 2.884 150.247 5 N 51(ARG) 1 N 50(LYS) 1 1 1 2.826 96.403 5 N 52(HIS) 1 O 48(ARG) 1 1 1 2.910 153.747 5 N 52(HIS) 1 O 49(LEU) 1 1 1 3.032 105.545 5 N 52(HIS) 1 N 51(ARG) 1 1 1 2.820 96.275 5 ND1 52(HIS) 1 O1P 5(C ) 2 1 1 2.744 149.168 5 N 53(GLU) 1 O 49(LEU) 1 1 1 2.819 156.536 5 N 53(GLU) 1 N 52(HIS) 1 1 1 2.810 95.565 5 N 54(LYS) 1 N 53(GLU) 1 1 1 2.764 101.963 5 N 55(VAL) 1 O 52(HIS) 1 1 1 2.846 145.495 5 N 55(VAL) 1 N 54(LYS) 1 1 1 2.762 101.398 5 N 56(HIS) 1 O 53(GLU) 1 1 1 2.989 129.295 5 N 56(HIS) 1 N 55(VAL) 1 1 1 2.809 98.141 5 N 57(ALA) 1 O 53(GLU) 1 1 1 3.079 149.433 5 N 57(ALA) 1 N 56(HIS) 1 1 1 2.770 100.283 5 N 58(GLY) 1 O 54(LYS) 1 1 1 2.751 141.007 5 N 58(GLY) 1 N 57(ALA) 1 1 1 2.761 100.449 5 N 59(TYR) 1 O 71(GLY) 1 1 1 2.784 146.322 5 N 61(CYS) 1 O 69(PHE) 1 1 1 2.851 163.083 5 N 63(LYS) 1 N 62(LYS) 1 1 1 2.668 105.029 5 N 64(ASP) 1 N 63(LYS) 1 1 1 2.730 103.154 5 N 66(SER) 1 N 65(ASP) 1 1 1 2.769 101.353 5 N 67(CYS) 1 O 64(ASP) 1 1 1 3.183 147.622 5 N 67(CYS) 1 N 66(SER) 1 1 1 2.722 104.182 5 N 69(PHE) 1 N 68(SER) 1 1 1 2.719 106.321 5 N 71(GLY) 1 O 59(TYR) 1 1 1 2.871 170.511 5 N 73(THR) 1 N 72(LYS) 1 1 1 2.716 105.235 5 N 74(TRP) 1 O2* 5(C ) 2 1 1 3.210 168.500 5 NE1 74(TRP) 1 O2* 8(A ) 2 1 1 3.027 166.521 5 N 75(THR) 1 N 74(TRP) 1 1 1 2.828 96.478 5 N 75(THR) 1 O2 5(C ) 2 1 1 2.886 153.696 5 OG1 75(THR) 1 O2 5(C ) 2 1 1 3.329 129.245 5 OG1 75(THR) 1 N3 5(C ) 2 1 1 2.828 165.243 5 N 76(LEU) 1 O 73(THR) 1 1 1 3.099 111.140 5 N 76(LEU) 1 N 75(THR) 1 1 1 2.858 94.571 5 N 76(LEU) 1 OG1 75(THR) 1 1 1 3.023 110.935 5 N 77(TYR) 1 O 73(THR) 1 1 1 3.337 145.237 5 N 77(TYR) 1 O 74(TRP) 1 1 1 3.235 127.758 5 N 77(TYR) 1 N 76(LEU) 1 1 1 2.784 100.734 5 N 78(LEU) 1 O 74(TRP) 1 1 1 3.034 177.863 5 N 78(LEU) 1 N 77(TYR) 1 1 1 2.850 92.445 5 N 79(LYS) 1 O 75(THR) 1 1 1 2.780 164.781 5 N 79(LYS) 1 N 78(LEU) 1 1 1 2.831 97.166 5 N 80(HIS) 1 O 76(LEU) 1 1 1 2.914 147.584 5 N 80(HIS) 1 O 77(TYR) 1 1 1 3.107 108.437 5 N 80(HIS) 1 N 79(LYS) 1 1 1 2.820 97.456 5 N 81(VAL) 1 O 77(TYR) 1 1 1 2.879 153.900 5 N 81(VAL) 1 N 80(HIS) 1 1 1 2.817 97.722 5 N 82(ALA) 1 O 78(LEU) 1 1 1 3.236 159.819 5 N 82(ALA) 1 N 81(VAL) 1 1 1 2.833 95.964 5 N 83(GLU) 1 O 79(LYS) 1 1 1 3.324 144.070 5 N 83(GLU) 1 N 82(ALA) 1 1 1 2.775 101.156 5 N 84(CYS) 1 O 80(HIS) 1 1 1 2.822 160.392 5 N 84(CYS) 1 N 83(GLU) 1 1 1 2.842 99.389 5 N 85(HIS) 1 O 81(VAL) 1 1 1 2.827 144.200 5 N 85(HIS) 1 N 84(CYS) 1 1 1 2.756 104.174 5 N 86(GLN) 1 N 85(HIS) 1 1 1 2.808 99.912 5 N1 1(G ) 2 N3 55(C ) 2 1 1 2.955 163.467 5 N2 1(G ) 2 O2 55(C ) 2 1 1 2.861 177.725 5 N1 2(G ) 2 N3 54(C ) 2 1 1 2.927 171.959 5 N2 2(G ) 2 O2 54(C ) 2 1 1 2.834 176.098 5 N1 3(G ) 2 N3 53(C ) 2 1 1 2.940 167.461 5 N2 3(G ) 2 O2 53(C ) 2 1 1 2.838 176.555 5 N4 4(C ) 2 O6 52(G ) 2 1 1 2.951 164.736 5 O2* 5(C ) 2 OH 59(TYR) 1 1 1 2.986 111.753 5 N6 8(A ) 2 O4* 5(C ) 2 1 1 2.825 141.532 5 N4 9(C ) 2 O6 16(G ) 2 1 1 2.891 168.831 5 N4 10(C ) 2 O6 15(G ) 2 1 1 2.931 165.386 5 N3 11(U ) 2 O4 13(U ) 2 1 1 2.919 159.537 5 O2* 12(C ) 2 O2P 13(U ) 2 1 1 3.151 158.810 5 N1 15(G ) 2 N3 10(C ) 2 1 1 2.925 166.906 5 N2 15(G ) 2 O2 10(C ) 2 1 1 2.808 173.514 5 N1 16(G ) 2 N3 9(C ) 2 1 1 2.962 152.995 5 N2 16(G ) 2 O2 9(C ) 2 1 1 2.896 163.380 5 N1 17(G ) 2 O2 51(U ) 2 1 1 3.015 157.795 5 N2 17(G ) 2 N3 6(A ) 2 1 1 3.175 173.802 5 N2 17(G ) 2 O2P 8(A ) 2 1 1 2.733 158.510 5 O2* 18(C ) 2 O2P 7(U ) 2 1 1 2.992 125.893 5 N4 18(C ) 2 O6 50(G ) 2 1 1 3.011 167.614 5 N4 19(C ) 2 O6 49(G ) 2 1 1 2.899 177.128 5 N3 20(U ) 2 N1 48(A ) 2 1 1 2.840 168.924 5 N1 21(G ) 2 N3 47(C ) 2 1 1 2.940 170.929 5 N2 21(G ) 2 O2 47(C ) 2 1 1 2.820 176.106 5 N1 22(G ) 2 N3 46(C ) 2 1 1 2.942 167.025 5 N2 22(G ) 2 O2 46(C ) 2 1 1 2.821 175.560 5 N3 23(U ) 2 N1 45(A ) 2 1 1 2.815 157.927 5 N3 24(U ) 2 O4 44(U ) 2 1 1 2.807 169.923 5 O2* 25(A ) 2 O2P 24(U ) 2 1 1 2.847 172.844 5 N6 25(A ) 2 O2P 43(A ) 2 1 1 3.091 145.096 5 N6 25(A ) 2 N7 43(A ) 2 1 1 2.886 149.055 5 N1 26(G ) 2 O2P 42(A ) 2 1 1 2.772 151.377 5 N2 26(G ) 2 O4 27(U ) 2 1 1 2.739 168.577 5 N2 26(G ) 2 O5* 42(A ) 2 1 1 2.859 165.545 5 N3 27(U ) 2 N7 42(A ) 2 1 1 2.830 152.831 5 N6 28(A ) 2 O2* 41(G ) 2 1 1 2.918 160.146 5 N6 28(A ) 2 N3 41(G ) 2 1 1 2.919 144.525 5 N4 29(C ) 2 O6 40(G ) 2 1 1 2.859 174.245 5 N4 30(C ) 2 O6 39(G ) 2 1 1 2.947 163.835 5 N3 31(U ) 2 O2 38(U ) 2 1 1 3.054 169.639 5 N4 32(C ) 2 O6 37(G ) 2 1 1 2.944 164.451 5 O2* 33(U ) 2 O6 36(G ) 2 1 1 2.849 127.577 5 N4 35(C ) 2 O2P 34(U ) 2 1 1 2.843 159.803 5 N1 36(G ) 2 O2 33(U ) 2 1 1 2.948 153.616 5 N2 36(G ) 2 O2 33(U ) 2 1 1 2.974 150.319 5 N1 37(G ) 2 N3 32(C ) 2 1 1 2.900 169.149 5 N2 37(G ) 2 O2 32(C ) 2 1 1 2.798 170.901 5 N3 38(U ) 2 O4 31(U ) 2 1 1 2.772 174.071 5 N1 39(G ) 2 N3 30(C ) 2 1 1 2.917 164.640 5 N2 39(G ) 2 O2 30(C ) 2 1 1 2.784 169.535 5 N1 40(G ) 2 N3 29(C ) 2 1 1 2.927 171.231 5 N2 40(G ) 2 O2 29(C ) 2 1 1 2.853 170.910 5 O2* 41(G ) 2 O4* 42(A ) 2 1 1 2.721 155.998 5 N1 41(G ) 2 O2P 27(U ) 2 1 1 2.818 163.270 5 N2 41(G ) 2 O2P 27(U ) 2 1 1 3.163 141.382 5 N2 41(G ) 2 N7 28(A ) 2 1 1 2.987 159.120 5 N6 42(A ) 2 O2 27(U ) 2 1 1 2.956 150.746 5 N6 43(A ) 2 N7 25(A ) 2 1 1 3.019 157.242 5 N3 44(U ) 2 O2 24(U ) 2 1 1 2.891 171.664 5 N6 45(A ) 2 O4 23(U ) 2 1 1 3.034 169.777 5 N4 46(C ) 2 O6 22(G ) 2 1 1 2.909 168.876 5 N4 47(C ) 2 O6 21(G ) 2 1 1 2.922 173.073 5 N6 48(A ) 2 O4 20(U ) 2 1 1 3.024 175.659 5 N1 49(G ) 2 N3 19(C ) 2 1 1 2.916 174.287 5 N2 49(G ) 2 O2 19(C ) 2 1 1 2.838 172.075 5 N1 50(G ) 2 O6 17(G ) 2 1 1 3.175 120.788 5 N1 50(G ) 2 N3 18(C ) 2 1 1 2.975 156.589 5 N2 50(G ) 2 O4* 7(U ) 2 1 1 2.767 150.297 5 N2 50(G ) 2 O2 18(C ) 2 1 1 2.775 160.769 5 N3 51(U ) 2 O6 17(G ) 2 1 1 2.668 144.372 5 N1 52(G ) 2 N3 4(C ) 2 1 1 2.930 164.293 5 N2 52(G ) 2 O2 4(C ) 2 1 1 2.793 171.032 5 N4 53(C ) 2 O6 3(G ) 2 1 1 2.917 170.273 5 N4 54(C ) 2 O6 2(G ) 2 1 1 2.888 175.132 5 N4 55(C ) 2 O6 1(G ) 2 1 1 2.901 173.297 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, 2hgh_wc.csv] Trying to match bases to eachother for number of bases: 55 Considering number of hydrogen bonds: 188 Results contains number of sets of co-planar bases: 15 Results: Residue: 1( G) Mol: 2 Model: 1 Entry: 1 Residue: 55( C) Mol: 2 Model: 1 Entry: 1 Residue: 2( G) Mol: 2 Model: 1 Entry: 1 Residue: 54( C) Mol: 2 Model: 1 Entry: 1 Residue: 3( G) Mol: 2 Model: 1 Entry: 1 Residue: 53( C) Mol: 2 Model: 1 Entry: 1 Residue: 4( C) Mol: 2 Model: 1 Entry: 1 Residue: 52( G) Mol: 2 Model: 1 Entry: 1 Residue: 9( C) Mol: 2 Model: 1 Entry: 1 Residue: 16( G) Mol: 2 Model: 1 Entry: 1 Residue: 10( C) Mol: 2 Model: 1 Entry: 1 Residue: 15( G) Mol: 2 Model: 1 Entry: 1 Residue: 18( C) Mol: 2 Model: 1 Entry: 1 Residue: 50( G) Mol: 2 Model: 1 Entry: 1 Residue: 19( C) Mol: 2 Model: 1 Entry: 1 Residue: 49( G) Mol: 2 Model: 1 Entry: 1 Residue: 20( U) Mol: 2 Model: 1 Entry: 1 Residue: 48( A) Mol: 2 Model: 1 Entry: 1 Residue: 21( G) Mol: 2 Model: 1 Entry: 1 Residue: 47( C) Mol: 2 Model: 1 Entry: 1 Residue: 22( G) Mol: 2 Model: 1 Entry: 1 Residue: 46( C) Mol: 2 Model: 1 Entry: 1 Residue: 23( U) Mol: 2 Model: 1 Entry: 1 Residue: 45( A) Mol: 2 Model: 1 Entry: 1 Residue: 29( C) Mol: 2 Model: 1 Entry: 1 Residue: 40( G) Mol: 2 Model: 1 Entry: 1 Residue: 30( C) Mol: 2 Model: 1 Entry: 1 Residue: 39( G) Mol: 2 Model: 1 Entry: 1 Residue: 32( C) Mol: 2 Model: 1 Entry: 1 Residue: 37( G) Mol: 2 Model: 1 Entry: 1 Writing results to file: 2hgh_wc.csv Wattos started at: January 19, 2007 10:22:17 AM CST Wattos stopped at: January 19, 2007 10:22:29 AM CST Wattos took (#ms): 11620