Read libraries from system resource. Wattos started at: January 19, 2007 10:16:34 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/pdb1fje.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 65436 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 4019 Found number of new bond candidates: 3516 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: 168 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 35(SER) 2 O 31(LYS) 2 1 1 130.441 5 N 35(SER) 2 O 32(VAL) 2 1 1 116.106 5 N 35(SER) 2 N 34(ILE) 2 1 1 101.638 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 39(ALA) 2 O 35(SER) 2 1 1 132.689 5 N 39(ALA) 2 O 36(GLU) 2 1 1 123.010 5 N 39(ALA) 2 N 38(PHE) 2 1 1 102.138 5 Found number of new hydrogen bonds: 168 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 22(C ) 1 1 1 2.808 170.088 5 N2 1(G ) 1 O2 22(C ) 1 1 1 2.680 175.574 5 N1 2(G ) 1 N3 21(C ) 1 1 1 2.765 165.765 5 N2 2(G ) 1 O2 21(C ) 1 1 1 3.069 173.235 5 N4 3(C ) 1 O6 20(G ) 1 1 1 2.841 153.088 5 N4 4(C ) 1 O6 19(G ) 1 1 1 3.304 161.429 5 N2 5(G ) 1 N7 18(A ) 1 1 1 2.400 134.372 5 N2 5(G ) 1 N6 18(A ) 1 1 1 3.081 125.442 5 N6 6(A ) 1 O2 17(U ) 1 1 1 2.630 126.753 5 N6 7(A ) 1 N7 15(A ) 1 1 1 3.317 171.771 5 N6 8(A ) 1 O2* 14(A ) 1 1 1 2.599 125.808 5 N6 15(A ) 1 N7 7(A ) 1 1 1 2.651 156.541 5 N2 16(G ) 1 O4 17(U ) 1 1 1 3.006 172.469 5 N3 17(U ) 1 N7 6(A ) 1 1 1 3.128 154.987 5 N6 18(A ) 1 N2 5(G ) 1 1 1 3.081 152.067 5 N6 18(A ) 1 N3 5(G ) 1 1 1 2.425 133.552 5 N1 19(G ) 1 O2 4(C ) 1 1 1 3.247 123.164 5 N1 19(G ) 1 N3 4(C ) 1 1 1 2.868 177.600 5 N2 19(G ) 1 O2 4(C ) 1 1 1 2.330 177.380 5 N1 20(G ) 1 N3 3(C ) 1 1 1 3.047 151.256 5 N2 20(G ) 1 O2 3(C ) 1 1 1 3.181 158.409 5 N4 21(C ) 1 O6 2(G ) 1 1 1 2.349 176.971 5 N4 22(C ) 1 O6 1(G ) 1 1 1 2.827 166.168 5 N 12(THR) 2 N 11(THR) 2 1 1 2.700 105.163 5 N 14(PHE) 2 N 13(PRO) 2 1 1 2.765 101.004 5 N 16(LEU) 2 O 59(VAL) 2 1 1 3.031 133.808 5 N 17(PHE) 2 O 86(GLU) 2 1 1 3.064 157.728 5 N 18(ILE) 2 O 57(GLY) 2 1 1 2.719 164.555 5 N 19(GLY) 2 O 84(LYS) 2 1 1 2.893 145.253 5 N 21(LEU) 2 O 55(LYS) 2 1 1 2.832 151.238 5 N 22(ASN) 2 O 54(ARG) 2 1 1 2.518 141.798 5 N 24(ASN) 2 N 23(PRO) 2 1 1 2.727 105.098 5 N 25(LYS) 2 N 24(ASN) 2 1 1 2.736 101.395 5 N 29(GLU) 2 N 28(ALA) 2 1 1 2.716 101.407 5 N 30(LEU) 2 O 26(SER) 2 1 1 3.164 141.930 5 N 30(LEU) 2 N 29(GLU) 2 1 1 2.780 99.140 5 N 31(LYS) 2 O 27(VAL) 2 1 1 3.112 168.212 5 N 31(LYS) 2 N 30(LEU) 2 1 1 2.783 97.470 5 N 32(VAL) 2 O 28(ALA) 2 1 1 2.684 150.467 5 N 32(VAL) 2 N 31(LYS) 2 1 1 2.769 100.719 5 N 33(ALA) 2 O 29(GLU) 2 1 1 3.020 151.628 5 N 33(ALA) 2 N 32(VAL) 2 1 1 2.772 99.221 5 N 34(ILE) 2 O 30(LEU) 2 1 1 3.265 157.981 5 N 34(ILE) 2 N 33(ALA) 2 1 1 2.728 98.480 5 N 35(SER) 2 O 31(LYS) 2 1 1 2.661 130.441 5 N 35(SER) 2 O 32(VAL) 2 1 1 3.018 116.106 5 N 35(SER) 2 N 34(ILE) 2 1 1 2.702 101.638 5 N 36(GLU) 2 O 32(VAL) 2 1 1 2.630 146.918 5 N 36(GLU) 2 N 35(SER) 2 1 1 2.718 101.895 5 N 37(LEU) 2 O 33(ALA) 2 1 1 3.014 157.161 5 N 37(LEU) 2 N 36(GLU) 2 1 1 2.749 99.217 5 N 38(PHE) 2 O 34(ILE) 2 1 1 3.127 138.474 5 N 38(PHE) 2 N 37(LEU) 2 1 1 2.717 101.052 5 N 39(ALA) 2 O 35(SER) 2 1 1 3.092 132.689 5 N 39(ALA) 2 O 36(GLU) 2 1 1 3.008 123.010 5 N 39(ALA) 2 N 38(PHE) 2 1 1 2.683 102.138 5 N 40(LYS) 2 O 36(GLU) 2 1 1 3.091 144.590 5 N 40(LYS) 2 N 39(ALA) 2 1 1 2.699 101.761 5 N 41(ASN) 2 N 40(LYS) 2 1 1 2.703 101.942 5 N 42(ASP) 2 N 41(ASN) 2 1 1 2.720 103.511 5 N 43(LEU) 2 O 38(PHE) 2 1 1 2.752 168.372 5 N 43(LEU) 2 N 42(ASP) 2 1 1 2.681 101.452 5 N 46(VAL) 2 O 60(ASP) 2 1 1 2.688 142.512 5 N 47(ASP) 2 N 46(VAL) 2 1 1 2.735 101.214 5 N 47(ASP) 2 O 60(ASP) 2 1 1 3.300 160.624 5 N 49(ARG) 2 O 58(TYR) 2 1 1 3.225 155.448 5 N 54(ARG) 2 N 53(ASN) 2 1 1 2.644 102.649 5 N 55(LYS) 2 OD1 53(ASN) 2 1 1 2.410 113.145 5 N 55(LYS) 2 N 54(ARG) 2 1 1 2.722 103.287 5 N 56(PHE) 2 O 51(GLY) 2 1 1 3.209 168.774 5 N 57(GLY) 2 O 18(ILE) 2 1 1 2.759 136.481 5 N 58(TYR) 2 O 49(ARG) 2 1 1 3.328 175.066 5 N 59(VAL) 2 O 16(LEU) 2 1 1 2.965 133.931 5 N 60(ASP) 2 O 47(ASP) 2 1 1 2.550 117.076 5 N 61(PHE) 2 O 14(PHE) 2 1 1 2.466 165.321 5 N 63(SER) 2 N 62(GLU) 2 1 1 2.731 105.806 5 N 65(GLU) 2 N 64(ALA) 2 1 1 2.589 104.565 5 N 66(ASP) 2 OG 63(SER) 2 1 1 3.055 130.577 5 N 66(ASP) 2 N 65(GLU) 2 1 1 2.699 102.591 5 N 67(LEU) 2 O 63(SER) 2 1 1 3.085 142.357 5 N 67(LEU) 2 N 66(ASP) 2 1 1 2.645 101.473 5 N 68(GLU) 2 O 64(ALA) 2 1 1 2.953 147.549 5 N 68(GLU) 2 N 67(LEU) 2 1 1 2.750 99.644 5 N 69(LYS) 2 O 65(GLU) 2 1 1 3.211 148.010 5 N 69(LYS) 2 N 68(GLU) 2 1 1 2.755 99.599 5 N 70(ALA) 2 O 66(ASP) 2 1 1 2.565 129.995 5 N 70(ALA) 2 N 69(LYS) 2 1 1 2.604 101.131 5 N 71(LEU) 2 O 67(LEU) 2 1 1 2.922 126.803 5 N 71(LEU) 2 N 70(ALA) 2 1 1 2.688 102.131 5 N 72(GLU) 2 O 68(GLU) 2 1 1 3.321 165.627 5 N 72(GLU) 2 N 71(LEU) 2 1 1 2.776 93.983 5 N 73(LEU) 2 N 72(GLU) 2 1 1 2.666 105.032 5 N 74(THR) 2 N 73(LEU) 2 1 1 2.739 104.229 5 N 75(GLY) 2 N 74(THR) 2 1 1 2.680 107.727 5 N 76(LEU) 2 N 75(GLY) 2 1 1 2.763 99.258 5 N 78(VAL) 2 O 81(ASN) 2 1 1 2.687 128.702 5 N 83(ILE) 2 O 76(LEU) 2 1 1 2.456 142.548 5 N 84(LYS) 2 O 19(GLY) 2 1 1 2.714 155.973 5 N 86(GLU) 2 O 17(PHE) 2 1 1 3.143 137.381 5 N 96(VAL) 2 N 95(LYS) 2 1 1 2.699 105.332 5 N 98(ALA) 2 N 97(ARG) 2 1 1 2.719 101.659 5 N 99(ALA) 2 N 98(ALA) 2 1 1 2.788 99.934 5 N 100(ARG) 2 O 97(ARG) 2 1 1 2.918 123.538 5 N 100(ARG) 2 N 99(ALA) 2 1 1 2.841 97.153 5 N 101(THR) 2 O 98(ALA) 2 1 1 2.848 148.576 5 N 101(THR) 2 N 100(ARG) 2 1 1 2.705 101.288 5 N 102(LEU) 2 O 141(ILE) 2 1 1 2.638 160.033 5 N 103(LEU) 2 O 169(TYR) 2 1 1 2.614 157.097 5 N 104(ALA) 2 O 139(ALA) 2 1 1 2.383 150.866 5 N 105(LYS) 2 O 167(SER) 2 1 1 2.409 154.641 5 N 107(LEU) 2 N 106(ASN) 2 1 1 2.766 101.286 5 N 107(LEU) 2 O 137(GLY) 2 1 1 2.688 151.772 5 N 110(ASN) 2 N 109(PHE) 2 1 1 2.720 103.903 5 N 111(ILE) 2 N 110(ASN) 2 1 1 2.816 97.456 5 N 114(ASP) 2 N 113(GLU) 2 1 1 2.772 99.234 5 N 115(GLU) 2 O 112(THR) 2 1 1 2.970 108.914 5 N 116(LEU) 2 O 112(THR) 2 1 1 2.917 162.533 5 N 116(LEU) 2 N 115(GLU) 2 1 1 2.766 99.319 5 N 117(LYS) 2 O 113(GLU) 2 1 1 2.402 145.549 5 N 117(LYS) 2 N 116(LEU) 2 1 1 2.672 99.796 5 N 118(GLU) 2 O 114(ASP) 2 1 1 2.697 134.321 5 N 118(GLU) 2 N 117(LYS) 2 1 1 2.687 103.776 5 N 119(VAL) 2 O 115(GLU) 2 1 1 2.889 145.592 5 N 119(VAL) 2 N 118(GLU) 2 1 1 2.730 100.546 5 N 120(PHE) 2 O 116(LEU) 2 1 1 2.517 158.055 5 N 120(PHE) 2 N 119(VAL) 2 1 1 2.751 99.225 5 N 122(ASP) 2 N 121(GLU) 2 1 1 2.727 104.384 5 N 123(ALA) 2 N 122(ASP) 2 1 1 2.738 102.376 5 N 124(LEU) 2 O 142(GLU) 2 1 1 2.865 127.743 5 N 125(GLU) 2 N 124(LEU) 2 1 1 2.827 98.068 5 N 127(ARG) 2 O 140(TYR) 2 1 1 2.581 153.462 5 NE 127(ARG) 2 O2 10(C ) 1 1 1 2.755 128.068 5 N 129(VAL) 2 O 138(ILE) 2 1 1 2.578 160.187 5 N 133(GLY) 2 N 132(ASP) 2 1 1 2.726 104.447 5 N 137(GLY) 2 N 136(LYS) 2 1 1 2.823 97.636 5 N 138(ILE) 2 O 129(VAL) 2 1 1 3.120 157.449 5 N 138(ILE) 2 N 137(GLY) 2 1 1 2.775 100.887 5 N 139(ALA) 2 O 104(ALA) 2 1 1 2.774 147.884 5 N 140(TYR) 2 O 127(ARG) 2 1 1 2.406 157.920 5 N 141(ILE) 2 O 102(LEU) 2 1 1 2.596 120.779 5 N 142(GLU) 2 O 125(GLU) 2 1 1 2.604 154.603 5 N 143(PHE) 2 O 100(ARG) 2 1 1 2.989 170.244 5 N 145(SER) 2 N 144(LYS) 2 1 1 2.705 104.129 5 N 147(ALA) 2 N 146(GLU) 2 1 1 2.815 94.501 5 N 148(ASP) 2 OG 145(SER) 2 1 1 2.874 147.374 5 N 148(ASP) 2 N 147(ALA) 2 1 1 2.711 101.204 5 N 149(ALA) 2 O 145(SER) 2 1 1 2.960 167.350 5 N 150(GLU) 2 O 146(GLU) 2 1 1 2.610 146.806 5 N 150(GLU) 2 N 149(ALA) 2 1 1 2.736 101.679 5 N 151(LYS) 2 O 147(ALA) 2 1 1 2.752 153.175 5 N 151(LYS) 2 N 150(GLU) 2 1 1 2.832 97.235 5 N 152(ASN) 2 O 148(ASP) 2 1 1 2.925 168.578 5 N 152(ASN) 2 N 151(LYS) 2 1 1 2.784 98.489 5 N 153(LEU) 2 O 149(ALA) 2 1 1 2.836 148.595 5 N 153(LEU) 2 N 152(ASN) 2 1 1 2.817 96.155 5 N 154(GLU) 2 O 150(GLU) 2 1 1 2.937 166.110 5 N 154(GLU) 2 N 153(LEU) 2 1 1 2.828 96.343 5 N 155(GLU) 2 O 151(LYS) 2 1 1 2.695 139.273 5 N 155(GLU) 2 N 154(GLU) 2 1 1 2.740 100.541 5 N 156(LYS) 2 O 152(ASN) 2 1 1 2.827 144.437 5 N 161(ILE) 2 O 164(ARG) 2 1 1 2.906 159.661 5 N 163(GLY) 2 N 162(ASP) 2 1 1 2.786 98.850 5 N 164(ARG) 2 O 161(ILE) 2 1 1 2.388 144.939 5 N 164(ARG) 2 N 163(GLY) 2 1 1 2.748 100.030 5 N 166(VAL) 2 O 158(GLY) 2 1 1 2.341 146.380 5 N 167(SER) 2 O 105(LYS) 2 1 1 2.732 135.205 5 N 168(LEU) 2 OE1 157(GLN) 2 1 1 2.399 150.031 5 N 169(TYR) 2 O 103(LEU) 2 1 1 2.390 159.444 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, 1fje_wc.csv] Trying to match bases to eachother for number of bases: 22 Considering number of hydrogen bonds: 168 Results contains number of sets of co-planar bases: 4 Results: Residue: 1( G) Mol: 1 Model: 1 Entry: 1 Residue: 22( C) Mol: 1 Model: 1 Entry: 1 Residue: 2( G) Mol: 1 Model: 1 Entry: 1 Residue: 21( C) Mol: 1 Model: 1 Entry: 1 Residue: 3( C) Mol: 1 Model: 1 Entry: 1 Residue: 20( G) Mol: 1 Model: 1 Entry: 1 Residue: 4( C) Mol: 1 Model: 1 Entry: 1 Residue: 19( G) Mol: 1 Model: 1 Entry: 1 Writing results to file: 1fje_wc.csv Wattos started at: January 19, 2007 10:16:34 AM CST Wattos stopped at: January 19, 2007 10:16:45 AM CST Wattos took (#ms): 10581