Read libraries from system resource. Wattos started at: January 19, 2007 10:21:35 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/pdb2err.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 49080 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 1863 Found number of new bond candidates: 1664 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: 62 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 67(LYS) 1 O 63(ARG) 1 1 1 135.217 5 N 67(LYS) 1 O 64(ALA) 1 1 1 126.899 5 N 67(LYS) 1 N 66(GLU) 1 1 1 99.632 5 Found number of new hydrogen bonds: 62 Atom Res#(Nam) Mol# Atom Res#(Nam) Mol# Model# Entry# Value_1 Value_2 RefValue RefSD Type Minimum Average Maximum Under cutoff N 11(LEU) 1 O 53(VAL) 1 1 1 2.841 147.294 5 N 12(HIS) 1 O 81(ASN) 1 1 1 3.007 145.271 5 N 13(VAL) 1 O 51(GLY) 1 1 1 2.811 154.976 5 N 14(SER) 1 O 79(GLU) 1 1 1 2.826 164.965 5 N 15(ASN) 1 O 49(GLY) 1 1 1 2.952 111.298 5 ND2 15(ASN) 1 O 77(LYS) 1 1 1 2.849 170.269 5 N 16(ILE) 1 N 15(ASN) 1 1 1 2.776 106.236 5 N 16(ILE) 1 O 49(GLY) 1 1 1 3.126 134.882 5 N 20(PHE) 1 N 19(ARG) 1 1 1 2.776 105.687 5 N 25(LEU) 1 O 21(ARG) 1 1 1 3.066 158.533 5 N 26(ARG) 1 O 22(ASP) 1 1 1 3.005 166.928 5 N 26(ARG) 1 N 25(LEU) 1 1 1 2.929 97.220 5 N 27(GLN) 1 O 23(PRO) 1 1 1 3.027 157.815 5 N 27(GLN) 1 N 26(ARG) 1 1 1 2.834 99.970 5 N 28(MET) 1 O 24(ASP) 1 1 1 3.006 151.733 5 N 29(PHE) 1 O 25(LEU) 1 1 1 2.827 165.187 5 N 30(GLY) 1 O 26(ARG) 1 1 1 2.811 118.407 5 N 30(GLY) 1 N 29(PHE) 1 1 1 2.770 98.466 5 N 31(GLN) 1 O 27(GLN) 1 1 1 3.031 131.037 5 N 31(GLN) 1 N 30(GLY) 1 1 1 2.839 98.194 5 N 32(PHE) 1 O 29(PHE) 1 1 1 2.831 145.096 5 N 32(PHE) 1 N 31(GLN) 1 1 1 2.902 100.073 5 N 33(GLY) 1 O 29(PHE) 1 1 1 2.996 165.597 5 N 33(GLY) 1 N 32(PHE) 1 1 1 2.840 101.119 5 N 35(ILE) 1 N 34(LYS) 1 1 1 2.748 113.131 5 N 36(LEU) 1 O 54(THR) 1 1 1 2.871 171.494 5 N 37(ASP) 1 N 36(LEU) 1 1 1 2.890 97.806 5 N 39(GLU) 1 O 52(PHE) 1 1 1 2.804 146.856 5 N 41(ILE) 1 O 50(PHE) 1 1 1 3.113 165.201 5 N 45(ARG) 1 N 44(GLU) 1 1 1 2.812 104.840 5 N 46(GLY) 1 N 45(ARG) 1 1 1 2.882 101.453 5 N 49(GLY) 1 N 48(LYS) 1 1 1 2.805 109.147 5 N 50(PHE) 1 N 49(GLY) 1 1 1 2.758 105.961 5 N 51(GLY) 1 O 13(VAL) 1 1 1 2.895 162.390 5 N 52(PHE) 1 O 39(GLU) 1 1 1 2.819 154.406 5 N 53(VAL) 1 O 11(LEU) 1 1 1 2.969 154.517 5 N 54(THR) 1 O 37(ASP) 1 1 1 2.808 146.997 5 N 61(ALA) 1 N 60(ASP) 1 1 1 2.846 101.415 5 N 62(ASP) 1 N 61(ALA) 1 1 1 2.862 98.307 5 N 63(ARG) 1 O 59(ALA) 1 1 1 2.870 173.060 5 N 64(ALA) 1 O 60(ASP) 1 1 1 2.863 156.395 5 N 64(ALA) 1 N 63(ARG) 1 1 1 2.877 97.097 5 N 65(ARG) 1 O 61(ALA) 1 1 1 2.940 167.331 5 N 66(GLU) 1 O 62(ASP) 1 1 1 2.916 174.750 5 N 67(LYS) 1 O 63(ARG) 1 1 1 2.931 135.217 5 N 67(LYS) 1 O 64(ALA) 1 1 1 3.143 126.899 5 N 67(LYS) 1 N 66(GLU) 1 1 1 2.812 99.632 5 N 68(LEU) 1 O 64(ALA) 1 1 1 2.951 159.590 5 N 69(HIS) 1 O 65(ARG) 1 1 1 2.819 155.570 5 N 69(HIS) 1 N 68(LEU) 1 1 1 2.787 104.598 5 N 70(GLY) 1 O 78(ILE) 1 1 1 2.857 152.878 5 N 71(THR) 1 O 68(LEU) 1 1 1 2.961 164.359 5 N 71(THR) 1 N 70(GLY) 1 1 1 2.815 106.556 5 N 73(VAL) 1 O 76(ARG) 1 1 1 2.874 167.665 5 N 76(ARG) 1 N 75(GLY) 1 1 1 2.895 97.816 5 N 78(ILE) 1 O 71(THR) 1 1 1 3.045 166.547 5 N 79(GLU) 1 O 14(SER) 1 1 1 2.867 164.826 5 N 81(ASN) 1 O 12(HIS) 1 1 1 2.867 128.760 5 N1 2(G ) 2 O 16(ILE) 1 1 1 2.767 159.618 5 N2 2(G ) 2 O 16(ILE) 1 1 1 3.038 142.169 5 N3 5(U ) 2 O 82(ASN) 1 1 1 3.028 157.207 5 N1 6(G ) 2 O 84(THR) 1 1 1 2.790 167.940 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, 2err_wc.csv] Trying to match bases to eachother for number of bases: 7 Considering number of hydrogen bonds: 62 WARNING: requested less than 1 new rows in getNewRowIdList: 0 Results contains number of sets of co-planar bases: 0 Results: Writing results to file: 2err_wc.csv Wattos started at: January 19, 2007 10:21:35 AM CST Wattos stopped at: January 19, 2007 10:21:39 AM CST Wattos took (#ms): 4323