Read libraries from system resource. Wattos started at: April 20, 2007 11:50:27 AM CDT 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/pdb1lo1.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 45080 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 2601 Found number of new bond candidates: 2332 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: 54 Found number of new hydrogen bonds: 54 Atom Res#(Nam) Mol# Atom Res#(Nam) Mol# Model# Entry# Value_1 Value_2 RefValue RefSD Type Minimum Average Maximum Under cutoff N 7(CYS) 1 O 12(ASP) 1 1 1 2.775 167.322 5 N 9(VAL) 1 N 8(LEU) 1 1 1 2.732 106.150 5 N 16(GLY) 1 N 15(SER) 1 1 1 2.826 95.401 5 N 20(GLY) 1 N 19(TYR) 1 1 1 2.883 97.869 5 N 21(VAL) 1 N 20(GLY) 1 1 1 2.823 104.985 5 N 23(SER) 1 O 16(GLY) 1 1 1 3.152 163.033 5 N 26(ALA) 1 N 25(GLU) 1 1 1 2.816 102.308 5 N 27(CYS) 1 N 26(ALA) 1 1 1 2.876 93.117 5 N 30(PHE) 1 N 29(ALA) 1 1 1 2.870 95.703 5 N 32(LYS) 1 O 28(LYS) 1 1 1 3.026 173.681 5 N 32(LYS) 1 N 31(PHE) 1 1 1 2.821 95.461 5 N 34(THR) 1 N 33(ARG) 1 1 1 2.842 96.152 5 N 35(ILE) 1 O 31(PHE) 1 1 1 3.291 156.835 5 N 36(GLN) 1 O 32(LYS) 1 1 1 2.795 163.069 5 N 37(GLY) 1 O 33(ARG) 1 1 1 2.922 141.842 5 N 37(GLY) 1 N 36(GLN) 1 1 1 2.802 97.763 5 N 38(ASN) 1 O 35(ILE) 1 1 1 3.056 151.495 5 N 38(ASN) 1 N 37(GLY) 1 1 1 2.763 107.505 5 N 39(ILE) 1 O 34(THR) 1 1 1 2.934 158.982 5 N 45(ALA) 1 N 44(PRO) 1 1 1 2.808 103.401 5 N 54(ARG) 1 N 53(LYS) 1 1 1 2.875 97.178 5 N 56(ARG) 1 O 52(THR) 1 1 1 2.934 163.671 5 N 56(ARG) 1 N 55(ARG) 1 1 1 2.818 98.929 5 N 58(SER) 1 N 57(LYS) 1 1 1 2.826 96.308 5 N 63(ARG) 1 N 62(CYS) 1 1 1 2.848 96.383 5 N 65(MET) 1 N 64(PHE) 1 1 1 2.849 95.836 5 N 66(LYS) 1 O 62(CYS) 1 1 1 2.866 160.594 5 N 67(ALA) 1 O 63(ARG) 1 1 1 2.896 170.152 5 N 67(ALA) 1 N 66(LYS) 1 1 1 2.858 96.403 5 N 70(VAL) 1 O 66(LYS) 1 1 1 2.887 171.112 5 N 71(GLY) 1 O 67(ALA) 1 1 1 3.161 169.209 5 N 71(GLY) 1 N 70(VAL) 1 1 1 2.859 96.053 5 N 72(MET) 1 O 67(ALA) 1 1 1 2.903 165.451 5 N 75(GLU) 1 N 74(LYS) 1 1 1 2.901 94.824 5 N 76(GLY) 1 O 73(LEU) 1 1 1 2.895 149.143 5 N 76(GLY) 1 N 75(GLU) 1 1 1 2.782 105.330 5 N 77(VAL) 1 N 76(GLY) 1 1 1 2.887 97.813 5 N 80(ASP) 1 N 79(LEU) 1 1 1 2.697 107.686 5 N 81(ARG) 1 N 80(ASP) 1 1 1 2.785 100.779 5 N1 1(G ) 2 N3 13(C ) 4 1 1 2.899 173.543 5 N3 3(T ) 2 N1 11(A ) 4 1 1 2.938 176.413 5 N1 7(G ) 2 N3 7(C ) 4 1 1 2.927 179.054 5 N1 8(G ) 2 N3 6(C ) 4 1 1 2.963 171.013 5 N3 9(T ) 2 N1 5(A ) 4 1 1 2.918 175.667 5 N6 11(A ) 2 O4 3(T ) 4 1 1 2.847 174.025 5 N1 13(G ) 2 N3 1(C ) 4 1 1 2.919 178.033 5 N2 13(G ) 2 O2 1(C ) 4 1 1 2.899 175.918 5 N1 2(G ) 4 N3 12(C ) 2 1 1 2.924 176.471 5 N3 3(T ) 4 N1 11(A ) 2 1 1 2.946 178.269 5 N1 4(G ) 4 N3 10(C ) 2 1 1 2.933 175.877 5 N3 8(T ) 4 N1 6(A ) 2 1 1 2.927 175.446 5 N3 9(T ) 4 N1 5(A ) 2 1 1 2.878 171.588 5 N1 10(G ) 4 N3 4(C ) 2 1 1 2.941 174.105 5 N1 12(G ) 4 N3 2(C ) 2 1 1 2.949 176.511 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, 1lo1_wc.csv] Trying to match bases to eachother for number of bases: 26 Considering number of hydrogen bonds: 54 Results contains number of sets of co-planar bases: 2 Results: Residue: 11( A) Mol: 2 Model: 1 Entry: 1 Residue: 3( T) Mol: 4 Model: 1 Entry: 1 Residue: 13( G) Mol: 2 Model: 1 Entry: 1 Residue: 1( C) Mol: 4 Model: 1 Entry: 1 Writing results to file: 1lo1_wc.csv Wattos started at: April 20, 2007 11:50:27 AM CDT Wattos stopped at: April 20, 2007 11:50:36 AM CDT Wattos took (#ms): 8427