Read libraries from system resource. Wattos started at: January 19, 2007 10:16:24 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/pdb1f6u.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 29940 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 1810 Found number of new bond candidates: 1557 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: 75 Found number of new hydrogen bonds: 75 Atom Res#(Nam) Mol# Atom Res#(Nam) Mol# Model# Entry# Value_1 Value_2 RefValue RefSD Type Minimum Average Maximum Under cutoff N 4(GLY) 1 N 3(LYS) 1 1 1 2.698 95.734 5 N 5(ASN) 1 O 2(GLN) 1 1 1 2.895 150.554 5 N 5(ASN) 1 N 4(GLY) 1 1 1 2.652 100.384 5 N 6(PHE) 1 O 3(LYS) 1 1 1 2.915 150.284 5 N 6(PHE) 1 N 5(ASN) 1 1 1 2.699 95.692 5 N 7(ARG) 1 O 4(GLY) 1 1 1 2.736 154.750 5 N 7(ARG) 1 N 6(PHE) 1 1 1 2.632 101.484 5 N 8(ASN) 1 O 5(ASN) 1 1 1 2.979 161.301 5 N 8(ASN) 1 N 7(ARG) 1 1 1 2.616 101.496 5 ND2 8(ASN) 1 O 12(THR) 1 1 1 2.710 126.440 5 N 9(GLN) 1 O 6(PHE) 1 1 1 2.962 163.947 5 N 9(GLN) 1 N 8(ASN) 1 1 1 2.600 101.083 5 NE2 9(GLN) 1 O 22(GLY) 1 1 1 2.996 166.917 5 N 10(ARG) 1 O 7(ARG) 1 1 1 2.932 173.916 5 N 10(ARG) 1 N 9(GLN) 1 1 1 2.669 98.492 5 N 11(LYS) 1 O 8(ASN) 1 1 1 2.766 165.013 5 N 11(LYS) 1 N 10(ARG) 1 1 1 2.649 99.629 5 N 12(THR) 1 O 9(GLN) 1 1 1 2.909 149.652 5 N 12(THR) 1 N 11(LYS) 1 1 1 2.730 94.083 5 N 15(CYS) 1 O 20(LYS) 1 1 1 2.779 158.306 5 N 16(PHE) 1 O6 11(G ) 3 1 1 3.003 163.844 5 N 17(ASN) 1 N 16(PHE) 1 1 1 2.636 101.264 5 N 19(GLY) 1 O 15(CYS) 1 1 1 2.703 120.609 5 N 19(GLY) 1 N 18(CYS) 1 1 1 2.633 97.914 5 N 20(LYS) 1 SG 18(CYS) 1 1 1 3.243 126.649 5 N 20(LYS) 1 N 19(GLY) 1 1 1 2.715 96.766 5 N 22(GLY) 1 O 13(VAL) 1 1 1 2.874 144.285 5 N 23(HIS) 1 N 22(GLY) 1 1 1 2.702 97.554 5 N 25(ALA) 1 O6 11(G ) 3 1 1 2.893 148.798 5 N 26(LYS) 1 N 25(ALA) 1 1 1 2.717 94.684 5 N 27(ASN) 1 O 24(ILE) 1 1 1 2.749 161.647 5 N 27(ASN) 1 N 26(LYS) 1 1 1 2.650 98.267 5 ND2 27(ASN) 1 O 24(ILE) 1 1 1 2.659 117.075 5 N 28(CYS) 1 O 25(ALA) 1 1 1 2.902 138.821 5 N 30(ALA) 1 N 29(ARG) 1 1 1 2.631 100.655 5 N 32(ARG) 1 N 31(PRO) 1 1 1 2.836 91.044 5 N 36(CYS) 1 O 41(LYS) 1 1 1 2.787 164.131 5 N 37(TRP) 1 O6 9(G ) 3 1 1 2.954 154.276 5 N 38(LYS) 1 N 37(TRP) 1 1 1 2.560 101.650 5 N 40(GLY) 1 O 36(CYS) 1 1 1 2.791 131.165 5 N 40(GLY) 1 N 39(CYS) 1 1 1 2.723 93.336 5 N 41(LYS) 1 N 40(GLY) 1 1 1 2.685 98.552 5 N 43(GLY) 1 O 34(LYS) 1 1 1 3.006 167.657 5 N 44(HIS) 1 N 43(GLY) 1 1 1 2.698 97.710 5 N 46(MET) 1 O6 9(G ) 3 1 1 2.847 140.275 5 N 47(LYS) 1 OE1 45(GLN) 1 1 1 2.745 158.201 5 N 47(LYS) 1 N 46(MET) 1 1 1 2.814 92.016 5 N 48(ASP) 1 O 45(GLN) 1 1 1 2.686 140.025 5 N 48(ASP) 1 N 47(LYS) 1 1 1 2.600 101.073 5 N 49(CYS) 1 O 46(MET) 1 1 1 2.726 152.897 5 N 49(CYS) 1 N 48(ASP) 1 1 1 2.655 97.910 5 N 51(GLU) 1 N 50(THR) 1 1 1 2.666 98.841 5 N1 1(G ) 3 N3 19(C ) 3 1 1 2.848 163.416 5 N2 1(G ) 3 O2 19(C ) 3 1 1 2.911 173.430 5 N1 2(G ) 3 N3 18(C ) 3 1 1 2.875 168.987 5 N2 2(G ) 3 O2 18(C ) 3 1 1 2.880 156.717 5 N4 3(C ) 3 O6 17(G ) 3 1 1 2.901 166.212 5 N1 4(G ) 3 N3 16(C ) 3 1 1 2.847 166.500 5 N2 4(G ) 3 O2 16(C ) 3 1 1 2.916 169.019 5 N6 5(A ) 3 O2 14(U ) 3 1 1 2.643 128.741 5 N4 6(C ) 3 O6 13(G ) 3 1 1 2.877 160.572 5 N3 7(U ) 3 N1 12(A ) 3 1 1 2.877 160.848 5 N1 9(G ) 3 O 35(GLY) 1 1 1 2.849 138.083 5 N1 11(G ) 3 O 14(LYS) 1 1 1 2.912 142.668 5 N6 12(A ) 3 O4 7(U ) 3 1 1 2.896 171.957 5 N1 13(G ) 3 N3 6(C ) 3 1 1 2.891 161.129 5 N2 13(G ) 3 O2 6(C ) 3 1 1 2.867 155.460 5 N6 15(A ) 3 N1 5(A ) 3 1 1 2.879 160.600 5 N6 15(A ) 3 O2 14(U ) 3 1 1 2.882 157.362 5 N4 16(C ) 3 O6 4(G ) 3 1 1 2.910 167.291 5 N4 16(C ) 3 O2* 14(U ) 3 1 1 2.898 168.113 5 N1 17(G ) 3 N3 3(C ) 3 1 1 2.852 170.252 5 N2 17(G ) 3 O2 3(C ) 3 1 1 2.890 161.284 5 N4 18(C ) 3 O6 2(G ) 3 1 1 2.911 171.117 5 N4 19(C ) 3 O6 1(G ) 3 1 1 2.902 167.140 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, 1f6u_wc.csv] Trying to match bases to eachother for number of bases: 19 Considering number of hydrogen bonds: 75 Results contains number of sets of co-planar bases: 6 Results: Residue: 1( G) Mol: 3 Model: 1 Entry: 1 Residue: 19( C) Mol: 3 Model: 1 Entry: 1 Residue: 2( G) Mol: 3 Model: 1 Entry: 1 Residue: 18( C) Mol: 3 Model: 1 Entry: 1 Residue: 3( C) Mol: 3 Model: 1 Entry: 1 Residue: 17( G) Mol: 3 Model: 1 Entry: 1 Residue: 4( G) Mol: 3 Model: 1 Entry: 1 Residue: 16( C) Mol: 3 Model: 1 Entry: 1 Residue: 6( C) Mol: 3 Model: 1 Entry: 1 Residue: 13( G) Mol: 3 Model: 1 Entry: 1 Residue: 7( U) Mol: 3 Model: 1 Entry: 1 Residue: 12( A) Mol: 3 Model: 1 Entry: 1 Writing results to file: 1f6u_wc.csv Wattos started at: January 19, 2007 10:16:24 AM CST Wattos stopped at: January 19, 2007 10:16:32 AM CST Wattos took (#ms): 8583