Read libraries from system resource. Wattos started at: January 19, 2007 10:20:51 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/pdb1zc5.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 26480 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 1705 Found number of new bond candidates: 1428 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: 46 Found number of new hydrogen bonds: 46 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 41(C ) 1 1 1 3.003 165.629 5 N2 1(G ) 1 O2 41(C ) 1 1 1 2.986 171.845 5 N1 2(G ) 1 N3 40(C ) 1 1 1 2.944 167.762 5 N2 2(G ) 1 O2 40(C ) 1 1 1 2.964 152.234 5 N4 3(C ) 1 O6 4(G ) 1 1 1 3.120 114.288 5 N4 3(C ) 1 O6 39(G ) 1 1 1 3.001 153.315 5 N1 4(G ) 1 O2 38(U ) 1 1 1 2.725 151.153 5 N1 4(G ) 1 N3 38(U ) 1 1 1 3.202 134.188 5 N4 7(C ) 1 O6 32(G ) 1 1 1 2.952 158.839 5 N3 8(U ) 1 N1 31(A ) 1 1 1 2.992 172.115 5 N1 9(G ) 1 N3 30(C ) 1 1 1 2.978 165.126 5 N2 9(G ) 1 O2 30(C ) 1 1 1 3.005 160.544 5 N1 10(G ) 1 N3 29(C ) 1 1 1 2.982 160.668 5 N2 10(G ) 1 O2 29(C ) 1 1 1 2.944 162.389 5 N4 11(C ) 1 O6 28(G ) 1 1 1 2.997 156.041 5 N4 12(C ) 1 O6 27(G ) 1 1 1 2.985 162.598 5 N3 13(U ) 1 N1 26(A ) 1 1 1 2.943 174.961 5 N3 14(U ) 1 N1 25(A ) 1 1 1 3.001 161.361 5 N4 15(C ) 1 O6 24(G ) 1 1 1 2.972 165.109 5 N4 16(C ) 1 O6 23(G ) 1 1 1 2.972 168.636 5 N3 17(U ) 1 O6 22(G ) 1 1 1 2.948 167.217 5 N3 17(U ) 1 N1 22(G ) 1 1 1 3.251 131.545 5 N1 22(G ) 1 O2 17(U ) 1 1 1 2.719 150.830 5 N1 22(G ) 1 N3 17(U ) 1 1 1 3.251 140.433 5 N1 23(G ) 1 N3 16(C ) 1 1 1 3.000 167.351 5 N2 23(G ) 1 O2 16(C ) 1 1 1 2.955 167.815 5 N1 24(G ) 1 N3 15(C ) 1 1 1 3.015 168.868 5 N2 24(G ) 1 O2 15(C ) 1 1 1 2.966 162.278 5 N6 25(A ) 1 O4 14(U ) 1 1 1 2.965 164.786 5 N6 26(A ) 1 O4 13(U ) 1 1 1 3.022 160.746 5 N1 27(G ) 1 N3 12(C ) 1 1 1 2.948 165.503 5 N2 27(G ) 1 O2 12(C ) 1 1 1 2.948 161.977 5 N1 28(G ) 1 N3 11(C ) 1 1 1 2.985 158.783 5 N2 28(G ) 1 O2 11(C ) 1 1 1 2.961 161.685 5 N4 29(C ) 1 O6 10(G ) 1 1 1 3.028 161.135 5 N4 30(C ) 1 O6 9(G ) 1 1 1 2.974 160.032 5 N6 31(A ) 1 O4 8(U ) 1 1 1 2.905 151.439 5 N1 32(G ) 1 N3 7(C ) 1 1 1 3.057 168.451 5 N2 32(G ) 1 O2 7(C ) 1 1 1 3.152 164.537 5 N3 37(U ) 1 N1 5(A ) 1 1 1 2.963 170.447 5 N3 38(U ) 1 O6 4(G ) 1 1 1 2.940 160.175 5 N3 38(U ) 1 N1 4(G ) 1 1 1 3.202 133.534 5 N1 39(G ) 1 N3 3(C ) 1 1 1 2.915 159.050 5 N2 39(G ) 1 O2 3(C ) 1 1 1 2.992 150.378 5 N4 40(C ) 1 O6 2(G ) 1 1 1 3.075 172.359 5 N4 41(C ) 1 O6 1(G ) 1 1 1 2.955 159.109 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, 1zc5_wc.csv] Trying to match bases to eachother for number of bases: 41 Considering number of hydrogen bonds: 46 Results contains number of sets of co-planar bases: 13 Results: Residue: 1( G) Mol: 1 Model: 1 Entry: 1 Residue: 41( C) Mol: 1 Model: 1 Entry: 1 Residue: 2( G) Mol: 1 Model: 1 Entry: 1 Residue: 40( C) Mol: 1 Model: 1 Entry: 1 Residue: 3( C) Mol: 1 Model: 1 Entry: 1 Residue: 39( G) Mol: 1 Model: 1 Entry: 1 Residue: 7( C) Mol: 1 Model: 1 Entry: 1 Residue: 32( G) Mol: 1 Model: 1 Entry: 1 Residue: 8( U) Mol: 1 Model: 1 Entry: 1 Residue: 31( A) Mol: 1 Model: 1 Entry: 1 Residue: 9( G) Mol: 1 Model: 1 Entry: 1 Residue: 30( C) Mol: 1 Model: 1 Entry: 1 Residue: 10( G) Mol: 1 Model: 1 Entry: 1 Residue: 29( C) Mol: 1 Model: 1 Entry: 1 Residue: 11( C) Mol: 1 Model: 1 Entry: 1 Residue: 28( G) Mol: 1 Model: 1 Entry: 1 Residue: 12( C) Mol: 1 Model: 1 Entry: 1 Residue: 27( G) Mol: 1 Model: 1 Entry: 1 Residue: 13( U) Mol: 1 Model: 1 Entry: 1 Residue: 26( A) Mol: 1 Model: 1 Entry: 1 Residue: 14( U) Mol: 1 Model: 1 Entry: 1 Residue: 25( A) Mol: 1 Model: 1 Entry: 1 Residue: 15( C) Mol: 1 Model: 1 Entry: 1 Residue: 24( G) Mol: 1 Model: 1 Entry: 1 Residue: 16( C) Mol: 1 Model: 1 Entry: 1 Residue: 23( G) Mol: 1 Model: 1 Entry: 1 Writing results to file: 1zc5_wc.csv Wattos started at: January 19, 2007 10:20:51 AM CST Wattos stopped at: January 19, 2007 10:20:59 AM CST Wattos took (#ms): 7961