Read libraries from system resource. Wattos started at: January 19, 2007 10:19:40 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/pdb1t28.ent, PDB] Read total number of atoms from PDB formatted coordinate list: 1103 Tolerance (0.1 Angstrom suggested) Doing CalcBond with arguments: [0.1] Done. Checked number of potential pairs: 1448 Found number of new bond candidates: 1209 WARNING: Got more bonds than allowed for this atom's (HO*2) element type (1). Bonds (2) read: WARNING: Atom Res#(Nam) Mol# Atom Res#(Nam) Mol# Model# Entry# Value_1 Value_2 RefValue RefSD Type Minimum Average Maximum Under cutoff O2* 1(G ) 1 HO*2 1(G ) 1 1 1 0.948 6 HO*2 1(G ) 1 H5*1 2(G ) 1 1 1 0.776 6 WARNING: Got more bonds than allowed for this atom's (H5*1) element type (1). Bonds (2) read: WARNING: Atom Res#(Nam) Mol# Atom Res#(Nam) Mol# Model# Entry# Value_1 Value_2 RefValue RefSD Type Minimum Average Maximum Under cutoff HO*2 1(G ) 1 H5*1 2(G ) 1 1 1 0.776 6 C5* 2(G ) 1 H5*1 2(G ) 1 1 1 1.078 6 WARNING: Got more bonds than allowed for this atom's (HO*2) element type (1). 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 O2* 8(G ) 1 HO*2 8(G ) 1 1 1 0.953 6 HO*2 8(G ) 1 O2* 9(U ) 1 1 1 1.077 6 HO*2 8(G ) 1 HO*2 9(U ) 1 1 1 0.643 6 WARNING: Got more bonds than allowed for this atom's (C5*) element type (4). Bonds (5) read: WARNING: Atom Res#(Nam) Mol# Atom Res#(Nam) Mol# Model# Entry# Value_1 Value_2 RefValue RefSD Type Minimum Average Maximum Under cutoff O5* 9(U ) 1 C5* 9(U ) 1 1 1 1.430 6 C5* 9(U ) 1 C4* 9(U ) 1 1 1 1.529 6 C5* 9(U ) 1 O2* 9(U ) 1 1 1 1.595 6 C5* 9(U ) 1 H5*1 9(U ) 1 1 1 1.090 6 C5* 9(U ) 1 H5*2 9(U ) 1 1 1 1.091 6 WARNING: Got more bonds than allowed for this atom's (C4*) element type (4). Bonds (7) read: WARNING: Atom Res#(Nam) Mol# Atom Res#(Nam) Mol# Model# Entry# Value_1 Value_2 RefValue RefSD Type Minimum Average Maximum Under cutoff C5* 9(U ) 1 C4* 9(U ) 1 1 1 1.529 6 C4* 9(U ) 1 O4* 9(U ) 1 1 1 1.448 6 C4* 9(U ) 1 C3* 9(U ) 1 1 1 1.499 6 C4* 9(U ) 1 C2* 9(U ) 1 1 1 0.886 6 C4* 9(U ) 1 O2* 9(U ) 1 1 1 1.261 6 C4* 9(U ) 1 H4* 9(U ) 1 1 1 1.110 6 C4* 9(U ) 1 H2* 9(U ) 1 1 1 1.308 6 WARNING: Got more bonds than allowed for this atom's (O4*) element type (2). Bonds (4) read: WARNING: Atom Res#(Nam) Mol# Atom Res#(Nam) Mol# Model# Entry# Value_1 Value_2 RefValue RefSD Type Minimum Average Maximum Under cutoff C4* 9(U ) 1 O4* 9(U ) 1 1 1 1.448 6 O4* 9(U ) 1 C2* 9(U ) 1 1 1 0.983 6 O4* 9(U ) 1 O2* 9(U ) 1 1 1 0.995 6 O4* 9(U ) 1 C1* 9(U ) 1 1 1 1.437 6 WARNING: Got more bonds than allowed for this atom's (C2*) element type (4). Bonds (6) read: WARNING: Atom Res#(Nam) Mol# Atom Res#(Nam) Mol# Model# Entry# Value_1 Value_2 RefValue RefSD Type Minimum Average Maximum Under cutoff C4* 9(U ) 1 C2* 9(U ) 1 1 1 0.886 6 O4* 9(U ) 1 C2* 9(U ) 1 1 1 0.983 6 C3* 9(U ) 1 C2* 9(U ) 1 1 1 1.524 6 C2* 9(U ) 1 O2* 9(U ) 1 1 1 1.465 6 C2* 9(U ) 1 C1* 9(U ) 1 1 1 1.506 6 C2* 9(U ) 1 H2* 9(U ) 1 1 1 1.090 6 WARNING: Got more bonds than allowed for this atom's (O2*) element type (2). Bonds (6) read: WARNING: Atom Res#(Nam) Mol# Atom Res#(Nam) Mol# Model# Entry# Value_1 Value_2 RefValue RefSD Type Minimum Average Maximum Under cutoff HO*2 8(G ) 1 O2* 9(U ) 1 1 1 1.077 6 C5* 9(U ) 1 O2* 9(U ) 1 1 1 1.595 6 C4* 9(U ) 1 O2* 9(U ) 1 1 1 1.261 6 O4* 9(U ) 1 O2* 9(U ) 1 1 1 0.995 6 C2* 9(U ) 1 O2* 9(U ) 1 1 1 1.465 6 O2* 9(U ) 1 HO*2 9(U ) 1 1 1 0.999 6 WARNING: Got more bonds than allowed for this atom's (H4*) element type (1). Bonds (2) read: WARNING: Atom Res#(Nam) Mol# Atom Res#(Nam) Mol# Model# Entry# Value_1 Value_2 RefValue RefSD Type Minimum Average Maximum Under cutoff C4* 9(U ) 1 H4* 9(U ) 1 1 1 1.110 6 H4* 9(U ) 1 H2* 9(U ) 1 1 1 0.782 6 WARNING: Got more bonds than allowed for this atom's (H2*) element type (1). 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 C4* 9(U ) 1 H2* 9(U ) 1 1 1 1.308 6 C2* 9(U ) 1 H2* 9(U ) 1 1 1 1.090 6 H4* 9(U ) 1 H2* 9(U ) 1 1 1 0.782 6 WARNING: Got more bonds than allowed for this atom's (HO*2) element type (1). Bonds (2) read: WARNING: Atom Res#(Nam) Mol# Atom Res#(Nam) Mol# Model# Entry# Value_1 Value_2 RefValue RefSD Type Minimum Average Maximum Under cutoff HO*2 8(G ) 1 HO*2 9(U ) 1 1 1 0.643 6 O2* 9(U ) 1 HO*2 9(U ) 1 1 1 0.999 6 WARNING: Got more bonds than allowed for this atom's (C5*) element type (4). Bonds (5) read: WARNING: Atom Res#(Nam) Mol# Atom Res#(Nam) Mol# Model# Entry# Value_1 Value_2 RefValue RefSD Type Minimum Average Maximum Under cutoff O5* 33(C ) 1 C5* 33(C ) 1 1 1 1.438 6 C5* 33(C ) 1 C4* 33(C ) 1 1 1 1.551 6 C5* 33(C ) 1 O2* 33(C ) 1 1 1 1.435 6 C5* 33(C ) 1 H5*1 33(C ) 1 1 1 1.091 6 C5* 33(C ) 1 H5*2 33(C ) 1 1 1 1.090 6 WARNING: Got more bonds than allowed for this atom's (C4*) element type (4). Bonds (7) read: WARNING: Atom Res#(Nam) Mol# Atom Res#(Nam) Mol# Model# Entry# Value_1 Value_2 RefValue RefSD Type Minimum Average Maximum Under cutoff C5* 33(C ) 1 C4* 33(C ) 1 1 1 1.551 6 C4* 33(C ) 1 O4* 33(C ) 1 1 1 1.436 6 C4* 33(C ) 1 C3* 33(C ) 1 1 1 1.529 6 C4* 33(C ) 1 C2* 33(C ) 1 1 1 0.812 6 C4* 33(C ) 1 O2* 33(C ) 1 1 1 1.197 6 C4* 33(C ) 1 H4* 33(C ) 1 1 1 1.120 6 C4* 33(C ) 1 H2* 33(C ) 1 1 1 1.199 6 WARNING: Got more bonds than allowed for this atom's (O4*) element type (2). Bonds (4) read: WARNING: Atom Res#(Nam) Mol# Atom Res#(Nam) Mol# Model# Entry# Value_1 Value_2 RefValue RefSD Type Minimum Average Maximum Under cutoff C4* 33(C ) 1 O4* 33(C ) 1 1 1 1.436 6 O4* 33(C ) 1 C2* 33(C ) 1 1 1 1.048 6 O4* 33(C ) 1 O2* 33(C ) 1 1 1 1.064 6 O4* 33(C ) 1 C1* 33(C ) 1 1 1 1.429 6 WARNING: Got more bonds than allowed for this atom's (C2*) element type (4). Bonds (6) read: WARNING: Atom Res#(Nam) Mol# Atom Res#(Nam) Mol# Model# Entry# Value_1 Value_2 RefValue RefSD Type Minimum Average Maximum Under cutoff C4* 33(C ) 1 C2* 33(C ) 1 1 1 0.812 6 O4* 33(C ) 1 C2* 33(C ) 1 1 1 1.048 6 C3* 33(C ) 1 C2* 33(C ) 1 1 1 1.499 6 C2* 33(C ) 1 O2* 33(C ) 1 1 1 1.440 6 C2* 33(C ) 1 C1* 33(C ) 1 1 1 1.529 6 C2* 33(C ) 1 H2* 33(C ) 1 1 1 1.088 6 WARNING: Got more bonds than allowed for this atom's (O2*) element type (2). Bonds (5) read: WARNING: Atom Res#(Nam) Mol# Atom Res#(Nam) Mol# Model# Entry# Value_1 Value_2 RefValue RefSD Type Minimum Average Maximum Under cutoff C5* 33(C ) 1 O2* 33(C ) 1 1 1 1.435 6 C4* 33(C ) 1 O2* 33(C ) 1 1 1 1.197 6 O4* 33(C ) 1 O2* 33(C ) 1 1 1 1.064 6 C2* 33(C ) 1 O2* 33(C ) 1 1 1 1.440 6 O2* 33(C ) 1 HO*2 33(C ) 1 1 1 0.998 6 WARNING: Got more bonds than allowed for this atom's (H4*) element type (1). Bonds (2) read: WARNING: Atom Res#(Nam) Mol# Atom Res#(Nam) Mol# Model# Entry# Value_1 Value_2 RefValue RefSD Type Minimum Average Maximum Under cutoff C4* 33(C ) 1 H4* 33(C ) 1 1 1 1.120 6 H4* 33(C ) 1 H2* 33(C ) 1 1 1 0.675 6 WARNING: Got more bonds than allowed for this atom's (H2*) element type (1). 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 C4* 33(C ) 1 H2* 33(C ) 1 1 1 1.199 6 C2* 33(C ) 1 H2* 33(C ) 1 1 1 1.088 6 H4* 33(C ) 1 H2* 33(C ) 1 1 1 0.675 6 WARNING: Got bonds that are potentially too much: 46 WARNING: Atom Res#(Nam) Mol# Atom Res#(Nam) Mol# Model# Entry# Value_1 Value_2 RefValue RefSD Type Minimum Average Maximum Under cutoff O2* 1(G ) 1 HO*2 1(G ) 1 1 1 0.948 6 HO*2 1(G ) 1 H5*1 2(G ) 1 1 1 0.776 6 C5* 2(G ) 1 H5*1 2(G ) 1 1 1 1.078 6 O2* 8(G ) 1 HO*2 8(G ) 1 1 1 0.953 6 HO*2 8(G ) 1 O2* 9(U ) 1 1 1 1.077 6 HO*2 8(G ) 1 HO*2 9(U ) 1 1 1 0.643 6 O5* 9(U ) 1 C5* 9(U ) 1 1 1 1.430 6 C5* 9(U ) 1 C4* 9(U ) 1 1 1 1.529 6 C5* 9(U ) 1 O2* 9(U ) 1 1 1 1.595 6 C5* 9(U ) 1 H5*1 9(U ) 1 1 1 1.090 6 C5* 9(U ) 1 H5*2 9(U ) 1 1 1 1.091 6 C4* 9(U ) 1 O4* 9(U ) 1 1 1 1.448 6 C4* 9(U ) 1 C3* 9(U ) 1 1 1 1.499 6 C4* 9(U ) 1 C2* 9(U ) 1 1 1 0.886 6 C4* 9(U ) 1 O2* 9(U ) 1 1 1 1.261 6 C4* 9(U ) 1 H4* 9(U ) 1 1 1 1.110 6 C4* 9(U ) 1 H2* 9(U ) 1 1 1 1.308 6 O4* 9(U ) 1 C2* 9(U ) 1 1 1 0.983 6 O4* 9(U ) 1 O2* 9(U ) 1 1 1 0.995 6 O4* 9(U ) 1 C1* 9(U ) 1 1 1 1.437 6 C3* 9(U ) 1 C2* 9(U ) 1 1 1 1.524 6 C2* 9(U ) 1 O2* 9(U ) 1 1 1 1.465 6 C2* 9(U ) 1 C1* 9(U ) 1 1 1 1.506 6 C2* 9(U ) 1 H2* 9(U ) 1 1 1 1.090 6 O2* 9(U ) 1 HO*2 9(U ) 1 1 1 0.999 6 H4* 9(U ) 1 H2* 9(U ) 1 1 1 0.782 6 O5* 33(C ) 1 C5* 33(C ) 1 1 1 1.438 6 C5* 33(C ) 1 C4* 33(C ) 1 1 1 1.551 6 C5* 33(C ) 1 O2* 33(C ) 1 1 1 1.435 6 C5* 33(C ) 1 H5*1 33(C ) 1 1 1 1.091 6 C5* 33(C ) 1 H5*2 33(C ) 1 1 1 1.090 6 C4* 33(C ) 1 O4* 33(C ) 1 1 1 1.436 6 C4* 33(C ) 1 C3* 33(C ) 1 1 1 1.529 6 C4* 33(C ) 1 C2* 33(C ) 1 1 1 0.812 6 C4* 33(C ) 1 O2* 33(C ) 1 1 1 1.197 6 C4* 33(C ) 1 H4* 33(C ) 1 1 1 1.120 6 C4* 33(C ) 1 H2* 33(C ) 1 1 1 1.199 6 O4* 33(C ) 1 C2* 33(C ) 1 1 1 1.048 6 O4* 33(C ) 1 O2* 33(C ) 1 1 1 1.064 6 O4* 33(C ) 1 C1* 33(C ) 1 1 1 1.429 6 C3* 33(C ) 1 C2* 33(C ) 1 1 1 1.499 6 C2* 33(C ) 1 O2* 33(C ) 1 1 1 1.440 6 C2* 33(C ) 1 C1* 33(C ) 1 1 1 1.529 6 C2* 33(C ) 1 H2* 33(C ) 1 1 1 1.088 6 O2* 33(C ) 1 HO*2 33(C ) 1 1 1 0.998 6 H4* 33(C ) 1 H2* 33(C ) 1 1 1 0.675 6 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: 45 WARNING: Got more than two hydrogen bond for this donor (N4). 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 N4 33(C ) 1 O6 2(G ) 1 1 1 96.392 5 N4 33(C ) 1 N1 2(G ) 1 1 1 123.766 5 N4 33(C ) 1 N4 34(C ) 1 1 1 112.479 5 Found number of new hydrogen bonds: 45 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 O2 34(C ) 1 1 1 2.920 119.608 5 N1 1(G ) 1 N3 34(C ) 1 1 1 2.956 138.514 5 N1 2(G ) 1 N3 33(C ) 1 1 1 3.119 135.738 5 N1 2(G ) 1 N4 33(C ) 1 1 1 2.474 125.887 5 N2 2(G ) 1 N3 33(C ) 1 1 1 2.884 144.158 5 O2* 3(U ) 1 O5* 4(C ) 1 1 1 2.428 133.486 5 N3 3(U ) 1 O6 32(G ) 1 1 1 3.238 134.454 5 O2* 4(C ) 1 O5* 5(A ) 1 1 1 2.229 155.292 5 N4 4(C ) 1 O6 31(G ) 1 1 1 3.108 127.276 5 O2* 5(A ) 1 O5* 6(U ) 1 1 1 2.288 149.777 5 O2* 7(C ) 1 O4* 8(G ) 1 1 1 2.546 100.942 5 N4 7(C ) 1 N3 6(U ) 1 1 1 2.955 100.054 5 N4 7(C ) 1 O6 28(G ) 1 1 1 2.797 138.273 5 O2* 8(G ) 1 O4* 9(U ) 1 1 1 2.063 113.322 5 O2* 8(G ) 1 O2* 9(U ) 1 1 1 1.909 140.132 5 N1 8(G ) 1 N3 27(C ) 1 1 1 3.010 132.058 5 N2 8(G ) 1 O2 27(C ) 1 1 1 3.329 132.628 5 O2* 9(U ) 1 O3* 8(G ) 1 1 1 3.032 102.486 5 O2* 9(U ) 1 O2* 8(G ) 1 1 1 1.909 97.809 5 N3 9(U ) 1 N1 26(A ) 1 1 1 3.312 144.480 5 N4 23(C ) 1 O2P 22(A ) 1 1 1 2.912 99.194 5 O2* 24(A ) 1 O1P 25(G ) 1 1 1 2.632 96.477 5 O2* 25(G ) 1 O5* 26(A ) 1 1 1 2.691 121.704 5 O2* 25(G ) 1 O4* 26(A ) 1 1 1 2.608 137.904 5 N1 25(G ) 1 O2* 10(U ) 1 1 1 2.771 125.955 5 O2* 26(A ) 1 O5* 27(C ) 1 1 1 2.359 169.802 5 N6 26(A ) 1 O4 9(U ) 1 1 1 3.057 153.666 5 O2* 27(C ) 1 O4* 28(G ) 1 1 1 3.339 133.823 5 N4 27(C ) 1 O6 8(G ) 1 1 1 2.615 122.364 5 N1 28(G ) 1 N3 7(C ) 1 1 1 2.885 157.484 5 N2 28(G ) 1 O2 7(C ) 1 1 1 3.082 169.639 5 O2* 29(G ) 1 O5* 30(U ) 1 1 1 2.241 168.639 5 N1 29(G ) 1 O2 6(U ) 1 1 1 2.921 116.510 5 O2* 30(U ) 1 O5* 31(G ) 1 1 1 2.259 159.536 5 N3 30(U ) 1 N1 5(A ) 1 1 1 2.998 127.990 5 O2* 31(G ) 1 O4* 32(G ) 1 1 1 3.064 123.812 5 N1 31(G ) 1 N3 4(C ) 1 1 1 2.929 128.470 5 N2 31(G ) 1 O2 4(C ) 1 1 1 2.721 112.362 5 N2 31(G ) 1 N3 4(C ) 1 1 1 3.190 122.568 5 O2* 32(G ) 1 O4* 33(C ) 1 1 1 2.050 113.896 5 O2* 32(G ) 1 O2* 33(C ) 1 1 1 2.198 146.397 5 N4 33(C ) 1 O6 2(G ) 1 1 1 2.666 96.392 5 N4 33(C ) 1 N1 2(G ) 1 1 1 2.474 123.766 5 N4 33(C ) 1 N4 34(C ) 1 1 1 3.161 112.479 5 N4 34(C ) 1 O6 1(G ) 1 1 1 3.208 135.657 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, 1t28_wc.csv] Trying to match bases to eachother for number of bases: 34 Considering number of hydrogen bonds: 45 Results contains number of sets of co-planar bases: 6 Results: Residue: 1( G) Mol: 1 Model: 1 Entry: 1 Residue: 34( C) Mol: 1 Model: 1 Entry: 1 Residue: 2( G) Mol: 1 Model: 1 Entry: 1 Residue: 33( C) Mol: 1 Model: 1 Entry: 1 Residue: 4( C) Mol: 1 Model: 1 Entry: 1 Residue: 31( G) Mol: 1 Model: 1 Entry: 1 Residue: 7( C) Mol: 1 Model: 1 Entry: 1 Residue: 28( G) Mol: 1 Model: 1 Entry: 1 Residue: 8( G) Mol: 1 Model: 1 Entry: 1 Residue: 27( C) Mol: 1 Model: 1 Entry: 1 Residue: 9( U) Mol: 1 Model: 1 Entry: 1 Residue: 26( A) Mol: 1 Model: 1 Entry: 1 Writing results to file: 1t28_wc.csv Wattos started at: January 19, 2007 10:19:40 AM CST Wattos stopped at: January 19, 2007 10:19:43 AM CST Wattos took (#ms): 3058