Read libraries from system resource.
Wattos started at: April 20, 2007 11:54:10 AM CDT
Program arguments [1] :[-at]
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Read libraries from system resource.
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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/pdb1sy8.ent, PDB]
Read total number of atoms from PDB formatted coordinate list: 3803


Tolerance (0.1 Angstrom suggested)
Doing CalcBond with arguments: [0.1]

Done. Checked number of potential pairs: 441
Found number of new bond candidates: 404


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: 10
Found number of new hydrogen bonds: 10
Atom Res#(Nam) Mol# Atom Res#(Nam) Mol# Model# Entry# Value_1  Value_2 RefValue    RefSD Type   Minimum  Average  Maximum Under cutoff
N3      1(T  )    1 N1      6(A  )    2      1      1   2.954  179.079                       5
N1      2(G  )    1 N3      5(C  )    2      1      1   2.912  173.560                       5
N6      3(A  )    1 O4      4(T  )    2      1      1   2.879  177.207                       5
N3      4(T  )    1 N1      3(A  )    2      1      1   2.953  178.848                       5
N6      6(A  )    1 O4      1(T  )    2      1      1   2.881  174.567                       5
N3      1(T  )    2 N1      6(A  )    1      1      1   2.954  179.079                       5
N1      2(G  )    2 N3      5(C  )    1      1      1   2.912  173.520                       5
N6      3(A  )    2 O4      4(T  )    1      1      1   2.880  177.214                       5
N3      4(T  )    2 N1      3(A  )    1      1      1   2.953  178.848                       5
N6      6(A  )    2 O4      1(T  )    1      1      1   2.882  174.619                       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, 1sy8_wc.csv]
Trying to match bases to eachother for number of bases: 12
Considering number of hydrogen bonds: 10
Results contains number of sets of co-planar bases: 4
Results:
Residue:   1(   T) Mol:   1 Model:   1 Entry:  1
Residue:   6(   A) Mol:   2 Model:   1 Entry:  1

Residue:   3(   A) Mol:   1 Model:   1 Entry:  1
Residue:   4(   T) Mol:   2 Model:   1 Entry:  1

Residue:   4(   T) Mol:   1 Model:   1 Entry:  1
Residue:   3(   A) Mol:   2 Model:   1 Entry:  1

Residue:   6(   A) Mol:   1 Model:   1 Entry:  1
Residue:   1(   T) Mol:   2 Model:   1 Entry:  1

Writing results to file: 1sy8_wc.csv


Wattos started at: April 20, 2007 11:54:10 AM CDT
Wattos stopped at: April 20, 2007 11:54:13 AM CDT
Wattos took (#ms): 2942