Read libraries from system resource.
Wattos started at: April 20, 2007 11:49:23 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/pdb1kr8.ent, PDB]
Read total number of atoms from PDB formatted coordinate list: 3108


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

Done. Checked number of potential pairs: 286
Found number of new bond candidates: 240


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: 9
Found number of new hydrogen bonds: 9
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      7(C  )    1      1      1   2.852  169.909                       5
N2      1(G  )    1 O2      7(C  )    1      1      1   2.747  170.551                       5
N4      2(C  )    1 O6      6(G  )    1      1      1   2.790  165.983                       5
N2      3(G  )    1 N7      5(A  )    1      1      1   2.901  173.760                       5
N6      5(A  )    1 O4*     3(G  )    1      1      1   2.879  125.588                       5
N6      5(A  )    1 N3      3(G  )    1      1      1   2.844  158.781                       5
N1      6(G  )    1 N3      2(C  )    1      1      1   2.831  153.497                       5
N2      6(G  )    1 O2      2(C  )    1      1      1   2.747  169.664                       5
N4      7(C  )    1 O6      1(G  )    1      1      1   2.801  174.116                       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, 1kr8_wc.csv]
Trying to match bases to eachother for number of bases: 7
Considering number of hydrogen bonds: 9
Results contains number of sets of co-planar bases: 2
Results:
Residue:   1(   G) Mol:   1 Model:   1 Entry:  1
Residue:   7(   C) Mol:   1 Model:   1 Entry:  1

Residue:   2(   C) Mol:   1 Model:   1 Entry:  1
Residue:   6(   G) Mol:   1 Model:   1 Entry:  1

Writing results to file: 1kr8_wc.csv


Wattos started at: April 20, 2007 11:49:23 AM CDT
Wattos stopped at: April 20, 2007 11:49:26 AM CDT
Wattos took (#ms): 2913