mdv1.log

mfold

 mfold version 3.2 by Michael Zuker & Doug Turner 
 Enter run type
     0  Regular run (default)
     1  Save run
     2  Continuation run
  
 Enter save file name (default fold.sav)

 Input sequence file name  (q to quit)  

 Available sequence(s) in mdv1-local.seq                          

   1) MDV-1 (-) RNA                                     

 Choose sequence by number [default is  1],                     or enter  F  for a new file: 

   Length of retrieved sequence =    221



 MDV-1 (-) RNA                                             221 nucleotides

 Enter start of fragment (default 1)
 Enter end of fragment (default    221)
 Enter asymmetric interior loop of size 3 energy file name
 (default asint1x2.dat)
 Enter asymmetric interior loop of size 5 energy file name
 (default asint2x3.dat)
 Enter dangle energy file name (default dangle.dat)
 Enter loop energy file name (default loop.dat)
 Enter misc. loop energy file name (default miscloop.dat)
 Enter symmetric interior loop of size 2 energy file
  name (default sint2.dat)
 Enter symmetric interior loop of size 4 energy file
  name (default sint4.dat)
 Enter symmetric interior loop of size 6 energy file
  name (default sint6.dat)
 Enter stack energy file name (default stack.dat)
 Enter tetraloop energy file name (default tloop.dat)
 Enter triloop energy file name (default triloop.dat)
 Enter tstackh energy file name (default tstackh.dat)
 Enter tstacki energy file name (default tstacki.dat)

          1  Energy Parameter           7  Double Prohibit 
          2  Single Force               8  Prohibit Range  
          3  Double Force               9  Maximum distance
          4  Closed Excision           10  Begin folding   
          5  Open Excision             11  Show current    
          6  Single Prohibit           12  Clear current   

 Enter Choice   

            Energy Parameters (10ths or 100ths kcal/mole)

          1 Extra stack energy                        [    0]
          2 Extra bulge energy                        [    0]
          3 Extra loop energy (interior)              [    0]
          4 Extra loop energy (hairpin)               [    0]
          5 Extra loop energy (multi)                 [  340]
          6 Multi loop energy/single-stranded base    [    0]
          7 Maximum size of interior loop             [   30]
          8 Maximum lopsidedness of an interior loop  [   30]
          9 Multi loop energy/closing base pair       [   40]
         10 Helix penalty per non-GC closing pair     [   50]
         11 GGG hairpin bonus                         [ -220]
         12 poly-C loop penalty: slope                [   30]
         13 poly-C loop penalty: intercept            [  160]
         14 poly-C loop penalty: hairpin of size 3    [  140]
         15 Intermolecular initiation free energy     [  410]
         16 GAIL Rule - 1 for version 3 rules only    [    1]
Enter Parameter to be changed (<return> for main menu)
Enter new value

            Energy Parameters (10ths or 100ths kcal/mole)

          1 Extra stack energy                        [    0]
          2 Extra bulge energy                        [    0]
          3 Extra loop energy (interior)              [    0]
          4 Extra loop energy (hairpin)               [    0]
          5 Extra loop energy (multi)                 [  340]
          6 Multi loop energy/single-stranded base    [    0]
          7 Maximum size of interior loop             [   30]
          8 Maximum lopsidedness of an interior loop  [   30]
          9 Multi loop energy/closing base pair       [   40]
         10 Helix penalty per non-GC closing pair     [   50]
         11 GGG hairpin bonus                         [ -220]
         12 poly-C loop penalty: slope                [   30]
         13 poly-C loop penalty: intercept            [  160]
         14 poly-C loop penalty: hairpin of size 3    [  140]
         15 Intermolecular initiation free energy     [  410]
         16 GAIL Rule - 1 for version 3 rules only    [    1]
Enter Parameter to be changed (<return> for main menu)
Enter new value

            Energy Parameters (10ths or 100ths kcal/mole)

          1 Extra stack energy                        [    0]
          2 Extra bulge energy                        [    0]
          3 Extra loop energy (interior)              [    0]
          4 Extra loop energy (hairpin)               [    0]
          5 Extra loop energy (multi)                 [  340]
          6 Multi loop energy/single-stranded base    [    0]
          7 Maximum size of interior loop             [   30]
          8 Maximum lopsidedness of an interior loop  [   30]
          9 Multi loop energy/closing base pair       [   40]
         10 Helix penalty per non-GC closing pair     [   50]
         11 GGG hairpin bonus                         [ -220]
         12 poly-C loop penalty: slope                [   30]
         13 poly-C loop penalty: intercept            [  160]
         14 poly-C loop penalty: hairpin of size 3    [  140]
         15 Intermolecular initiation free energy     [  410]
         16 GAIL Rule - 1 for version 3 rules only    [    1]
Enter Parameter to be changed (<return> for main menu)

          1  Energy Parameter           7  Double Prohibit 
          2  Single Force               8  Prohibit Range  
          3  Double Force               9  Maximum distance
          4  Closed Excision           10  Begin folding   
          5  Open Excision             11  Show current    
          6  Single Prohibit           12  Clear current   

 Enter Choice   
 Enter save file name (default fold.sav)
 Enter helix file name 
 >
vmin =  -145.3. Enter energy increment >
Enter number of levels >
Removing non-optimal helices of length less than 2
mdv1.plot replaced by new file.
 Enter save file name (default fold.sav)
 Enter p-num file name 
 >
vmin =  -145.3. Enter energy increment >
    ====>  Output file is mdv1.h-num

 mfold version 3.2 by Michael Zuker & Doug Turner 
 Enter run type
     0  Regular run (default)
     1  Save run
     2  Continuation run
  
 Enter run mode
     0  Sub-optimal plot (default)
     1  n-best
     2  Multiple Molecules
  

 Enter percentage for sort (default 0)  

 Enter number of tracebacks (default 1)  

 Enter window size (default 0)  
  
 Enter save file name (default fold.sav)
 Enter file name for continuation dump(return for terminal)
  No choices currently defined
   Energy Parameters


             Energy Parameters (10ths kcal/mole)

           1 Extra stack energy                        [    0]
           2 Extra bulge energy                        [    0]
           3 Extra loop energy (interior)              [    0]
           4 Extra loop energy (hairpin)               [    0]
           5 Extra loop energy (multi)                 [  340]
           6 Multi loop energy/single-stranded base    [    0]
           7 Maximum size of interior loop             [   30]
           8 Maximum lopsidedness of an interior loop  [   30]
           9 Multi loop energy/closing base pair       [   40]
          10 Helix penalty per non-GC closing pair     [   50]
          11 GGG hairpin bonus                         [ -220]
          12 poly-C loop penalty: slope                [   30]
          13 poly-C loop penalty: intercept            [  160]
          14 poly-C loop penalty: hairpin of size 3    [  140]
          15 Intermolecular initiation free energy     [  410]
          16 GAIL Rule - 1 for version 3 rules only    [    1]


 Listing of energy files? (y/N)
Do you want printer output? (Y,n) 
Output to terminal? (Y,n) 
Enter output file name (default MDV_1_____RNA.out_________________________________          )
Do you want ct file? (y,N) 
Enter ct file name (default MDV_1_____RNA.ct _________________________________          )
Do you want a detailed ddG table? (y,N) 
Enter detailed ddG table file name (default MDV_1_____RNA.det_________________________________          )
  
 End reached at traceback     6



 boxplot_ng Version 3.2 


 Trying to open  mdv1.plot
 number of helices is 91
 There are 91 helices in the plot file.
 Postscript file is     mdv1.ps
 Creating gif 612 by 792 
 gif file is            mdv1.jpg

 GIFDAT file is mdv1.gifdat
 Normal exit from boxplot_ng 

CurrentFile= mdv1-temp_1.ct
CurrentFile= mdv1-temp_2.ct
CurrentFile= mdv1-temp_3.ct
CurrentFile= mdv1-temp_4.ct
CurrentFile= mdv1-temp_5.ct
CurrentFile= mdv1-temp_6.ct



 sir_graph_ng 


 Rotation angle: 0.00 degrees
 Input File: mdv1_1.ct
 Sequence length: 221
 Using 356.0 degrees of the circle 



 Output:  mdv1_1.ps 

 Normal exit from sir_graph_ng 




 sir_graph_ng 


 Rotation angle: 0.00 degrees
 Input File: mdv1_1.ct
 Sequence length: 221
 Using 356.0 degrees of the circle 



 Output:  mdv1_1.gif 
 gif File: mdv1_1.gif
 gif resolution 1224 x 1584

 Normal exit from sir_graph_ng 




 sir_graph_ng 


 Rotation angle: 0.00 degrees
 Input File: mdv1_2.ct
 Sequence length: 221
 Using 356.0 degrees of the circle 



 Output:  mdv1_2.ps 

 Normal exit from sir_graph_ng 




 sir_graph_ng 


 Rotation angle: 0.00 degrees
 Input File: mdv1_2.ct
 Sequence length: 221
 Using 356.0 degrees of the circle 



 Output:  mdv1_2.gif 
 gif File: mdv1_2.gif
 gif resolution 1224 x 1584

 Normal exit from sir_graph_ng 




 sir_graph_ng 


 Rotation angle: 0.00 degrees
 Input File: mdv1_3.ct
 Sequence length: 221
 Using 356.0 degrees of the circle 



 Output:  mdv1_3.ps 

 Normal exit from sir_graph_ng 




 sir_graph_ng 


 Rotation angle: 0.00 degrees
 Input File: mdv1_3.ct
 Sequence length: 221
 Using 356.0 degrees of the circle 



 Output:  mdv1_3.gif 
 gif File: mdv1_3.gif
 gif resolution 1224 x 1584

 Normal exit from sir_graph_ng 




 sir_graph_ng 


 Rotation angle: 0.00 degrees
 Input File: mdv1_4.ct
 Sequence length: 221
 Using 356.0 degrees of the circle 



 Output:  mdv1_4.ps 

 Normal exit from sir_graph_ng 




 sir_graph_ng 


 Rotation angle: 0.00 degrees
 Input File: mdv1_4.ct
 Sequence length: 221
 Using 356.0 degrees of the circle 



 Output:  mdv1_4.gif 
 gif File: mdv1_4.gif
 gif resolution 1224 x 1584

 Normal exit from sir_graph_ng 




 sir_graph_ng 


 Rotation angle: 0.00 degrees
 Input File: mdv1_5.ct
 Sequence length: 221
 Using 356.0 degrees of the circle 



 Output:  mdv1_5.ps 

 Normal exit from sir_graph_ng 




 sir_graph_ng 


 Rotation angle: 0.00 degrees
 Input File: mdv1_5.ct
 Sequence length: 221
 Using 356.0 degrees of the circle 



 Output:  mdv1_5.gif 
 gif File: mdv1_5.gif
 gif resolution 1224 x 1584

 Normal exit from sir_graph_ng 




 sir_graph_ng 


 Rotation angle: 0.00 degrees
 Input File: mdv1_6.ct
 Sequence length: 221
 Using 356.0 degrees of the circle 



 Output:  mdv1_6.ps 

 Normal exit from sir_graph_ng 




 sir_graph_ng 


 Rotation angle: 0.00 degrees
 Input File: mdv1_6.ct
 Sequence length: 221
 Using 356.0 degrees of the circle 



 Output:  mdv1_6.gif 
 gif File: mdv1_6.gif
 gif resolution 1224 x 1584

 Normal exit from sir_graph_ng