> how do u know my decoy above 8A.
On the X axis of your clustering tree you have got rmsd values… You should be able to find the exact rmsd cutoff used for clustering in the *.info file you should have got in the clustering directory. It should be a line like:
TARGET: 100 THRESHOLD: 1.271307
just after the AC lines.
> i am generate 9999 decoy
For such a long protein it might be much too few. Especially if you get poor clustering.
> run cluster_info_silent.out with 5,15,45,75 3,4
With such options the program did not find any cluster with the size above 15 when using rmsd threshold between 3 and 4 A. So it increased the rmsd threshold until it got the top cluster of size 15.
Please post the AC lines from your *.info file so I could advice you how you should modify the clustering options.
And if you have computational power generate another 20000 decoys You can try different options/protocols or try to fold a homolog.