is this the AC lines?
COMMAND: ../../C/cluster_info_silent.out bbphad.out _ cluster1/tmp 5,15,45,75 3,4
AC: target 15 threshold 8.21 clusters 69 coverage 466
AC: target 16 threshold 8.21 clusters 69 coverage 466
AC: target 17 threshold 8.21 clusters 69 coverage 466
AC: target 18 threshold 8.37 clusters 88 coverage 616
AC: target 19 threshold 8.37 clusters 88 coverage 616
AC: target 20 threshold 8.37 clusters 88 coverage 616
AC: target 21 threshold 8.39 clusters 89 coverage 628
AC: target 22 threshold 8.40 clusters 91 coverage 639
AC: target 23 threshold 8.40 clusters 91 coverage 639
AC: target 24 threshold 8.40 clusters 91 coverage 639
AC: target 25 threshold 8.55 clusters 115 coverage 819
AC: target 27 threshold 8.55 clusters 115 coverage 819
AC: target 29 threshold 8.61 clusters 120 coverage 870
AC: target 31 threshold 8.64 clusters 126 coverage 916
AC: target 33 threshold 8.64 clusters 126 coverage 916
AC: target 35 threshold 8.65 clusters 128 coverage 931
AC: target 38 threshold 8.80 clusters 156 coverage 1192
AC: target 41 threshold 8.87 clusters 165 coverage 1295
AC: target 44 threshold 8.87 clusters 166 coverage 1305
AC: target 47 threshold 8.88 clusters 167 coverage 1311
AC: target 51 threshold 8.97 clusters 181 coverage 1453
AC: target 55 threshold 8.99 clusters 185 coverage 1493
AC: target 60 threshold 9.10 clusters 201 coverage 1700
AC: target 65 threshold 9.16 clusters 220 coverage 1867
AC: target 71 threshold 9.22 clusters 227 coverage 1994
TARGET: 15 THRESHOLD: 8.209858
what’s ur comment?
> > 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.
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