Hello all<br><br>I have refined and built model a dataset of 3.0A resolution dataset. This model is assocaied with a ligand. After final refinement and model building i found  a big blob of  Fo-Fc density of around 4sigma level at the N-terminal of the fianl model. My protein doesnot carry any tag at the N-terminal. But, the template i have used for the molecular replacement carrying a tag at the N-termianl, which can occupy only 1/4th of this positive density after superpostion. My crystallisation conditions component cannot occupy such higher level of positive density. Since my protein binds to a ligand, i looked carefully to the positive density and it seems very similar to the ligand density but its obscure. Refinement after fitting the ligand leads to very high B-factor of  the ligan, which vary for various atoms from 50-90 and simultaneously positive density goes off. I also tried to change the occupancy of the ligand but as i reduce the occupancy the B factor comes down at the noraml expected average B factor value but again Fo-Fc density appears in the map over ligand. If i leave to refine the occupancy to the programme automatically, this lead to the zero occupancy of the few atoms in the ligand and avearge B factor remains normal.  suggestions  would be appreciated.<br>
<br>Thanks in advance<br>Peter<br><br>