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Hi Lisa, Why are you so sure there are 4 molecules in the ASU? There may only be 3 and forcing a fourth molecule is causing lots of clashes. In a similar case, I have seen phaser put two molecules right on top of each other when I forced it to search for too many molecules. In your case I would look at the solution (crystal packing) in coot and see whether the clashes are due to some loops (or domains) which may move upon ligand binding, or whether one of the molecules is at a completely wrong position and if you get a good crystal packing (crystal contacts in all directions) with fewer molecules. You can also start refinement with fewer molecules and see if additional density for missing molecule(s) appears. Good luck! Herman ________________________________ From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of LISA Sent: Thursday, April 19, 2012 8:20 AM To: [log in to unmask] Subject: [ccp4bb] phaser: high z score but no sol Hi all, I am trying to solve one structure by molecular replacement with phaser in CCP4. This a complex of a multi-domain domains with small ligand. I have structues of this protein in apo state and with other similar ligand. The space group of this crystal is P21. This crystal should have 4 molecules in ASU. I used the full protein as model but did get any sol and LLG is below zero. Then each domain were used as the search models in phaser with rotation and tranlsation. I can the get high z score (>20), and LLG is raising. It looks like I get the right sol, but it have more 50 clashes. Why phaser give wrong sol with so high z socre? Can anyone give me some suggestion to solve my strucutes? Thank you. Best Lisa