Dear CCP4 BBers,
I am currently refining a model of a protein containing three iron sulphur clusters using Refmac (v5.8.0078) and am getting some unusual results. One of the clusters (3fe 4s) seems to behave resonably and the refined electron density looks very nice. The atoms in the others clusters (4Fe4S and 4Fe3S), however, migrate towards the centre of the cluster producing Fo-Fc difference maps with strong negative density at the centre surrounded by blobs of positive density where the atoms should be.
I have checkedthe refmac dictionaries and there are entries for each of the clusters, so I shouldn't have to explicitly include a cif file for the clusters as an input right? In fact, when I did try to include a dictionary file for one of the clusters refmac gave a warning message in the log about duplicate monomers dictionaries and it made no difference to the refinement/maps anyway.
On checking the refmac log file there is no specific mention that there are hetero-groups in the pdb file and no explicit mention that it is using any dictionaries during the refinement. How can I tell if refmac is reading/using the dictionaries? Also bonds within the clusters are flagged up as outliers and deviating by more than 10 sigma from ideal suggesting that they are not getting read?
I realise that something chemically odd could be going on at the centres, but if I omit them from the model and calculate maps very strong density comes back around where the atoms sat before refinement, so I am pretty confident that they are in the right place to start with.
Any help with this problem would be greatly appreciated, I'm sure there is something obvious that I am missing but can't see what that is at the moment. It is particularly confusing since one cluster apparently behaves while the others do not. I could, of course, try phenix or buster, but I would like to get to the bottom of the problem with refmac if possible.
Thanks very much in advance,
Steve
Dr Stephen Carr
Research Complex at Harwell (RCaH)
Rutherford Appleton Laboratory
Harwell Oxford
Didcot
Oxon OX11 0FA
United Kingdom
Email [log in to unmask]
tel 01235 567717
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