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 [email protected] tel 01235 567717 This email and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorized recipient of the addressee, please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to this email. Any views or opinions presented are solely those of the author and do not necessarily represent those of the Research Complex at Harwell. There is no guarantee that this email or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. We use an electronic filing system. Please send electronic versions of documents, unless paper is specifically requested. This email may have a protective marking, for an explanation, please see: http://www.mrc.ac.uk/About/informationandstandards/documentmarking/index.htm.
