I have been having a problem of worse R factors in phenix. However this was between runs on 1.8.1-1168 and 1.8.2-1309. It transpired that although I had switched reference structure on in both, in 1.8.1 it had found a format error and ignored the reference without telling me. 1.8.2 forced me to correct the error and then used it (and it made the R factors worse). I don't know if this explains any of the other recent problems reported. Best wishes Nick -- Prof Nicholas H. Keep Executive Dean of School of Science Professor of Biomolecular Science Crystallography, Institute for Structural and Molecular Biology, Department of Biological Sciences Birkbeck, University of London, Malet Street, Bloomsbury LONDON WC1E 7HX email [email protected] Telephone 020-7631-6852 (Room G54a Office) 020-7631-6800 (Department Office) Fax 020-7631-6803 If you want to access me in person you have to come to the crystallography entrance and ring me or the department office from the internal phone by the door