Hi Krisztian, I have seen refmac fall over in a similar situation (low-ish res, partially floppy model) during TLS refinement. You could try to rescue it by - using fixed TLS parameters from a previous (successful) refinement - setting initial B-values to a fixed value - including the peptide in one of the larger TLS groups (whichever chain/domain it happens to be bound to)
JED. > -------------------------------------------------------------------------- AstraZeneca UK Limited is a company incorporated in England and Wales with registered number: 03674842 and a registered office at 2 Kingdom Street, London, W2 6BD. Confidentiality Notice: This message is private and may contain confidential, proprietary and legally privileged information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorised use or disclosure of the contents of this message is not permitted and may be unlawful. Disclaimer: Email messages may be subject to delays, interception, non-delivery and unauthorised alterations. Therefore, information expressed in this message is not given or endorsed by AstraZeneca UK Limited unless otherwise notified by an authorised representative independent of this message. No contractual relationship is created by this message by any person unless specifically indicated by agreement in writing other than email. Monitoring: AstraZeneca UK Limited may monitor email traffic data and content for the purposes of the prevention and detection of crime, ensuring the security of our computer systems and checking Compliance with our Code of Conduct and Policies. -----Original Message----- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > Krisztian Fodor > Sent: 20 December 2011 13:57 > To: CCP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb] Refmac with TLS terminates early when occupancy > changed > > > Hello Guys, > > I am trying to refine a 3.2 A complex structure with Refmac using TLS. > It seems that I need to decrease the occupancy for a 38 amino acid > peptide in the structure. However, after changing the occupancy to > 0.50, > Refmac terminates after 4 rounds of TLS refinement. > > The only "error message" I can see is this towards the end of the log > file: > Problem > xyz 6480 -1.4325285 -0.92473793 etc. > > And then it says that it is writing out coordinate files etc. which is > obviously not happening, because the run was terminated too early. > > Is this a bug? Any suggestions? > > Thanks a lot, > Krisztian > > > -- > Krisztian Fodor, PhD > EMBL Hamburg c/o DESY > Notkestrasse 85 > 22603 Hamburg, Germany > Email: fo...@embl-hamburg.de > Phone: +49 40 89902221 > Fax: +49 40 89902149
