-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear Md. Munan Shaik, a couple of aspects you might check: - - first build the model AS MUCH AS POSSIBLE before running the first refinement cycle - - switch off automatic weight determination in refmac and use a low weight (e.g. 0.005) and many cycles of refinement - - check that the geometry does not distort (rmsd angles and bond lengths reported in the refmac log-file must not go too high). if it does, lower the weight even further.
if your model stems from higher resolution data and is actually in good agreement with the model you are going at, refinement might ruin the good model if you use inappropriate settings, causing Rfree to go up. Cheers, Tim On 09/14/2011 04:34 PM, Md Shaik wrote: > Dear ccp4, > > I am refining one structure at low resolution (3.5 A). I solved the > structure in space group P622 by molecular replacement. The Rw/Rf > after some cycle of rigid body refinement in Refmac5 is 34/37. But > when I am trying to refine with Restrain refinement in Refmac the Rw > is going down but the Rf is going up. This same happens with the > phenix refinement. The protein is quite big 520 residues and one > molecule is present in the crystal asymmetric unit. The maps are > also not so bad except some region. > > Please give me suggestion, what should I have to care during low > resolution refinement? or is there any other tricks for this types > of data? > > Thanks in advance. > > > Md. Munan Shaik PhD Student Department of Biotehnology School of > Bioscience and Biotechnology via G. Colombo 03 Padova 35131, Italy > Mobile: 00393275671896 E-mail: munanbt2...@yahoo.com > munan.sh...@unipd.it > > - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFOcMiWUxlJ7aRr7hoRAgjmAJ9DGXYXUGHFWW7pJG2weuFMvg8r1ACfUqTq YhxbtdQNuV7rKC/klAKtgjM= =bQQT -----END PGP SIGNATURE-----
