Re: [ccp4bb] r-factor does not reduce

[Roger Rowlett]

It would not necessarily be unusual for an initial MR solution to have an R-factor of 45-48%, depending on the MR program used and quality of the search model. However, after an initial restrained refinement in Refmac, a good solution should drop pretty smartly from there. Some issues to consider: 1. Do you have the correct space group? (e.g., P422 vs. P41212 vs. P43212, etc.). If you use Phaser or EPMR, it can do an automatic search of all related space groups. 2. Does the MR solution have the correct number of protein chains in the ASU and does it pack well? Too many clashes, large area of empty space in the unit cell? If the solution does not pack well, you may have an incorrect MR solution. Inspect your MR model in Pymol or another favorite program to examine unit cell packing. 3. Have you tried alternative MR programs? Phaser and EPMR are among the quickest and most efficient. 4. How closely related is your search model to the target? For more distantly related models, have you used chainsaw or manually edited the search model to truncate non-identical side chains? Cheers. Sylvia Fanucchi wrote: Hi everyone   I am new to solving crystal structures so apologies for the simple question   I am solving a structure using molecular replacement. I have refined my structure with refmac however the R-factor and R-free do not seem to go down with successive rounds of refinement. The initial value was 0.49 (after 20 cycles of rigid body refinement). After analysing the output and a further 20 cycles of refinement, the R-factor is now 0.48. I would like to know if it is ever worthwhile to continue refining a structure when the initial R factors are so high? If so, what could I do to improve the refinement?   Thanks for your suggestions   Best regards Sylvia Fanucchi Ph.D Protein Structure-Function Research Unit East Campus, Gate House Room 416 School of Molecular and Cell Biology University of the Witwatersrand Johannesburg 2050 South Africa Tel: +27 (11) 717-6348 Fax: +27 (11) 717-6351 E-mail: sylvia.fanuc...@wits.ac.za    This communication is intended for the addressee only. It is confidential. If you have received this communication in error, please notify us immediately and destroy the original message. You may not copy or disseminate this communication without the permission of the University. Only authorized signatories are competent to enter into agreements on behalf of the University and recipients are thus advised that the content of this message may not be legally binding on the University and may contain the personal views and opinions of the author, which are not necessarily the views and opinions of The University of the Witwatersrand, Johannesburg. All agreements between the University and outsiders are subject to South African Law unless the University agrees in writing to the contrary. -- Roger S. Rowlett Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu