Dear Sean,
I have noticed this and more to the point the geometry as assessed
by MOLPROBITY is much worse for
the latest version of REFMAC (3.0068).
I have tested a few other versions of REFMAC and the results vary
quite a lot.
For exactly the same run, I get the best results with an old version
Refmac_5.2.0019!
For my structure, exactly the same run gives the R-factors 0.218,
0.268 with 5.2.0019
(compare 0.2326 R-free 0.2915 for latest Refmac version 3.0068)
and the also the best MOLPROBITY scores for (clashscore 9.03 for ,
compared with 22.0 for 3.0068). And the map is actually noticeably
better after refining with
Refmac_5.2.0019.
I have been in touch with Garib about this and he is looking into it.
Stephen
Hi all,
I have just installed the new CCP4I package for Windows, and refined a
structure I was working on using an older version (CCP4I 6.0.2), and the
refinement statistics are significantly worse when using the same input files.
Under Refmac 5.2 the details were:
$$
Ncyc Rfact Rfree FOM LLG rmsBOND rmsANGLE rmsCHIRAL $$
$$
0 0.150 0.189 0.886 481182.9 0.011 1.208 0.147
1 0.147 0.188 0.887 480211.9 0.010 1.170 0.147
2 0.147 0.188 0.887 480049.6 0.010 1.152 0.147
3 0.147 0.188 0.887 479927.9 0.010 1.147 0.147
4 0.147 0.188 0.887 479847.2 0.010 1.144 0.147
5 0.147 0.188 0.887 479805.5 0.010 1.143 0.148
$$
Where Refmac 5.5 gives:
$$
Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND rmsANGL
zANGL rmsCHIRAL $$
$$
0 0.1738 0.2163 0.874 465814. 25317.2 0.0106 0.439 1.208
0.519 0.147
1 0.1723 0.2158 0.875 465007. 25296.4 0.0102 0.410 1.178
0.510 0.147
2 0.1716 0.2155 0.875 464584. 25285.4 0.0102 0.403 1.158
0.506 0.147
3 0.1711 0.2155 0.875 464297. 25278.2 0.0101 0.401 1.145
0.503 0.146
4 0.1708 0.2155 0.875 464090. 25271.8 0.0101 0.399 1.137
0.501 0.146
5 0.1706 0.2155 0.876 463961. 25269.1 0.0101 0.398 1.131
0.500 0.146
$$
I have been through the header of both files to check that all of the settings
are the same. One thing I did notice is that the Estimated number of
reflections is now 111528, where Refmac 5.2 had this value at 101968. I don't
know whether this is relevant to the problem I'm seeing, but it does seem
suspicious. The new Refmac has also apparently read one more reflection than
the old (84317 vs 84316).
Has anyone else seen this problem, and is there anything I can do to fix it (I
was liking my old statistics!)?
Thanks in advance,
Sean
--
**********************************************************************
Dr. Stephen Cusack,
Head of Grenoble Outstation of EMBL
Group leader in structural biology of protein-RNA complexes and viral proteins
Joint appointment in EMBL Gene Expression Programme
Director of CNRS-UJF-EMBL Mixed Unit (UMR 5233) for Virus Host Cell
Interactions (UVHCI)
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Email: [email protected]
Website: http://www.embl.fr
Tel: (33) 4 76 20 7238 Secretary (33) 4 76 20 7306
Fax: (33) 4 76 20 7786 or (33) 4 76 20 7199
Postal address: EMBL Grenoble Outstation, 6 Rue Jules Horowitz, BP181, 38042
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