Hello All,
Not long ago I posted for some help with my twinned dataset at 1.95 A, and have
confirmed the twinning of P6(5) into P6(5)22. Molecular replacement was
successful and the twin refinement in Refmac yieled R/Rfree of 21%/26%, with a
twin fraction of 0.46.
Although the electron density map looks good, I am not sure if I should have
too much confidence in it because I was not able to obtain 'strong electron
densities' from omitted sections of the model in a refinement. I don't know if
this is an indicator for bias introduced somewhere.
I would like to ask what may be some procedures I can try for checking and
removing these biases, and a few additional related questions.
As suggested to me previously, I have generated a total omit map with sfcheck
in ccp4i, using the refined pdb and unrefined data in P6(5). The .map file look
a little worse in quality (is this because of the twinning?) but is still
reasonable, with a few breaks in the main chain and side chains. Interestingly,
when I do a real space refinement against the total omit map, I get slightly
better Rfree at the earlier rounds of Refmac which diverges into the numbers
above. Why is this the case?
Cycle R fact R free
0 0.2301 0.2523
1 0.2205 0.2534
2 0.2164 0.2545
3 0.2140 0.2554
4 0.2123 0.2559
5 0.2117 0.2570
6 0.2116 0.2575
7 0.2112 0.2582
8 0.2112 0.2584
9 0.2109 0.2587
10 0.2106 0.2597
Secondly, I read that I should make sure the Free R flags should be consistent
throughout the twin-related indices. What may be the adverse outcome if this
isn't enforced? Is Refmac aware of this in a twin-refinement? If not, which
tool could I use for this?
I would very much appreciate any comments and suggestions.
Best,
Peter Chan
