Overfitting (?) in local refinement

Local Refinement
1

Hi,
I am working on a ‘small’ (~85kDa) membrane protein with low snr particles (~270k). NU refinement doesn’t work well (~6-7A), however using local refinement excluding a flexible domain (~20kDa) appears to ‘work’ (excluded by mask, no particle subtraction). My issue is what I believe to be overfitting - while I see density improvements in the tm regions down to ~3.5A, the loop regions gets overfitted to a point when maps are not interpretable (refinement keeps goooooing until tm regions break down too, <3A).

I’ve varied mask dilation/padding (0-5 & 10-30), turned on gaussian priors (3/2). When I ‘restrict’ refinement sufficiently with these parameters (i.e. no overfitting) the refinement stops @ ~4-4.5A. My issue is that there is clearly high res information beyond this resolution in the tm regions…

Anyone had a similar issues before? Thoughts? Suggestions?

Cheers,
Mika

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2

Are you enabling recentering of rotations & shifts during local refinement? If not, I would recommend trying that (as otherwise you are limited by the initial search range)

3

Thanks for your reply Oli!

I’m right now running a test with both on - I’ll post the results in a couple of hours

4

Hi Mika,

I am facing the same overfitting issue. Have you figured out this problem? How did you work around it?

Thanks,
Chen

5

Hi Chen

unfortunately not… We have collected more data and I’m still working on them, but the ‘issue’ is still there. I believe it goes back to it being a small particle, low SNR, and some flexibility in the (small) fiducial marker. I hope to find a solution and post it here… but if you get there first then please let me know!
Cheers
Mika