It
general means that you have some information at the higher frequency region or
you are refining noise (overfitting). The later may happen if you are running a
quite older version of auto3dem and you have manually set your resolution to
the Nyquist limit.
1. If you have single defocus dataset, this means you don't have information on
certain frequency. You may see the FSC curve drops to zero, raises up and then
drops to zero again. By combining multiple defocus dataset, this may disappear.
2. If you refine the dataset at very low frequency (say 20 Å), this may suggest you can increase your frequency limit to the higher frequency range (assuming you are manually running auto3dem)
3. If you refine your structure to the Nyquist, this may be an indication that you are refining high frequency noise.
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