Local refinement (new) result with some noise signal

I did a local refinement(new) job with particle subtraction first, the result was ok except for some noise signal in the map bottom(see picture below). The noise signal was in the interface of particle subtraction. Dose that mean I did not subtract particles completely or the refinement parameters did not fit?

At the same time, I did a local refinement (legacy) job with the same particles and mask, the result was worse but noise signal was less(see picture below).

I want to use the local refinement(new) job result but with less noise signal. What should I do to improve it?
Thanks a lot!


Yes, signal subtraction is always incomplete. Do “focused” local refinement, using a mask for area of interest in the job. Or if you have lots of particles do 3D class no alignment with low resolution focus and it will likely put 1 class with the major fraction of noise so you can remove

Ok, thanks a lot!I will give it a try.