Recently when I run homogeneous refinement (legacy) on version v2.13.2, I noticed that resolution stayed at 5.9 Å after second iteration, the third and fourth iteration have the same result as second (attached picture). I processed the same micrographs on another computer by cryosparc, which did not have this problem and gave a high resolution model. Dose anyone have any idea to fix this bug?
Were any parameters changed between the runs?
Here it looks like your reconstruction is proceeding up to the nyquist resolution of the images - did you set the refinement box size to a small value, or did you downsample the particles before refinement?
Something seems off, because at 0.615A pixel size, extracted at 640 and binned to 256, the pixel size should end up as 1.5375 giving a Nyquist rate of 3.075A. However, the FSC curves you posted show that the refinement was done with a Nyquist rate of 5.9A (pixel size 2.95A).
Any chance there was a typo in the import job, with the pixel size set wrong?