The results of my local refinements look very strange. Although some real features of the molecule emerge (i.e. I can see the backbone better in certain locations), the map is really distorted and shows a lot of “spikes” and disconnected parts. Can anyone please explain the origin of this problem; I’m somewhat new to cryo-EM and cryoSparc. I have seen similarly strange results in the past, when running global homogenous refinements or NU-refinements. The GSFSC resolution gets much better, but the map looks like it “splashed”. Any help is greatly appreciated. The molecule that I am working with is relatively small < 200 kDa.