Cannot obtain correct apoferritin STA reconstruction following WarpTools tutorial

[rui wang]

Hello, I am trying to reproduce the WarpTools(version 2.0.0) cryo-ET tutorial using the provided apoferritin dataset(EMPIAR-10491) and followed the tutorial workflow in WarpTools. The entire processing pipeline in WarpTools completed successfully without any obvious errors, including motion correction, CTF estimation, tilt-series alignment(Etomo), tomogram reconstruction, particle picking(WarpTools TM), and export(3d subtomo) to RELION4. However, after performing subtomogram averaging and refinement in RELION, I am unable to obtain the expected apoferritin structure. The tomograms appear reasonable, and I have not found any obvious problems in the processing logs.  Has anyone encountered a similar issue or could suggest what I should check first?
For reference, I have attached representative images of the reconstructed tomograms, extracted particles, and the final STA map obtained from RELION. I am relatively new to cryo-ET and still learning the workflow, so I would greatly appreciate any suggestions or guidance from the community. Thank you very much for your time and help.