Dear Pan,
I apologise if the following comes across as overly harsh, but this is something that needs to be said (to many in structural biology, not just you):
If you skip the manual component of model building and rely on automated building/refinement tools combined with summary validation statistics to do the job for you, it's a near certainty that the model you deposit will end up with preventable errors. The only real questions are: (a) how many, and (b) how serious. While hopefully we will eventually get to the point where automated building and refinement find the right answer almost all the time, and validation near-infallibly tells us which places are correct and don't need to be manually checked... we're not there yet. Right now, automated rebuilding tends to be too "good" at finding conformations that aren't Ramachandran and rotamer outliers and don't clash (much), but are still wrong. The wwPDB is full of such depositions... here's an example from literally the first (very recent) structure I looked at today. I won't name it (that's not my point), but it's a 3.4 angstrom cryo-EM map with zero Ramachandran and rotamer outliers, and a clashscore of 6. While overall it seems quite good, the pictured site is modelled as in bad_trans_pro.jpg - while there are no Rama/rota outliers, that's only because the geometry's been force-fit into a chemically-infeasible conformation with two amides pointing at each other (which would undoubtedly be flagged as a major clash in MolProbity). Remodelling to a cis proline gives a much more sensible solution, and as a bonus fits the density rather better (both in the backbone and the sidechain of the preceding Phe).
The point of my mini-rant: your role in the process shouldn't be to simply press buttons to start each successive automated task. If you want a good model, you need to get in there and diagnose, on a local level, why these outliers and clashes are appearing. It's quite likely that most of them will be fairly innocuous and easy to address, but unless you check for yourself you can't rule out the potential for more serious problems.
In terms of tools for this sort of interactive inspection and rebuilding, have you tried ISOLDE (https://isolde.cimr.cam.ac.uk)? This sort of moderate-to-low resolution regime is exactly what I designed it to handle.
Best regards,
Tristan
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