Welcome, schow!
Maybe someone more expert than I will chime in, but here’s my non-expert reply.
The dip in the corrected FSC is normal. It’s where phase randomization begins in the calculation of the corrected FSC. You will always see this.
In my experience, if the dip is very large, it can indicate potential problems, such as duplicate particles, or masking problems. I’ve encountered both problems, and when I corrected them the dip was smaller that what you’re showing, although what you show is not that bad and probably usable.
Some suggestions:
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Note the B-factor from the Guinier plot of your refinement, and use the refinement volume and mask output as the input for a Local Resolution job. Then use the output volume of the Local Resolution Job as input for a Local Filtering job, and enter the noted B-factor for sharpening (as a negative number). This will improve your map. You can also download the LocRes volume from the Local Resolution job, and the output of the Local Filtering job and display it within Chimera using Volume->Surface Color to color the filtered map according to the local resolution. That, plus your eye will tell you what you can confidently model and what you can’t.
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Run a Heterogeneous refinement to look for different populations. How much you can get out of this will depend on how many particles you have to work with (and how variable your protein is).
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Run a 3D variability job to look for domain movement. If you identify major movement from this or the hetero-refinenent, you can run a Local Refinement to improve the resolution in the area of interest.
Best,
RJ