Frealign generates a log file in the working directory called "frealign.log". It contains status updates that can be used to monitor the progress of the refinement or search. Furthermore, a scratch directory is created (unless one already exists) that contains all intermediate files and results. Unless specified otherwise in mparameters, the scratch directory will be in the working directory and will be called "scratch".
After each cycle, a new parameter file with updated alignment parameters as well as a new 3D reconstruction are generated. Cycle numbers will be incremented automatically for each cycle. The final lines of each new parameter file show statistics about the 3D reconstruction, for example the Fourier Shell Correlation (FSC) curve.