We have a bit of a problem with our refinement 
Some of the classsums look a bit off centered and it gets worse as I do more rounds of refinement. Our structure looks more funny as I refine further. We wonder if it's worth removing the bad classsums in the initial rounds of refinements to get the rough shape of the molecule (if yes, how?).
I started with a Gaussian sphere as initial model and used these commands:
refine 2 mask=25 pad=128 hard=25 ang=10 classkeep=1 classiter=8 median phasecls refine 10 mask=25 pad=128 hard=25 ang=10 classkeep=1 classiter=5 median phasecls refine 14 mask=25 pad=128 hard=25 ang=10 classkeep=1 classiter=3 median phasecls refine 16 mask=25 pad=128 hard=25 ang=8 classkeep=1 classiter=8 median phasecls refine 24 mask=25 pad=128 hard=25 ang=8 classkeep=1 classiter=5 median phasecls refine 32 mask=25 pad=128 hard=25 ang=8 classkeep=1 classiter=3 shrink=8 median phasecls refine 42 mask=25 pad=128 hard=25 ang=8 classkeep=1 classiter=3 shrink=8 median phasecls refine 44 mask=25 pad=128 hard=25 ang=6 classkeep=1 classiter=8 shrink=8 median phasecls