I already checked the spindle and has no runout(0.01-0.02) and also no deflection. The cutter is a 4mm x22mm (not the best quality) and for sure will deflect. Tomorrow I will check this too.
However, the cut was done first at 2000mm/min and second at 1000mm/mm and decreasing the feed rate /deep of the cut improve the result, but not dramatically(from 39.7 to 39.8).In case of cutter deflection changing the speed/deep should improve the result.