When using the Altera_PLL IP with Stratix® V, Arria® V and Cyclone® V devices, the Quartus® Prime software will chose the VCO frequency of the PLL based on the user entered input frequency and output frequencies by calculating suitable M and N counter values (fvco=fin*M/N). The VCO frequency consequently determines the achievable phase step resolution for the achievable phase shift values (phase step resolution = VCO frequency/8). However, the phase step resolution may not be as granular as desired by the user.
An alternative method would be to set one of the output clocks as very high and to leave this output unconnected. This would force the VCO to be a higher frequency, allowing access to finer phase shift steps.