We evaluate the frequency error from distributed cavity phase in the caesium fountain clock PTB-CSF2 at the Physikalisch-Technische Bundesanstalt with a combination of frequency measurements and ab initio calculations. The associated uncertainty is 1.3E-16, with a frequency bias of 0.4E-16. The agreement between the measurements and calculations explains the previously observed frequency shifts at elevated microwave amplitude. We also evaluate the frequency bias and uncertainty due to the microwave lensing of the atomic wavepackets. We report a total PTB-CSF2 systematic uncertainty of 4.1E-16.