The .hd11 file specifies that time series output is to be generated additionally. See the .hd11 file.
The model simulation sequence simply specifies the name of the MIKE 11 .sim11 file, and the model parameter file is the .xns11r file. When pressing the "Edit" button, the AutoCal editor will open Notepad to allow for editing the .xns11r template file.
AutoCal treats .xns11r file somewhat differently than other parameter files used for auto-calibration. The data in .xns11r are to be interpolated into Manning numbers in all intermediate cross sections. When using the cross section editor this happens automatically, but when changing the .xns11r file externally using AutoCal the Manning numbers still need to be interpolated and processed data needs to be recalculated. This is all taken care of by AutoCal.
Using Notepad the Manning number (for uniform resistance distribution) at the three locations is set to 1.01e-035, 1.02e-035 and 1.03e-035.
Finally, the Parameter optimisation is chosen as the Simulation option.