You are also asked to put comments into the file. Finally you are asked which residues you want to write in the output file. The question will repeat such that you can select complicated sets of residues if you want. These can all be set using other options described below. Select the line width to use.
Line width is given in units of pixels of the scanned image.
The default starting value is 3, so you probably want to change it before starting a refinement. In initial stages of refinement, no scale should be refined at all. Three scales are refined for X, Y, and Z separately. At the early stages of refinement this should be set to 0. In the final stages you probably want to raise it in steps to 3.