Method: Copy the format of the table on the left.  Substitute the data from your pdb file for the data in the table.
 

Strategy: Use the coordinates of the native proteinase K structure output by ARP/wARP as a starting point for the refinement of the PMSF complex.  Refine using maximum likelihood restrained refinement for 5 cycles. Calculate difference Fourier maps (fo-fc and 2fo-fc) and look for large peaks in the fo-fc density.  One of these peaks should correspond to PMSF, the others may be due to water molecules, side chain movements, or bits of the model that were not built by ARP/wARP previously.

Procedures: Login to Bernal, Laue, or Bragg. Change directories to your working directory. Type the word "ccp4i" to start the CCP4 programs GUI. Define yourself as the user in the "Directories & Projects Dir" button.  Select the options as shown in the example on the right.   Check the R-work and R-free.  Begin an O session by typing "ono" and in the graphic window type "@difmacro".  This command will read in the refined proteinase K model and a few libraries that will aid in model building.  Tear off the following sub-menus form the "menus" menu: Objects, User, Fake Dials.  You should be able to see three objects: the proteinase K model (prok1); the 2fo-fc difference Fourier map (2fofc); and the fo-fc difference Fourier map contoured in positive(pos/blue) and negative (neg/red) contour levels.  You will see a sidechain movement near Trp A9; fix it with RSR-rotamer. You will see a missing dipeptide between A171-A174 (why would this be missing from the model?); build it in with "build_resi prok1 a172 f" followed by "build_resi prok1 a173 f". Adjust the conformation by "grab residue". Lastly, you will see some density for the PMSF.  Read in pms.pdb and position it near the active site serine.  Write out coordinates for your modified protein (prok_pmsf1.pdb) and coordinates for you pmsf molecule (pms.pdb).  Catenate the pmsf coordinates to the bottom of prok_pmsf1.pdb and use this file for the next round of refinement.