8. Provide detailed refinement information
In this section, the applied methods and algorithms as well as parameters, options and protocols within them have to be described along with the justifications for the choices made. It is important to explain how extensive refinement has been made, including force fields, time steps, calculation details, stopping criterion, etc. whatever is relevant for the used method.
Example: The model was refined by energy minimization with the program CHARMM (version 41, release c40b2) (Brooks et al., 2009) using the all-hydrogen parameter set 22 in a stepwise manner whereby the conserved regions were constrained and the largest deviations were on the insertions/deletions. First the new loops were minimized. After 1000 cycles, the insertion/deletion regions were subjected to simulated annealing from 2000 to 300 K, followed by minimization for 500 cycles. Then the Cα atoms of the conserved regions, ATP, and Mg atoms were harmonically constrained, and the structure was minimized until the rms gradient was below 0.001 kcal/(mol·Å).