Hi Carsten,

I was wondering if anyone had experience/advice for real space refinement with phenix using marginal data to 3A. I just did a run (SA, real-space refinement against diff_map, 2 fold NCS, grouped APD, fix_rotamers enabled) were the resulting structure showed lots of disconnected sidechains and some broken main chains. I am just repeating the run w/o real space refinement, may be the combination of SA and real space refinement was a bit harsh, but am wondering what kind of parameters make most sense to tweak in order to avoid having the molecules fall apart.

this could be a weight issue (weight between real-space target and restraints). In general I didn't find it too beneficial doing real-space refinement globally, although I've seen cases where it made a good difference (but at higher than 3A resolution). You may try to switch to "simple" target (to make it run much faster) and turn on the weight optimization:

real_space_refinement {
    mode = *simple diff_map
    target_weights = value *grid_search gradients_ratio
    rmsd_max_bonds = 0.05
    rmsd_max_angles = 5
    grid_search_scales = 0.25 0.5 0.75 1 1.25 1.5 1.75 2 2.5 3
}

"fix_rotamers=true" (local real-space refinement for the residues that really need it, as determined automatically) is much better option. I thoroughly tested it up to 3A resolution and in all test cases it worked just great. Try it and see what happens for your data.

Pavel.