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While waiting for and trying the other more intelligent
suggestions, you might also try letting arp/warp have a
go at your stuck solution.
If in fact the space group is correct and you MR solution
has some validity but is not quite good enough to make
rebuilding easy, A/W might kick in and build your model
for you.

I am playing with such a case: MR from a distant homolog,
with no attempt to to taylor the model to be more like the
target sequence. After refinement in CNS stalls at
R/Rfree 0.43/0.44 (no manual rebuilding), A/W builds
(in one example) 1818 residues and docks 1530 in sequence
(out of ~2250 total). Using resolution 9 to 1.9 A.

In a way A/W's approach would be taking the suggestion to
revert to polyalanine (in case of permuted segments) one step
farther- revert to free atoms.

I use the CCP4i gui. Select Model Building, arp/warp,
task "automated building starting from existing model",
give it your current model and an mtz file with Fobs and
SigFobs, and let it run.

Ed

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