Dear Refmac developers,
I am trying to reproduce some successful refmac runs but cannot get the
previous results despite playing around with the parameters.
I did those runs in Feb 2014 (Refmac 5.8.0049) but unfortunately have
overwritten the log files in a backup. I still have the pdbs, mtz and my
notes.
I was using jelly body and Prosmart at a resolution of 3.1 A, which
worked superb and I could track some unexpected conformational changes.
In several successive runs each with 100 cycles Rwork and Rfree were
decreasing slowly and continuously and finally showed two rigid body
movements.
When I now repeat those runs (same pdb, same mtz input files and using
the prosmart restraint file from the former runs) I get very similar
Rwork/Refree but not the rigid body movements of these domains again in
the resulting pdb.
If I loosen the restraints in jelly body Rwork decreases but Rfree
stays, indicating some overfitting. And also in the resulting pdbs the
previously observbed conformational change is not observed. I tried also
to increase the number of cycles to some insane numbers (>600), but this
did not improve the situation.
Any ideas what might go wrong? I am really fond of jelly body and would
like now to check a series of new data sets at low resolution for the
extent of the observed (and verified) conformational change.
Best regards,
Guenter
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