[phenixbb] Constrained occ refinement -- sum not equal 1

Schubert, Carsten [PRDUS] CSCHUBER at its.jnj.com
Wed Feb 4 12:15:46 PST 2009


I am trying to sort out some issues with the constrained occupancy refinement in phenix 1.4.3. The structure I am working on is fairly high resolution ~1.4A and it looks as if a couple of the alternative conformations would benefit from occupancy refinement, no hydrogens are present yet.

I defined the constrained groups like this:

    occupancies {
      individual = None
      remove_selection = None
      constrained_group {
        selection = chain A and resid 66 and altid A
        selection = chain A and resid 66 and altid B

I expected that the sum of occupancies would be restrained to 1, which they should according to the manual, but the refinement gives me occupancies of 0.7 for altid A and 0.34 for altid B, starting values were both 0.5.  Similar discrepancies were also present in other groups, like 0.5 A, 0.37 B etc. The latter is the largest deviation from 1 I have seen in thus far. The alternate conformations were generated in coot, by splitting at the CA position.

Is this a rounding error I just have to contend with or is there some other parameter I need to tweak?



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