Haiying,
As far as I can tell you've got a successful solution in molecular
replacement via Phaser and then gone and refined it in the wrong space
group.
Based on what you've told us: you took your initial data in primitive
orthorhombic and solved for the structure in Phaser while sampling all
possible space groups. Phaser is telling you that your *original* data
indexing is truly space group P22(1)2(1) and if you take that m.r.
solution/data combination and simple *assign* the space group it should
work in Refmac. In fact Phaser should have written the correct space
group in the PDB file header.
If you refine your original MTZ native data file with the PDB file
Phaser wrote, what do you get ?
You seem to have reindexed the data but not rotated the model (or re-run
molecular replacement). That makes the model and data out-of-sync.
Phaser does not reindex the data internally, and that's why it tries
eight space groups in primitive orthorhombic rather than just the
minimal set P222, P222(1), P2(1)2(1)2, P2(1)2(1)2(1). The others that
it tries are alternative settings of these space groups (where appropriate).
If you want to refine in P2(1)2(1)2 then reindex the data (h,k,l) ->
(k,l,h) and re-run molecular replacement with the reindexed MTZ file.
If the above is a misinterpretation of what you wrote, my alternative
advice on this is:
1. throw the thing at Arp/wArp and look hard at the maps you get out.
The structure might have changed more than you thought.
2. rescale the data in P1 and put it into Pointless and/or Xtriage to
check for twinning and point group assignment
3. I'm fairly sure that the (72.6, 78.0, 112.5) and (66.5, 70.5, 137.0)
cells are unrelated but #2 will show that.
4. If all else fails solve it in P1 and find the space group "by
inspection" afterwards
Phil Jeffrey
Princeton
