Hi Partha -
A few thoughts:
1. If you attach logs, at least gzip them ...
2. From the fact that Rfree goes down when twinning is switched off, I
would think there is no twining.
3. The intensity distribution (moment of E, etc) suggest no twining.
The twining operator you use is the crystallographic two fold, I think.
4. During refinement the relative fraction of twin is a refined
parameter, to make you model+twining fit the data. The initial twin
fraction is only an estimate.
5. Did you consider P3121 or P3221 at all? I think its unlikely, but
easy to check in Phaser as alternative space group.
6. Do these R/Rfree include TLS refinement and waters? if not they are
quite Ok, given the missing residues
7. I see you only have 430 free reflections. I would argue they are
too few to get a reliable Rfree and would aim for more, 10% instead of
5% will give you about 900. Be careful though in not choosing a new
Rfree for the refinement from now on.
Good luck -
A.
On 8 Jul 2010, at 20:03, Parthasarathy Sampathkumar wrote:
Dear All,
Back ground:
This is my first experience with a twined dataset. Crystals belong
to a small domain of 132 aa, out of which ~40 residues appears to be
disordered (~30 of those from C-terminal and C-term His6 tag).
Initial space group: P3 with unit cell dimensions: 62.507 62.507
55.117 90.00 90.00 120.00; Resolution 2.35Angs.
Pointless suggested P321 (space group # 150) as possibility. I
determined structure by MR with Phaser (1 molecule in ASU). After
several model building and refinement cycles R and Rfree got stuck
at 24.0% and 31.6% respectively.
Therefore, I considered P3 space group (now Two molecules in the
ASU) with a twin component. I was only able to add handful residues
to the model already refined in P321. My current R and Rfree factors
are 21.0% and 29.1%, respectively for Two molecules refined in P3
space group.
Questions:
1. H-test in cTruncate suggested a twin fraction of 0.43 for the
twin operator -h-k, k, -l. Where as Refmac5 with Amplitude based
twin refinement gave an initial value of 0.508 for the same
operator. Why these values are different between cTruncate and
Refmac5 (is this because I asked Refmac5 do amplitude Twin
refinement instead of Intensity based)?
2. I noticed in Refmac5 log file that twin fractions changes for
every cycle of refinement. During my most recent Refmac5 run Initial
estimate of 0.508 for -h-k, k, -l operator changed to 0.504 at the
end of 20th cycle. The corresponding values were 0.519 and 0.529,
respectively, in a previous round. Since twin estimates were based
on measured Intensities (in turn amplitudes) why would they change
with refinement (am I missing something here)?
3. When I repeated my final round of Refmac5 WithOut Twin Refinement
my R and R-free factors are 22.9% and 28.6%, respectively, which
also appears to be OK for 2.35 Angs. data (in fact, slightly better
R-free). These values are likely to improve little bit after
completing the solvent model. So, is this crystal really twinned?
I have attached log files of cTruncate and most recent Refmac5 run
with Twin refinement. Apologies for attachments (at least no image
files).
Thank you all in advance for educating me.
-Partha
<34_truncate_anl.log><40_refmac5.log>
