oops, I should have expanded my comments to include the sort of funky lattice order-disorder Zbyszek so cleverly diagnosed.  Scratch that "perfect twinning" comment in my last message.
________________________________________
From: CCP4 bulletin board [[log in to unmask]] on behalf of Phoebe A. Rice [[log in to unmask]]
Sent: Tuesday, March 19, 2013 10:34 AM
To: [log in to unmask]
Subject: Re: [ccp4bb] Strange density in solvent channel and high Rfree

Hi Zbyszek,
  If the issue is perfect twinning, I agree - good point!
  But you don't want to confuse people who simply have nearly-but-not-quite crystallographic symmetry (OK, I'm being a bit pedagogical here, but a lot of newbies read the BB).  We had a case of P31 that was so close to P61 we actually solved the molecular replacement problem in P61, then expanded it back and re-rigid-bodied it.  We've played similar games with translational pseudo-symmetry (ignoring the weak spots at first).  In cases like that it is important to properly reprocess the data in the lower symmetry space group (or smaller unit cell) because there is real information in those small differences.  However, the point about Rfree holds for twinning or rotational pseudo-symmetry: the Rfree flags should be expanded by the xtal symmetry operators, not re-picked in the lower symmetry space group.
           Phoebe

++++++++++++++++++++++++++++++++++++++++++

Phoebe A. Rice
Dept. of Biochemistry & Molecular Biology
The University of Chicago
773 834 1723; [log in to unmask]
http://bmb.bsd.uchicago.edu/Faculty_and_Research/
http://www.rsc.org/shop/books/2008/9780854042722.asp

________________________________________
From: CCP4 bulletin board [[log in to unmask]] on behalf of Zbyszek Otwinowski [[log in to unmask]]
Sent: Tuesday, March 19, 2013 9:37 AM
To: [log in to unmask]
Subject: Re: [ccp4bb] Strange density in solvent channel and high Rfree

It is a clear-cut case of crystal packing disorder. The tell-tale sign is
that data can be merged in the higher-symmetry lattice, while the number
of molecules in the asymmetric unit (3 in P21) is not divisible by the
higher symmetry factor (2, by going from P21 to P21212).
From my experience, this is more likely a case of order-disorder than
merohedral twinning. The difference between these two is that structure
factors are added for the alternative conformations in the case of
order-disorder, while intensities (structure factors squared) are added in
the case of merohedral twinning.

Now an important comment on how to proceed in the cases where data can be
merged in a higher symmetry, but the structure needs to be solved in a
lower symmetry due to a disorder.

!Such data needs to be merged in the higher symmetry,assigned R-free flag,
and THEN expanded to the lower symmetry. Reprocessing the data in a lower
symmetry is an absolutely wrong procedure and it will artificially reduce
R-free, as the new R-free flags will not follow data symmetry!

Moreover, while this one is likely to be a case of order-disorder, and
these are infrequent, reprocessing the data in a lower symmetry seems to
be frequently abused, essentially in order to reduce R-free. Generally,
when data CAN be merged in a higher symmetry, the only proper procedure in
going to a lower-symmetry structure is by expanding these higher-symmetry
data to a lower symmetry, and not by rescaling and merging the data in a
lower symmetry.

Zbyszek Otwinowski

> Dear all,
> We have solved the problem. Data processing in P1 looks better (six
> molecules in ASU), and Zanuda shows a P 1 21 1 symmetry (three molecules
> in
> ASU), Rfactor/Rfree drops to 0.20978/0.25719 in the first round
> of refinement (without put waters, ligands, etc.).
>
> Indeed, there were one more molecule in ASU, but the over-merged data in
> an orthorhombic lattice hid the correct solution.
>
> Thank you very much for all your suggestions, they were very important to
> solve this problem.
>
> Cheers,
>
> Andrey
>
> 2013/3/15 Andrey Nascimento <[log in to unmask]>
>
>> *Dear all,*
>>
>> *I have collected a good quality dataset of a protein with 64% of
>> solvent
>> in P 2 21 21 space group at 1.7A resolution with good statistical
>> parameters (values for last shell: Rmerge=0.202; I/Isig.=4.4;
>> Complet.=93%
>> Redun.=2.4, the overall values are better than last shell). The
>> structure
>> solution with molecular replacement goes well, the map quality at the
>> protein chain is very good, but in the final of refinement, after
>> addition
>> of a lot of waters and other solvent molecules, TLS refinement, etc. ...
>> the Rfree is a quite high yet, considering this resolution
>> (1.77A).(Rfree=
>> 0.29966 and Rfactor= 0.25534). Moreover, I reprocess the data in a lower
>> symmetry space group (P21), but I got the same problem, and I tried all
>> possible space groups for P222, but with other screw axis I can not even
>> solve the structure.*
>>
>> *A strange thing in the structure are the large solvent channels with a
>> lot of electron density positive peaks!? I usually did not see too many
>> peaks in the solvent channel like this. This peaks are the only reason
>> for
>> these high R's in refinement that I can find. But, why are there too
>> many
>> peaks in the solvent channel???*
>>
>> *I put a .pdf file (ccp4bb_maps.pdf) with some more information and map
>> figures in this link: https://dl.dropbox.com/u/16221126/ccp4bb_maps.pdf*
>>
>> *
>> *
>>
>> *Do someone have an explanation or solution for this?*
>>
>> * *
>>
>> *Cheers,*
>>
>> *Andrey*
>>
>


Zbyszek Otwinowski
UT Southwestern Medical Center at Dallas
5323 Harry Hines Blvd.
Dallas, TX 75390-8816
Tel. 214-645-6385
Fax. 214-645-6353