[ccp4bb]: arp warp bad data warning

[Maneesh Yadav <yadavm@scripps.edu>]

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Hi all,
I have been having a lot of trouble refining a crystal structure, so I
tried to use arp warp to add the waters and do the final refinement.
My R,Rfree value has been stuck at the about 30%, 33% (before solvent).
The assymetric unit is half of a C2 symmetrical tetrameric 4 helix
bundle (the C2 axis is along the hydrophobic core).  The sg is P4132 and
unit cell dimensions are 79x79x79. The resolution of the data is 2.07 A.
There are no apparent problems during processing of images.

I've tried lowering the symmetry and the general feel I get from looking
at other messages is that at these statistics, you can lower the symmetry
but you are increasing the overall number of parameters per observation,
even with collecting more data; so lowering is just as bad as any other
choice you have in order to try lowering the R-factor.

Arp warp will bring down the values to 25%, 31%; but it complains loudly
if I try to use the bulk solvent.  My data *seem* fine, and the wilson
plot looks like that of a standard protein (linear up to 4A and then a dip
between 5.5-7.0 A).  The chi sq vs. resolution ( I don't really know
understand this statistic, is it the deriviative of the Wilson in
someway?)  has a large spike at 6.0A (as it seems to have for every data
set I have, across many different crystals/days of collection).  Arp warp
seems to be very sure of itself in telling me that
my low resolution data is bad and I should cutoff at 3.25A (!).  Is it the
honest truth, or is there something I should know about the usage of arp
warp?

Does anyone have any commments?