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Dear Ray,
I would not use the refinement stage to consider a structure as finished, but
whether or not you can build anything meaningful. At 2.5A you are probably
going to reach a stage where you can make small changes, but you have the
impression that you are not getting anywhere but moving in a circle. Provided
the set of statistics is reasonable, you can then publish your structure. It
is more than a single number, after all, and you know more about your
structure and your data than a computer program.
If you are indeed only talking about refinement, could monitor the the -LL of
refmac5 vs. the number of refinement cycles. If you allow e.g. 100-500 cycles
to run, it should become more or less a constant line.
Cheers,
Tim
On Thursday, October 15, 2015 05:12:29 PM Ray Brown wrote:
> I have a question about when to actually stop refinement with Refmac5. What
> is a properly carried out refinement with good statistics? All I could find
> was this advice:
> 'zBOND and zANGL are the Z-scores of the deviations of bond lengths and
> angles from ideal values: at high resolution these should approach 1.0
> while at low resolution, where structures are tightly restrained to ideal
> values, they should approach 0.0.' What values of zBOND and zANGL are
> expected for a well-built and correctly refined protein structure at a
> resolution of 2.5 angstroms? Should the geometric weights in Refmac5 be
> adjusted/varied so as to produce statistics of rmsBOND 2.0, rmsANGL 2.0 and
> rmsCHIRAL 0.2? Are these values appropriate for this resolution? Some
> practical advice and your experience would very much be appreciated. Ray
> Brown
- --
- --
Paul Scherrer Institut
Tim Gruene
- - persoenlich -
OFLC/102
CH-5232 Villigen PSI
phone: +41 (0)56 310 5754
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