Small molecule crystallographers all know what convergence means. Most
small molecules are refined
by full-matix least-squares until the mean parameter shift/esd is less
than 0.01 and often less than 0.001.
The esds are found by inverting the least-squares matrix. A CheckCIF
alert is generated if the mean
shift/esd is more than 0.05 and it is an alert-A if it is more than 0.2.
An alert-A without a good explanation
is often regarded as a reason for rejecting a paper.
George
On 08/06/2016 07:25 AM, Dale Tronrud wrote:
> On 8/5/2016 4:58 PM, Murpholino Peligro wrote:
>> Excellent question! So there is no way to know if the refinement
>> "converged"?
>> I always ploted the R values (R_free and R_work) against number of
>> refinements and if the difference was very small (I guess less than 1%)
>> I would say that refinement was done..i.e. it converged. So was I wrong?
> Looking only at global stats can get you into serious trouble. One
> atom can be moving quite a lot and not cause a blip in an over-all
> number. That atom would quite likely be the metal atom in the middle of
> your active site! Most refinement protocols today tend to carefully
> restrain the ligand distances to your metals. One reason they do that
> is because it is hard to resolve these short distances. The other
> reason is that electron dense atoms tend to bounce back and forth if you
> don't build the second derivatives into your optimization. If you run
> more cycles of refinement you can relax the distance restraints, which
> is good because those restraints might be wrong.
>
> It used to be that refinement programs would list the atoms with the
> biggest shifts in the last cycle so the user could check for
> convergence. At times this practice has been dropped by some. I
> haven't checked the recent versions of the big packages to see what
> tools they provide.
>
> As I said, I beat it to death to make sure. There is no harm to
> running extra cycles other than time it takes.
>
> Dale Tronrud
>
>> Thanks
>>
>> 2016-08-05 18:17 GMT-05:00 Dale Tronrud<[log in to unmask]
>> <mailto:[log in to unmask]>>:
>>
>>
>> I have never seen a refinement "converge" in the mathematical sense.
>> The optimization algorithms we use are not expected to converge until
>> you have run a number of cycles greater than some multiple of the number
>> of parameters in the model. No one is ever going to do this.
>>
>> The mistake I have seen, and what is being recommended against, is to
>> just run some standard number of cycles and quit without checking to see
>> if anything is still happening. Some programs have a standard of three
>> "big" rounds of refinement but the R values and over all geometry might
>> still be changing at the end of that, particularly early in a project.
>> You certainly shouldn't stop if the major stats are in flux (either
>> going up OR down).
>>
>> More subtly individual atoms may still be moving while the overall
>> stats look stable. You should check that the largest shifts in your
>> final rounds are "small". This is a fuzzy definition, but if you are
>> interested in distances to a precision of 0.1 A you certainly shouldn't
>> be stopping if you still have atoms moving in steps approaching that
>> size.
>>
>> Refinement is fast these days. I tend to beat my refinements to
>> death just to be sure. If the standard practice is three "big" rounds
>> I'll run ten.
>>
>> There is no such thing as "over refinement" only "over fitting".
>>
>> Dale Tronrud
>>
>>
>> On 8/5/2016 3:22 PM, Keller, Jacob wrote:
>> >>>- make sure refinement is done till convergence.
>> >
>> >
>> >
>> > I have never understood and still do not understand what is meant by
>> > convergence—in my experience, refinements are always incremental, with
>> > various improvements here and there, but there’s never been any magic
>> > moment of convergence. Is there a rigorous meaning to this term? Is it
>> > just when the refinement program stops improving things?
>> >
>> >
>> >
>> > Jacob Keller
>> >
>> >
>> >
>>
>>
--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or -33068
Fax. +49-551-39-22582
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