Hi Robbie,
Thank you for your very clear explanation and suggestions.
Am I right in thinking that what this means is that the zBOND and zANGLE values
in Refmac5 refinement should be made to be close to 1.000?
Best
Ray
--------------------------------------------
On Tue, 3/12/19, Robbie Joosten <[log in to unmask]> wrote:
Subject: Re: [ccp4bb] Refmac5 refinement question
To: [log in to unmask]
Date: Tuesday, March 12, 2019, 4:58 AM
Hi Ray,
This is how I see it: Because different bond
length and angle target tolerances/sigmas you cannot compare
them on an absolute scale. What is less likely? A two 0.020A
deviation in the CD1-CG in PHE or a the same deviation in
the CD1-CG bond in LEU. If you think they are equally
likely, you can use rmsd, if not you probably realise that
you are comparing apples and oranges.
Enter
rmsZ. Instead of comparing the absolute deviations you
compare the deviations expressed in sigma (the Z-score).
This brings everything on the same scale so you can actually
compare them (provided the restraints themselves, especially
the sigmas, make sense).
Now let's
assume that your deviations (expressed as Z-scores) have a
normal distribution. Then the rmsZ says something about the
broadness of this distribution. With rmsZ equal to 1 your
distribution is as wide as that of the source of the
restraints (i.e. small molecule structures in the COD, in
the case of Refmac). Assuming that your data are a bit
worse, you can argue that you do not have any strong
evidence to allow wider distributions. That means your rmsZ
should not be greater than 1. There seems to be a bit of a
downward trend with resolution and rmsZ: lower resolution,
lower rmsZ. However the correlation is not very strong and
therefor I would say that any rmsZ < 1.00 is fine. Refmac
gives these numbers for bond lengths and angles, not for
chiral volumes, but those all have the same sigma
(AFAIK).
Don't go for
hard numbers with deviations, unless you find a good
rationale to do so (if you do, please share it). I've
seen too many case of grossly over/underrestrained models
where a much better fit to the data (and other validation
criteria) can be obtained by just playing a bit with the
geometric restraint weights.
HTH,
Robbie
-----Original
Message-----
From: CCP4 bulletin board
[mailto:[log in to unmask]]
On Behalf Of Raymond Brown
Sent: Monday,
March 11, 2019 17:11
To: [log in to unmask]
Subject: [ccp4bb] Refmac5 refinement
question
Hi folks,
What are acceptable values for
RMS Bond length, RMS Bond angle and RMS Chiral volume?
The tutorial suggests RMS Bond
length of 0.0200?
I would
like to hear your suggestions and/or rationale.
Many thanks
Ray Brown
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