Re: [ccp4bb]: refmac5 geometry restraints

["Eleanor J. Dodson" <ccp4@ysbl.york.ac.uk>]

***  For details on how to be removed from this list visit the  ***
***          CCP4 home page http://www.ccp4.ac.uk         ***

Wolfram Tempel wrote:
> 
> ***  For details on how to be removed from this list visit the  ***
> ***          CCP4 home page http://www.ccp4.ac.uk         ***
> 
> Dear colleagues:
> this is about some trouble I am having with methionine bond lengths.
> This problem is NOT shown on PROCEHECK's geometrical distortion summary
> page but comes up in PDB/ADIT's "validation" summary letter.
> 
> Deviation  Residue  Chain  Sequence  AT1  -  AT2    Bond    Dictionary
>               Name     ID     Number                 Distance    Value
> ------------------------------------------------------------------------
>    -0.358     MET        A    101      SD   -  CE     1.433     1.791
>    -0.228     MET        B    101      SD   -  CE     1.563     1.791
>    -0.218     MET        B    132      SD   -  CE     1.573     1.791
> 


I think this might be an artefact of your structure?
 For a typical protein I refined yesterday with the newest refmac I get
these distances:
 M   76 SD   C   M   76 CG   C      1.868           1 0. 0. 0.   1.000  
29.85
 M   76 SD   C   M   76 CE   C      1.721           1 0. 0. 0.   1.000  
33.66
....
 M   55 SD   D   M   55 CG   D      1.845           1 0. 0. 0.   1.000  
21.88
 M   55 SD   D   M   55 CE   D      1.677           1 0. 0. 0.   1.000  
20.26
etc..
 M   32 SD   A   M   32 CG   A      1.783           1 0. 0. 0.   1.000  
10.93
 M   32 SD   A   M   32 CE   A      1.679           1 0. 0. 0.   1.000  
14.10

 M   76 SD   A   M   76 CG   A      1.755           1 0. 0. 0.   1.000  
19.23
 M   76 SD   A   M   76 CE   A      1.692           1 0. 0. 0.   1.000  
18.86


 and so on..

Eleanor