Huge E(XREF)

zeily nurachman zeily at bio.titech.ac.jp
Thu Oct 22 21:18:05 EST 1998


At  2:40 PM 98.10.22 +0100, dima at cryst.bioc.cam.ac.uk wrote:
>Hello crystallographers !!!
>
>I am refining the structure (XPLOR 3.851) and during the positional refinement
>(powell minimization)
>I am getting very large energies for XREF term. Can anybody explain why is
>this happening? Is it
>related to scaling? The structure solved by MR (mutant structure), spacegroup
>C2221, data is very
>good (Rmerge=4%, last shell 30%, 60% of reflections with I/sigma > 3 in the
>last shell) and complete
>(90%) resolution 2.5, the model is 95 % complete, bulk solvent used.
>
>XRTEST: number of selected reflections   30206
> XRFILL: #scatt.= 5532 #anomalous=  0 #special pos.=  0 occupancies=1
> XFFT: using grid [ 90, 96,384] and sublattice [ 90( 91), 96( 97),192]
> TRRESI: ->[TEST SET (TEST=1)] Fobs/Fcalc scale=   0.446 R=       0.408
> TRRESI: ->[WORKING SET (TEST=0)] Fobs/Fcalc scale=   0.449 R=       0.396
> --------------- cycle=     7 ------ stepsize=    0.0000
>-----------------------
> | Etotal =86284.423  grad(E)=44.989     E(BOND)=760.244    E(ANGL)=3144.373  
>|
> | E(DIHE)=208.594    E(IMPR)=749.659    E(VDW )=1989.093   E(HARM)=0.242     
>|
> | E(NCS )=47.109     E(XREF)=73841.679  E(PVDW)=5543.431                     
>|
>
>-------------------------------------------------------------------------------
>
>
>Cheers
>Dima
>===================================================
>Mr Dimitri Y Chirgadze
>Department of Biochemistry
>University of Cambridge
>80 Tennis Court Road
>Cambridge CB2 1GA
>UK
>
>Tel: 44(0)1223 766029
>Fax: 44(0)1223 766082
>E-mail: dima at cryst.bioc.cam.ac.uk
>===================================================

Dear,

Is your initial model more than one monomer, e.g homodimer?
If so, please generate each mer seperately, and combine it 
in generate molecule step (generate.inp). Then, you could check
weight. If it succees, I think you could go forward to the next steps
refinement.

Regards


Zeily Nurachman
Tokyo Institute of Technology
Department of Life Science
Tanaka Lab (Struc. Anal. Lab), R 507
4529 Nagatsuta-cho, Midori-ku, 
Yokohama-shi 227, Japan
Ph      +81-45-924-5710
fax     +81-45-924-5808




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