I guess you are using as input mtz the output mtz from the previous cycle?
This will be limited to the requested previous resolution..

it is good practice to always use as input the full data - eg 
mystuff-scala.mtz output from the scala/ctruncate step..

If the input file has the full resolution then your requested limits 
should be respected..

Unlike your supervisor I would probably have run the rigid body 
refinement against limited data then gone straight to using thefull 
resolution available - restrained refinement of B factors works better 
the higher the resolution, and provides a very useful way of smudging 
out errors. Wrong bits often have B factors which go through the roof, 
and it is then very obvious in the maps
  But there are many ways to kill a goose, and ditto for refinement 
strategy..
Eleanor



On 10/30/2010 01:46 AM, Tom Huxford wrote:
> Hi all,
>
> I'm working with good quality relatively complete x-ray diffraction data
> collected to a resolution limit 2.6 Å from a crystal of a protein with a
> small molecule ligand bound.  I ran MR from 10-4 Å and then did maximum
> likelihood rigid body refinement in Refmac5 against data from 50-3.5 Å.
> Now I would like to run restrained refinement from 50-3 Å.  The reason
> for doing this is that, in order to minimize the divergence between
> R-cryst and R-free during refinement my advisor who, by the way, is
> forwarding this e-mail for me (and editing it so please don't bash him
> too mercilessly) suggested I first build in the ligand and newly
> positioned polypeptide loops and refine against data at a lower
> resolution limit before opening it up to all the available data.
> Apparently this has worked well for him in the past (and it has!). The
> problem is that I'm to the point where I'd like to extend the resolution
> down to 3 Å during restrained refinement but even if I set the range
> from 50-3 Å in the ccp4i window refinement only happens from 50-3.5 Å.
> If I take a step back and do the rigid body refinement from 50-3 Å and
> then carry out restrained refinement from 50-3 Å it works fine.  Why
> would the limits imposed by rigid body refinement cause the subsequent
> restrained refinement to be stuck at the rigid body refinement's
> resolution limits?
>
> Thanks for any thoughts,
>
> Jon Fleming
> Graduate Student
> Structural Biochemistry Laboratory (Huxford Lab)
> Department of Chemistry & Biochemistry
> San Diego State University