You probably have metal coordination restraints that are no longer valid - each time you run phenix.refine with the solvent update enabled, the numbering of waters will change and the old restraints become invalid.  The utilities menu in the phenix.refine GUI has an option to clear these out entirely; you can then run ReadySet again to generate new restraints.

-Nat


On Mon, Mar 3, 2014 at 10:31 PM, SD Y <ccp4_sc@hotmail.com> wrote:
Hi,

Could you please tell me why am I getting this error " No atom selected: "name O and chain W and resname HOH and resseq 69". 

Log file ends as follows:

============================= Scattering factors =============================


                ----------X-ray scattering dictionary----------                

Number of scattering types: 7
  Type  Number    sf(0)   Gaussians
   Zn2+     1     27.88       1
   S       10     15.96       2
   P        2     14.95       2
   Mg2+     3      9.96       1
   O      635      7.97       2
   N      523      6.97       2
   C     1983      5.97       2
  sf(0) = scattering factor at diffraction angle 0.


========================== Anomalous scatterer groups =========================

All atoms refined with f_prime=0 and f_double_prime=0.

======================== Summary of geometry restraints =======================

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
Sorry
------------------------------

Thanks a lot
SDY

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