Hi David

Occupancis of input file are very suspicious and not all atoms of resides are present, some occupancies are zero. In refmac zero occupancy means it does not exist. It may explain the problem
In refinement we could add an option to make occuancies one if there are no alts but it would be dangerous thing to do.

Since occupancies are suspect I would check input pdb file carefully.


regards
Garib



On 24 Mar 2012, at 18:39, David Schuller wrote:

CCP4 6.2.0
Refmac_5.6.0117
Scientific Linux 6.1

In my current model, I notice that several sidechains are falling apart, despite having gone through a few rounds of refinement with REFMAC5 and model building with COOT. The worst examples were all Glu and Arg residues.

I tried switch to the REFMAC5 executable on the updates page, which was Refmac_5.6.0114, with no obvious difference.

Eventually I noticed that these are all residues containing atoms with occupancy less than 1.00, which must be a carry over from the MR search model. I set all the occupancies to 1.00 and this seems to have fixed the problem.

This seems counter-intuitive to me. If the occupancies are set low, shouldn't the geometry restraints be stronger relative to the density refinement?

Cheers,

ATOM   1479  N   GLU A   7     -51.844 -33.605  37.318  1.00 60.26           N
ATOM   1480  CA  GLU A   7     -53.137 -33.849  37.966  1.00 59.28           C
ATOM   1481  CB  GLU A   7     -52.997 -33.664  39.476  1.00 61.37           C
ATOM   1482  CG  GLU A   7     -52.799 -32.212  39.905  0.48 60.42           C
ATOM   1483  CD  GLU A   7     -53.349 -32.573  41.635  0.00 54.47           C
ATOM   1484  OE1 GLU A   7     -52.557 -31.998  42.106  0.83 52.26           O
ATOM   1485  OE2 GLU A   7     -55.014 -32.911  42.408  0.68 50.75           O
ATOM   1486  C   GLU A   7     -54.293 -32.985  37.412  1.00 62.61           C
ATOM   1487  O   GLU A   7     -55.444 -33.240  37.737  1.00 63.42           O
ATOM   3165  N   ARG A  77     -46.032 -33.003  26.272  1.00 55.82           N
ATOM   3166  CA  ARG A  77     -44.959 -32.368  27.071  1.00 60.92           C
ATOM   3167  CB  ARG A  77     -44.050 -31.428  26.231  1.00 54.56           C
ATOM   3168  CG  ARG A  77     -42.702 -31.102  26.892  1.00 69.21           C
ATOM   3169  CD  ARG A  77     -42.278 -29.628  26.867  0.46 63.93           C
ATOM   3170  NE  ARG A  77     -41.587 -29.303  25.625  0.79 61.76           N
ATOM   3171  CZ  ARG A  77     -41.607 -28.610  24.146  0.00 37.32           C
ATOM   3172  NH1 ARG A  77     -43.177 -26.956  23.467  0.85 60.52           N
ATOM   3173  NH2 ARG A  77     -41.267 -28.245  23.427  0.95 58.82           N
ATOM   3174  C   ARG A  77     -45.585 -31.698  28.281  1.00 64.89           C
ATOM   3175  O   ARG A  77     -45.949 -32.377  29.262  1.00 77.93           O


--
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All Things Serve the Beam
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                              David J. Schuller
                              modern man in a post-modern world
                              MacCHESS, Cornell University
                              [log in to unmask]

Garib N Murshudov 
Structural Studies Division
MRC Laboratory of Molecular Biology
Hills Road 
Cambridge 
CB2 0QH UK
Email: garib@mrc-lmb.cam.ac.uk 
Web http://www.mrc-lmb.cam.ac.uk