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
--
=======================================================================
All Things Serve the Beam
=======================================================================
David J. Schuller
modern man in a post-modern world
MacCHESS, Cornell University
[email protected]
