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Dear all!
I am refining a structure against a 2.1 A resolution remote dataset of a
Se-Met MAD experiment. Since the R/Rfree is stuck at 21/27 % I tried to
use TLS refinement. This yielded a much better R/Rfree of 19/24.1 but I
got this 'Problem in MAKE_U_POSITIVE' warning. Analysing the models
before and after TLS showed the following results:
no ncs, no tls:
average B (overall)
chain A: 48.7
chain B: 45.6
chain C: 33.9
chain D: 20.2
R/Rfree 21/27 % (CNS gives nearly the same results)
no ncs, one tls group per protomer:
average B (overall)
chain A: 13.1
chain B: 12.9
chain C: 14.5
chain D: 12.9
R/Rfree 19/24.1
tlsanl and different refmac trials with fixed starting Bs for subsequent
tls refinement (35-60) showed that protomers C and D seem to cause the
problems. Therefore I tried a refinement protocol with just chains A and
B in two different tls groups, leaving out chains C and D.
no ncs, tls on protomers A+B:
average B (overall)
chain A: 28.4
chain B: 28.5
chain C: 34.6
chain D: 21.8
R/Rfree 20/26
The matrix weight was 0.17 in all cases. Bbulk was fixed to 200 (refined
to 295 without fixing)
I would like to know if it is legitimate to use tls only on parts of the
asymetric unit and/or if there are any other things I should look for.
additional informations:
The structure solution was straight forward. The experimental density
for all 4 subunits was good.
spacegroup: P2(1)
cell axis: 90.570 57.020 152.697 90.000 103.352 90.000
wilson B from XSCALE: 33.23
Rsym (overall/last shell): 5 (25)
reflections: 86204 (7972)
overloads: 143 out of 1343616
As far as I can see the data looks good so far. the Wilson line is ok
according to what I see in truncate.
(it didn't pass the arp/warp check, but until now I haven't come across
a dataset that passed it).
The dataset doesn't show any sign of radiation damage (checked this
looking at the xdsstat output.)
