On 11 Sep 2009, at 09:46, Alasdair K. Mackenzie wrote:
I have been running some TLS refinement which does wonders for my R/
Rfree
values, but seems to give some spurious Bfactors/ADPs for the
waters, e.g.
B= 2.
I am getting this too but not just for waters - some example lines
from the pdb files output when the same input files are refined with
REFMAC 5.2.0019 (CCP4 6.0) and Refmac_5.5.0102 (CCP4 6.1)
In all cases 10 cycles TLS refinement followed by 10 cycles
restrained refinement. TLS groups (5) as suggested by TLSMD were
defined by a TLSIN file and the TLS parameters were initialised to zero.
REMARK 3 PROGRAM : REFMAC 5.2.0019
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 5
REMARK 3 ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY
ATOM 1 N GLY A 1 57.296 -46.837 36.250 1.00
30.89 N
ATOM 2 CA GLY A 1 57.071 -47.826 37.339 1.00
29.53 C
ATOM 3 C GLY A 1 55.665 -48.421 37.355 1.00
28.37 C
ATOM 4 O GLY A 1 55.248 -49.012 38.369 1.00
30.06 O
ATOM 5 N ARG A 2 54.946 -48.312 36.249 1.00
26.00 N
ATOM 6 CA ARG A 2 53.537 -48.738 36.223 1.00
24.66 C
ATOM 7 CB ARG A 2 52.894 -48.328 34.894 1.00
25.61 C
ATOM 8 CG ARG A 2 52.791 -46.825 34.732 1.00
30.86 C
ATOM 9 CD ARG A 2 51.932 -46.448 33.555 1.00
35.59 C
ATOM 10 NE ARG A 2 52.688 -46.482 32.319 1.00
40.25 N
ATOM 11 CZ ARG A 2 53.137 -45.407 31.681 1.00
42.01 C
ATOM 12 NH1 ARG A 2 52.900 -44.188 32.148 1.00
41.24 N
ATOM 13 NH2 ARG A 2 53.829 -45.563 30.561 1.00
44.36 N
ATOM 14 C ARG A 2 53.418 -50.252 36.366 1.00
23.17 C
ATOM 15 O ARG A 2 54.313 -51.001 35.902 1.00
22.56 O
ATOM 16 N SER A 3 52.314 -50.708 36.961 1.00
20.25 N
ATOM 17 CA SER A 3 52.008 -52.147 36.927 1.00
19.82 C
ATOM 18 CB SER A 3 50.706 -52.452 37.673 1.00
20.71 C
ATOM 19 OG SER A 3 49.601 -51.837 37.041 1.00
20.34 O
ATOM 20 C SER A 3 51.851 -52.647 35.501 1.00
19.77 C
REMARK 3 PROGRAM : REFMAC 5.5.0102
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 5
REMARK 3 ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY
ATOM 1 N GLY A 1 57.316 -46.814 36.305 1.00
12.20 N
ATOM 2 CA GLY A 1 57.070 -47.790 37.390 1.00
8.55 C
ATOM 3 C GLY A 1 55.665 -48.410 37.347 1.00
6.78 C
ATOM 4 O GLY A 1 55.239 -49.035 38.362 1.00
10.43 O
ATOM 5 N ARG A 2 54.969 -48.342 36.238 1.00
3.00 N
ATOM 6 CA ARG A 2 53.526 -48.722 36.241 1.00
2.00 C
ATOM 7 CB ARG A 2 52.865 -48.356 34.895 1.00
2.17 C
ATOM 8 CG ARG A 2 52.837 -46.851 34.750 1.00
8.65 C
ATOM 9 CD ARG A 2 51.980 -46.398 33.603 1.00
12.50 C
ATOM 10 NE ARG A 2 52.692 -46.488 32.373 1.00
20.40 N
ATOM 11 CZ ARG A 2 53.158 -45.450 31.693 1.00
22.50 C
ATOM 12 NH1 ARG A 2 52.983 -44.201 32.118 1.00
18.27 N
ATOM 13 NH2 ARG A 2 53.819 -45.694 30.575 1.00
23.75 N
ATOM 14 C ARG A 2 53.413 -50.249 36.396 1.00
2.00 C
ATOM 15 O ARG A 2 54.309 -51.009 35.916 1.00
2.00 O
ATOM 16 N SER A 3 52.311 -50.700 36.987 1.00
2.00 N
ATOM 17 CA SER A 3 52.014 -52.145 36.912 1.00
2.00 C
ATOM 18 CB SER A 3 50.694 -52.464 37.655 1.00
2.00 C
ATOM 19 OG SER A 3 49.581 -51.843 37.061 1.00
2.00 O
ATOM 20 C SER A 3 51.876 -52.639 35.489 1.00
2.00 C
If I include the keywords "TLSD WATERS EXCLUDE" it doesn't fix the
problem:
REMARK 3 PROGRAM : REFMAC 5.5.0102
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 5
REMARK 3 ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY
ATOM 1 N GLY A 1 57.282 -46.747 36.351 1.00
8.67 N
ATOM 2 CA GLY A 1 57.095 -47.808 37.373 1.00
5.77 C
ATOM 3 C GLY A 1 55.679 -48.420 37.348 1.00
4.19 C
ATOM 4 O GLY A 1 55.251 -49.030 38.375 1.00
7.25 O
ATOM 5 N ARG A 2 54.970 -48.346 36.248 1.00
2.00 N
ATOM 6 CA ARG A 2 53.529 -48.731 36.249 1.00
2.00 C
ATOM 7 CB ARG A 2 52.864 -48.370 34.899 1.00
2.00 C
ATOM 8 CG ARG A 2 52.850 -46.851 34.760 1.00
6.23 C
ATOM 9 CD ARG A 2 51.990 -46.387 33.620 1.00
8.88 C
ATOM 10 NE ARG A 2 52.689 -46.471 32.384 1.00
16.95 N
ATOM 11 CZ ARG A 2 53.131 -45.433 31.688 1.00
19.89 C
ATOM 12 NH1 ARG A 2 52.959 -44.177 32.104 1.00
16.48 N
ATOM 13 NH2 ARG A 2 53.778 -45.681 30.566 1.00
21.58 N
ATOM 14 C ARG A 2 53.413 -50.256 36.400 1.00
2.00 C
ATOM 15 O ARG A 2 54.315 -51.016 35.913 1.00
2.00 O
ATOM 16 N SER A 3 52.320 -50.718 36.986 1.00
2.00 N
ATOM 17 CA SER A 3 52.013 -52.148 36.908 1.00
2.00 C
ATOM 18 CB SER A 3 50.689 -52.479 37.638 1.00
2.00 C
ATOM 19 OG SER A 3 49.579 -51.840 37.067 1.00
2.00 O
ATOM 20 C SER A 3 51.877 -52.639 35.480 1.00
2.00 C
I'd be happy to send the data for this structure to the developers if
it would help in identify the source of the problem.
Cheers,
Huw
--
Dr Huw Jenkins
Astbury Centre for Structural Molecular Biology
University of Leeds
