Dear ccp4bb, I have noticed I get strange results when I have been attempting to refine a protein-DNA complex in refmac 5.5.0088. I see a large variation in the B-factors of connected atoms for the DNA while the protein atoms all seem to refine to sensible values, for example,
before refinement ATOM 2160 P Ad Z 2 26.238 -46.384 -6.900 1.00132.37 P ATOM 2161 O1P Ad Z 2 26.966 -46.846 -8.102 1.00132.16 O ATOM 2162 O2P Ad Z 2 26.972 -45.589 -5.892 1.00132.16 O ATOM 2163 O5* Ad Z 2 24.935 -45.563 -7.357 1.00132.09 O ATOM 2164 C5* Ad Z 2 25.029 -44.404 -8.207 1.00131.15 C ATOM 2165 C4* Ad Z 2 23.809 -43.486 -8.137 1.00130.50 C ATOM 2166 O4* Ad Z 2 22.628 -44.204 -8.584 1.00130.90 O ATOM 2167 C1* Ad Z 2 21.474 -43.738 -7.912 1.00132.14 C ATOM 2168 N9 Ad Z 2 20.586 -44.878 -7.656 1.00132.86 N ATOM 2169 C8 Ad Z 2 20.874 -45.936 -6.844 1.00133.05 C ATOM 2170 N7 Ad Z 2 19.931 -46.841 -6.773 1.00133.11 N ATOM 2171 C5 Ad Z 2 18.942 -46.347 -7.599 1.00133.07 C ATOM 2172 C4 Ad Z 2 19.319 -45.140 -8.155 1.00133.06 C ATOM 2173 N3 Ad Z 2 18.567 -44.410 -9.004 1.00133.19 N ATOM 2174 C2 Ad Z 2 17.383 -44.993 -9.259 1.00133.13 C ATOM 2175 N1 Ad Z 2 16.883 -46.154 -8.797 1.00133.05 N ATOM 2176 C6 Ad Z 2 17.673 -46.856 -7.946 1.00133.00 C ATOM 2177 N6 Ad Z 2 17.231 -48.008 -7.459 1.00132.98 N ATOM 2178 C2* Ad Z 2 21.949 -43.038 -6.641 1.00130.70 C ATOM 2179 C3* Ad Z 2 23.473 -42.943 -6.745 1.00129.56 C ATOM 2180 O3* Ad Z 2 24.028 -41.608 -6.453 1.00127.12 O ATOM 425 N TRP A 70 22.973 -26.906 -0.217 1.00 76.89 N ATOM 426 CA TRP A 70 22.385 -26.863 -1.557 1.00 77.16 C ATOM 427 CB TRP A 70 23.469 -26.569 -2.611 1.00 76.94 C ATOM 428 CG TRP A 70 22.947 -26.097 -4.000 1.00 76.52 C ATOM 429 CD1 TRP A 70 22.021 -25.123 -4.252 1.00 75.29 C ATOM 430 NE1 TRP A 70 21.839 -24.989 -5.603 1.00 75.65 N ATOM 431 CE2 TRP A 70 22.660 -25.868 -6.259 1.00 75.66 C ATOM 432 CD2 TRP A 70 23.380 -26.580 -5.281 1.00 75.71 C ATOM 433 CE3 TRP A 70 24.299 -27.554 -5.691 1.00 75.33 C ATOM 434 CZ3 TRP A 70 24.476 -27.779 -7.056 1.00 75.47 C ATOM 435 CH2 TRP A 70 23.750 -27.051 -8.009 1.00 75.84 C ATOM 436 CZ2 TRP A 70 22.837 -26.092 -7.634 1.00 76.15 C ATOM 437 C TRP A 70 21.647 -28.154 -1.886 1.00 77.50 C ATOM 438 O TRP A 70 22.270 -29.143 -2.316 1.00 77.24 O (The residues in the pdb as output from coot 0.5.2) after refinement ATOM 4339 P A Z 2 26.115 -46.360 -6.953 1.00161.28 P ATOM 4340 O1P A Z 2 26.825 -46.773 -8.177 1.00115.03 O ATOM 4341 O2P A Z 2 26.880 -45.599 -5.929 1.00 80.54 O ATOM 4342 O5* A Z 2 24.826 -45.511 -7.390 1.00127.62 O ATOM 4343 C5* A Z 2 24.963 -44.268 -8.095 1.00500.00 C ATOM 4346 C4* A Z 2 23.717 -43.401 -7.975 1.00225.44 C ATOM 4348 O4* A Z 2 22.559 -44.187 -8.350 1.00156.09 O ATOM 4349 C1* A Z 2 21.406 -43.694 -7.694 1.00104.26 C ATOM 4351 N9 A Z 2 20.510 -44.825 -7.408 1.00104.67 N ATOM 4352 C8 A Z 2 20.744 -45.842 -6.524 1.00254.53 C ATOM 4354 N7 A Z 2 19.785 -46.733 -6.464 1.00117.22 N ATOM 4355 C5 A Z 2 18.849 -46.275 -7.373 1.00 93.98 C ATOM 4356 C4 A Z 2 19.271 -45.104 -7.969 1.00 96.16 C ATOM 4357 N3 A Z 2 18.583 -44.406 -8.898 1.00500.00 N ATOM 4358 C2 A Z 2 17.410 -44.988 -9.198 1.00215.48 C ATOM 4360 N1 A Z 2 16.872 -46.121 -8.708 1.00102.77 N ATOM 4361 C6 A Z 2 17.597 -46.787 -7.774 1.00122.19 C ATOM 4362 N6 A Z 2 17.111 -47.910 -7.255 1.00116.30 N ATOM 4365 C2* A Z 2 21.891 -42.938 -6.457 1.00297.54 C ATOM 4368 C3* A Z 2 23.418 -42.883 -6.565 1.00170.10 C ATOM 4370 O3* A Z 2 23.994 -41.570 -6.268 1.00179.14 O ATOM 846 N TRP A 70 22.483 -26.850 -0.143 1.00 59.32 N ATOM 847 CA TRP A 70 22.017 -26.748 -1.526 1.00 59.25 C ATOM 849 CB TRP A 70 23.181 -26.454 -2.468 1.00 59.30 C ATOM 852 CG TRP A 70 22.781 -26.038 -3.869 1.00 59.32 C ATOM 853 CD1 TRP A 70 21.994 -24.979 -4.207 1.00 59.49 C ATOM 855 NE1 TRP A 70 21.884 -24.891 -5.573 1.00 59.57 N ATOM 857 CE2 TRP A 70 22.613 -25.897 -6.147 1.00 58.75 C ATOM 858 CD2 TRP A 70 23.200 -26.637 -5.110 1.00 58.53 C ATOM 859 CE3 TRP A 70 24.009 -27.725 -5.439 1.00 58.37 C ATOM 861 CZ3 TRP A 70 24.205 -28.036 -6.786 1.00 58.38 C ATOM 863 CH2 TRP A 70 23.611 -27.282 -7.790 1.00 58.88 C ATOM 865 CZ2 TRP A 70 22.808 -26.210 -7.493 1.00 59.39 C ATOM 867 C TRP A 70 21.365 -28.043 -1.920 1.00 59.50 C ATOM 868 O TRP A 70 22.020 -28.969 -2.411 1.00 59.13 O A bit more background is probably needed, the data resolution is 3.0 Angstrom and the protein is dimeric so I have applied tight NCS restraints to the protein chains and the DNA bases have been made to strictly obey Watson-Crick geometry by the use of LINK records, I have not use NCS restraints for the DNA. I have also refined using TLS for the protein chains (1 per chain), but not the DNA followed by individual isotropic B-factors. I am running ccp4-6.1.1 on a linux box running centos-5.3. I still get the same B-factors if I do not refine using tls or if I remove the LINK records. I have tried reducing the sigma-values for B-factors between atoms and also adjusted the B-factor weighting with no success. I have also tried limiting the range of allowed B-factors to no effect. Previously I have successfully ran the same sort of refinement in refmac-5.2 and not seen this odd distribution of temperature factors. So really my questions are; am I doing something obviously wrong? or is this some sort of bug? best regards Steve Dr Stephen Carr, Membrane Protein Laboratory, Diamond Light Source Ltd, Harwell Science and Innovation Campus, Chilton, Didcot, OX11 0DE Tel: (44)1235 778896 Email stephen.c...@diamond.ac.uk This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
