Dear all, specifically refmac developers, I have an unexpected observation, when refining alternate main chain conformations for residues 22 and following in refmac. Residue 21 has one conformation, residues 22-25 have two conformations. There are four chains. I have coordinates with PRO 21, A PRO 22 and B PRO 22, A PRO 23 and B PRO 23, ... In chain A and B A PRO 22 is connected to A PRO 23 and B PRO 22 is connected to B PRO 23. Refmac handles this correctly in chain A
ATOM 134 N PRO A 21 55.911 -46.023 11.391 1.00 71.64 N ATOM 135 CA PRO A 21 54.636 -45.699 10.771 1.00 69.48 C ATOM 136 C PRO A 21 53.652 -45.003 11.712 1.00 75.85 C ATOM 137 O PRO A 21 53.737 -45.128 12.943 1.00 71.90 O ATOM 138 CB PRO A 21 54.132 -47.050 10.291 1.00 73.57 C ATOM 139 CG PRO A 21 54.732 -48.029 11.268 1.00 78.87 C ATOM 140 CD PRO A 21 56.095 -47.462 11.621 1.00 80.25 C ATOM 148 N APRO A 22 52.618 -44.384 11.088 0.40 83.27 N ATOM 149 N BPRO A 22 52.759 -44.118 11.211 0.60 75.47 N ATOM 150 CA APRO A 22 51.512 -43.751 11.796 0.40 84.16 C ATOM 151 CA BPRO A 22 51.849 -43.395 12.104 0.60 72.98 C ATOM 152 C APRO A 22 50.228 -44.579 11.869 0.40 87.98 C ATOM 153 C BPRO A 22 50.964 -44.325 12.947 0.60 75.21 C ATOM 154 O APRO A 22 49.906 -45.361 10.962 0.40 78.72 O ATOM 155 O BPRO A 22 50.724 -45.466 12.556 0.60 75.40 O ATOM 156 CB APRO A 22 51.372 -42.540 10.866 0.40 81.67 C ATOM 157 CB BPRO A 22 51.028 -42.492 11.157 0.60 70.57 C ATOM 158 CG APRO A 22 51.449 -43.146 9.482 0.40 81.76 C ATOM 159 CG BPRO A 22 51.348 -42.942 9.743 0.60 70.36 C ATOM 160 CD APRO A 22 52.449 -44.275 9.624 0.40 80.93 C ATOM 161 CD BPRO A 22 52.605 -43.766 9.788 0.60 71.03 C ATOM 176 N APRO A 23 49.460 -44.406 12.970 0.40 93.31 N ATOM 177 N BPRO A 23 50.456 -43.886 14.129 0.60 74.50 N ATOM 178 CA APRO A 23 48.118 -44.976 13.080 0.40 94.09 C ATOM 179 CA BPRO A 23 49.554 -44.724 14.943 0.60 74.34 C ATOM 180 C APRO A 23 47.344 -44.828 11.770 0.40 86.61 C ATOM 181 C BPRO A 23 48.202 -45.107 14.318 0.60 79.21 C ATOM 182 O APRO A 23 46.587 -43.879 11.580 0.40 78.80 O ATOM 183 O BPRO A 23 47.978 -44.905 13.125 0.60 87.29 O ATOM 184 CB APRO A 23 47.502 -44.164 14.238 0.40 99.79 C ATOM 185 CB BPRO A 23 49.389 -43.885 16.249 0.60 66.55 C ATOM 186 CG APRO A 23 48.683 -43.763 15.109 0.40 99.18 C ATOM 187 CG BPRO A 23 49.687 -42.465 15.832 0.60 65.08 C ATOM 188 CD APRO A 23 49.861 -43.632 14.158 0.40 98.24 C ATOM 189 CD BPRO A 23 50.763 -42.584 14.757 0.60 62.91 C in chain B, though, ATOM 10241 N PRO B 21 29.572 -19.212 60.309 1.00 70.15 N ATOM 10242 CA PRO B 21 28.640 -18.729 59.295 1.00 76.47 C ATOM 10243 C PRO B 21 28.922 -19.180 57.863 1.00 79.17 C ATOM 10244 O PRO B 21 30.034 -19.590 57.528 1.00 73.13 O ATOM 10245 CB PRO B 21 28.749 -17.216 59.453 1.00 79.61 C ATOM 10246 CG PRO B 21 30.155 -16.998 59.938 1.00 80.13 C ATOM 10247 CD PRO B 21 30.483 -18.180 60.824 1.00 74.66 C ATOM 10255 N APRO B 22 27.930 -18.968 56.964 0.40 81.02 N ATOM 10256 N BPRO B 22 27.885 -19.324 57.007 0.60 86.55 N ATOM 10257 CA APRO B 22 28.181 -18.795 55.531 0.40 79.63 C ATOM 10258 CA BPRO B 22 28.083 -19.897 55.672 0.60 85.45 C ATOM 10259 C APRO B 22 28.404 -17.322 55.153 0.40 74.57 C ATOM 10260 C BPRO B 22 28.612 -18.882 54.668 0.60 82.28 C ATOM 10261 O APRO B 22 27.496 -16.474 55.330 0.40 65.21 O ATOM 10262 O BPRO B 22 29.491 -18.064 55.017 0.60 75.63 O ATOM 10263 CB APRO B 22 26.878 -19.368 54.958 0.40 78.44 C ATOM 10264 CB BPRO B 22 26.664 -20.355 55.335 0.60 88.40 C ATOM 10265 CG APRO B 22 25.820 -18.874 55.924 0.40 77.98 C ATOM 10266 CG BPRO B 22 25.785 -19.289 55.969 0.60 84.77 C ATOM 10267 CD APRO B 22 26.494 -18.892 57.288 0.40 78.10 C ATOM 10268 CD BPRO B 22 26.483 -18.959 57.278 0.60 83.77 C ATOM 10284 N BPRO B 23 30.919 -19.516 53.713 0.60 85.16 N ATOM 10285 N APRO B 23 28.739 -17.919 53.643 0.40 86.84 N ATOM 10286 CA BPRO B 23 31.539 -18.641 52.718 0.60 90.72 C ATOM 10287 CA APRO B 23 28.833 -16.879 52.624 0.40 83.23 C ATOM 10288 C BPRO B 23 30.686 -17.504 52.141 0.60 88.67 C ATOM 10289 C APRO B 23 27.467 -16.309 52.244 0.40 77.44 C ATOM 10290 O BPRO B 23 29.501 -17.371 52.448 0.60 83.42 O ATOM 10291 O APRO B 23 26.674 -16.987 51.604 0.40 68.59 O ATOM 10292 CB BPRO B 23 31.943 -19.662 51.628 0.60 84.94 C ATOM 10293 CB APRO B 23 29.502 -17.595 51.440 0.40 87.02 C ATOM 10294 CG BPRO B 23 30.829 -20.684 51.662 0.60 82.63 C ATOM 10295 CG APRO B 23 30.267 -18.744 52.065 0.40 87.95 C ATOM 10296 CD BPRO B 23 30.364 -20.728 53.118 0.60 79.44 C ATOM 10297 CD APRO B 23 29.474 -19.131 53.299 0.40 84.63 C the peptide bond between C BPRO B 22 and N BPRO B 23 was pushed apart (2.45 A). The reason seems to be the reverse order of the A and B alternate conformation in residue 23 compared to residue 22. I thought, the order of the ATOM Lines in the PDB file should not matter. After switching the order of the ATOM lines, the wrong connections resolved. This is in ### CCP4 8.0.017: Refmac version 5.8.0425 : 10/24/23## In ### CCP4 8.0.016: Refmac version 5.8.0419 : 07/18/23## I additionally got in the log file ATTENTION: atom:OXT GLY 640 A1_ is missing in the structure ATTENTION: atom:OXT PRO 22 B4_ is missing in the structure ATTENTION: atom:OXT THR 643 B4_ is missing in the structure ATTENTION: atom:OXT GLY 640 C7_ is missing in the structure ATTENTION: atom:OXT VAL 639 D0_ is missing in the structure which also points at the erroneous break between PRO B 22 and PRO B 23. Is this meant to be so? Greetings Gottfried ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
