Dear All,
I have a question regarding the output of Zanuda. We are working on a structure solved in P 32 1 2 with one molecule in the asymmetric unit. The structure was solved by molecular replacement and refines well to R = 20.6%, Rfree = 25.2% with data to 1.8Å and 90% of the model built. Most of the missing residues are 15 residue long section that is predicted to form a helix and although there is some ambiguous density it is not possible to construct anything. To check the solution I submitted the structure to Zanuda which suggested that the symmetry was too high and the correct space group should be P 32. I have refined the structure in P 32 and although the stats are better (R = 19.9%, Rfree = 23.1%) there is no improvement in the density and the two copies remain largely identical. However when I resubmitted this structure to Zanuda it suggests that the symmetry is too low and the correct space group is P 32 1 2. But looking at the log file I am not sure why this should be so. The program does pick P 32 in step 2 but then selects P 32 1 2 at the end of step 3 even though the R free is better in P 32 (R is slightly worse). I'm not sure what I am missing here. I have tried molecular replacement in P 1 followed by refinement and still get P 32 1 2 picked over P 32 which has the best R and Rfree. I have attached an extract from the log files at the end of this email. Does anyone have any suggestions? Thanks in advance, Alastair McEwen P 32 logfile Step 1. R-factors for the starting model. Transformation into a supergroup. current time: Nov 27 14:19 CET expected end of job (rough estimate): Nov 27 14:30 CET --------------------------------------------------------------------- | Subgroup | Spacegroup | R.m.s.d. | Refinement in tested group | | | | from the |--------------------------------| | Ref | | starting | Rigid | Restrained | | | | model, A |----------|---------------------| | | | | R | R | R-free | |----------|------------|----------|----------|----------|----------| | >> 2 | P 32 | 0.0006 | -- | 0.2716 | 0.3084 | | 6 | P 32 1 2 | 0.1035 | -- | -- | -- | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Step 2. Refinements in subgroups. There are 4 subgroups to test. current time: Nov 27 14:19 CET expected end of job: Nov 27 14:32 CET ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | >> 2 | P 32 | 0.0006 | -- | 0.2716 | 0.3084 | --------------------------------------------------------------------- | 1 | P 1 | 0.1728 | 0.2777 | 0.2521 | 0.3288 | | 2 | P 32 | 0.1738 | 0.2779 | 0.2509 | 0.3279 | | 3 | C 1 2 1 | 0.2080 | 0.2872 | 0.2519 | 0.3315 | | 6 | P 32 1 2 | 0.2040 | 0.2899 | 0.2526 | 0.3434 | --------------------------------------------------------------------- | << 2 | P 32 | 0.1738 | 0.2779 | 0.2509 | 0.3279 | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Step 3. Refinement of the best model. Candidate symmetry elements are added one by one. current time: Nov 27 14:25 CET expected end of job: Nov 27 14:32 CET ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | >> 2 | P 32 | 0.1738 | 0.2779 | 0.2509 | 0.3279 | --------------------------------------------------------------------- | 1 | P 1 | 0.1728 | 0.2778 | 0.2521 | 0.3290 | | 2 | P 32 | 0.2231 | -- | 0.2467 | 0.3305 | | 6 | P 32 1 2 | 0.2679 | -- | 0.2452 | 0.3444 | --------------------------------------------------------------------- | << 6 | P 32 1 2 | 0.2679 | -- | 0.2452 | 0.3444 | --------------------------------------------------------------------- R-factor in the original subgroup is NOT the best. The original spacegroup assignment seems to be incorrect P1 logfile Step 1. R-factors for the starting model. Transformation into a supergroup. current time: Dec 11 11:18 CET expected end of job (rough estimate): Dec 11 11:32 CET --------------------------------------------------------------------- | Subgroup | Spacegroup | R.m.s.d. | Refinement in tested group | | | | from the |--------------------------------| | Ref | | starting | Rigid | Restrained | | | | model, A |----------|---------------------| | | | | R | R | R-free | |----------|------------|----------|----------|----------|----------| | >> 1 | P 1 | 0.0000 | -- | 0.2753 | 0.3090 | | 6 | P 32 1 2 | 0.1947 | -- | -- | -- | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Step 2. Refinements in subgroups. There are 6 subgroups to test. current time: Dec 11 11:18 CET expected end of job: Dec 11 11:35 CET ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | >> 1 | P 1 | 0.0000 | -- | 0.2753 | 0.3090 | --------------------------------------------------------------------- | 1 | P 1 | 0.1973 | 0.2780 | 0.2482 | 0.3480 | | 2 | C 1 2 1 | 0.2431 | 0.2837 | 0.2517 | 0.3449 | | 3 | C 1 2 1 | 0.2196 | 0.2863 | 0.2525 | 0.3473 | | 4 | P 32 | 0.2859 | 0.2855 | 0.2503 | 0.3393 | | 5 | C 1 2 1 | 0.2815 | 0.2907 | 0.2530 | 0.3483 | | 6 | P 32 1 2 | 0.2914 | 0.2935 | 0.2574 | 0.3493 | --------------------------------------------------------------------- | << 4 | P 32 | 0.2859 | 0.2855 | 0.2503 | 0.3393 | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Step 3. Refinement of the best model. Candidate symmetry elements are added one by one. current time: Dec 11 11:29 CET expected end of job: Dec 11 11:37 CET ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | >> 4 | P 32 | 0.2859 | 0.2855 | 0.2503 | 0.3393 | --------------------------------------------------------------------- | 1 | P 1 | 0.2767 | 0.2863 | 0.2482 | 0.3455 | | 4 | P 32 | 0.3320 | -- | 0.2497 | 0.3409 | | 6 | P 32 1 2 | 0.3698 | -- | 0.2550 | 0.3578 | --------------------------------------------------------------------- | << 6 | P 32 1 2 | 0.3698 | -- | 0.2550 | 0.3578 | --------------------------------------------------------------------- R-factor in the original subgroup is NOT the best. The original spacegroup assignment seems to be incorrect. *************************************************** Alastair McEwen, PhD Structural Biology and Genomics Technology Platform Integrated Structural Biology IGBMC 1 rue Laurent Fries 67404 ILLKIRCH - FRANCE tel: +33 (0)3 88 65 57 92 ***************************************************
