[ccp4bb] PHENIX & BSS refinement

[Jose Casasnovas]

We have seen that the recent versions of phenix (1.3) the structure refinement ends with a bulk solvent correction step, something I found quite unusual (absent in other refinement programs and in older versions of phenix, 1.24.1).  We have also seen that the B factor jumps up in this last step (see bellow).  Is anybody aware of this?  Do you know how to get rid of this final bss step?  This step is redundant, as bss is also done at the beginning of each ref cycle.

Header of a pdb file after refinement with phenix version 1.3:

REMARK  R-factors, x-ray target values and norm of gradient of x-ray target
REMARK  stage     r-work r-free  xray_target_w  xray_target_t
REMARK    0    :  0.3729 0.3776   5.594260e+00   5.604698e+00
REMARK    1_bss:  0.3135 0.3236   5.460255e+00   5.490057e+00   BSS refinement step
REMARK    1_xyz:  0.3096 0.3226   5.451384e+00   5.487128e+00   refinement of coordinates 
REMARK    1_adp:  0.2608 0.2858   5.300551e+00   5.386607e+00   refinement of ADPs
REMARK    2_bss:  0.2601 0.2843   5.299065e+00   5.384776e+00
REMARK    2_xyz:  0.2545 0.2847   5.285488e+00   5.386100e+00
REMARK    2_adp:  0.2460 0.2821   5.261319e+00   5.375879e+00
REMARK    3_bss:  0.2456 0.2788   5.257944e+00   5.366116e+00
REMARK    3_xyz:  0.2457 0.2809   5.261113e+00   5.371113e+00
REMARK    3_adp:  0.2427 0.2804   5.252685e+00   5.370838e+00
REMARK    3_bss:  0.2427 0.2804   5.252685e+00   5.370838e+00  ???????????

Bfactors
REMARK  stage      b_max   b_min   b_ave
REMARK    0    :   30.00   30.00   30.00
REMARK    1_bss:   30.00   30.00   30.00
REMARK    1_xyz:   30.00   30.00   30.00
REMARK    1_adp:  118.26    1.18   35.04
REMARK    2_bss:  118.26    1.18   35.04
REMARK    2_xyz:  118.26    1.18   35.04
REMARK    2_adp:  157.72    0.00   37.99
REMARK    3_bss:  157.72    0.00   37.99
REMARK    3_xyz:  157.72    0.00   37.99
REMARK    3_adp:  166.60    0.00   38.73
REMARK    3_bss:  203.00   36.40   75.12 ??????

Thanks a lot for your help.

Jose M Casasnovas

Centro Nacional de Biotecnología (lab. B16)
CSIC, Campus UAM
Darwin 3
28049 Madrid
Spain
Ph.  34 915854917(8)
Fax. 34 915854506
email: jcasasno...@cnb.csic.es   !!!!!! NEW E-MAIL