I am currently refining a structure at 2.4A resolution. I would like to increase the geometry target weight during refinement, however when I decrease wxc_scale (to 0.25 or 0.1) there is no change in the bond deviations or R factors compared to refinement with the default wxc_scale. I noticed in the refinement logfile under XYZ refinement wc=0. This does not change when I change the wc value in the command line (wc=2.0 for example) as suggested in a previous email. I also see no change when I use the optimize_wxc=true command. Examples of the command line input and output log files are below. I am currently using version 1.6-289 and would appreciate any help in resolving this issue as it seems the geometry is not being properly weighted during refinement. Thanks, Breann Breann L. Brown Department of Molecular Pharmacology, Physiology and Biotechnology Brown University Box GE-3 Providence, RI 02912
phenix.refine data.mtz model.pdb ligand.cif twin_law strategy=tls+individual_adp tls.params main.ncs=true wxc_scale=0.1 wc=2.0
========================== Target weights: x-ray data ========================= |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.000000 wxc_scale = 0.100 wc = 0.000 | | angle between x-ray and geometry gradient vectors: None (deg) | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 11.057053 wxu_scale = 2.160 wu = 1.000 | | angle between Xray and ADP gradient vectors: 143.484 (deg) | |-----------------------------------------------------------------------------| ------------------------------------------------------------------------ stage angl bond chir dihe plan repu geom_target 0 : 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01 1_bss: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01 1_adp: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01 2_bss: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01 2_adp: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01 3_bss: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01 3_adp: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01 4_bss: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01 4_adp: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01 5_bss: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01 5_adp: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01 6_bss: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01 6_adp: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01 7_bss: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01 7_adp: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01 8_bss: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01 8_adp: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01 9_bss: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01 9_adp: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01 10_bss: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01 10_adp: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01 10_bss: 2.493 0.027 0.239 23.648 0.008 4.106 3.6797e-01 ------------------------------------------------------------------------ Maximal deviations: stage angl bond chir dihe plan repu |grad| 0 : 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01 1_bss: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01 1_adp: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01 2_bss: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01 2_adp: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01 3_bss: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01 3_adp: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01 4_bss: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01 4_adp: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01 5_bss: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01 5_adp: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01 6_bss: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01 6_adp: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01 7_bss: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01 7_adp: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01 8_bss: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01 8_adp: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01 9_bss: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01 9_adp: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01 10_bss: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01 10_adp: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01 10_bss: 29.287 0.287 2.517 83.486 0.050 1.724 3.9155e-01 -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Pavel Afonine Sent: Tuesday, February 23, 2010 1:40 PM To: PHENIX user mailing list Subject: Re: [phenixbb] weights optimization, add hydrogens Hi Ursula,
I am refining a 2.0 A structure in Phenix using mostly the graphical interface. The maps are very good and the R factors are low (0.208/0.173). But the geometry is not so great with bond deviations of 0.208 and Angle deviations of 1.85. What is the best thing to do to try to improve the geometry. Should I try to optimize the weights?
the R-factors seem good indeed. Yes, Although the angle deviations seem ok to me, I'm concerned about the bond deviations... Yes, you can try two things: - increase the restraints strength by increasing the corresponding weight: from the command line: "wc=VALUE", where VALUE is a number somewhat larger than 1.0; from the GUI: Refinement settings -> All parameters -> Refinement target weights... -> Stereochemistry weight scale - Run automatic weight optimization (note, this may take a while to run): from the command line: use keyword: "optimize_wxc=true"; from the GUI: Refinement settings -> All parameters -> Refinement target weights... -> Optimize X-ray/stereochemistry weight Alternatively, you can send me your PDB and data file and I will tell you what exactly is not right and how to fix it. Pavel.