[phenixbb] Phenix.refine distorts geometry during rigid body refinement

Pavel Afonine pafonine at lbl.gov
Wed Sep 14 12:00:35 PDT 2011

Hi Ian,

can you send me a PDB file (and any parameter files, if any) so I can 
reproduce the problem?


On 9/14/11 11:35 AM, Ian Slaymaker wrote:
> I am bringing a PDB refined in Refmac back to phenix.refine. After an
> initial rigid body refinement to compare numbers (one chain per
> group), the geometry (specifically the bond length rmsd) had
> surprisingly increased. Phenix.validate confirmed the Refmac (initial)
> geometry numbers and then afterwards confirmed the distorted geometry.
> What is strange is that when opened in COOT, the initial and final
> models are completely super imposed.
> REMARK Start: r_work = 0.3375 r_free = 0.3624 bonds = 0.006 angles = 0.768
> REMARK Final: r_work = 0.3379 r_free = 0.3626 bonds = 0.145 angles = 1.019
> can you help me figure out what is going on here? These are the final
> few refinements of a 4.1 A structure.
> Thanks,
> Ian

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