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

Ian Slaymaker iamslaymaker at gmail.com
Wed Sep 14 11:35:48 PDT 2011

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.

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