This has been discussed multiple times on bb, also BMC p640.
The restraint target standard uncertainty provides an upper limit54 for a reasonable bond or angle r.m.s.d. from targets within the model (approximately 0.02 Å and 1.9deg, respectively), but makes no further assumption where these values de facto should be in an optimal refi nement of a protein structure.73 Assume at one extreme a low-resolution torsion angle refi nement with fixed bond lengths, where the bond length deviation from targets will be zero. At the other extreme, an unrestrained refi nement at ultra-high resolution will refl ect the bond length variation as observed in small molecules, around ~0.02 Å. In between the values will vary, depending on the properly selected overall restraint weight that minimizes R-free (or preferably LL-free).73 The notion that the r.m.s.d. from targets should be the same for all structures and that it should be close to small molecule values is not correct. br From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jiamu Du Sent: Wednesday, April 13, 2011 2:06 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] about RMSD bond lengths and angles Dear All, I am wondering about the ranges of RMSD bond lengths and angles. What are the acceptable ranges for these two values? Is there some statistics for them? Thanks and best wishes.
