Hi Faisal, There is no such thing as the ideal deviation from ideal geometry. As long as your rmsZ values are below 1 (which they are), it's okay. Note that, in contrast to popular belief, rmsd has no useful meaning for bonds and angles.
Genarally, rmsZ goes down with resolution but the correlation is not that high. It does not mean that rmsZ should be a particular value at a certain resolution. That said, you should optimise your restraints to get the most likely model. In Refmac that means minimizing -LLfree. You can do this by hand, but there are also automated procedures to do that. Shameless plug: PDB_REDO has such an automated procedure. HTH, Robbie Joosten Date: Wed, 3 Oct 2012 03:19:48 +0530 From: [email protected] Subject: [ccp4bb] ideal rms bond length To: [email protected] Dear all i request you to please answer my basic query about the ideal acceptable rmsbond length obtained during refmac refinement..is the data acceptable in mine case which is as follows.. Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.2090 0.2079 0.875 226315. 11985.5 0.0278 1.389 2.718 1.261 0.198 1 0.2064 0.2284 0.850 226313. 12201.1 0.0285 1.427 2.733 1.271 0.204 2 0.2076 0.2373 0.837 226944. 12289.9 0.0248 1.242 2.598 1.200 0.187 3 0.2092 0.2429 0.828 227495. 12341.7 0.0222 1.107 2.458 1.128 0.173 4 0.2100 0.2468 0.822 227753. 12372.4 0.0211 1.053 2.377 1.086 0.166 5 0.2104 0.2500 0.818 227942. 12395.7 0.0204 1.021 2.326 1.061 0.161 6 0.2108 0.2522 0.814 228075. 12411.5 0.0200 0.999 2.289 1.042 0.158 7 0.2111 0.2537 0.812 228162. 12421.8 0.0197 0.984 2.265 1.030 0.156 8 0.2113 0.2550 0.810 228228. 12430.5 0.0194 0.971 2.243 1.020 0.154 9 0.2114 0.2559 0.809 228300. 12436.1 0.0192 0.962 2.228 1.012 0.153 10 0.2116 0.2568 0.808 228348. 12441.7 0.0191 0.957 2.218 1.008 0.152 11 0.2118 0.2574 0.807 228394. 12446.2 0.0190 0.951 2.210 1.004 0.151 12 0.2119 0.2581 0.806 228421. 12449.6 0.0189 0.948 2.203 1.001 0.151 13 0.2119 0.2585 0.805 228440. 12452.7 0.0189 0.944 2.198 0.998 0.150 14 0.2120 0.2590 0.805 228461. 12455.0 0.0188 0.941 2.194 0.996 0.150 15 0.2121 0.2593 0.804 228480. 12456.9 0.0188 0.939 2.190 0.995 0.150 -- Regards Faisal School of Life Sciences JNU
