Dear Faisal -
There are a few problems with your refinement.
First and foremost, your R factors increase instead of decreasing! This
is associated with a decrease in geometry rmsd, suggesting that Refmac
is trying to fix an incorrect model using an excessively tight geometry
weight.
Second, your geometry rmsd values are still quite high. You don't say
what resolution you have to work with, but given your R factors, I would
expect you have something in the 2 to 2.5 A range. Your rmsBOND values
would typically be below 0.015 at this resolution. It's possible you
have a few areas of your model with very bad geometry which are raising
the global values even though everything else is mostly OK.
Third, I wonder why your R and Rfree are so close at the start of
refinement. The low R values suggest a late-stage refined model, not an
initial molecular replacement solution or something similar. If you're
starting with an isomorphous structure, you need to use the same free R
set as was used in the previous refinement in order to keep your R free
set uncontaminated.
You should examine your model carefully and look for regions that don't
have strong electron density to support them. Also look for bad
geometry: bond and angle deviations greater than 5 sigma (these will be
in the Refmac log file), bad rotamers, bad Ramachandran position, etc.
Regions which are of poor quality should be removed from the model and
rebuilt into unbiased density in later refinement rounds. (Or if the
electron density stays poor, leave the region out of the model.)
Good luck,
Matt
On 10/2/12 5:49 PM, Faisal Tarique wrote:
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
--
Matthew Franklin, Ph. D.
Senior Scientist
New York Structural Biology Center
89 Convent Avenue, New York, NY 10027
(212) 939-0660 ext. 9374
