Hello everyone,
Thank everybody for the good suggestions.
Especially I thank Prof. Eleanor Dodson for her many times' help.
Finally, I found that there is an ice ring in the data as the suggestion of Prof. Eleanor Dodson.
After I cut out ice rings, Rfact and Rfree are 0.175 and 0.227 at 1.8 A.
Best regards,
zhongzhou chen
[log in to unmask]
2007-08-06
> Dear Sir or madam,
>
> I have some questions about refmac5.
>
> I am new to Refmac. I optimized the structure with CNS (Rwork:
> 23%, Rfree: 25%).
>
> Cell : 71.480 71.480 151.813 90.000 90.000 90.000
> Space group p43212
> resolution 100 1.97
>
> protein contain 350 amino acids.
> Nmol/asym: 1
>
> number of amino acids built: 330
> number of waters:330
> three glycerols
> six sulfate ions.
>
>
>
> My friends told me that refmac5 will get lower Rfree and Rfactor.
>
> I refined the pdb structure from CNS using restrained refinement.
>
> Ncyc Rfact Rfree FOM LLG rmsBOND rmsANGLE
> rmsCHIRAL $$
> $$
>
> using TLS:
> 0 0.215 0.221 0.763 165320.6 0.006
> 1.250 0.092
> 1 0.189 0.230 0.751 162623.7 0.022
> 1.680 0.116
> 2 0.187 0.233 0.751 162500.2 0.022
> 1.724 0.119
> 3 0.185 0.239 0.747 162269.0 0.022
> 1.790 0.123
> 4 0.185 0.241 0.748 162314.8 0.022
> 1.809 0.124
> 5 0.185 0.244 0.744 162248.1 0.023
> 1.831 0.126
> 6 0.185 0.245 0.744 162353.0 0.023
> 1.839 0.126
> 7 0.185 0.247 0.743 162226.2 0.023
> 1.858 0.128
> 8 0.186 0.248 0.741 162430.4 0.023
> 1.852 0.128
> 9 0.185 0.248 0.741 162300.2 0.023
> 1.857 0.128
> 10 0.185 0.249 0.740 162317.2 0.023
> 1.861 0.129
>
>
> without TLS:
> Ncyc Rfact Rfree FOM LLG rmsBOND rmsANGLE
> rmsCHIRAL $$
> $$
> 0 0.217 0.223 0.764 166172.2 0.006
> 1.250 0.092
> 1 0.192 0.234 0.752 163514.5 0.022
> 1.676 0.116
> 2 0.190 0.237 0.752 163400.6 0.022
> 1.715 0.119
> 3 0.188 0.242 0.747 163218.2 0.022
> 1.783 0.124
> 4 0.188 0.244 0.747 163276.6 0.022
> 1.802 0.125
> 5 0.188 0.248 0.744 163167.9 0.023
> 1.828 0.127
> 6 0.188 0.248 0.744 163271.0 0.023
> 1.832 0.127
> 7 0.188 0.251 0.743 163144.5 0.023
> 1.849 0.128
> 8 0.189 0.251 0.742 163331.2 0.023
> 1.845 0.129
> 9 0.188 0.252 0.741 163209.3 0.023
> 1.850 0.129
> 10 0.188 0.253 0.741 163249.6 0.023
> 1.854 0.129
>
>
> May I ask some questions?
>
> 1. Can I use the structure in zero cycle to deposit in pdb bank?
> Because its rfree is lowest and it just come from CNS result
> without any change of B
>
> factor?
>
> 2. Why Rfree increase during refinement?
>
> 3. Usually, delta(Rwork,Rfree) is lower than 3.0 percent for a
> good structure.
> However, there is 7% if using the final refinement structure.
> How can I do to reduce Rfree?
>
> 4. I use the TLS to refine during restrained refinement. Why the
> result structure show
>
> that there is no tls groups?
>
> The TLS format
> RANGE 'A 11.' 'A 60.' ALL
> ORIGIN -5.756 -6.929 21.439
> T -0.0229 -0.0472 -0.0103 -0.0487 -0.0019 0.0414
> L 0.8419 0.3881 3.8499 -0.2446 -1.1643 0.8341
> S -0.0615 -0.0707 -0.0949 -0.1532 0.1007 0.1020 0.2434 -0.2249
>
>
>
> The pdb output file is shown as below.
>
> REMARK 3 TLS DETAILS
> REMARK 3 NUMBER OF TLS GROUPS : NULL
>
>
>
> thanks
>
>
> Best regards,
>
> zhong chen
> [log in to unmask]
> 2007-07-12
>
>
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