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
[EMAIL PROTECTED]
2007-07-12
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