1) Rfree in the first cycle seem to be more apparent than actual. You
need to check you free reflection conversion. It may turn out that you
have more reflections for free than for working R.
2) You may need to use tighter restraints. For example by changing
weight matrix value to smaller number or by using weight auto.
I would not deposit with 0 cycles.
regards
Garib
On 12 Jul 2007, at 21:38, zhongzhou chen wrote:
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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