Yang Li,
I personally always take this kind of thing as "instability" in
refinement. Your independent reflection numbers might be much less
than the to-be-refined parameters, and still you sacrificed some for
R-free calculation. I think there is no reason at this resolution
edge (~3A), making bonds possibly resolvable, that NCS should not be
used, except that you would like to see difference between 2
structures in ASU. Unfortunately, at this situation, the difference
may not be reliable even if you could see.
There was a so-called Ping-Pong refinement strategy (from
Deisenhofer?) may be used for your case in a low resolution try.
However, personally I would be very careful with this a-way-out-of-no-
way strategy. A good dataset is always better than any tricks. Good
luck.
LJL
On Feb 20, 2008, at 11:23 PM, yang li wrote:
Dear All,
I have a 3A structure, the quality of the data is not very
good. Now I have refined it to Rfree=40.7 in Refmac.
But it wonnot go further down. Then I used CNS to do annealing,
then use refmac to do rigid body refinement.
The Rfree converged to 0.34, but if I use restrain refinement it
will go up gradually. Then I use CNS refine
script to refine the anneal.pdb, then the rigid body of refmac
refinement converged at Rfree=0.33, but the refmac restrain
refinement will still increase the Rfree--given weighting=0.03,
after 80 cycle Rfree is 0.38 and seems like still increasing.
Then I gave weighting=0.02, after 180 cycle, the Rfree is 0.37. I
very wonder if I give 1000 cycle to run, Rfree
will go back to 0.4. Can anybody give me some suggestions?
By the way, it is a dimer and I didnot use NCS restarin during
refinement. Below is from refmac log:
Ncyc Rfact Rfree FOM LLG rmsBOND rmsANGLE
rmsCHIRAL $$
$$
0 0.303 0.326 0.738 81869.2 0.012
1.575 0.104
1 0.288 0.337 0.722 81411.2 0.013
1.321 0.080
2 0.284 0.343 0.717 81312.9 0.011
1.303 0.081
3 0.282 0.347 0.713 81308.2 0.010
1.312 0.083
4 0.282 0.349 0.710 81326.4 0.010
1.313 0.083
5 0.281 0.352 0.708 81339.9 0.010
1.321 0.084
6 0.280 0.353 0.707 81356.4 0.010
1.322 0.085
7 0.280 0.355 0.705 81380.9 0.010
1.332 0.086
8 0.280 0.355 0.704 81390.5 0.010
1.330 0.086
9 0.279 0.359 0.702 81400.6 0.010
1.342 0.087
10 0.279 0.357 0.701 81405.1 0.010
1.340 0.086
11 0.279 0.360 0.700 81435.3 0.010
1.349 0.087
12 0.278 0.358 0.700 81425.8 0.011
1.363 0.086
13 0.278 0.362 0.698 81436.3 0.010
1.352 0.087
14 0.278 0.361 0.698 81438.1 0.010
1.347 0.086
15 0.278 0.364 0.696 81456.5 0.010
1.354 0.087
16 0.277 0.363 0.696 81452.3 0.011
1.352 0.087
17 0.278 0.365 0.695 81456.7 0.010
1.356 0.087
18 0.277 0.363 0.695 81450.3 0.011
1.348 0.087
19 0.277 0.366 0.694 81447.6 0.010
1.355 0.087
20 0.276 0.364 0.694 81448.2 0.011
1.350 0.087
21 0.277 0.366 0.693 81451.4 0.010
1.355 0.087
22 0.276 0.364 0.694 81442.4 0.011
1.350 0.087
23 0.277 0.366 0.693 81440.8 0.010
1.354 0.087
24 0.276 0.364 0.693 81434.4 0.011
1.350 0.087
25 0.277 0.365 0.693 81453.9 0.010
1.356 0.087
26 0.276 0.363 0.693 81446.5 0.011
1.352 0.087
27 0.276 0.365 0.693 81448.6 0.010
1.356 0.087
28 0.276 0.363 0.693 81438.2 0.011
1.352 0.087
29 0.276 0.364 0.693 81433.7 0.010
1.356 0.088
30 0.276 0.362 0.693 81430.1 0.011
1.352 0.087
31 0.276 0.364 0.692 81427.0 0.010
1.355 0.087
32 0.275 0.362 0.693 81421.2 0.011
1.354 0.087
33 0.276 0.364 0.692 81428.6 0.010
1.356 0.087
34 0.275 0.362 0.692 81421.9 0.011
1.355 0.087
35 0.275 0.364 0.691 81439.0 0.010
1.358 0.087
36 0.275 0.362 0.691 81435.9 0.011
1.356 0.087
37 0.275 0.364 0.691 81446.4 0.010
1.360 0.088
38 0.275 0.362 0.691 81444.6 0.010
1.358 0.087
39 0.275 0.364 0.690 81453.3 0.010
1.361 0.088
40 0.275 0.362 0.691 81443.5 0.010
1.360 0.087
41 0.275 0.363 0.690 81453.2 0.010
1.362 0.088
42 0.274 0.362 0.691 81443.8 0.010
1.361 0.088
43 0.275 0.364 0.690 81468.1 0.010
1.364 0.088
44 0.274 0.362 0.690 81471.5 0.010
1.363 0.088
45 0.274 0.364 0.689 81509.4 0.010
1.366 0.088
46 0.274 0.363 0.689 81498.1 0.010
1.364 0.088
47 0.274 0.364 0.689 81512.9 0.010
1.368 0.088
48 0.274 0.363 0.689 81499.2 0.010
1.366 0.088
49 0.274 0.365 0.688 81513.6 0.010
1.369 0.088
50 0.274 0.363 0.689 81509.3 0.010
1.368 0.088
51 0.274 0.365 0.688 81505.7 0.010
1.372 0.088
52 0.274 0.363 0.689 81498.6 0.010
1.370 0.088
53 0.274 0.365 0.688 81499.5 0.010
1.374 0.088
54 0.273 0.363 0.689 81488.1 0.010
1.372 0.088
55 0.273 0.365 0.688 81490.0 0.010
1.375 0.089
56 0.273 0.364 0.688 81495.7 0.010
1.374 0.088
57 0.273 0.365 0.688 81494.9 0.010
1.377 0.089
58 0.273 0.365 0.688 81476.1 0.010
1.376 0.089
59 0.273 0.366 0.687 81496.9 0.010
1.378 0.089
60 0.273 0.365 0.688 81496.1 0.010
1.376 0.089
61 0.273 0.367 0.687 81494.6 0.010
1.378 0.089
62 0.273 0.365 0.688 81480.5 0.010
1.377 0.089
63 0.273 0.367 0.687 81486.5 0.010
1.379 0.090
64 0.273 0.366 0.687 81483.1 0.010
1.378 0.090
65 0.273 0.367 0.687 81483.9 0.010
1.380 0.090
66 0.273 0.366 0.687 81479.1 0.010
1.378 0.090
67 0.273 0.367 0.687 81479.6 0.010
1.380 0.090
68 0.273 0.366 0.687 81479.4 0.010
1.379 0.090
69 0.273 0.367 0.687 81480.1 0.010
1.381 0.090
70 0.273 0.367 0.687 81489.5 0.010
1.379 0.090
71 0.273 0.368 0.687 81492.0 0.010
1.381 0.090
72 0.273 0.367 0.687 81486.0 0.010
1.379 0.090
73 0.273 0.368 0.687 81483.4 0.010
1.381 0.090
74 0.273 0.366 0.687 81479.5 0.010
1.379 0.090
75 0.273 0.367 0.687 81483.7 0.010
1.382 0.090
76 0.273 0.366 0.687 81486.5 0.010
1.380 0.090
77 0.273 0.367 0.686 81487.8 0.010
1.381 0.090
78 0.273 0.367 0.687 81494.2 0.010
1.380 0.090
79 0.273 0.368 0.686 81498.2 0.010
1.381 0.090
80 0.274 0.367 0.686 81499.0 0.010
1.379 0.090
81 0.274 0.368 0.686 81492.4 0.010
1.382 0.091
82 0.274 0.367 0.687 81493.9 0.010
1.381 0.090
83 0.274 0.368 0.686 81508.0 0.010
1.381 0.091
84 0.274 0.367 0.687 81505.1 0.010
1.381 0.091
85 0.274 0.369 0.686 81505.6 0.010
1.381 0.091
86 0.274 0.367 0.687 81504.1 0.010
1.381 0.091
87 0.274 0.369 0.686 81507.0 0.010
1.380 0.091
88 0.274 0.367 0.687 81506.4 0.010
1.382 0.091
89 0.273 0.369 0.686 81509.2 0.010
1.380 0.091
90 0.274 0.367 0.687 81506.5 0.010
1.381 0.091
91 0.274 0.369 0.686 81510.8 0.010
1.379 0.091
92 0.274 0.367 0.687 81516.3 0.010
1.380 0.091
93 0.273 0.369 0.687 81511.2 0.010
1.380 0.091
94 0.273 0.367 0.687 81502.3 0.010
1.380 0.091
95 0.273 0.369 0.686 81508.2 0.010
1.380 0.091
96 0.274 0.367 0.687 81508.7 0.010
1.380 0.091
97 0.273 0.369 0.687 81507.3 0.010
1.379 0.091
98 0.273 0.367 0.687 81506.2 0.010
1.379 0.091
99 0.273 0.369 0.687 81506.3 0.010
1.379 0.091
100 0.273 0.367 0.687 81511.4 0.010
1.379 0.091
101 0.273 0.369 0.687 81519.2 0.010
1.379 0.091
102 0.273 0.367 0.687 81514.9 0.010
1.380 0.091
103 0.273 0.369 0.687 81510.1 0.010
1.379 0.091
104 0.273 0.367 0.687 81504.4 0.010
1.380 0.091
105 0.273 0.369 0.687 81519.7 0.010
1.380 0.091
106 0.273 0.367 0.687 81505.1 0.010
1.379 0.091
107 0.273 0.369 0.687 81522.2 0.010
1.379 0.091
108 0.273 0.367 0.687 81503.6 0.010
1.379 0.091
109 0.273 0.369 0.687 81516.1 0.010
1.379 0.091
110 0.273 0.367 0.687 81507.9 0.010
1.379 0.091
111 0.273 0.369 0.687 81514.9 0.010
1.379 0.091
112 0.273 0.367 0.688 81502.1 0.010
1.379 0.091
113 0.273 0.368 0.687 81505.8 0.010
1.379 0.091
114 0.273 0.367 0.687 81507.0 0.010
1.380 0.091
115 0.273 0.369 0.687 81512.7 0.010
1.379 0.091
116 0.273 0.367 0.688 81504.4 0.010
1.380 0.091
117 0.273 0.368 0.687 81512.0 0.010
1.379 0.091
118 0.273 0.368 0.688 81512.5 0.010
1.379 0.090
119 0.273 0.369 0.687 81514.2 0.010
1.378 0.091
120 0.273 0.368 0.688 81518.6 0.010
1.379 0.090
121 0.273 0.369 0.687 81520.0 0.010
1.378 0.090
122 0.273 0.368 0.688 81524.6 0.010
1.379 0.090
123 0.273 0.369 0.687 81522.5 0.010
1.377 0.090
124 0.273 0.368 0.688 81525.0 0.010
1.379 0.090
125 0.273 0.369 0.687 81511.2 0.010
1.378 0.090
126 0.273 0.368 0.688 81515.6 0.010
1.379 0.090
127 0.273 0.370 0.687 81511.5 0.010
1.378 0.090
128 0.273 0.369 0.687 81520.6 0.010
1.380 0.090
129 0.273 0.370 0.687 81522.1 0.010
1.377 0.089
130 0.273 0.369 0.687 81525.5 0.010
1.374 0.088
131 0.273 0.370 0.686 81528.8 0.010
1.372 0.088
132 0.273 0.369 0.687 81528.9 0.010
1.371 0.088
133 0.273 0.370 0.686 81524.1 0.010
1.370 0.088
134 0.273 0.369 0.687 81527.9 0.010
1.371 0.088
135 0.273 0.371 0.686 81535.6 0.010
1.370 0.088
136 0.273 0.370 0.686 81536.0 0.010
1.370 0.088
137 0.273 0.371 0.686 81530.4 0.010
1.369 0.088
138 0.273 0.370 0.686 81532.5 0.010
1.369 0.088
139 0.273 0.371 0.686 81531.8 0.010
1.368 0.088
140 0.273 0.370 0.686 81527.9 0.010
1.369 0.088
141 0.273 0.371 0.686 81530.8 0.010
1.369 0.088
142 0.273 0.370 0.686 81522.6 0.010
1.370 0.088
143 0.273 0.372 0.685 81524.6 0.010
1.369 0.088
144 0.273 0.370 0.686 81514.4 0.010
1.370 0.088
145 0.273 0.372 0.685 81528.9 0.010
1.370 0.088
146 0.273 0.370 0.686 81515.6 0.010
1.370 0.088
147 0.273 0.372 0.685 81524.7 0.010
1.369 0.088
148 0.273 0.370 0.686 81522.6 0.010
1.370 0.088
149 0.273 0.372 0.685 81531.6 0.010
1.369 0.088
150 0.273 0.370 0.686 81519.6 0.010
1.370 0.088
151 0.273 0.372 0.685 81536.0 0.010
1.369 0.088
152 0.273 0.370 0.686 81527.7 0.010
1.370 0.088
153 0.273 0.371 0.685 81536.1 0.010
1.369 0.088
154 0.273 0.370 0.686 81526.6 0.010
1.371 0.088
155 0.273 0.371 0.685 81531.2 0.010
1.370 0.088
156 0.273 0.370 0.686 81523.3 0.010
1.370 0.088
157 0.273 0.370 0.685 81518.6 0.010
1.370 0.088
158 0.273 0.369 0.686 81516.9 0.010
1.372 0.088
159 0.273 0.370 0.685 81523.8 0.010
1.370 0.088
160 0.273 0.369 0.686 81512.8 0.010
1.371 0.088
161 0.273 0.370 0.685 81514.7 0.010
1.370 0.088
162 0.273 0.369 0.685 81515.2 0.010
1.368 0.088
163 0.273 0.371 0.685 81525.4 0.010
1.370 0.088
164 0.273 0.369 0.685 81508.3 0.010
1.369 0.088
165 0.273 0.371 0.684 81522.5 0.010
1.370 0.088
166 0.273 0.369 0.685 81525.8 0.010
1.368 0.088
167 0.273 0.371 0.684 81531.7 0.010
1.371 0.088
168 0.273 0.369 0.684 81534.7 0.010
1.369 0.088
169 0.273 0.371 0.684 81537.8 0.010
1.371 0.088
170 0.273 0.370 0.684 81534.8 0.010
1.369 0.088
171 0.273 0.371 0.683 81552.7 0.011
1.372 0.088
172 0.273 0.370 0.683 81552.5 0.010
1.370 0.088
173 0.273 0.371 0.683 81552.1 0.010
1.372 0.088
174 0.273 0.370 0.683 81545.7 0.010
1.370 0.088
175 0.273 0.371 0.683 81556.1 0.010
1.373 0.088
176 0.273 0.370 0.683 81560.3 0.010
1.371 0.088
177 0.273 0.371 0.682 81568.8 0.010
1.372 0.088
178 0.273 0.370 0.683 81567.8 0.010
1.371 0.088
179 0.273 0.371 0.682 81568.0 0.010
1.374 0.088
180 0.273 0.370 0.683 81565.7 0.010
1.372 0.088
Lijun Liu, PhD
Institute of Molecular Biology
HHMI & Department of Physics
University of Oregon
Eugene, OR 97403
541-346-4080
