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Revision as of 22:30, 17 March 2011

1,732 bytes removed ,  17 March 2011
→‎Automatically building almost 3/4 of the main chain
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[[File:1y13-raddam-contrast-raddam.png]]
[[File:1y13-raddam-contrast-raddam.png]]


== Automatically building almost 3/4 of the main chain ==
== Automatically building the main chain of 452 out of 519 residues ==


Based on the sites obtained by SHELXD, we run
Based on the sites obtained by SHELXD, we run
  shelxe.beta -a -q -h -b -s0.585 -m40 raddam raddam_fa
  shelxe.beta -a -q -h -b -s0.585 -m40 raddam raddam_fa
This already builds a significant number of residues, but also gives an improved list of heavy atom sites - there are actually 6 sites instead of the 5 that SHELXD wrote out (yes, we had asked SHELXD for 3 sites since there are 3 Met residues, but SHELXD as always was smarter than we are). We "mv raddam.hat raddam_fa.res" for another run of SHELXE:
This already builds a significant number of residues, but also gives an improved list of heavy atom sites - there are actually 6 sites instead of the 5 that SHELXD wrote out (yes, we had asked SHELXD for 3 sites since there are 3 Met residues, but SHELXD as always was smarter than we are). We "mv raddam.hat raddam_fa.res" for another run of SHELXE:
  shelxe.beta -a -q -h6 -b -s0.585 -m40 raddam raddam_fa
  shelxe.beta -a -q -h6 -b -s0.585 -m40 -n3 raddam raddam_fa
and get
and get
<pre>
<pre>
   374 residues left after pruning, divided into chains as follows:
   452 residues left after pruning, divided into chains as follows:
  A:  43   B: 37   C:  17   D:  19   E:   7   F:  16   G: 16   H:  5  I:  13
  A:  15   B:   5   C:  22   D:  22   E: 27   F:  62   G: 263   H:  36
J:  5  K:  9  L:  40  M:  81  N:  12  O:  15  P:  7  Q:  5  R:  8
S:  13  T:  6


  CC for partial structure against native data =  34.56 %
  CC for partial structure against native data =  39.83 %


  ------------------------------------------------------------------------------
  ------------------------------------------------------------------------------
Line 607: Line 605:
  Global autotracing cycle  4
  Global autotracing cycle  4


  <wt> = 0.300, Contrast = 0.484, Connect. = 0.705 for dens.mod. cycle 1
  <wt> = 0.300, Contrast = 0.447, Connect. = 0.705 for dens.mod. cycle 1
  <wt> = 0.300, Contrast = 0.704, Connect. = 0.780 for dens.mod. cycle 2
  <wt> = 0.300, Contrast = 0.660, Connect. = 0.781 for dens.mod. cycle 2
  <wt> = 0.300, Contrast = 0.761, Connect. = 0.799 for dens.mod. cycle 3
  <wt> = 0.300, Contrast = 0.723, Connect. = 0.801 for dens.mod. cycle 3
  <wt> = 0.300, Contrast = 0.795, Connect. = 0.805 for dens.mod. cycle 4
  <wt> = 0.300, Contrast = 0.762, Connect. = 0.807 for dens.mod. cycle 4
  Pseudo-free CC = 65.99 %
  Pseudo-free CC = 64.88 %
  <wt> = 0.300, Contrast = 0.817, Connect. = 0.810 for dens.mod. cycle 5
  <wt> = 0.300, Contrast = 0.785, Connect. = 0.810 for dens.mod. cycle 5
  <wt> = 0.300, Contrast = 0.834, Connect. = 0.813 for dens.mod. cycle 6
  <wt> = 0.300, Contrast = 0.806, Connect. = 0.813 for dens.mod. cycle 6
  <wt> = 0.300, Contrast = 0.844, Connect. = 0.816 for dens.mod. cycle 7
  <wt> = 0.300, Contrast = 0.820, Connect. = 0.815 for dens.mod. cycle 7
  <wt> = 0.300, Contrast = 0.852, Connect. = 0.818 for dens.mod. cycle 8
  <wt> = 0.300, Contrast = 0.831, Connect. = 0.817 for dens.mod. cycle 8
  <wt> = 0.300, Contrast = 0.856, Connect. = 0.820 for dens.mod. cycle 9
  <wt> = 0.300, Contrast = 0.839, Connect. = 0.819 for dens.mod. cycle 9
  Pseudo-free CC = 70.07 %
  Pseudo-free CC = 69.74 %
  <wt> = 0.300, Contrast = 0.859, Connect. = 0.821 for dens.mod. cycle 10
  <wt> = 0.300, Contrast = 0.845, Connect. = 0.820 for dens.mod. cycle 10
  <wt> = 0.300, Contrast = 0.860, Connect. = 0.822 for dens.mod. cycle 11
  <wt> = 0.300, Contrast = 0.849, Connect. = 0.821 for dens.mod. cycle 11
  <wt> = 0.300, Contrast = 0.861, Connect. = 0.822 for dens.mod. cycle 12
  <wt> = 0.300, Contrast = 0.851, Connect. = 0.822 for dens.mod. cycle 12
  <wt> = 0.300, Contrast = 0.861, Connect. = 0.823 for dens.mod. cycle 13
  <wt> = 0.300, Contrast = 0.853, Connect. = 0.823 for dens.mod. cycle 13
  <wt> = 0.300, Contrast = 0.861, Connect. = 0.823 for dens.mod. cycle 14
  <wt> = 0.300, Contrast = 0.854, Connect. = 0.823 for dens.mod. cycle 14
  Pseudo-free CC = 70.84 %
  Pseudo-free CC = 70.80 %
  <wt> = 0.300, Contrast = 0.860, Connect. = 0.824 for dens.mod. cycle 15
  <wt> = 0.300, Contrast = 0.854, Connect. = 0.824 for dens.mod. cycle 15
  <wt> = 0.300, Contrast = 0.860, Connect. = 0.824 for dens.mod. cycle 16
  <wt> = 0.300, Contrast = 0.855, Connect. = 0.824 for dens.mod. cycle 16
  <wt> = 0.300, Contrast = 0.859, Connect. = 0.824 for dens.mod. cycle 17
  <wt> = 0.300, Contrast = 0.855, Connect. = 0.824 for dens.mod. cycle 17
  <wt> = 0.300, Contrast = 0.858, Connect. = 0.824 for dens.mod. cycle 18
  <wt> = 0.300, Contrast = 0.854, Connect. = 0.824 for dens.mod. cycle 18
  <wt> = 0.300, Contrast = 0.857, Connect. = 0.824 for dens.mod. cycle 19
  <wt> = 0.300, Contrast = 0.854, Connect. = 0.824 for dens.mod. cycle 19
  Pseudo-free CC = 70.93 %
  Pseudo-free CC = 71.03 %
  <wt> = 0.300, Contrast = 0.856, Connect. = 0.824 for dens.mod. cycle 20
  <wt> = 0.300, Contrast = 0.854, Connect. = 0.824 for dens.mod. cycle 20
<wt> = 0.300, Contrast = 0.856, Connect. = 0.824 for dens.mod. cycle 21
<wt> = 0.300, Contrast = 0.855, Connect. = 0.824 for dens.mod. cycle 22
<wt> = 0.300, Contrast = 0.854, Connect. = 0.825 for dens.mod. cycle 23
<wt> = 0.300, Contrast = 0.853, Connect. = 0.824 for dens.mod. cycle 24
Pseudo-free CC = 70.85 %
<wt> = 0.300, Contrast = 0.853, Connect. = 0.824 for dens.mod. cycle 25
<wt> = 0.300, Contrast = 0.852, Connect. = 0.824 for dens.mod. cycle 26
<wt> = 0.300, Contrast = 0.851, Connect. = 0.825 for dens.mod. cycle 27
<wt> = 0.300, Contrast = 0.850, Connect. = 0.824 for dens.mod. cycle 28
<wt> = 0.300, Contrast = 0.850, Connect. = 0.824 for dens.mod. cycle 29
Pseudo-free CC = 70.69 %
<wt> = 0.300, Contrast = 0.849, Connect. = 0.824 for dens.mod. cycle 30
<wt> = 0.300, Contrast = 0.849, Connect. = 0.825 for dens.mod. cycle 31
<wt> = 0.300, Contrast = 0.848, Connect. = 0.824 for dens.mod. cycle 32
<wt> = 0.300, Contrast = 0.848, Connect. = 0.824 for dens.mod. cycle 33
<wt> = 0.300, Contrast = 0.847, Connect. = 0.824 for dens.mod. cycle 34
Pseudo-free CC = 70.51 %
<wt> = 0.300, Contrast = 0.847, Connect. = 0.824 for dens.mod. cycle 35
<wt> = 0.300, Contrast = 0.846, Connect. = 0.824 for dens.mod. cycle 36
<wt> = 0.300, Contrast = 0.846, Connect. = 0.824 for dens.mod. cycle 37
<wt> = 0.300, Contrast = 0.845, Connect. = 0.824 for dens.mod. cycle 38
<wt> = 0.300, Contrast = 0.845, Connect. = 0.824 for dens.mod. cycle 39
Pseudo-free CC = 70.35 %
<wt> = 0.300, Contrast = 0.844, Connect. = 0.824 for dens.mod. cycle 40


  Estimated mean FOM and mapCC as a function of resolution
  Estimated mean FOM and mapCC as a function of resolution
  d    inf - 4.62 - 3.64 - 3.17 - 2.88 - 2.67 - 2.51 - 2.38 - 2.27 - 2.18 - 2.11
  d    inf - 4.62 - 3.64 - 3.17 - 2.88 - 2.67 - 2.51 - 2.38 - 2.27 - 2.18 - 2.11
  <FOM>  0.712 0.774 0.761 0.710 0.694 0.682 0.622 0.598 0.582 0.534
  <FOM>  0.736 0.786 0.768 0.721 0.701 0.681 0.618 0.595 0.587 0.540
  <mapCC> 0.841 0.923 0.941 0.927 0.920 0.926 0.926 0.915 0.877 0.853
  <mapCC> 0.862 0.932 0.946 0.934 0.924 0.924 0.922 0.913 0.882 0.858
  N        4206  4227  4214  4135  4185  4207  4292  4406  4320  3702
  N        4206  4227  4214  4135  4185  4207  4292  4406  4320  3702


  Estimated mean FOM = 0.668   Pseudo-free CC = 70.35 %
  Estimated mean FOM = 0.674   Pseudo-free CC = 71.18 %


  Density (in map sigma units) at input heavy atom sites
  Density (in map sigma units) at input heavy atom sites


   Site    x        y        z    occ*Z    density
   Site    x        y        z    occ*Z    density
     1  0.2273   0.7578  0.1190 34.0000    30.83
     1  0.2276   0.7578  0.1189 34.0000    29.98
     2  0.1770   0.5343   0.2167 29.6922   29.13
     2  0.1568   0.6345   0.3049 32.2898   30.44
     3  0.1568   0.6341   0.3057 27.3088   29.14
     3  0.1767   0.5344   0.2160 32.2388   29.67
     4  0.3059  0.4523   0.1308 25.2552   23.34
     4  0.3059  0.4535   0.1297 26.0746   23.51
     5  0.0287   0.8253   0.1396 20.5870   20.24
     5  0.0280   0.8243   0.1410 22.7324   21.02
     6  0.0389   0.9744   0.0501 14.1270   19.44
     6  0.0383   0.9748   0.0492 21.5050   21.18


  Site    x      y      z  h(sig) near old  near new
  Site    x      y      z  h(sig) near old  near new
   1  0.2276 0.7578 0.1189 30.8 1/0.04 8/17.51 10/19.34 2/19.52 5/21.94
   1  0.1569 0.6345 0.3048 30.4 2/0.02 9/13.36 3/15.73 2/19.52 7/22.13
   2  0.1568 0.6345 0.3049 29.3 3/0.11 8/3.01 3/15.74 1/19.52 7/22.22
   2  0.2278 0.7578 0.1188 30.0 1/0.02 1/19.52 6/21.97 7/22.48 9/25.02
   3  0.1767  0.5344 0.2160 29.3 2/0.10 2/15.74 8/16.49 4/19.41 1/26.90
   3  0.1767  0.5345 0.2158 29.7  3/0.03 9/2.90 1/15.73 4/19.45 2/26.88
   4  0.3059 0.4535 0.1297 23.7 4/0.19 3/19.41 9/26.54 6/26.81 6/28.31
   4  0.3060 0.4536 0.1292 23.5 4/0.07 3/19.45 9/21.16 8/26.49 5/26.83
   5  0.0280 0.8243 0.1410 20.6 5/0.23 6/19.72 9/21.55 7/21.87 1/21.94
   5  0.0382 0.9748 0.0490 21.2  6/0.02 8/2.63 8/15.66 5/15.88 6/19.80
   6  0.0383 0.9748 0.0492 19.5 6/0.15 9/2.58 9/15.62 6/15.91 5/19.72
   6  0.0278 0.8240 0.1416 21.1  5/0.08 5/19.80 8/21.59 7/21.87 2/21.97
   7  0.1847 0.9579 0.1793 -5.2 5/21.79 5/21.87 2/22.22 1/22.59 9/22.61
   7  0.1854 0.9571 0.1787 -5.0 5/21.86 6/21.87 1/22.13 2/22.48 8/22.57
   8  0.1842 0.6442 0.3069 -4.9 3/3.02 2/3.01 3/16.49 1/17.51 10/22.77
   8  0.0427 0.9993 0.0530 -5.0 6/2.62 5/2.63 8/15.31 5/15.66 6/21.59
   9  0.0430 0.9990 0.0523 -4.8 6/2.59 6/2.58 9/15.17 6/15.62 5/21.55
   9  0.1787 0.5611 0.2228 -4.7 3/2.91 3/2.90 1/13.36 4/21.16 2/25.02
  10  0.3437  0.8355  0.0209  4.6  1/19.38  1/19.34 8/22.77 2/23.02 5/27.73
 
</pre>
</pre>


At this point the structure is obviously solved, and we could use buccanneer or Arp/wArp to add side chains and the rest of the model. 3-fold NCS surely helps!
At this point the structure is obviously solved, and we could use buccanneer or Arp/wArp to add side chains and the rest of the model. 3-fold NCS surely helps!


== Could we do better? ==
== Could we do better? ==
Kay
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