[phenixbb] Trouble with occupancy refinement
Pavel Afonine
pafonine at lbl.gov
Mon Feb 8 17:22:44 PST 2016
Hi,
I agree: having different occupancies for covalently linked atoms
doesn't make much sense! If ligand is partially occupied then simply
refine its overall occupancy.
Pavel
On 2/7/16 14:44, Christian Roth wrote:
> Dear Chris,
>
> personally I wouldn't go for different occupancies in one ligand and
> set everything to 1 or everything to a values of your choice
> (constraint groups necessary). I would also check the electron density
> and the RSRZ for your ligands. The B-factors look quite high.
> Concerning the outliers, that is due to slight variations in the
> boundaries. Your outliers are probably exactly on a boundary. I
> wouldn't worry too much about that. They are fine.
>
> Cheers
>
> Christian
>
>
> On Sat, Feb 6, 2016 at 12:19 PM, Chris Fage <cdfage at gmail.com
> <mailto:cdfage at gmail.com>> wrote:
>
> Hello,
>
> The non-unity occupancies were scattered among different glucose
> (and BICINE) molecules, as shown below. But, again, I think the
> occupancy refinement doesn't contribute much to the final model/maps.
>
> Another concern of mind is that phenix.refine reports no
> Ramachandran outliers in the results, but the plot in Coot lists
> 5. I'm tempted to trust Coot here and attempt to fix these
> boundary cases.
>
> Best,
> Chris
>
> HETATM10716 N1 BCN S 1 33.836 34.201 59.534 0.18
> 23.53 N
>
> HETATM10717 C1 BCN S 1 34.230 32.958 58.836
> 0.70179.13 C
>
> HETATM10718 C2 BCN S 1 34.891 33.313 57.492
> 1.00115.73 C
>
> HETATM10719 O21 BCN S 1 34.957 34.518 57.119
> 1.00109.54 O
>
> HETATM10720 O22 BCN S 1 35.367 32.401 56.762
> 1.00108.31 O
>
> HETATM10721 C3 BCN S 1 34.436 34.251 60.889
> 1.00133.37 C
>
> HETATM10722 C4 BCN S 1 35.959 33.990 60.820
> 1.00145.21 C
>
> HETATM10723 O4 BCN S 1 36.512 34.130 62.106
> 1.00128.90 O
>
> HETATM10724 C5 BCN S 1 32.359 34.284 59.630
> 1.00138.45 C
>
> HETATM10725 C6 BCN S 1 31.834 33.285 60.690 1.00149.79
> C
>
> HETATM10726 O6 BCN S 1 31.344 32.131 60.054
> 1.00182.66 O
>
> TER
>
> HETATM10727 C1 GLC T 1 29.246 35.417 65.683
> 1.00146.58 C
>
> HETATM10728 O1 GLC T 1 28.834 34.126 66.073
> 0.96127.55 O
>
> HETATM10729 O5 GLC T 1 28.195 36.040 64.979
> 1.00124.69 O
>
> HETATM10730 C5 GLC T 1 28.505 37.368 64.624
> 1.00122.20 C
>
> HETATM10731 C6 GLC T 1 27.259 38.050 64.075
> 1.00119.08 C
>
> HETATM10732 O6 GLC T 1 26.187 37.862 64.970
> 1.00119.13 O
>
> HETATM10733 C4 GLC T 1 29.637 37.367 63.604
> 1.00136.04 C
>
> HETATM10734 O4 GLC T 1 29.990 38.695 63.289
> 1.00149.55 O
>
> HETATM10735 C3 GLC T 1 30.857 36.629 64.144
> 1.00123.84 C
>
> HETATM10736 O3 GLC T 1 31.753 36.382 63.084
> 1.00155.37 O
>
> HETATM10737 C2 GLC T 1 30.484 35.302 64.800
> 1.00125.03 C
>
> HETATM10738 O2 GLC T 1 31.567 34.865 65.591
> 0.63132.05 O
>
> TER
>
> HETATM10739 C1 GLC U 1 66.828 61.786 109.714
> 1.00143.00 C
>
> HETATM10740 O1 GLC U 1 67.797 62.779 109.467
> 0.00156.33 O
>
> HETATM10741 O5 GLC U 1 67.461 60.579 110.071
> 1.00138.44 O
>
> HETATM10742 C5 GLC U 1 66.549 59.587 110.494
> 1.00130.87 C
>
> HETATM10743 C6 GLC U 1 67.332 58.348 110.912
> 1.00126.41 C
>
> HETATM10744 O6 GLC U 1 66.446 57.387 111.438
> 1.00130.55 O
>
> HETATM10745 C4 GLC U 1 65.554 59.239 109.389
> 1.00143.93 C
>
> HETATM10746 O4 GLC U 1 64.505 58.479 109.947 1.00
> 96.88 O
>
> HETATM10747 C3 GLC U 1 64.961 60.468 108.707
> 1.00123.83 C
>
> HETATM10748 O3 GLC U 1 64.402 60.081 107.473
> 0.00105.55 O
>
> HETATM10749 C2 GLC U 1 66.006 61.547 108.457
> 1.00183.06 C
>
> HETATM10750 O2 GLC U 1 65.369 62.743 108.070
> 1.00139.75 O
>
> TER
>
> HETATM10751 C1 GLC V 1 54.972 17.830 19.939
> 1.00169.39 C
>
> HETATM10752 O1 GLC V 1 53.783 17.971 20.683
> 1.00144.51 O
>
> HETATM10753 O5 GLC V 1 54.838 16.740 19.052
> 1.00159.54 O
>
> HETATM10754 C5 GLC V 1 55.968 16.571 18.224
> 1.00189.07 C
>
> HETATM10755 C6 GLC V 1 55.684 15.517 17.160
> 0.00157.50 C
>
> HETATM10756 O6 GLC V 1 56.642 15.622 16.130
> 0.00150.00 O
>
> HETATM10757 C4 GLC V 1 57.171 16.190 19.078
> 1.00197.13 C
>
> HETATM10758 O4 GLC V 1 58.312 16.053 18.263
> 0.00169.52 O
>
> HETATM10759 C3 GLC V 1 57.420 17.249 20.145
> 1.00158.70 C
>
> HETATM10760 O3 GLC V 1 58.385 16.779 21.059 1.00146.18
> O
>
> HETATM10761 C2 GLC V 1 56.137 17.593 20.894
> 1.00148.03 C
>
> HETATM10762 O2 GLC V 1 56.348 18.756 21.663
> 0.00152.95 O
>
> TER
>
> HETATM10763 C1 GLC W 1 31.538 68.920 102.287
> 1.00113.76 C
>
> HETATM10764 O1 GLC W 1 32.846 68.776 101.784
> 1.00103.09 O
>
> HETATM10765 O5 GLC W 1 30.704 67.928 101.734
> 1.00117.86 O
>
> HETATM10766 C5 GLC W 1 29.403 67.910 102.284
> 1.00115.04 C
>
> HETATM10767 C6 GLC W 1 28.609 66.817 101.581
> 1.00106.54 C
>
> HETATM10768 O6 GLC W 1 28.601 67.074 100.194
> 0.00111.10 O
>
> HETATM10769 C4 GLC W 1 28.697 69.256 102.122
> 1.00117.67 C
>
> HETATM10770 O4 GLC W 1 27.558 69.277 102.955
> 1.00115.60 O
>
> HETATM10771 C3 GLC W 1 29.585 70.446 102.474
> 1.00115.77 C
>
> HETATM10772 O3 GLC W 1 29.006 71.627 101.968
> 1.00111.82 O
>
> HETATM10773 C2 GLC W 1 30.984 70.282 101.897
> 1.00114.72 C
>
> HETATM10774 O2 GLC W 1 31.827 71.303 102.379
> 0.00116.48 O
>
> TER
>
> HETATM10775 C1 GLC X 1 54.211 45.223 25.697
> 1.00206.04 C
>
> HETATM10776 O1 GLC X 1 55.322 45.961 25.241
> 1.00187.48 O
>
> HETATM10777 O5 GLC X 1 54.574 44.469 26.835
> 1.00228.70 O
>
> HETATM10778 C5 GLC X 1 53.489 43.765 27.404
> 1.00223.60 C
>
> HETATM10779 C6 GLC X 1 53.941 43.080 28.688
> 1.00159.71 C
>
> HETATM10780 O6 GLC X 1 54.911 42.103 28.384
> 1.00166.38 O
>
> HETATM10781 C4 GLC X 1 52.939 42.753 26.403
> 1.00163.35 C
>
> HETATM10782 O4 GLC X 1 51.806 42.113 26.943
> 0.00168.67 O
>
> HETATM10783 C3 GLC X 1 52.564 43.445 25.098
> 0.00164.83 C
>
> HETATM10784 O3 GLC X 1 52.207 42.489 24.126
> 0.00154.76 O
>
> HETATM10785 C2 GLC X 1 53.724 44.292 24.593
> 1.00198.64 C
>
> HETATM10786 O2 GLC X 1 53.308 45.050 23.479
> 1.00201.68 O
>
> TER
>
> HETATM10787 C1 GLC Y 1 36.970 50.317 37.435
> 1.00100.18 C
>
> HETATM10788 O1 GLC Y 1 37.809 50.485 36.323
> 1.00106.33 O
>
> HETATM10789 O5 GLC Y 1 35.664 50.350 36.918 1.00
> 98.74 O
>
> HETATM10790 C5 GLC Y 1 34.675 50.321 37.911 1.00
> 96.58 C
>
> HETATM10791 C6 GLC Y 1 33.320 50.170 37.238 1.00
> 94.30 C
>
> HETATM10792 O6 GLC Y 1 32.352 49.935 38.233 1.00
> 97.38 O
>
> HETATM10793 C4 GLC Y 1 34.760 51.605 38.726 1.00
> 94.56 C
>
> HETATM10794 O4 GLC Y 1 33.716 51.637 39.676 0.78
> 97.91 O
>
> HETATM10795 C3 GLC Y 1 36.127 51.715 39.398 1.00 96.51
> C
>
> HETATM10796 O3 GLC Y 1 36.299 53.002 39.950 1.00
> 97.63 O
>
> HETATM10797 C2 GLC Y 1 37.230 51.499 38.366 1.00
> 98.97 C
>
> HETATM10798 O2 GLC Y 1 38.505 51.392 38.983
> 1.00101.52 O
>
> TER
>
> HETATM10799 C1 GLC Z 1 42.915 71.571 76.690
> 1.00101.13 C
>
> HETATM10800 O1 GLC Z 1 42.711 71.632 75.297
> 0.00103.04 O
>
> HETATM10801 O5 GLC Z 1 43.618 72.718 77.112
> 1.00100.13 O
>
> HETATM10802 C5 GLC Z 1 43.763 72.783 78.514
> 1.00103.11 C
>
> HETATM10803 C6 GLC Z 1 44.396 74.119 78.887
> 1.00100.33 C
>
> HETATM10804 O6 GLC Z 1 43.852 74.583 80.101
> 1.00102.36 O
>
> HETATM10805 C4 GLC Z 1 44.596 71.607 79.018
> 1.00101.96 C
>
> HETATM10806 O4 GLC Z 1 44.627 71.613 80.428 0.00
> 99.19 O
>
> HETATM10807 C3 GLC Z 1 44.030 70.278 78.527
> 1.00100.06 C
>
> HETATM10808 O3 GLC Z 1 44.956 69.245 78.783 1.00
> 95.83 O
>
> HETATM10809 C2 GLC Z 1 43.723 70.326 77.035 1.00
> 94.68 C
>
> HETATM10810 O2 GLC Z 1 42.998 69.176 76.663 1.00
> 91.83 O
>
>
> On Fri, Feb 5, 2016 at 7:34 PM, Christian Roth
> <christianroth034 at gmail.com> wrote:
>
> Hi Chris, what would concern me is that one glucose have atoms
> with different occupancies or all of them. That is chemically
> unlikely. You should define sensible constraint groups, I think.
>
> Cheers Christian
>
> On 5 Feb 2016 18:09, "Chris Fage" <cdfage at gmail.com> wrote:
>
> Hi Pavel,
>
> The B-factors of these atoms are quite high (most are
> 100+), so maybe the occupancy is compensating as you said.
> After refinement, the maps don't look much different.
> Perhaps it's not worth bothering with occupancy
> refinement, then?
>
> I think you got my question. I was asking if it is unusual
> that only 5/93 occupancies were refined to values other
> than 0 or 1.
>
> Best,
> Chris
>
> On Fri, Feb 5, 2016 at 6:38 PM, Pavel Afonine
> <pafonine at lbl.gov> wrote:
>
> Hi Chris,
>
> I've built several glucose molecules from my
> cryosolution into regions of weaker electron
> density. Attempting to refine the occupancies of
> the corresponding atoms, I set the value of each
> to 0.25 in the pdb file. However, after running
> phenix.refine, most of the atoms still have
> occupancies of 1.00:
>
>
> perhaps they are fully occupied but highly mobile
> which explains weak density? Or B-factor refines to
> larger value so that occupancy tries to compensate?
> How maps look like after refinement?
>
> 14 atoms with occ = 0.00
> 5 atoms with 0.00 < occ < 1.00
> 74 atoms with occ = 1.00
>
> Is this unusual?
>
>
> Do you mean is it unusual to have 5 atoms in your
> structure with occupancies between 0 and 1? Hm.. I
> don't know, may be not! I think I'm not understanding
> what's the real question here..
>
> Pavel
>
>
>
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