Re: [phenixbb] Trouble with occupancy refinement

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 mailto:[email protected]> 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 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" 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 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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