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@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@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@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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