[phenixbb] weird B factor refinement
Pavel Afonine
pafonine at lbl.gov
Thu Mar 24 09:53:21 PDT 2011
Hi,
- is there density for it?
- can it be partially occupied (alternative conformations) ?
- can it be Se?
- if so, try resetting B-factor back to similar values of surrounding
atoms and refine occupancy just for that atom.
If nothing helps please send me the data and model files and I will have
a look.
Pavel.
> Hi all,
> I am refining a structure and have turned on TLS refinement.
> Since I have done this, I see a weird behavior in some sulphur atom's
> B factor, and their near atoms.
> I paste below an example.
> Has anybody else seen this? Looks like a bug...
> Thanks a lot in advance,
> ciao,
> s
>
> ATOM 655 N PHE A 82 66.343 -40.145 -6.536 1.00 25.85
> N
> ANISOU 655 N PHE A 82 3247 3386 3190 162 103 157
> N
> ATOM 656 CA PHE A 82 65.631 -38.890 -6.206 1.00 23.86
> C
> ANISOU 656 CA PHE A 82 2967 3126 2971 192 102 153
> C
> ATOM 657 C PHE A 82 64.134 -39.032 -6.460 1.00 27.82
> C
> ANISOU 657 C PHE A 82 3494 3640 3436 176 116 173
> C
> ATOM 658 O PHE A 82 63.709 -39.388 -7.568 1.00 46.67
> O
> ANISOU 658 O PHE A 82 5852 6065 5815 251 147 222
> O
> ATOM 659 CB PHE A 82 66.174 -37.668 -6.970 1.00 14.67
> C
> ANISOU 659 CB PHE A 82 1831 1971 1772 176 119 175
> C
> ATOM 660 CG PHE A 82 65.501 -36.397 -6.574 1.00 25.83
> C
> ANISOU 660 CG PHE A 82 3217 3375 3223 210 117 169
> C
> ATOM 661 CD1 PHE A 82 64.399 -35.932 -7.285 1.00 19.12
> C
> ANISOU 661 CD1 PHE A 82 2363 2528 2371 221 125 179
> C
> ATOM 662 CD2 PHE A 82 65.919 -35.707 -5.429 1.00 37.72
> C
> ANISOU 662 CD2 PHE A 82 4725 4876 4732 206 117 168
> C
> ATOM 663 CE1 PHE A 82 63.734 -34.784 -6.874 1.00 23.74
> C
> ANISOU 663 CE1 PHE A 82 2979 3122 2919 200 145 205
> C
> ATOM 664 CE2 PHE A 82 65.275 -34.544 -5.018 1.00 34.01
> C
> ANISOU 664 CE2 PHE A 82 4257 4438 4226 262 171 240
> C
> ATOM 665 CZ PHE A 82 64.176 -34.080 -5.744 1.00 33.79
> C
> ANISOU 665 CZ PHE A 82 4254 4389 4196 197 145 203
> C
> ATOM 666 N CYS A 83 63.337 -38.791 -5.425 1.00* 35.53*
> N
> ANISOU 666 N CYS A 83 4471 4615 4413 176 117 175
> N
> ATOM 667 CA CYS A 83 61.879 -38.960 -5.524 1.00* 55.90*
> C
> ANISOU 667 CA CYS A 83 7050 7200 6991 181 121 181
> C
> ATOM 668 C CYS A 83 61.332 -37.537 -5.259 1.00* 48.88*
> C
> ANISOU 668 C CYS A 83 6132 6340 6100 265 163 240
> C
> ATOM 669 O CYS A 83 61.949 -36.777 -4.512 1.00* 50.54*
> O
> ANISOU 669 O CYS A 83 6344 6544 6313 262 165 239
> O
> ATOM 670 CB CYS A 83 61.343 -40.122 -4.596 1.00* 2.87*
> C
> ANISOU 670 CB CYS A 83 332 481 275 174 114 172
> C
> ATOM 671 SG CYS A 83 61.739 -41.776 -5.153 1.00*212.79*
> S
> ANISOU 671 SG CYS A 83 26919 27069 26861 166 105 162
> S
> ATOM 672 N ASP A 84 60.251 -37.131 -5.925 1.00 46.73
> N
> ANISOU 672 N ASP A 84 5887 6042 5827 199 138 202
> N
> ATOM 673 CA ASP A 84 59.894 -35.684 -6.003 1.00 53.97
> C
> ANISOU 673 CA ASP A 84 6774 6990 6743 291 187 268
> C
> ATOM 674 C ASP A 84 59.468 -34.966 -4.713 1.00 54.16
> C
> ANISOU 674 C ASP A 84 6797 6968 6812 239 140 198
> C
> ATOM 675 O ASP A 84 59.898 -33.835 -4.448 1.00 54.40
> O
> ANISOU 675 O ASP A 84 6861 7005 6804 211 158 221
> O
> ATOM 676 CB ASP A 84 58.829 -35.479 -7.062 1.00 52.17
> C
> ANISOU 676 CB ASP A 84 6574 6736 6511 218 157 225
> C
> ATOM 677 CG ASP A 84 59.320 -35.845 -8.416 1.00 59.41
> C
> ANISOU 677 CG ASP A 84 7456 7647 7469 252 143 207
> C
> ATOM 678 OD1 ASP A 84 60.375 -35.284 -8.783 1.00 61.87
> O
> ANISOU 678 OD1 ASP A 84 7770 7956 7782 252 144 207
> O
> ATOM 679 OD2 ASP A 84 58.683 -36.697 -9.087 1.00 57.64
> O
> ANISOU 679 OD2 ASP A 84 7230 7428 7243 253 141 207
> O
>
>
> --
> Sebastiano Pasqualato, PhD
> Crystallography Unit
> IFOM-IEO Campus
> Cogentech - Consortium for Genomic Technologies
> via Adamello, 16
> 20139 - Milano
> Italy
>
> tel +39 02 9437 5172
> fax +39 02 9437 5990
>
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