[sharp-discuss] very low B-factors
Gregory D. Bowman
gdbowman@uclink.berkeley.edu
Wed, 16 Jul 2003 17:42:35 -0700
Hello -
I am working with a 2-wavelength MAD dataset to about 3.2A resolution. From a
related crystal, I know the 17 Se sites pretty confidently, and these sites
seem to refine OK in SOLVE for the dataset I am having trouble with (so I am
pretty sure the sites are all real). With SHARP, the B-factor of one site
refines to 1.0. If I do not refine occupancies, the B-factor still dips pretty
low in the first cycle (B=2.5) but manages to recover somewhat by the final
cycle (B=56.7), though it is still relatively low for this resolution. Is it
the case that I simply do not have enough information to refine these
parameters at this resolution? Some of the logfile is below.
Thanks for any advice.
Greg
==============================
NOTE - site 6 is the offender. I apologise if the formatting does not carry
though in the email.
-------------------------------------------------------
refining both B and occupancies:
--------------------------------
First cycle of refining B/occupancies: Everything seems OK
001__G-SITE-001 HAT_OCC 1.1969 0.5500 1.7469
HAT_B 149.2960 -1.6175 147.6785
001__G-SITE-002 HAT_OCC 1.5708 0.7393 2.3100
HAT_B 155.8439 -1.5838 154.2601
001__G-SITE-003 HAT_OCC 1.5014 0.6834 2.1847
HAT_B 186.3591 -1.2411 185.1180
001__G-SITE-004 HAT_OCC 1.4379 0.6495 2.0874
HAT_B 199.2562 -1.3835 197.8728
001__G-SITE-005 HAT_OCC 1.8110 0.8303 2.6413
HAT_B 213.9898 -0.5395 213.4502
001__G-SITE-006 HAT_OCC 1.6478 0.7564 2.4041
HAT_B 155.2214 -1.8708 153.3506
001__G-SITE-007 HAT_OCC 1.1981 0.5572 1.7553
HAT_B 174.7769 -1.0286 173.7482
001__G-SITE-008 HAT_OCC 1.3638 0.6294 1.9932
HAT_B 185.8664 -0.9468 184.9196
001__G-SITE-009 HAT_OCC 1.6190 0.7405 2.3595
HAT_B 193.9789 -1.0006 192.9783
001__G-SITE-010 HAT_OCC 1.4603 0.6834 2.1437
HAT_B 200.6610 -0.5527 200.1083
001__G-SITE-011 HAT_OCC 1.4920 0.6880 2.1800
HAT_B 168.2568 -1.9167 166.3402
001__G-SITE-012 HAT_OCC 1.4472 0.7089 2.1562
HAT_B 225.7435 -0.9393 224.8042
001__G-SITE-013 HAT_OCC 0.9212 0.4453 1.3665
HAT_B 163.8727 -0.9562 162.9165
001__G-SITE-014 HAT_OCC 1.1805 0.4887 1.6692
HAT_B 264.7068 -0.5238 264.1831
001__G-SITE-015 HAT_OCC 1.3148 0.5880 1.9028
HAT_B 250.8974 -1.0426 249.8548
001__G-SITE-016 HAT_OCC 1.4841 0.6934 2.1775
HAT_B 300.0000 0.0000 300.0000 ->]
001__G-SITE-017 HAT_OCC 0.6966 0.3615 1.0581
HAT_B 300.0000 0.0000 300.0000 ->]
--------------------------------
The very next small cycle: B-factor of SITE 6 drops by about 75
001__G-SITE-001 HAT_OCC 1.7469 0.0017 1.7486
HAT_B 147.6785 -42.3724 105.3061
001__G-SITE-002 HAT_OCC 2.3100 -0.0154 2.2946
HAT_B 154.2601 -31.3099 122.9502
001__G-SITE-003 HAT_OCC 2.1847 -0.0207 2.1640
HAT_B 185.1180 8.1799 193.2979
001__G-SITE-004 HAT_OCC 2.0874 -0.0284 2.0590
HAT_B 197.8728 19.6576 217.5304
001__G-SITE-005 HAT_OCC 2.6413 0.0608 2.7021
HAT_B 213.4502 14.4088 227.8590
001__G-SITE-006 HAT_OCC 2.4041 0.0002 2.4044
HAT_B 153.3506 -75.3947 77.9559
001__G-SITE-007 HAT_OCC 1.7553 -0.0193 1.7360
HAT_B 173.7482 6.3321 180.0803
001__G-SITE-008 HAT_OCC 1.9932 0.0283 2.0215
HAT_B 184.9196 18.8103 203.7298
001__G-SITE-009 HAT_OCC 2.3595 0.0342 2.3937
HAT_B 192.9783 15.1212 208.0994
001__G-SITE-010 HAT_OCC 2.1437 -0.0026 2.1411
HAT_B 200.1083 11.6774 211.7856
001__G-SITE-011 HAT_OCC 2.1800 -0.0634 2.1166
HAT_B 166.3402 -56.0831 110.2571
001__G-SITE-012 HAT_OCC 2.1562 0.0179 2.1741
HAT_B 224.8042 38.3077 263.1119
001__G-SITE-013 HAT_OCC 1.3665 -0.0235 1.3430
HAT_B 162.9165 22.0442 184.9607
001__G-SITE-014 HAT_OCC 1.6692 0.0306 1.6998
HAT_B 264.1831 9.4390 273.6221
001__G-SITE-015 HAT_OCC 1.9028 0.0364 1.9392
HAT_B 249.8548 -4.5829 245.2718
001__G-SITE-016 HAT_OCC 2.1775 -0.0052 2.1722
HAT_B 300.0000 0.0000 300.0000 <-]
001__G-SITE-017 HAT_OCC 1.0581 0.0441 1.1022
HAT_B 300.0000 0.0000 300.0000 <-]
-------------------------------------
A few cycles later: B-factor of SITE 6 is now 1.0, and stays that way
001__G-SITE-001 HAT_OCC 0.9540 0.0608 1.0148
HAT_B 100.8967 2.4084 103.3051
001__G-SITE-002 HAT_OCC 1.3670 0.0974 1.4644
HAT_B 124.2807 -6.2762 118.0045
001__G-SITE-003 HAT_OCC 1.4122 0.0847 1.4969
HAT_B 165.5046 -13.7893 151.7153
001__G-SITE-004 HAT_OCC 1.3042 0.1374 1.4417
HAT_B 159.0778 14.0159 173.0936
001__G-SITE-005 HAT_OCC 1.8778 0.2253 2.1031
HAT_B 227.7046 -4.6517 223.0529
001__G-SITE-006 HAT_OCC 1.0219 -0.2701 0.7518
HAT_B 41.3661 -40.3661 1.0000 [<-
001__G-SITE-007 HAT_OCC 1.0922 0.0566 1.1488
HAT_B 150.3008 -15.5740 134.7268
001__G-SITE-008 HAT_OCC 1.4094 0.1122 1.5216
HAT_B 201.8194 -18.7466 183.0728
001__G-SITE-009 HAT_OCC 1.6166 0.2004 1.8171
HAT_B 201.2297 -4.5830 196.6467
001__G-SITE-010 HAT_OCC 1.4988 0.1621 1.6608
HAT_B 215.9288 -10.5880 205.3408
001__G-SITE-011 HAT_OCC 1.1856 0.0182 1.2038
HAT_B 103.9965 5.4042 109.4008
001__G-SITE-012 HAT_OCC 0.8806 0.0912 0.9717
HAT_B 55.0457 88.9120 143.9577
001__G-SITE-013 HAT_OCC 0.9247 0.1006 1.0253
HAT_B 155.5759 6.6344 162.2103
001__G-SITE-014 HAT_OCC 1.1636 0.2149 1.3785
HAT_B 287.3449 11.9467 299.2916
001__G-SITE-015 HAT_OCC 1.2764 0.0898 1.3662
HAT_B 238.9843 -36.9708 202.0135
001__G-SITE-016 HAT_OCC 1.3258 0.1084 1.4342
HAT_B 294.1810 -26.6462 267.5348
001__G-SITE-017 HAT_OCC 0.7161 0.1652 0.8813
HAT_B 300.0000 0.0000 300.0000 <-]
001_001_001_001 NANO_BGLO 0.0000 0.0000 0.0000 [<-
=================================
not refining occupancies(occup=1.0)
--------------------------------------------------------
first cycle of B-factor refinement: B-factor of SITE 6 drops by 152
001__G-SITE-001 HAT_B 149.2960 -79.1425 70.1535
001__G-SITE-002 HAT_B 155.8439 -46.2592 109.5847
001__G-SITE-003 HAT_B 186.3591 -12.7966 173.5625
001__G-SITE-004 HAT_B 199.2562 -34.9708 164.2854
001__G-SITE-005 HAT_B 213.9898 -22.3762 191.6136
001__G-SITE-006 HAT_B 155.2214 -152.6520 2.5694
001__G-SITE-007 HAT_B 174.7769 -11.0692 163.7076
001__G-SITE-008 HAT_B 185.8664 -52.2808 133.5855
001__G-SITE-009 HAT_B 193.9789 -32.2719 161.7070
001__G-SITE-010 HAT_B 200.6610 -16.0723 184.5886
001__G-SITE-011 HAT_B 168.2568 -60.1715 108.0853
001__G-SITE-012 HAT_B 225.7435 -138.1051 87.6384
001__G-SITE-013 HAT_B 163.8727 -15.9228 147.9499
001__G-SITE-014 HAT_B 264.7068 1.3815 266.0884
001__G-SITE-015 HAT_B 250.8974 -25.9098 224.9876
001__G-SITE-016 HAT_B 300.0000 -6.1918 293.8082
001__G-SITE-017 HAT_B 300.0000 0.0000 300.0000 <-]
------------
fourth cycle ("convergence")
001__G-SITE-001 HAT_B 92.8436 1.0171 93.8607 9.9228
001__G-SITE-002 HAT_B 119.0792 -0.3648 118.7144 8.7481
001__G-SITE-003 HAT_B 161.8942 5.2916 167.1858 11.5122
001__G-SITE-004 HAT_B 150.6342 3.9114 154.5456 11.5175
001__G-SITE-005 HAT_B 162.5293 4.9221 167.4514 10.9640
001__G-SITE-006 HAT_B 28.2706 12.8946 41.1652 2.8821
001__G-SITE-007 HAT_B 151.2232 4.0154 155.2387 13.1730
001__G-SITE-008 HAT_B 154.2849 3.8372 158.1221 11.7087
001__G-SITE-009 HAT_B 150.7050 2.1013 152.8063 11.0317
001__G-SITE-010 HAT_B 162.1460 6.4316 168.5776 12.3290
001__G-SITE-011 HAT_B 128.7785 3.6294 132.4079 8.5903
001__G-SITE-012 HAT_B 140.2975 21.5858 161.8834 10.1248
001__G-SITE-013 HAT_B 126.4959 -1.4780 125.0180 15.4597
001__G-SITE-014 HAT_B 223.7989 13.2720 237.0708 23.3402
001__G-SITE-015 HAT_B 154.6024 20.9541 175.5565 13.3123
001__G-SITE-016 HAT_B 236.7864 20.8837 257.6702 20.7670
001__G-SITE-017 HAT_B 300.0000 0.0000 300.0000 0.0000 ->]
-------------
last cycle (2 more small cycles)
001__G-SITE-001 HAT_B 87.9400 -5.2957 82.6443 12.1455
001__G-SITE-002 HAT_B 116.5185 -2.0488 114.4697 9.1728
001__G-SITE-003 HAT_B 167.9062 -0.4840 167.4222 11.8020
001__G-SITE-004 HAT_B 154.3282 -1.0146 153.3136 12.0092
001__G-SITE-005 HAT_B 168.5729 -0.4999 168.0730 11.3471
001__G-SITE-006 HAT_B 50.8219 5.8795 56.7014 5.8259
001__G-SITE-007 HAT_B 156.5339 -0.1544 156.3795 13.5625
001__G-SITE-008 HAT_B 158.7488 -0.4433 158.3056 12.1579
001__G-SITE-009 HAT_B 151.7882 -1.0714 150.7168 11.1549
001__G-SITE-010 HAT_B 169.1792 -0.2711 168.9081 12.8765
001__G-SITE-011 HAT_B 131.4322 -1.5125 129.9198 9.1421
001__G-SITE-012 HAT_B 167.3042 -0.7311 166.5730 13.2964
001__G-SITE-013 HAT_B 124.8798 -0.7616 124.1182 15.5111
001__G-SITE-014 HAT_B 238.3301 -0.2120 238.1182 25.2273
001__G-SITE-015 HAT_B 182.6898 1.4207 184.1104 16.7740
001__G-SITE-016 HAT_B 262.7511 -0.2747 262.4764 24.3344
001__G-SITE-017 HAT_B 300.0000 0.0000 300.0000 0.0000 ->]
============