Dear Phenix-Team,
I did a refinement of 5 macrocycles and it worked really well for 4
cycles, but in the last cycle the R/Rfee increased by nearly 1 percent.
Specifically in the last ADP refinement. I don't really understand why.
Do you have any comments what might be the problem. it seems that the as
optimal chosen weight is not the optimal weight at all.
I have copied the relevant part of the logfile in.
Thanks in advance for your help.
Best Regards
Christian
----------Individual ADP refinement----------
R-FACTORS <Bi-Bj> <B> WEIGHT TARGETS
work free delta data restr
22.88 25.57 2.69 7.305 69.519 0.356 1.056
25.57 27.18 1.61 5.329 75.682 0.005 1.128
24.30 26.40 2.10 6.197 74.591 0.021 1.087
23.56 26.22 2.66 10.610 72.524 0.082 1.065
23.95 27.03 3.08 14.233 73.918 0.165 1.082
23.67 26.53 2.86 15.745 73.489 0.247 1.073
23.55 26.04 2.49 15.268 73.145 0.329 1.067
23.46 26.14 2.68 17.052 73.654 0.412 1.065
23.25 26.16 2.91 17.712 73.655 0.494 1.061
23.17 26.26 3.09 18.359 73.638 0.576 1.061
22.80 26.15 3.35 15.697 72.615 0.659 1.051
22.73 26.19 3.46 15.989 72.549 0.741 1.050
22.63 26.20 3.57 15.613 72.287 0.823 1.048
max suggested <Bi-Bj> for this run: 10.00
max allowed Rfree-Rwork gap: 6.0
range of equivalent Rfree: 1.0
Best ADP weight: 0.021
Accepted refinement result:
24.30 26.40 2.10 6.197 74.591 0.021 1.087
|-ADP statistics (Wilson B =
38.175)------------------------------------------|
| Atom | Number of | Isotropic or equivalent| Anisotropy
lmin/max |
| type |iso aniso | min max mean | min max mean
|
| - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - -
- |
| all : 22327 10961 22.54 481.16 74.59 0.25 0.84 0.33
|
| all(noH): 11454 10961 22.73 481.16 70.40 0.25 0.84 0.33
|
| Sol. : 410 0 24.44 104.66 49.01 None None None
|
| Mac. : 11044 10961 22.73 481.16 71.19 0.25 0.84 0.33
|
| Hyd. : 10873 0 22.54 389.64 79.01 None None None
|
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
|
| Distribution of isotropic (or equivalent) ADP for non-H atoms:
|
| Bin# value range #atoms | Bin# value range #atoms
|
| 0: 22.735 - 68.577: 7910 | 5: 251.946 - 297.788: 42
|
| 1: 68.577 - 114.419: 1983 | 6: 297.788 - 343.631: 25
|
| 2: 114.419 - 160.262: 941 | 7: 343.631 - 389.473: 19
|
| 3: 160.262 - 206.104: 407 | 8: 389.473 - 435.315: 5
|
| 4: 206.104 - 251.946: 113 | 9: 435.315 - 481.157: 9
|
| =>continue=>
|
| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
|
| Distribution of anisotropy:
|
| Bin# value range #atoms | Bin# value range #atoms
|
| 0: 0.250 - 0.309: 6325 | 5: 0.546 - 0.605: 227
|
| 1: 0.309 - 0.368: 1851 | 6: 0.605 - 0.664: 110
|
| 2: 0.368 - 0.428: 1094 | 7: 0.664 - 0.723: 49
|
| 3: 0.428 - 0.487: 801 | 8: 0.723 - 0.783: 15
|
| 4: 0.487 - 0.546: 474 | 9: 0.783 - 0.842: 15
|
| =>continue=>
|
|-----------------------------------------------------------------------------|
=========================== Idealize ADP of riding H
==========================
r_work=0.2430 r_free=0.2640
r_work=0.2440 r_free=0.2645
----------X-ray data----------
|--(resolution: 2.20 - 48.79 A, n_refl.=183093 (all), 5.00 %
free)-----------|
|
|
| r_work= 0.2440 r_free= 0.2645 coordinate error (max.-lik. estimate):
0.29 A |
|
|
| x-ray target function (ml) for work reflections: 1.088996
|
|-----------------------------------------------------------------------------|
|-----------------------------------------------------------------------------|
| Bin Resolution Compl. No. Refl. R-factors Targets
|
|number range work test work test work
test|
| 1: 48.7982 - 6.8296 0.99 5785 298 0.2106 0.2093 2.1338
2.1779|
| 2: 6.8296 - 5.4232 1.00 5818 342 0.2291 0.2632 1.8091
1.8784|
| 3: 5.4232 - 4.7383 1.00 5733 351 0.1950 0.2248 1.8106
1.9715|
| 4: 4.7383 - 4.3053 1.00 5810 297 0.1865 0.2091 1.8418
1.9422|
| 5: 4.3053 - 3.9969 1.00 5770 351 0.1947 0.2125 1.7965
1.8123|
| 6: 3.9969 - 3.7614 1.00 5854 317 0.2059 0.2273 1.7389
1.8541|
| 7: 3.7614 - 3.5730 1.00 5807 315 0.2165 0.2248 1.6958
1.7279|
| 8: 3.5730 - 3.4175 1.00 5743 309 0.2116 0.2532 1.6098
1.7535|
| 9: 3.4175 - 3.2860 1.00 5844 333 0.2255 0.2873 1.5248
1.6889|
| 10: 3.2860 - 3.1726 0.99 5763 329 0.2437 0.2678 1.4283
1.4634|
| 11: 3.1726 - 3.0735 1.00 5828 271 0.2467 0.2763 1.2886
1.403|
| 12: 3.0735 - 2.9856 1.00 5803 326 0.2456 0.2590 1.179
1.2299|
| 13: 2.9856 - 2.9070 1.00 5782 340 0.2506 0.2807 1.1218
1.155|
| 14: 2.9070 - 2.8361 1.00 5762 305 0.2575 0.3100 1.0497
1.0718|
| 15: 2.8361 - 2.7716 1.00 5892 309 0.2555 0.2665 0.96762
1.1343|
| 16: 2.7716 - 2.7127 1.00 5681 293 0.2698 0.3171 0.92297
1.0768|
| 17: 2.7127 - 2.6584 0.99 5948 246 0.2877 0.2608 0.86751
0.93978|
| 18: 2.6584 - 2.6082 1.00 5814 297 0.2929 0.2990 0.79337
0.80596|
| 19: 2.6082 - 2.5617 0.99 5806 266 0.3032 0.3671 0.75287
0.77999|
| 20: 2.5617 - 2.5182 1.00 5886 261 0.3065 0.2973 0.73691
0.83083|
| 21: 2.5182 - 2.4776 1.00 5777 298 0.3082 0.3174 0.68817
0.79164|
| 22: 2.4776 - 2.4395 0.99 5758 274 0.3293 0.3626 0.64915
0.72304|
| 23: 2.4395 - 2.4036 1.00 5864 337 0.3385 0.3388 0.62574
0.73292|
| 24: 2.4036 - 2.3698 1.00 5791 322 0.3418 0.3387 0.59163
0.66116|
| 25: 2.3698 - 2.3377 0.99 5667 329 0.3491 0.3861 0.55553
0.58025|
| 26: 2.3377 - 2.3074 0.99 5876 285 0.3572 0.3901 0.55473
0.60051|
| 27: 2.3074 - 2.2785 1.00 5813 305 0.3605 0.3906 0.51979
0.59044|
| 28: 2.2785 - 2.2511 0.99 5738 303 0.3831 0.3878 0.48079
0.53204|
| 29: 2.2511 - 2.2249 0.98 5716 289 0.4042 0.4574 0.49415
0.54579|
| 30: 2.2249 - 2.1999 0.98 5810 256 0.4013 0.4243 0.43974
0.41396|
|-----------------------------------------------------------------------------|
|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase
error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51,
880-887)|
|
|
| Bin Resolution No. Refl. FOM Phase Scale Alpha
Beta |
| # range work test error factor
|
| 1: 48.7982 - 6.8296 5785 298 0.83 22.51 0.97 0.01
10.98|
| 2: 6.8296 - 5.4232 5818 342 0.80 26.62 0.97 0.01
6.91|
| 3: 5.4232 - 4.7383 5733 351 0.84 22.92 1.00 0.01
6.67|
| 4: 4.7383 - 4.3053 5810 297 0.86 20.63 1.00 0.01
6.47|
| 5: 4.3053 - 3.9969 5770 351 0.85 21.50 1.00 0.01
5.76|
| 6: 3.9969 - 3.7614 5854 317 0.84 22.93 1.01 0.01
5.36|
| 7: 3.7614 - 3.5730 5807 315 0.83 24.02 1.02 0.01
4.81|
| 8: 3.5730 - 3.4175 5743 309 0.81 26.14 1.02 0.01
4.72|
| 9: 3.4175 - 3.2860 5844 333 0.77 29.41 0.98 0.01
4.39|
| 10: 3.2860 - 3.1726 5763 329 0.75 31.32 1.01 0.01
3.58|
| 11: 3.1726 - 3.0735 5828 271 0.77 29.32 1.06 0.01
2.56|
| 12: 3.0735 - 2.9856 5803 326 0.79 28.13 1.04 0.01
1.97|
| 13: 2.9856 - 2.9070 5782 340 0.79 28.31 1.02 0.01
1.76|
| 14: 2.9070 - 2.8361 5762 305 0.76 30.59 1.00 0.01
1.65|
| 15: 2.8361 - 2.7716 5892 309 0.75 31.96 0.99 0.01
1.55|
| 16: 2.7716 - 2.7127 5681 293 0.76 31.00 0.98 0.01
1.34|
| 17: 2.7127 - 2.6584 5948 246 0.75 32.10 1.01 0.01
1.16|
| 18: 2.6584 - 2.6082 5814 297 0.76 31.04 1.12 0.01
0.99|
| 19: 2.6082 - 2.5617 5806 266 0.74 33.23 1.09 0.01
1.00|
| 20: 2.5617 - 2.5182 5886 261 0.74 32.81 1.08 0.01
0.94|
| 21: 2.5182 - 2.4776 5777 298 0.73 33.99 1.06 0.01
0.92|
| 22: 2.4776 - 2.4395 5758 274 0.68 38.36 1.05 0.01
0.95|
| 23: 2.4395 - 2.4036 5864 337 0.68 37.76 1.05 0.01
0.87|
| 24: 2.4036 - 2.3698 5791 322 0.68 37.81 1.04 0.01
0.81|
| 25: 2.3698 - 2.3377 5667 329 0.66 40.12 1.02 0.01
0.82|
| 26: 2.3377 - 2.3074 5876 285 0.66 40.04 1.02 0.01
0.80|
| 27: 2.3074 - 2.2785 5813 305 0.64 41.52 1.00 0.01
0.80|
| 28: 2.2785 - 2.2511 5738 303 0.61 43.75 0.96 0.01
0.75|
| 29: 2.2511 - 2.2249 5716 289 0.61 43.65 1.00 0.01
0.72|
| 30: 2.2249 - 2.1999 5810 256 0.62 43.45 0.97 0.01
0.68|
|alpha: min = 0.01 max = 0.01 mean =
0.01|
|beta: min = 0.67 max = 12.97 mean =
2.76|
|figures of merit: min = 0.00 max = 1.00 mean =
0.74|
|phase err.(work): min = 0.00 max = 90.00 mean =
31.89|
|phase err.(test): min = 0.00 max = 89.95 mean =
31.57|
|-----------------------------------------------------------------------------|
==================================== Final
====================================
============================= updating all scales
=============================
start: r_work=0.2440 r_free=0.2645 n_reflections: 183093
start: r_work=0.4676 r_free=0.5197 (reset all scales to undefined)
cycle 0:
bulk-solvent and scaling: r_work=0.2443 r_free=0.2670
HD scattering refinement: r_work=0.2436 r_free=0.2671 k_h=-0.50
b_h=68.00
cycle 1:
bulk-solvent and scaling: r_work=0.2431 r_free=0.2659
HD scattering refinement: r_work=0.2429 r_free=0.2661 k_h=-0.80
b_h=76.00
remove outliers: r_work=0.2429 r_free=0.2661
correct solvent mask: r_work=0.2403 r_free=0.2646
final: r_work=0.2403 r_free=0.2646 n_reflections: 183093
overall anisotropic scale matrix:
V0: 0.7884,-1.3407,1.0850,-0.6410,0.0941,-0.9208
V1: -0.0081,-0.0224,0.0112,0.0027,0.0051,0.0136
======================== Statistics in resolution bins
========================
Total model structure factor:
F_model = k_total * (F_calc + k_mask * F_mask)
k_total = k_isotropic * k_anisotropic
Resolution Compl Nwork Nfree R_work <Fobs> <Fmodel> kiso
kani kmask
48.786-25.095 95.24 97 3 0.4187 1086.912 945.454 1.000
0.978 0.333
25.084-20.829 96.12 93 6 0.3183 823.323 739.609 1.000
1.069 0.332
20.816-17.332 95.77 128 8 0.2779 830.776 766.444 1.000
0.984 0.330
17.254-14.349 96.37 278 14 0.2092 778.625 740.522 1.000
0.771 0.303
14.321-11.898 98.22 469 29 0.1781 880.823 854.378 1.000
0.825 0.300
11.885-9.873 99.07 806 50 0.1587 839.382 814.201 1.000
0.810 0.300
9.866-8.193 99.54 1447 65 0.1797 706.818 683.600 1.000
0.854 0.300
8.191-6.800 99.78 2564 127 0.2032 565.003 544.081 1.000
0.859 0.275
6.798-5.642 99.96 4380 260 0.2212 465.483 447.550 1.000
0.842 0.270
5.641-4.682 99.85 7661 461 0.1911 532.250 514.206 1.000
0.869 0.225
4.682-3.885 99.91 13619 747 0.1911 546.495 530.277 1.000
0.970 0.220
3.885-3.224 99.84 23640 1298 0.2156 401.920 389.232 1.000
1.053 0.125
3.224-2.675 99.61 41527 2193 0.2543 219.824 208.597 1.000
1.027 0.020
2.675-2.200 99.31 77230 3893 0.3355 120.901 104.169 1.000
1.008 0.010
Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
k_overall=0.9148 b_overall=-2.3712
================= overall refinement statistics: step by step
=================
****************** REFINEMENT STATISTICS STEP BY STEP ******************
leading digit, like 1_, means number of macro-cycle
0 : statistics at the very beginning when nothing is done yet
1_bss: bulk solvent correction and/or (anisotropic) scaling
1_xyz: refinement of coordinates
1_adp: refinement of ADPs (Atomic Displacement Parameters)
------------------------------------------------------------------------
stage r-work r-free bonds angles b_min b_max b_ave n_water shift
0 : 0.4542 0.5034 0.014 1.36 22.3 139.6 58.4 410 0.000
1_bss: 0.2297 0.2604 0.014 1.36 21.8 139.1 57.9 410 0.000
1_settarget: 0.2297 0.2604 0.014 1.36 21.8 139.1 57.9 410 0.000
1_addcbetar: 0.2297 0.2604 0.014 1.36 21.8 139.1 57.9 410 0.000
1_weight: 0.2297 0.2604 0.014 1.36 21.8 139.1 57.9 410 0.000
1_nqh: 0.2297 0.2605 0.014 1.36 21.8 139.1 57.9 410 0.000
1_xyzrec: 0.2249 0.2590 0.006 0.97 21.8 139.1 57.9 410 0.052
1_regHxyz: 0.2250 0.2591 0.006 0.97 21.8 139.1 57.9 410 0.057
1_adp: 0.2316 0.2642 0.006 0.97 21.9 185.5 60.4 410 0.057
1_regHadp: 0.2334 0.2657 0.006 0.97 21.9 185.5 60.4 410 0.057
2_bss: 0.2326 0.2642 0.006 0.97 21.1 184.8 59.7 410 0.057
2_settarget: 0.2326 0.2642 0.006 0.97 21.1 184.8 59.7 410 0.057
2_weight: 0.2326 0.2642 0.006 0.97 21.1 184.8 59.7 410 0.057
2_nqh: 0.2326 0.2642 0.006 0.97 21.1 184.8 59.7 410 0.058
2_xyzrec: 0.2316 0.2632 0.005 0.85 21.1 184.8 59.7 410 0.061
2_regHxyz: 0.2316 0.2632 0.005 0.85 21.1 184.8 59.7 410 0.064
2_adp: 0.2308 0.2605 0.005 0.85 19.8 213.7 61.5 410 0.064
2_regHadp: 0.2310 0.2604 0.005 0.85 19.8 213.7 61.5 410 0.064
3_bss: 0.2307 0.2610 0.005 0.85 18.9 212.8 60.6 410 0.064
3_settarget: 0.2307 0.2610 0.005 0.85 18.9 212.8 60.6 410 0.064
3_weight: 0.2307 0.2610 0.005 0.85 18.9 212.8 60.6 410 0.064
3_nqh: 0.2307 0.2610 0.005 0.85 18.9 212.8 60.6 410 0.064
3_xyzrec: 0.2337 0.2598 0.004 0.83 18.9 212.8 60.6 410 0.057
3_regHxyz: 0.2337 0.2597 0.004 0.83 18.9 212.8 60.6 410 0.060
3_adp: 0.2354 0.2563 0.004 0.83 26.0 194.2 62.6 410 0.060
3_regHadp: 0.2357 0.2564 0.004 0.83 26.0 194.2 62.6 410 0.060
4_bss: 0.2341 0.2571 0.004 0.83 20.0 188.2 56.6 410 0.060
4_settarget: 0.2341 0.2571 0.004 0.83 20.0 188.2 56.6 410 0.060
4_weight: 0.2341 0.2571 0.004 0.83 20.0 188.2 56.6 410 0.060
4_nqh: 0.2341 0.2571 0.004 0.83 20.0 188.2 56.6 410 0.060
4_xyzrec: 0.2328 0.2564 0.004 0.83 20.0 188.2 56.6 410 0.056
4_regHxyz: 0.2328 0.2564 0.004 0.83 20.0 188.2 56.6 410 0.060
4_adp: 0.2344 0.2569 0.004 0.83 19.3 325.3 63.8 410 0.060
4_regHadp: 0.2353 0.2576 0.004 0.83 19.3 325.3 63.8 410 0.060
5_bss: 0.2321 0.2580 0.004 0.83 19.3 324.6 63.1 410 0.060
5_settarget: 0.2321 0.2580 0.004 0.83 19.3 324.6 63.1 410 0.060
5_weight: 0.2321 0.2580 0.004 0.83 19.3 324.6 63.1 410 0.060
5_nqh: 0.2321 0.2580 0.004 0.83 19.3 324.6 63.1 410 0.060
5_xyzrec: 0.2325 0.2588 0.004 0.82 19.3 324.6 63.1 410 0.056
5_regHxyz: 0.2325 0.2588 0.004 0.82 19.3 324.6 63.1 410 0.060
5_adp: 0.2430 0.2640 0.004 0.82 22.7 481.2 70.4 410 0.060
5_regHadp: 0.2440 0.2645 0.004 0.82 22.7 481.2 70.4 410 0.060
end: 0.2403 0.2646 0.004 0.82 22.7 481.2 70.4 410 0.060
------------------------------------------------------------------------
CPU time actual refinement: 10207.44
============================== Exporting results
==============================
Writing refined structure to PDB file:
/y/people/christian/projects/BtGH84/John/phenix/Refine_18/BtGH84activator_refine_18.pdb
n_use = 22327
n_use_u_both = 10961
n_use_u_iso = 11366
n_use_u_aniso = 0
n_grad_site = 0
n_grad_u_iso = 0
n_grad_u_aniso = 0
n_grad_occupancy = 0
n_grad_fp = 0
n_grad_fdp = 0
total number of scatterers = 22327
=============================== Detailed timings
==============================
Micro-tasks:
mask = 0.00
f_calc = 0.00
alpha_beta = 26.67
target = 5.80
gradients_wrt_atomic_parameters = 0.00
fmodel = 0.00
r_factors = 273.36
phase_errors = 132.42
foms = 1.54
TOTAL for micro-tasks = 439.79
NUMBER OF MASK CALCS= 0
Time per interpreted Python bytecode instruction: 1.763 micro seconds
Total CPU time: 2.87 hours
from_scatterers_fft: 988 calls, 348.82 s
gradients_fft: 534 calls, 461.04 s
=========================== phenix.refine: finished
===========================
# Date 2014-06-16 Time 21:27:40 BST +0100 (1402950460.37 s)
wall clock time: 12291.21 s
Start R-work = 0.2297, R-free = 0.2604
Final R-work = 0.2403, R-free = 0.2646
