[phenixbb] strange increase of R/Rfree in the last tow steps of a macrocycle

Christian Roth christian.roth at bbz.uni-leipzig.de
Tue Jun 17 04:18:16 PDT 2014


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


More information about the phenixbb mailing list