[phenixbb] strange increase of R/Rfree in the last tow steps of a macrocycle
Pavel Afonine
pafonine at lbl.gov
Tue Jun 17 05:25:12 PDT 2014
Hi Christian,
could you please send me the data and model and any ligand cif files
(off list)? I need to have a closer look..
Thanks,
Pavel
On 6/17/14, 4:18 AM, Christian Roth wrote:
> 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
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