[phenixbb] lower Rfree in phenix.maps compared to phenix.refine and phenix.reciprocal_space_arrays
Gregers Rom Andersen
gra at mb.au.dk
Thu Jul 31 00:08:07 PDT 2014
Dear bb
I have encountered a quite significant difference between Rfree reported by phenix.maps, refine and reciprocal_space_arrays. I have used default values in the GUI, and don't find differences in reflections statistics reported in the phenix.maps log that could explain the difference. I have another example also, but with a smaller difference between phenix.maps and phenix.refine. Both are quite large structures with maximum resolution between 3.5 and 4. Any explanation?
phenix.maps
-------------------------------------------------------------------------------
Bulk solvent correction and anisotropic scaling:
|--(resolution: 3.68 - 29.45 A, n_refl.=22769 (all), 10.16 % free)------------|
| |
| r_work= 0.2550 r_free= 0.2823 coordinate error (max.-lik. estimate): 0.60 A |
| |
| x-ray target function (ml) for work reflections: 6.433959 |
|-----------------------------------------------------------------------------|
phenix.reciprocal_space_arrays
|--(resolution: 3.68 - 29.45 A, n_refl.=22769 (all), 10.16 % free)------------|
| |
| r_work= 0.2741 r_free= 0.3045 coordinate error (max.-lik. estimate): 0.69 A |
| |
| x-ray target function (ml) for work reflections: 6.492710 |
|-----------------------------------------------------------------------------|
phenix.refine, strategy=none 1 macrocycle
|--(resolution: 3.68 - 29.45 A, n_refl.=22769 (all), 10.16 % free)------------|
| |
| r_work= 0.2741 r_free= 0.3045 coordinate error (max.-lik. estimate): 0.69 A |
| |
| x-ray target function (ml) for work reflections: 6.492702 |
|-----------------------------------------------------------------------------|
gregers
Professor Gregers Rom Andersen
Department of Molecular Biology and Genetics
Aarhus University
Gustav Wiedsvej 10C DK8000 Aarhus C
phone +45 871 55507 fax +45 861 23178
email gra at mb.au.dk
-------------extract of log files--------
phenix.maps log
Parameters to compute maps::
maps {
input {
pdb_file_name = "/u/gra/myproject/juli2014/mave/ref_01.pdb"
reflection_data {
file_name = "/u/gra/myproject/juli2014/mave/reflections.mtz"
labels = "FP,SIGFP"
high_resolution = None
low_resolution = None
outliers_rejection = True
french_wilson_scale = True
french_wilson {
max_bins = 60
min_bin_size = 40
}
sigma_fobs_rejection_criterion = None
sigma_iobs_rejection_criterion = None
r_free_flags {
file_name = "/u/gra/myproject/juli2014/mave/reflections.mtz"
label = "R-free-flags43"
test_flag_value = 1
ignore_r_free_flags = False
}
}
}
=============================== Reflection data ===============================
F-obs:
/u/gra/myproject/juli2014/mave/reflections.mtz:FP,SIGFP
Miller array info: /u/gra/myproject/juli2014/mave/reflections.mtz:FP,SIGFP
Observation type: xray.amplitude
Type of data: double, size=22776
Type of sigmas: double, size=22776
Number of Miller indices: 22776
Anomalous flag: False
Unit cell: (168.063, 154.031, 78.988, 90, 90, 90)
Space group: P 21 21 2 (No. 18)
Systematic absences: 0
Centric reflections: 2864
Resolution range: 29.4462 3.67631
Completeness in resolution range: 0.992029
Completeness with d_max=infinity: 0.989401
Wavelength: 0.0000
Number of F-obs in resolution range: 22776
Number of F-obs<0 (these reflections will be rejected): 0
Number of F-obs=0 (these reflections will be used in refinement): 0
Refinement resolution range: d_max = 29.4462
d_min = 3.6763
R-free flags:
/u/gra/myproject/juli2014/mave/reflections.mtz:R-free-flags43
Miller array info: /u/gra/myproject/juli2014/mave/reflections.mtz:R-free-flags43
Observation type: None
Type of data: int, size=22776
Type of sigmas: None
Number of Miller indices: 22776
Anomalous flag: False
Unit cell: (168.063, 154.031, 78.988, 90, 90, 90)
Space group: P 21 21 2 (No. 18)
Systematic absences: 0
Centric reflections: 2864
Resolution range: 29.4462 3.67631
Completeness in resolution range: 0.992029
Completeness with d_max=infinity: 0.989401
Wavelength: 0.0000
Test (R-free flags) flag value: 1
Number of work/free reflections by resolution:
work free %free
bin 1: 29.4471 - 7.8747 [2434/2441] 2190 244 10.0%
bin 2: 7.8747 - 6.2702 [2347/2348] 2103 244 10.4%
bin 3: 6.2702 - 5.4834 [2297/2300] 2076 221 9.6%
bin 4: 5.4834 - 4.9847 [2284/2286] 2053 231 10.1%
bin 5: 4.9847 - 4.6289 [2272/2274] 2045 227 10.0%
bin 6: 4.6289 - 4.3569 [2294/2295] 2066 228 9.9%
bin 7: 4.3569 - 4.1393 [2240/2241] 1994 246 11.0%
bin 8: 4.1393 - 3.9595 [2254/2255] 2027 227 10.1%
bin 9: 3.9595 - 3.8074 [2277/2278] 2055 222 9.7%
bin 10: 3.8074 - 3.6763 [2077/2241] 1853 224 10.8%
overall 20462 2314 10.2%
-------------------------------------------------------------------------------
Input model file: /u/gra/myproject/juli2014/mave/ref_01.pdb
============================== Scattering factors =============================
----------X-ray scattering dictionary----------
Number of scattering types: 6
Type Number sf(0) Gaussians
S 48 15.91 1
P 28 14.91 1
Mg 2 11.95 2
O 2498 7.97 1
N 2146 6.97 1
C 7880 5.97 1
sf(0) = scattering factor at diffraction angle 0.
Number of scatterers: 12602
At special positions: 0
Unit cell: (168.063, 154.031, 78.988, 90, 90, 90)
Space group: P 21 21 2 (No. 18)
-------------------------------------------------------------------------------
Bulk solvent correction and anisotropic scaling:
|--(resolution: 3.68 - 29.45 A, n_refl.=22769 (all), 10.16 % free)------------|
| |
| r_work= 0.2550 r_free= 0.2823 coordinate error (max.-lik. estimate): 0.60 A |
| |
| x-ray target function (ml) for work reflections: 6.433959 |
|-----------------------------------------------------------------------------|
phenix.reciprocal_space_arrays
Default params::
hkl_file = None
pdb_file = None
f_obs_label = None
r_free_flags_label = None
remove_f_obs_outliers = True
bulk_solvent_and_scaling = True
hendrickson_lattman_coefficients_label = None
output_file_name = None
space_group = None
unit_cell = None
job_title = None
|--(resolution: 3.68 - 29.45 A, n_refl.=22769 (all), 10.16 % free)------------|
| |
| r_work= 0.2741 r_free= 0.3045 coordinate error (max.-lik. estimate): 0.69 A |
| |
| x-ray target function (ml) for work reflections: 6.492710 |
|-----------------------------------------------------------------------------|
|-----------------------------------------------------------------------------|
| Bin Resolution Compl. No. Refl. R-factors Targets |
|number range work test work test work test|
| 1: 29.4471 - 9.3567 0.99 1316 144 0.1750 0.1935 7.111 7.2567|
| 2: 9.3567 - 7.4666 1.00 1244 147 0.1844 0.2442 6.8649 7.0955|
| 3: 7.4666 - 6.5345 1.00 1243 135 0.2403 0.3183 6.6514 6.7683|
| 4: 6.5345 - 5.9424 1.00 1221 136 0.2622 0.3386 6.5345 6.547|
| 5: 5.9424 - 5.5195 1.00 1230 131 0.2482 0.3091 6.3934 6.5161|
| 6: 5.5195 - 5.1959 1.00 1199 141 0.2741 0.2699 6.3987 6.4315|
| 7: 5.1959 - 4.9370 1.00 1196 129 0.2528 0.2600 6.3987 6.4955|
| 8: 4.9370 - 4.7230 1.00 1227 136 0.2747 0.3240 6.4448 6.5001|
| 9: 4.7230 - 4.5418 1.00 1178 151 0.2867 0.3278 6.4205 6.5232|
| 10: 4.5418 - 4.3856 1.00 1224 113 0.2871 0.2980 6.4246 6.5162|
| 11: 4.3856 - 4.2489 1.00 1201 151 0.3209 0.4007 6.4221 6.5583|
| 12: 4.2489 - 4.1278 1.00 1174 137 0.3552 0.3395 6.4274 6.4033|
| 13: 4.1278 - 4.0194 1.00 1190 129 0.3917 0.3944 6.4059 6.366|
| 14: 4.0194 - 3.9216 1.00 1184 149 0.3931 0.3915 6.3718 6.38|
| 15: 3.9216 - 3.8326 1.00 1221 116 0.3952 0.3998 6.3442 6.3031|
| 16: 3.8326 - 3.7512 1.00 1168 138 0.4077 0.3949 6.334 6.3252|
| 17: 3.7512 - 3.6763 0.88 1040 130 0.4322 0.4220 6.3237 6.2334|
|-----------------------------------------------------------------------------|
-------------------------------
phenix.refine
refine {
strategy = individual_sites individual_sites_real_space rigid_body \
individual_adp group_adp tls occupancies group_anomalous
main {
number_of_macro_cycles = 1
============================= updating all scales =============================
start: r_work=0.3857 r_free=0.4073 n_reflections: 22776
start: r_work=0.3857 r_free=0.4073 (reset all scales to undefined)
bulk-solvent and scaling: r_work=0.2758 r_free=0.3049
remove outliers: r_work=0.2758 r_free=0.3049
correct solvent mask: r_work=0.2741 r_free=0.3045
final: r_work=0.2741 r_free=0.3045 n_reflections: 22769
overall anisotropic scale matrix:
V0: 0.0014,6.7700,1.3003,-6.1473,-1.1440,0.3484
V1: -0.0036,-0.0045,-0.0442,0.0324,0.0082,0.0028
======================== 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
29.446-20.724 97.09 90 10 0.2436 1579.386 1497.822 1.000 2.341 0.338
20.553-17.465 100.00 91 10 0.2757 1238.791 1140.148 1.000 1.886 0.335
17.444-14.852 99.35 137 16 0.2182 1221.185 1176.515 1.000 1.685 0.327
14.833-12.617 98.73 210 23 0.1958 1278.964 1244.386 1.000 1.494 0.307
12.608-10.717 98.98 349 39 0.1500 1428.238 1389.811 1.000 1.395 0.300
10.715-9.108 99.84 547 62 0.1416 1410.502 1384.438 1.000 1.354 0.290
9.104-7.738 100.00 883 99 0.1789 1027.723 1002.711 1.000 1.233 0.290
7.736-6.574 99.94 1427 159 0.2385 682.594 646.245 1.000 1.076 0.290
6.573-5.586 99.88 2288 254 0.2567 515.856 486.005 1.000 0.892 0.270
5.586-4.747 99.90 3710 411 0.2654 489.477 455.553 1.000 0.818 0.220
4.746-4.033 99.95 5973 671 0.3225 441.426 390.526 1.000 0.817 0.170
4.033-3.676 96.99 4751 559 0.4048 366.235 296.284 1.000 0.848 0.170
Approximation of k_total with k_overall*exp(-b_overall*s**2/4)
k_overall=1.1939 b_overall=26.4160
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