Environment configuration... Python => /usr/local/xtal/ccp4/ccp4-7.0/libexec/python2.7 CCTBX => /usr/local/xtal/ccp4/ccp4-7.0/lib/py2/site-packages CCP4 => /usr/local/xtal/ccp4/ccp4-7.0 CLIBD => /usr/local/xtal/ccp4/ccp4-7.0/lib/data CCP4_SCR => /tmp/tmp9XXm3a Starting directory: /home/bgb25/vps39/reprocess Working directory: /home/bgb25/vps39/reprocess Free space: 10521.59 GB Host: diamond Contact: xia2.support@gmail.com XIA2 0.5.902-gffa11588-dials-1.14 DIALS 1.14.13-g10ecfbb15-release CCP4 7.0.078 Command line: xia2 pipeline=dials freer=freer_ref.mtz space_group=P4222 xinfo=vps39.xinfo atom=zn --------------------- Spotfinding HREM --------------------- 41129 spots found on 1800 images (max 789 / bin) * * * * * *** ********* * * ************* * ******* * ************************************************************ ************************************************************ ************************************************************ ************************************************************ ************************************************************ ************************************************************ ************************************************************ ************************************************************ 1 image 1800 -------------------- Autoindexing HREM --------------------- All possible indexing solutions: tP 104.17 104.17 39.43 90.00 90.00 90.00 Indexing solution: tP 104.17 104.17 39.43 90.00 90.00 90.00 --------------------- Integrating HREM --------------------- Processed batches 1 to 1800 Standard Deviation in pixel range: 0.33 0.43 Integration status per image (60/record): oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo "o" => good "%" => ok "!" => bad rmsd "O" => overloaded "#" => many bad "." => weak "@" => abandoned Mosaic spread: 0.039 < 0.039 < 0.039 --------------------- Spotfinding PEAK --------------------- 18855 spots found on 900 images (max 372 / bin) * * * * ***** **** ******* ***** * * * ** *********************************** ****** * ************** ************************************************************ ************************************************************ ************************************************************ ************************************************************ ************************************************************ ************************************************************ ************************************************************ 1 image 900 -------------------- Autoindexing PEAK --------------------- All possible indexing solutions: tP 104.07 104.07 39.41 90.00 90.00 90.00 Indexing solution: tP 104.07 104.07 39.41 90.00 90.00 90.00 --------------------- Integrating PEAK --------------------- Processed batches 1 to 900 Standard Deviation in pixel range: 0.27 0.41 Integration status per image (60/record): oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo "o" => good "%" => ok "!" => bad rmsd "O" => overloaded "#" => many bad "." => weak "@" => abandoned Mosaic spread: 0.057 < 0.057 < 0.057 ------------------- Spotfinding PEAK_HR -------------------- 30488 spots found on 900 images (max 602 / bin) *** **** * * * * ************************** * ************************************** * ************ ****************************************** **************** ************************************************************ ************************************************************ ************************************************************ ************************************************************ ************************************************************ ************************************************************ 1 image 900 ------------------- Autoindexing PEAK_HR ------------------- All possible indexing solutions: tP 104.23 104.23 39.45 90.00 90.00 90.00 Indexing solution: tP 104.23 104.23 39.45 90.00 90.00 90.00 ------------------- Integrating PEAK_HR -------------------- Processed batches 1 to 900 Standard Deviation in pixel range: 0.29 0.37 Integration status per image (60/record): ooooooooooo.oooooooooooooooooooooooo.ooooooooooooooooooooooo ooooooooooo.o.oooooooooooooo.ooooooooooooooooooooooooooooooo oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo .ooooooo.oooooooooooooooooooooooooooooooooooooooooooo.o.oooo .oo.oooooooooo.ooo.oooooooo.ooooooo.ooo.oooooooooooooooooooo oooooo.oooooooooooo.oooooooooooooooo.ooooooooooo.ooooooooooo ooooo.oooooooooooooooooooooooooooooooooo.oo.ooooo.ooooo.oooo oooooooooo.oooooooo.ooooo..oooooooooooo.oooooooooo.oooo.oooo .oooooooooooooooooooo.oooo.oooooo.o..ooooooooooooo.oo.oo..o. oooooooooooo.ooooooo.ooooo.o.ooo.ooooooo.oo.ooooo.oooooooo.o oooo.oooooooo.ooooooo.oooooooooooooooooooo.oooooooo.oooooooo oooooo.ooooooo.ooooo.ooo.ooo.ooooooooo.ooooooooooooooooooooo oooooooooooooo.oo.ooooo.oooo.oooooooo.o.o.ooooooo.o.oooo.o.o oooooooooooooooo.oooo.ooooooo.ooo.o..ooooooo.oo..oooo.ooooo. ooooo.oooooooooooo.oo..ooooooooooooooooo..ooo.oooo.o.oooo.oo "o" => good "%" => ok "!" => bad rmsd "O" => overloaded "#" => many bad "." => weak "@" => abandoned Mosaic spread: 0.072 < 0.072 < 0.072 ------------------ Preparing 4024_h12_x1 ------------------- Likely spacegroups: P 42 2 2 Reindexing to first spacegroup setting: P 42 2 2 (h,k,l) ------------------- Scaling 4024_h12_x1 -------------------- Resolution for sweep peak/PEAK: 3.20 (merged > 1.0) Resolution for sweep peak/PEAK_HR: 3.07 (merged > 1.0) Resolution for sweep hrem/HREM: 2.98 (unmerged > 0.25) ------------------- Scaling 4024_h12_x1 -------------------- ------------------- Unit cell refinement ------------------- h12x1hrem: 104.17 104.17 39.43 90.00 90.00 90.00 h12x1peak: 104.16 104.16 39.43 90.00 90.00 90.00 Overall: 104.17 104.17 39.43 90.00 90.00 90.00 Overall twinning score: 2.90 Your data do not appear twinned ---------------- Local Scaling 4024_h12_x1 ----------------- hrem 0.0 0.00 (ok) peak -0.8 0.07 (ok) ------------------------------------------------------------ Project: vps39 Crystal: 4024_h12_x1 Sequence: Wavelength name: hrem Wavelength 0.97949 Sweeps: SWEEP HREM [WAVELENGTH hrem] TEMPLATE 4024_h12_x1_rm_1_####.cbf DIRECTORY /data/20151206_Diamond_I04/4024/4024_h12_x1/remote IMAGES (USER) 1 to 1800 MTZ file: /home/bgb25/vps39/reprocess/4024_h12_x1/hrem/HREM/integrate/dials_integrated.mtz Wavelength name: peak Wavelength 1.28096 Sweeps: SWEEP PEAK [WAVELENGTH peak] TEMPLATE 4024_h12_x1_pk_1_####.cbf DIRECTORY /data/20151206_Diamond_I04/4024/4024_h12_x1/peak IMAGES (USER) 1 to 900 MTZ file: /home/bgb25/vps39/reprocess/4024_h12_x1/peak/PEAK/integrate/dials_integrated.mtz SWEEP PEAK_HR [WAVELENGTH peak] TEMPLATE 4024_h12_x1_pkhr_2_####.cbf DIRECTORY /data/20151206_Diamond_I04/4024/4024_h12_x1/peak_hr IMAGES (USER) 1 to 900 MTZ file: /home/bgb25/vps39/reprocess/4024_h12_x1/peak/PEAK_HR/integrate/dials_integrated.mtz For vps39/4024_h12_x1/hrem Overall Low High High resolution limit 2.98 8.03 2.98 Low resolution limit 28.89 28.89 3.03 Completeness 100.0 99.3 100.0 Multiplicity 24.3 17.8 25.7 I/sigma 16.0 30.2 3.1 Rmerge(I) 0.124 0.076 1.154 Rmerge(I+/-) 0.120 0.073 1.137 Rmeas(I) 0.127 0.079 1.178 Rmeas(I+/-) 0.125 0.076 1.180 Rpim(I) 0.026 0.019 0.231 Rpim(I+/-) 0.034 0.021 0.315 CC half 0.999 0.999 0.944 Wilson B factor 104.460 Anomalous completeness 99.9 98.6 100.0 Anomalous multiplicity 13.7 11.7 14.1 Anomalous correlation 0.403 0.529 0.020 Anomalous slope 1.186 dF/F 0.057 dI/s(dI) 1.028 Total observations 116580 4961 6360 Total unique 4793 279 247 For vps39/4024_h12_x1/peak Overall Low High High resolution limit 3.07 8.33 3.07 Low resolution limit 73.65 73.67 3.12 Completeness 100.0 100.0 100.0 Multiplicity 22.2 18.1 12.0 I/sigma 16.4 31.0 2.4 Rmerge(I) 0.121 0.088 0.844 Rmerge(I+/-) 0.112 0.080 0.810 Rmeas(I) 0.124 0.091 0.881 Rmeas(I+/-) 0.117 0.084 0.880 Rpim(I) 0.027 0.023 0.252 Rpim(I+/-) 0.033 0.025 0.343 CC half 0.998 0.998 0.939 Wilson B factor 102.477 Anomalous completeness 100.0 100.0 100.0 Anomalous multiplicity 12.6 12.1 6.5 Anomalous correlation 0.699 0.738 0.011 Anomalous slope 1.386 dF/F 0.076 dI/s(dI) 1.422 Total observations 97700 4869 2367 Total unique 4399 269 197 Assuming spacegroup: P 42 2 2 Unit cell (with estimated std devs): 104.1653(5) 104.1653(5) 39.4281(2) 90.0 90.0 90.0 mtz format: Scaled reflections: /home/bgb25/vps39/reprocess/DataFiles/vps39_4024_h12_x1_free.mtz mtz_unmerged format: Scaled reflections (hrem): /home/bgb25/vps39/reprocess/DataFiles/vps39_4024_h12_x1_scaled_unmerged_hrem.mtz Scaled reflections (peak): /home/bgb25/vps39/reprocess/DataFiles/vps39_4024_h12_x1_scaled_unmerged_peak.mtz sca format: Scaled reflections (hrem): /home/bgb25/vps39/reprocess/DataFiles/vps39_4024_h12_x1_scaled_hrem.sca Scaled reflections (peak): /home/bgb25/vps39/reprocess/DataFiles/vps39_4024_h12_x1_scaled_peak.sca sca_unmerged format: Scaled reflections (hrem): /home/bgb25/vps39/reprocess/DataFiles/vps39_4024_h12_x1_scaled_unmerged_hrem.sca Scaled reflections (peak): /home/bgb25/vps39/reprocess/DataFiles/vps39_4024_h12_x1_scaled_unmerged_peak.sca Processing took 00h 16m 01s XIA2 used... aimless, ccp4, dials, pointless, xia2 Here are the appropriate citations (BIBTeX in xia2-citations.bib.) Evans, P. (2006) Acta Cryst. D62, 72-82. Evans, P. R. and Murshudov, G. N. (2013) Acta Cryst. D69, 1204-1214. Winn, M. D. et al. (2011) Acta Cryst. D67, 235-242. Winter, G. (2010) J. Appl. Cryst. 43, 186-190. Winter, G. et al. (2018) Acta Cryst. D74, 85-97. Status: normal termination