************************************************************** Superflip Version: 03/16/09 15:32 Palatinus, L. & Chapuis, G.(2007): J. Appl. Cryst. 40, 786-790 http://superspace.epfl.ch/superflip ************************************************************** ----------------------------------------------- Start of the calculation: 27.DEC 2010, 09:28:45 ----------------------------------------------- ################################################################### # Following data were read from the input file or set as default: # ################################################################### Job title: 2010sl0010a ------------------------ Information about files: ------------------------ Name of the input file: superflip.input Density will be writen in xplor format to file superflip.xplor Warning: If the outputfile exists, it will be overwritten by the new density. Logfile will contain only basic information about the calculation. Logfile will contain information about the data coverage. ----------------------------- Crystallographic information: ----------------------------- Superspace dimension: 3 Dimension of the physical space: 3 Direct cell parameters: 6.5932 7.4090 21.4824 90.0000 90.0000 90.0000 Volume: 1049.39429 Reciprocal cell parameters: 0.1517 0.1350 0.0465 90.0000 90.0000 90.0000 Volume: 0.00095 Wilson plot will be based on this composition: C52H32N4F12 4 symmetry operations found, their list follows: 1: 1 0 0 0.0000 2: -1 0 0 0.5000 3: -1 0 0 0.0000 0 1 0 0.0000 0 -1 0 0.0000 0 1 0 0.5000 0 0 1 0.0000 0 0 1 0.5000 0 0 -1 0.5000 4: 1 0 0 0.5000 0 -1 0 0.5000 0 0 -1 0.0000 The structure is non-centrosymmetric. -------------------------- Settings of the algorithm: -------------------------- Number of voxels: 20 24 60 Total: 28800 Number of voxels for polishing: 36 40 108 Total: 155520 The density modification method will be charge flipping. Delta will be determined automatically. The iteration will be stopped when the convergence is detected or after 10000 cycles. After the regular iteration 5 cycles of "density polishing" will be applied. The random number generator will be initialized automatically. The whole calculation will be repeated 1times. Random initial phases will be assigned to the structure factors. Isotropic Debye-Waller factor: 2.500 Proportion of reflections to be treated as weak: 0.200 All reflections with sin(th)/lambda < 0.400 not present in the input data set will be treated a missing. The amplitudes of the missing reflections will be left unconstrained. The resulting density will be shifted and averaged according to the symmetry operations given above. Following symmetry operations will be used to locate the origin of symmetry: 2 3 ################################## # Information about reflections: # ################################## Number of reflections in the input file: 7761 ------------------------- Averaging of reflections: ------------------------- Redundancy : 5.390 Rint : 7.110 Info: 20 reflections found that are extinct according to the symmetry. These reflections will be used in the calculation. Maximum indices in expanded reflection set: 8 9 27 Number of reflections treated as missing: 8 ------------ Wilson Plot: ------------ circles: /SUM(f^2) dots : linear fit y = -2.9825 + -3.921 * [sin(theta)/lambda]^2 0.04889-| o -| o o . Scale^2 -| . . -| o . o o -| o . . o o 0.03257-| o . . o o -| o o . . o o -| . . o -| o . . o -| o o o . . o 0.02170-| o . . o -| . . -| . . o -| . . -| o o . 0.01445-| . . . -| o . . o -| o o o . . -| o . . -| o o o o o 0.00963-| o o o . o I-------------------I-------------------I-------------------I-------------------I-------- 0.00 0.10 0.20 0.30 0.40 [sin(theta)/lambda]^2 Scale (F_obs = K * F_abs): 0.225 Biso: 1.961 ---------------------------------------------------------- Coverage statistics of the expanded reflections by shells: ---------------------------------------------------------- Resolution (sin(th)/l): 0.050 0.100 0.150 0.200 0.250 0.300 0.350 0.400 Resolution (d_min): 10.000 5.000 3.333 2.500 2.000 1.667 1.429 1.250 Obs. refl. in shell: 0 12 44 97 164 212 317 382 Total refl. in shell: 2 18 44 97 164 212 317 382 Coverage in shell: 0.0% 66.7% 100.0% 100.0% 100.0% 100.0% 100.0% 100.0% Commulative coverage: 0.0% 60.0% 87.5% 95.0% 97.5% 98.5% 99.1% 99.4% Resolution (sin(th)/l): 0.450 0.500 0.550 0.600 0.649 Resolution (d_min): 1.111 1.000 0.909 0.833 0.770 Obs. refl. in shell: 532 651 762 920 1093 Total refl. in shell: 532 651 762 920 1093 Coverage in shell: 100.0% 100.0% 100.0% 100.0% 100.0% Commulative coverage: 99.5% 99.7% 99.7% 99.8% 99.8% ############# # Iteration # ############# Estimated delta: 0.4459 Random seed: 92845640 Searching for a proper delta: Current delta = 0.44587 (k_ed = 1.00000) Total/flipped ratio = 1.231. Increasing delta. Current delta = 0.47709 (k_ed = 1.07000) Total/flipped ratio = 0.980. Criterion for delta fulfilled, continuing iteration. 20 R: 47.973 Charge: 152.81 Peaks: 1.08 Score: --- 30 R: 46.718 Charge: 149.23 Peaks: 1.19 Score: --- 40 R: 47.240 Charge: 145.21 Peaks: 1.25 Score: --- 50 R: 46.805 Charge: 143.59 Peaks: 1.30 Score: --- 60 R: 47.178 Charge: 143.81 Peaks: 1.37 Score: --- 70 R: 46.743 Charge: 141.76 Peaks: 1.37 Score: --- 80 R: 47.160 Charge: 144.43 Peaks: 1.33 Score: --- 90 R: 47.780 Charge: 141.05 Peaks: 1.45 Score: --- 100 R: 46.963 Charge: 137.88 Peaks: 1.52 Score: --- Calculation successfully converged after 169 cycles. Last iteration record: 169 R: 26.180 Charge: 89.80 Peaks: 2.36 Score: 9.97 5 cycles of noise suppression follow: 5 R: 20.647 Charge: 0.00 Peaks: 3.14 ##################################### # Checking the density for symmetry # ##################################### Symmetry operations compatible with the lattice and centering: Symmetry operation agreement factor 2_1(1,0,0): 1/2+x1 -x2 -x3 0.130 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2_1(0,0,1): -x1 -x2 1/2+x3 0.163 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2_1(0,1,0): -x1 1/2+x2 -x3 0.175 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX -1: -x1 -x2 -x3 73.385 XXXXXXXXXXXXX m(1,0,0): -x1 x2 x3 73.413 XXXXXXXXXXXXX n(0,0,1): 1/2+x1 1/2+x2 -x3 73.586 XXXXXXXXXXXXX c(0,1,0): x1 -x2 1/2+x3 73.722 XXXXXXXXXXXXX b(0,0,1): x1 1/2+x2 -x3 81.414 XXXXXXXXX n(0,1,0): 1/2+x1 -x2 1/2+x3 81.628 XXXXXXXXX 2(0,1,0): -x1 x2 -x3 85.603 XXXXXXX m(0,0,1): x1 x2 -x3 86.143 XXXXXXX a(0,0,1): 1/2+x1 x2 -x3 89.883 XXXXX n(1,0,0): -x1 1/2+x2 1/2+x3 90.159 XXXXX m(0,1,0): x1 -x2 x3 90.607 XXXXX c(1,0,0): -x1 x2 1/2+x3 91.028 XXXX 2(1,0,0): x1 -x2 -x3 91.807 XXXX b(1,0,0): -x1 1/2+x2 x3 92.897 XXXX a(0,1,0): 1/2+x1 -x2 x3 109.732 X 2(0,0,1): -x1 -x2 x3 131.906 X ------------------------------------------------- Space group derived from the symmetry operations: ------------------------------------------------- Symmetry operations: 1: x1 x2 x3 2_1(1,0,0): 1/2+x1 -x2 -x3 2_1(0,0,1): -x1 1/2-x2 1/2+x3 2_1(0,1,0): 1/2-x1 1/2+x2 1/2-x3 ------------------------------------- Tentative space group symbol: P212121 ------------------------------------- ############################################ # Search for the origin of the space group # ############################################ Position of the origin in the CF map: 0.9841 0.9578 0.6614 Agreement factors of individual generators: Number smb agreement 2 21 0.16 3 21 0.17 Overall agreement factor: 0.16 You can obtain more information about the reconstructed reflection phases by using 'expandedlog yes'. Current FOM is the best until now. Saving the density. Properties of the saved density: Run Rvalue Peaks Symm. Der.SG 1 20.65 3.14 0.16 P212121 Electron density written to file superflip.xplor Last run from 1 completed. Summary of all runs: Number of attempts : 1 Maximum cycles : 10000 Number of successes : 1 Success rate [%] : 100.0 Mean cycles per convergence(beta): 169 95% confidence interval for beta : 46 - 6675 95% confidence interval for SR : 0.78 - 1.00 --------------------------------------------- End of the calculation: 27.DEC 2010, 09:28:47 --------------------------------------------- Superflip version: 03/16/09 15:32