************************************************************** 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: 28.NOV 2010, 10:22:07 ----------------------------------------------- ################################################################### # Following data were read from the input file or set as default: # ################################################################### Job title: 2010sl0005a ------------------------ 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: 6.2066 7.7799 21.3938 90.0000 90.0000 90.0000 Volume: 1033.03662 Reciprocal cell parameters: 0.1611 0.1285 0.0467 90.0000 90.0000 90.0000 Volume: 0.00097 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: 32 40 108 Total: 138240 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: 13164 ------------------------- Averaging of reflections: ------------------------- Redundancy : 9.290 Rint : 5.903 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 10 27 Number of reflections treated as missing: 6 ------------ Wilson Plot: ------------ circles: /SUM(f^2) dots : linear fit y = -2.9271 + -4.628 * [sin(theta)/lambda]^2 0.04991-| . o -| o o . Scale^2 -| . . -| o o o -| o . 0.03106-| o . . o o -| o o . . o o o o o -| o o . o o -| o o . . o -| . . 0.01933-| . . . o -| . . -| . o -| o . -| . . 0.01203-| o o . . -| o . . -| o o o . . -| . . o -| o o o o o o 0.00748-| 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): 0.231 Biso: 2.314 ---------------------------------------------------------- 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 14 48 101 134 242 307 380 Total refl. in shell: 2 18 48 101 134 242 307 380 Coverage in shell: 0.0% 77.8% 100.0% 100.0% 100.0% 100.0% 100.0% 100.0% Commulative coverage: 0.0% 70.0% 91.2% 96.4% 98.0% 98.9% 99.3% 99.5% Resolution (sin(th)/l): 0.450 0.500 0.550 0.600 0.650 0.651 Resolution (d_min): 1.111 1.000 0.909 0.833 0.769 0.768 Obs. refl. in shell: 518 635 772 920 1039 8 Total refl. in shell: 518 635 772 920 1047 16 Coverage in shell: 100.0% 100.0% 100.0% 100.0% 99.2% 50.0% Commulative coverage: 99.7% 99.7% 99.8% 99.9% 99.7% 99.6% ############# # Iteration # ############# Estimated delta: 0.4315 Random seed: 102207904 Searching for a proper delta: Current delta = 0.43145 (k_ed = 1.00000) Total/flipped ratio = 1.224. Increasing delta. Current delta = 0.46165 (k_ed = 1.07000) Total/flipped ratio = 0.980. Criterion for delta fulfilled, continuing iteration. 20 R: 47.638 Charge: 147.09 Peaks: 1.07 Score: --- 30 R: 48.470 Charge: 138.51 Peaks: 1.18 Score: --- 40 R: 48.110 Charge: 141.38 Peaks: 1.22 Score: --- 50 R: 48.317 Charge: 139.91 Peaks: 1.17 Score: --- 60 R: 47.928 Charge: 137.42 Peaks: 1.20 Score: --- 70 R: 46.863 Charge: 139.63 Peaks: 1.25 Score: --- 80 R: 47.210 Charge: 136.83 Peaks: 1.22 Score: --- 90 R: 47.169 Charge: 136.19 Peaks: 1.27 Score: --- 100 R: 47.601 Charge: 135.03 Peaks: 1.31 Score: --- Calculation successfully converged after 184 cycles. Last iteration record: 184 R: 24.358 Charge: 82.43 Peaks: 2.38 Score: 12.33 5 cycles of noise suppression follow: 5 R: 18.360 Charge: 0.00 Peaks: 3.05 ##################################### # 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 0.063 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2_1(0,0,1): -x1 -x2 1/2+x3 0.089 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2_1(0,1,0): -x1 1/2+x2 -x3 0.092 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX m(1,0,0): -x1 x2 x3 70.949 XXXXXXXXXXXXXXX -1: -x1 -x2 -x3 71.037 XXXXXXXXXXXXXX n(0,0,1): 1/2+x1 1/2+x2 -x3 71.515 XXXXXXXXXXXXXX c(0,1,0): x1 -x2 1/2+x3 71.600 XXXXXXXXXXXXXX 2(1,0,0): x1 -x2 -x3 83.164 XXXXXXXX 2(0,1,0): -x1 x2 -x3 84.802 XXXXXXXX m(0,1,0): x1 -x2 x3 85.708 XXXXXXX b(0,0,1): x1 1/2+x2 -x3 86.763 XXXXXXX m(0,0,1): x1 x2 -x3 88.800 XXXXXX n(0,1,0): 1/2+x1 -x2 1/2+x3 88.968 XXXXXX b(1,0,0): -x1 1/2+x2 x3 89.141 XXXXX a(0,0,1): 1/2+x1 x2 -x3 99.912 X n(1,0,0): -x1 1/2+x2 1/2+x3 100.229 X c(1,0,0): -x1 x2 1/2+x3 101.239 X a(0,1,0): 1/2+x1 -x2 x3 106.876 X 2(0,0,1): -x1 -x2 x3 132.107 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: 0.9752 0.5262 0.7179 Agreement factors of individual generators: Number smb agreement 2 21 0.09 3 21 0.09 Overall agreement factor: 0.08 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 18.36 3.05 0.08 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): 184 95% confidence interval for beta : 50 - 7268 95% confidence interval for SR : 0.75 - 1.00 --------------------------------------------- End of the calculation: 28.NOV 2010, 10:22:10 --------------------------------------------- Superflip version: 03/16/09 15:32