************************************************************** 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.NOV 2010, 22:31:08 ----------------------------------------------- ################################################################### # Following data were read from the input file or set as default: # ################################################################### Job title: 2010sl0004a ------------------------ 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: 12.8476 3.7474 21.5262 90.0000 97.2910 90.0000 Volume: 1028.00110 Reciprocal cell parameters: 0.0785 0.2669 0.0468 90.0000 82.7090 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 0.5000 0 -1 0 0.0000 0 0 1 0.0000 0 0 -1 0.5000 0 0 -1 0.0000 4: 1 0 0 0.5000 0 -1 0 0.5000 0 0 1 0.5000 The structure is centrosymmetric. -------------------------- Settings of the algorithm: -------------------------- Number of voxels: 36 12 60 Total: 25920 Number of voxels for polishing: 72 20 108 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: 4 2 ################################## # Information about reflections: # ################################## Number of reflections in the input file: 14663 ------------------------- Averaging of reflections: ------------------------- Redundancy : 5.397 Rint : 7.537 Info: 357 reflections found that are extinct according to the symmetry. These reflections will be used in the calculation. Maximum indices in expanded reflection set: 16 4 28 Number of reflections treated as missing: 4 ------------ Wilson Plot: ------------ circles: /SUM(f^2) dots : linear fit y = -3.0172 + -3.802 * [sin(theta)/lambda]^2 0.04849-| o -| . o Scale^2 -| o . . -| . . -| o o o o 0.03218-| o . . o o o o -| o . . o o -| o . o o -| o o . . -| o o . . o o 0.02135-| . . o -| . . . o -| . . -| o . -| . . 0.01417-| o . . -| o . . -| o o o o . -| o o o o . . o -| o o . . o 0.00940-| 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): 0.221 Biso: 1.901 ---------------------------------------------------------- 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 7 28 84 107 191 267 305 Total refl. in shell: 4 7 28 84 107 191 267 305 Coverage in shell: 0.0% 100.0% 100.0% 100.0% 100.0% 100.0% 100.0% 100.0% Commulative coverage: 0.0% 63.6% 89.7% 96.7% 98.3% 99.0% 99.4% 99.6% 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 0.769 Obs. refl. in shell: 505 549 682 860 949 11 Total refl. in shell: 505 549 682 860 962 27 Coverage in shell: 100.0% 100.0% 100.0% 100.0% 98.6% 40.7% Commulative coverage: 99.7% 99.8% 99.9% 99.9% 99.6% 99.3% ############# # Iteration # ############# Estimated delta: 0.4475 Random seed: 223108960 Searching for a proper delta: Current delta = 0.44751 (k_ed = 1.00000) Total/flipped ratio = 1.215. Increasing delta. Current delta = 0.47884 (k_ed = 1.07000) Total/flipped ratio = 1.053. Increasing delta. Current delta = 0.51235 (k_ed = 1.14490) Total/flipped ratio = 0.901. Criterion for delta fulfilled, continuing iteration. 20 R: 54.850 Charge: 133.98 Peaks: 1.42 Score: --- 30 R: 52.314 Charge: 122.88 Peaks: 1.61 Score: --- 40 R: 50.073 Charge: 116.16 Peaks: 1.82 Score: --- 50 R: 45.206 Charge: 105.25 Peaks: 2.18 Score: --- 60 R: 29.575 Charge: 84.50 Peaks: 2.58 Score: --- 70 R: 26.870 Charge: 83.06 Peaks: 2.51 Score: --- 80 R: 27.411 Charge: 82.15 Peaks: 2.46 Score: --- 90 R: 27.164 Charge: 82.10 Peaks: 2.42 Score: --- 100 R: 28.003 Charge: 80.05 Peaks: 2.41 Score: --- Calculation successfully converged after 103 cycles. Last iteration record: 103 R: 28.021 Charge: 84.75 Peaks: 2.36 Score: 6.61 5 cycles of noise suppression follow: 5 R: 22.935 Charge: 0.00 Peaks: 3.30 ##################################### # Checking the density for symmetry # ##################################### Symmetry operations compatible with the lattice and centering: Symmetry operation agreement factor n(0,1,0): 1/2+x1 -x2 1/2+x3 0.693 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2_1(0,1,0): -x1 1/2+x2 -x3 5.225 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX -1: -x1 -x2 -x3 5.834 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX a(0,1,0): 1/2+x1 -x2 x3 95.729 XX m(0,1,0): x1 -x2 x3 95.750 XX c(0,1,0): x1 -x2 1/2+x3 96.465 XX 2(0,1,0): -x1 x2 -x3 100.734 X ------------------------------------------------- Space group derived from the symmetry operations: ------------------------------------------------- Symmetry operations: 1: x1 x2 x3 -1: -x1 -x2 -x3 n(0,1,0): 1/2+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: P21/n ----------------------------------- ############################################ # Search for the origin of the space group # ############################################ Position of the origin in the CF map: 0.6583 0.7508 0.8827 Agreement factors of individual generators: Number smb agreement 4 n 0.69 2 21 5.22 Overall agreement factor: 3.92 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 22.94 3.30 3.92 P21/n 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): 103 95% confidence interval for beta : 28 - 4068 95% confidence interval for SR : 0.91 - 1.00 --------------------------------------------- End of the calculation: 27.NOV 2010, 22:31:10 --------------------------------------------- Superflip version: 03/16/09 15:32