************************************************************** 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: 23.DEC 2010, 20:51:25 ----------------------------------------------- ################################################################### # Following data were read from the input file or set as default: # ################################################################### Job title: 2010sl0009a ------------------------ 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: 3.6878 48.7964 12.4014 90.0000 98.5510 90.0000 Volume: 2206.84131 Reciprocal cell parameters: 0.2742 0.0205 0.0815 90.0000 81.4490 90.0000 Volume: 0.00045 Wilson plot will be based on this composition: C104H48N8F40 2 symmetry operations found, their list follows: 1: 1 0 0 0.0000 2: 1 0 0 0.0000 0 1 0 0.0000 0 -1 0 0.0000 0 0 1 0.0000 0 0 1 0.5000 The structure is non-centrosymmetric. The symmetry operations are to be combined with the following centering vectors: 0.0000 0.0000 0.0000 0.5000 0.5000 0.0000 -------------------------- Settings of the algorithm: -------------------------- Number of voxels: 12 144 36 Total: 62208 Number of voxels for polishing: 20 250 64 Total: 320000 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 ################################## # Information about reflections: # ################################## Number of reflections in the input file: 9824 ------------------------- Averaging of reflections: ------------------------- Redundancy : 3.923 Rint :15.284 Info: 29 reflections found that are extinct according to the symmetry. These reflections will be used in the calculation. Maximum indices in expanded reflection set: 4 64 16 Number of reflections treated as missing: 28 ------------ Wilson Plot: ------------ circles: /SUM(f^2) dots : linear fit y = -3.9169 + -2.828 * [sin(theta)/lambda]^2 0.01989-| o -| . o . . o Scale^2 -| o . o . o o -| o o . . . o o o o o -| o . . . . o o o o 0.01189-| o o o . . . . o o -| o o . . . o -| o . . . . o -| o o . . . -| . . . . 0.00711-| . . . . o -| o o o o o -| o o o . . . . -| o o -| o 0.00425-| -| -| -| -| 0.00254-| 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): 0.141 Biso: 1.414 ---------------------------------------------------------- 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 20 66 122 180 248 364 410 Total refl. in shell: 8 26 66 122 180 260 366 410 Coverage in shell: 0.0% 76.9% 100.0% 100.0% 100.0% 95.4% 99.5% 100.0% Commulative coverage: 0.0% 58.8% 86.0% 93.7% 96.5% 96.1% 97.3% 98.1% Resolution (sin(th)/l): 0.450 0.500 0.550 0.600 0.650 0.657 Resolution (d_min): 1.111 1.000 0.909 0.833 0.769 0.761 Obs. refl. in shell: 608 730 809 1032 1052 28 Total refl. in shell: 608 732 819 1068 1160 184 Coverage in shell: 100.0% 99.7% 98.8% 96.6% 90.7% 15.2% Commulative coverage: 98.6% 98.9% 98.9% 98.4% 96.8% 94.3% ############# # Iteration # ############# Estimated delta: 0.2388 Random seed: 205126144 Searching for a proper delta: Current delta = 0.23876 (k_ed = 1.00000) Total/flipped ratio = 1.226. Increasing delta. Current delta = 0.25547 (k_ed = 1.07000) Total/flipped ratio = 1.069. Increasing delta. Current delta = 0.27335 (k_ed = 1.14490) Total/flipped ratio = 0.846. Criterion for delta fulfilled, continuing iteration. 20 R: 52.403 Charge: 165.68 Peaks: 1.12 Score: --- 30 R: 51.259 Charge: 158.61 Peaks: 1.27 Score: --- 40 R: 51.375 Charge: 159.52 Peaks: 1.33 Score: --- 50 R: 50.936 Charge: 152.22 Peaks: 1.39 Score: --- 60 R: 50.746 Charge: 153.11 Peaks: 1.45 Score: --- 70 R: 51.015 Charge: 152.12 Peaks: 1.39 Score: --- 80 R: 50.039 Charge: 151.87 Peaks: 1.36 Score: --- 90 R: 50.697 Charge: 152.01 Peaks: 1.43 Score: --- 100 R: 50.094 Charge: 154.29 Peaks: 1.33 Score: --- 200 R: 49.206 Charge: 148.66 Peaks: 1.50 Score: --- 300 R: 39.378 Charge: 125.33 Peaks: 1.79 Score: --- Calculation successfully converged after 367 cycles. Last iteration record: 367 R: 38.098 Charge: 119.55 Peaks: 1.79 Score: 1.48 5 cycles of noise suppression follow: 5 R: 30.547 Charge: 0.00 Peaks: 2.24 ##################################### # Checking the density for symmetry # ##################################### Centering vectors: 0.000 0.000 0.000 0.500 0.500 0.000 Symmetry operations compatible with the lattice and centering: Symmetry operation agreement factor c(0,1,0): x1 -x2 1/2+x3 1.534 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX -1: -x1 -x2 -x3 67.099 XXXXXXXXXXXXXXXX 2(0,1,0): -x1 x2 -x3 82.193 XXXXXXXXX m(0,1,0): x1 -x2 x3 88.431 XXXXXX ------------------------------------------------- Space group derived from the symmetry operations: ------------------------------------------------- Centering vectors: 0.000 0.000 0.000 0.500 0.500 0.000 Symmetry operations: 1: x1 x2 x3 c(0,1,0): x1 -x2 1/2+x3 -------------------------------- Tentative space group symbol: Cc -------------------------------- ############################################ # Search for the origin of the space group # ############################################ Position of the origin in the CF map: 0.0000 0.5895 0.0000 Agreement factors of individual generators: Number smb agreement 2 c 1.53 Overall agreement factor: 1.53 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 30.55 2.24 1.53 Cc 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): 367 95% confidence interval for beta : 99 - 14496 95% confidence interval for SR : 0.50 - 1.00 --------------------------------------------- End of the calculation: 23.DEC 2010, 20:51:31 --------------------------------------------- Superflip version: 03/16/09 15:32