The date today is 12-apr-01. Your license expires on 15-jul-07. ------------------------ COPYRIGHT NOTICE --------------------------------- Los Alamos National Laboratory This program was prepared by the Regents of the University of California at Los Alamos National Laboratory (the University) under Contract No. W-7405-ENG-36 with the U.S. Department of Energy (DOE). The University has certain rights in the program pursuant to the contract and the program should not be copied or distributed outside your organization. All rights in the program are reserved by the DOE and the University. Neither the U.S. Government nor the University makes any warranty, express or implied, or assumes any liability or responsibility for the use of this software. ******************************************************* * --- SOLVE --- * * * * Automated structure solution for MAD and MIR * * * * Please type "solvehelp" for on-line help * * or see "http://solve.lanl.gov" * ******************************************************* (version 2.00 of 12-Apr-2001 / Size = 6) Tom Terwilliger, Los Alamos National Laboratory, "terwilliger@LANL.gov" Space group number is: 5 Space group name from file name is: c2 The fft containing the asymmetric unit of the map runs from: 0 to 95 in x, where the cell translation is 96 0 to 17 in y, where the cell translation is 36 0 to 24 in z, where the cell translation is 48 You may wish to include in your "solve.setup" file the following line: FFTGRID 0 95 96 0 17 36 0 24 48 The EZD map file containing the output map runs from: 0 to 95 in x, where the cell translation is 96 0 to 17 in y, where the cell translation is 36 0 to 24 in z, where the cell translation is 48 You may wish to include in your "solve.setup" file the following line: EZDGRID 0 95 0 17 0 24 The patterson containing the asymmetric unit of the map runs from: 0 to 95 in x, where the cell translation is 96 0 to 18 in y, where the cell translation is 36 0 to 24 in z, where the cell translation is 48 You may wish to include in your "solve.setup" file the following line: PATTGRID 0 95 96 0 18 36 0 24 48 Rescaling standard dataset to put it on approximate absolute scale. NRES = 200; expected = 196000.0 ; observed in lowest resolution shell = 412272.9 ... Scale factor = 0.4754133 -------------------------------------------------- *** Analysis of this scaled MAD data set *** Fbar,sigma,Delano,sigma for 1 wavelengths written to: mad_fbar.scl F+,sigma,F-,sigma for 1 wavelengths written to: mad_fpfm.scl ** Completeness of Fbar data at each wavelength: ** Completeness of dataset 1 ( F > 2.000000 * sigma) SAD data for Se Reflections observed: Possible Found % complete shell dmin 1 6.000 239 233 97.5 2 4.500 317 314 99.1 3 4.200 120 119 99.2 4 3.975 120 120 100.0 5 3.750 155 154 99.4 6 3.600 112 111 99.1 7 3.450 143 142 99.3 8 3.300 172 172 100.0 9 3.150 190 190 100.0 10 3.000 254 254 100.0 total 1822 1809 99.3 ** R-factors for F-bar data dispersive differences ** anomalous differences lambda 1 Differences by shell: shell dmin nobs Fbar delta R scale min max 1 6.000 232 311.509 19.321 0.062 1.000 0.982 1.042 2 4.500 311 298.883 17.568 0.059 1.004 0.979 1.032 3 4.200 119 287.355 17.591 0.061 1.002 0.981 1.027 4 3.975 120 252.634 16.200 0.064 0.999 0.976 1.023 5 3.750 154 247.537 15.235 0.062 0.999 0.974 1.017 6 3.600 110 217.438 14.323 0.066 1.000 0.979 1.022 7 3.450 142 185.648 14.809 0.080 0.999 0.981 1.027 8 3.300 171 185.812 12.930 0.070 1.000 0.974 1.025 9 3.150 190 181.405 12.349 0.068 1.000 0.981 1.020 10 3.000 252 170.665 10.956 0.064 1.000 0.980 1.022 Total: 1801 237.303 15.173 0.064 1.000 SAD analysis: defining pseudo-native based on Fbar for the SAD data and pseudo-derivative based on Fbar and del anom for the SAD data Script file suitable for running SOLVE written to: solve_mir.script **** SOLVE: Solutions to MIR or SIR datasets ****** Derivatives considered: 1 (NSET) Cross-vectors tested in HASSP: 20 (ICRMAX, DEFAULT=20) HASSP solutions saved per deriv: 30 (NTOPHASSP, DEFAULT=30) Fourier peaks saved per map: 30 (NTOPFOUR, DEFAULT=10) Sites per derivative: 4 (NSOLSITE, DEFAULT=20) Derivative solutions per seed: 5 (NTOPDERIV, DEFAULT=5) Seeds per derivative tested: 10 (NSEEDTEST,DEFAULT=10) Sorted seeds to use 5 (NSEEDSOLVE, DEFAULT=5) Number of final solutions saved: 5 (NTOPSOLVE, DEFAULT=5) Sites per derivative vary with derivative. Derivative Max sites 1 2 Solutions obtained will be compared to input solution (ICHECKSOLVE) Correlated phasing used (CORRELPHASE) Standard difference fouriers will be calculated for derivative 1 Datafile with 4 columns of data: Title:mad_fbar.scl Fnat,sig,(fbar,sig,delano,sig)n Data: Fbar SAD data for Se Data: Sig of Fbar SAD data for Se Data: Del Ano (F+ - F-) SAD data for Se Data: sig of Del Ano SAD data for Se Fnat,sigma taken from columns 1 2 Fder,sig,Delano,sig deriv 1 from cols: 1 2 3 4 Check solution to be compared to all solutions found: Derivative 1: Site X Y Z 1 0.140 0.360 0.280 2 0.440 0.160 0.380 ********************************************************** ANALYZE_SOLVE: analysis of top 1 solutions ************************************************************* Solution 1 *********************** Analysis of this solution ************* ****** Analysis of non-randomness of native Fourier map ****** A. Maps with distinct solvent regions havea high standard deviation of local r.m.s. electron density. For this map the SD of this local r.m.s. is 0.2146582 B. Maps with distinct solvent regions also have a high correlation of local r.m.s. electron density with density at neighboring locations. Typical values for poor maps in this structure solution are 4.5458950E-02 +/- 2.4037734E-02 For this map the correlation of r.m.s. density in neighboring boxes is 9.8282509E-02 The correlation coefficient is used here in scoring. ****** Analysis of derivative solutions with the difference Patterson ****** and with cross-validation difference Fouriers ----------------------------------------------- Derivative # 1 List of sites analyzed for compatibility with difference Patterson PEAK X Y Z OPTIMIZED RELATIVE OCCUPANCY 1 0.443 0.167 0.375 55.156 2 0.141 0.361 0.281 56.433 Evaluation of this test soln with 2 sites after optimizing occupancy of each site Cross-vectors for sites 1 and 1 (excluding origin; 1000 = 1 sigma): # U V W HEIGHT PRED HEIGHT SYMM# 1 -0.885 0.000 -0.750 5442.87 6084.45 2 Cross-vectors for sites 2 and 1 (excluding origin; 1000 = 1 sigma): # U V W HEIGHT PRED HEIGHT SYMM# 1 -0.302 0.194 -0.094 4702.00 3112.64 1 2 -0.583 0.194 -0.656 4019.86 3112.64 1 Cross-vectors for sites 2 and 2 (excluding origin; 1000 = 1 sigma): # U V W HEIGHT PRED HEIGHT SYMM# 1 -0.281 0.000 -0.562 5759.70 6369.39 2 Overall quality of this Patterson soln = 6168.29 Overall quality of the fit to patterson = 0.909112 Avg normalized peak height = 2758.54 Cross-validation fouriers calculated with all heavy atoms in all derivs except the site being evaluated and any sites equivalent to it. Site x y z occ B -- PEAK HEIGHT -- 1 0.440 0.160 0.379 0.633 15.000 6.96 2 0.140 0.358 0.282 0.810 29.070 6.99 Summary of scoring for this solution: -- over many solutions-- -- this solution -- Criteria MEAN SD VALUE Z-SCORE Pattersons: 2.40 0.774 4.09 2.18 Cross-validation Fourier: 4.25 2.76 10.3 2.21 NatFourier CCx100: 4.55 2.40 9.83 2.20 Mean figure of meritx100: 0.000E+00 5.69 38.4 6.74 Correction for Z-scores: -2.29 Overall Z-score value: 11.0 ****** Overall analysis of phasing for solution 1************ HEAVY: Refine heavy atom parameters File title: CRYSTALLOGRAPHIC PARAMETERS A = 76.00 B = 28.00 C = 42.00 alpha = 90.00 beta = 103.00 gamma = 90.00 PHASES CALCULATED EVERY 5 DEGREES RESIDUALS CALCULATED ON EXTRA ZEROTH CYCLE ONLY SIGMAS FROM data FILE WILL BE USED STATISTICS WILL BE PRINTED ON ZEROTH CYCLE, SHIFTS ON LAST PHASING WILL BE DONE TAKING INTO ACCOUNT THE CORRELATIONS AMONG DERIVATIVES THE GROUPS OF DERIVATIVES WITH CORRELATIONS WILL BE UPDATED THE BETA VALUES FOR EACH DERIV WILL BE SET TO 1.0 PHASE-AVERAGED RESIDUALS WILL BE USED FOR PHASING TYPE OF REFINEMENT SELECTED: UNPHASED ORIGIN-REMOVED PATTERSON REFINEMENT ONLY Bayesian Correlated Phasing will be used RESOLUTION LIMITS IN ANGSTROMS: 3.000 20.000 MINIMUM RATIO OF FDER TO RMS LACK-OF-CLOSURE FOR INCLUSION IN REFINEMENT OR PHASING= 0.000 MINIMUM NATIVE F: 0.000 MINIMUM FIGURE OF MERIT FOR PHASED REFINEMENT: 0.000 MINIMUM ALLOWED ISOTROPIC B: 0.000 PARAMETER SHIFTS GREATER THAN 0.0000 TIMES SIGMA WILL BE SCALED BY 0.5000 MINIMUM RATIO OF FNAT/SIGMA OR FDER/SIGMA TO INCLUDE: 1.000 NUMBER OF REFINEMENT CYCLES IS 2 DERIVATIVES REFINED DURING THESE CYCLES ARE : 0 0 TYPE OF OUTPUT SELECTED IS: +10 COLUMNS OF HENDRICKSON-LATTMAN COEFFICIENTS data COLUMNS FOR NATIVE F AND SIGMA: 1 2 data COLUMNS FOR BEST AND MOST PROB PHASES AND FIGURE OF MERIT: 0 0 0 OVERALL SCALE FACTOR FOR ALL data = 1.000 SCALE FACTOR FOR NATIVE SIGMAS = 1.000 DERIVATIVE INFORMATION FOR 1 COMPOUNDS COMPOUND 1 SAD data for Se COLUMNS FOR F, SIGMA, AND ANOM DIFF and sig (=F+ - F-) 1 2 3 4 THIS DERIVATIVE WILL BE USED IN PHASING ANOMALOUS DIFFERENCES WILL BE USED IN PHASING FOR THIS DERIVATIVE OVERALL SCALING FOR THIS DERIVATIVE WILL BE REFINED ONLY ANO DIFFERENCES WILL BE USED IN REFINEMENT AND PHASING FOR THIS DERIVATIVE. AFTER OVERALL SCALING OBSERVED STRUCTURE FACTORS AND SIGMAS WILL BE DIVIDED BY : 1.000*EXP( 0.000*(SIN theta/LAMBDA)**2 ) THEN SIGMAS WILL BE MULTIPLIED BY 1.000 CARRYING OUT STANDARD REFINEMENT Total of 2 cycles will be done Derivs refined will be 0 0 SUMMARY OF RESULTS ON FINAL CYCLE: NUMBER OF REFLECTIONS READ = 1810 NUMBER OF F .GT. FMIN = 1809 NUMBER OF F IN RES. LIMITS = 1809 NUMBER OF F .GT. MIN = 1548 NUMBER OF F USED TO REFINE = 0 FIGURE OF MERIT < 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 # OF REFLECTIONS 462 170 172 162 176 150 154 173 145 45 FIGURE OF MERIT WITH RESOLUTION DMIN: TOTAL 9.91 6.56 5.22 4.46 3.96 3.60 3.32 3.09 N: 1809 102 150 200 218 246 276 298 319 MEAN FIG MERIT: 0.38 0.30 0.37 0.35 0.36 0.39 0.41 0.41 0.40 COMPOUND 1 SAD data for Se DMIN: TOTAL 9.91 6.56 5.22 4.46 3.96 3.60 3.32 3.09 ANOM DIFFS: 1551. 70. 115. 169. 189. 210. 243. 265. 290. RMS OBS DIFF: 19.9 26.7 23.8 23.2 23.0 20.4 18.5 16.7 14.8 RMS CALC DIFF: 14.4 19.9 17.5 16.4 15.5 14.3 13.9 11.8 11.6 RMS RESIDUAL: 14.0 19.1 16.3 17.2 17.2 14.2 12.1 11.6 9.8 RATIO ISO/ANO: 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 ESTIMATES OF LACK-OF-CLOSURE RESIDUALS LESS AVERAGE VALUE OF SIGMAS IN data (AS INPUT TO NEXT CYCLE) CENTRIC LOC: 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 ANOMALOUS LOC: 0.0 3.7 1.5 2.8 0.0 3.2 3.6 0.0 RMS FPH : 443.8 316.7 343.9 338.5 287.8 233.5 221.0 196.5 RMS FH : 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 RMS SIGMA: 15.7 11.2 12.1 12.0 10.2 8.2 7.8 7.0 PARAMETER SHIFTS FOR DERIV 1 : SAD data for Se SCALE FACTOR OVERALL B CURRENT VALUES: 1.0000 0.0000 SITE ATOM OCCUP X Y Z B CURRENT VALUES: 1 ANO1 0.6332 0.4402 0.1600 0.3795 15.0000 CURRENT VALUES: 2 ANO1 0.8103 0.1399 0.3582 0.2822 29.0703 ************************************************************* ************************************************************* *** Summary of solutions and their relationships to each other and to check solution *** ---------------------------------------------------------- solution # 1 with overall quality = 11.03216 Derivative 1 with 2 sites. Overall scale = 1.000000 and overall b of 0.0000000E+00 0.4401501 0.1600000 0.3794678 0.6331899 15.00000 0.1398734 0.3581975 0.2822208 0.8102973 29.07034 Best match of solution 1 -> solution 2: -------- solution 1 -------- -------------solution 2 ------ site x y z site x y z DIST (A) Derivative 1 1 0.440 0.160 0.379 2 0.440 0.160 0.380 0.03 2 0.140 0.358 0.282 1 0.140 0.360 0.280 0.11 Comparison of this solution with check solution: Number of sites in this solution matching check= 2 ... and number not matching = 0 by derivative, this is... Deriv nsame ndifferent 1 2 0 All sites in this solution are contained in check soln