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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 2.09 of 02-Apr-2005 / Size = 6) Tom Terwilliger, Los Alamos National Laboratory, "terwilliger@LANL.gov" Dataset title: SOLVE 06-Apr-05 Space group number is: 5 Space group name from file name is: c2 Rescaling standard dataset to put it on approximate absolute scale. NRES = 200; expected = 196000.0 ; observed in lowest resolution shell = 489643.2 ... Scale factor = 0.4002915 -------------------------------------------------- *** 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 Pt Reflections observed: Possible Found % complete shell dmin 1 6.000 239 235 98.3 2 4.500 317 316 99.7 3 4.200 120 119 99.2 4 3.975 120 120 100.0 5 3.750 155 155 100.0 6 3.600 112 112 100.0 7 3.450 143 142 99.3 8 3.300 172 171 99.4 9 3.150 190 190 100.0 10 3.000 254 254 100.0 total 1822 1814 99.6 ** R-factors for F-bar data dispersive differences ** Anomalous differences lambda 1 (f" = 5.000000 ) Differences by shell: shell dmin nobs Fbar R scale SIGNAL NOISE S/N 1 6.000 235 307.724 0.079 0.998 27.96 13.15 2.13 2 4.500 314 301.800 0.073 1.005 25.56 11.90 2.15 3 4.200 119 289.654 0.074 1.001 24.07 11.72 2.05 4 3.975 120 251.377 0.080 0.998 23.64 10.10 2.34 5 3.750 155 249.422 0.079 0.998 23.61 10.06 2.35 6 3.600 111 225.244 0.088 0.999 23.11 9.07 2.55 7 3.450 142 192.784 0.101 0.999 23.12 7.76 2.98 8 3.300 171 190.314 0.089 1.000 19.87 7.94 2.50 9 3.150 189 186.536 0.084 1.000 18.17 7.34 2.48 10 3.000 253 177.901 0.083 1.001 17.32 7.09 2.44 Total: 1809 240.774 0.081 1.000 22.94 10.00 2.37 Recommended resolution cut-off = 3.00 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 Pt Data: Sig of Fbar SAD data for Pt Data: Del Ano (F+ - F-) SAD data for Pt Data: sig of Del Ano SAD data for Pt 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 0.2269217 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 3.6363978E-02 +/- 2.8206760E-02 For this map the correlation of r.m.s. density in neighboring boxes is 0.1060753 The correlation coefficient is used here in scoring. Skew of the map is: 0.1197042 ****** 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 0.141 0.361 0.281 76.859 2 0.438 0.167 0.385 69.500 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 -0.281 0.000 -0.562 10586.4 11814.6 2 Cross-vectors for sites 2 and 1 (excluding origin; 1000 = 1 sigma): # U V W HEIGHT PRED HEIGHT SYMM# 1 0.297 -0.194 0.104 8196.26 5341.68 1 2 -0.578 -0.194 -0.667 7865.75 5341.68 1 Cross-vectors for sites 2 and 2 (excluding origin; 1000 = 1 sigma): # U V W HEIGHT PRED HEIGHT SYMM# 1 -0.875 0.000 -0.771 8177.69 9660.44 2 Overall quality of this Patterson soln = 10019.1 Overall quality of the fit to patterson = 1.90927 Avg normalized peak height = 4480.66 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 0.140 0.360 0.280 1.230 25.260 8.96 2 0.440 0.162 0.381 1.040 16.937 8.92 Summary of scoring for this solution: -- over many solutions-- -- this solution -- Criteria MEAN SD VALUE Z-SCORE Pattersons: 3.61 1.74 7.47 2.21 Cross-validation Fourier: 4.91 5.00 14.9 2.00 NatFourier CCx100: 3.64 2.82 10.6 2.47 Mean figure of meritx100: 0.000E+00 5.82 49.1 8.44 Correction for Z-scores: -3.33 Overall Z-score value: 11.8 ****** Overall analysis of phasing for solution 1************ HEAVY: Refine heavy atom parameters File title: SOLVE 06-Apr-05 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 1 INPUT data FILE WITH 4 COLUMNS IS: mad_fbar.scl COLUMN 0 : mad_fbar.scl Fnat,sig,(fbar,sig,delano,sig)n COLUMN 1 : Fbar SAD data for Pt COLUMN 2 : Sig of Fbar SAD data for Pt COLUMN 3 : Del Ano (F+ - F-) SAD data for Pt COLUMN 4 : sig of Del Ano SAD data for Pt 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 Pt 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 Sim weighting on heavy-atoms used assuming FO/F" = 6.478219 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 = 1814 NUMBER OF F .GT. FMIN = 1814 NUMBER OF F IN RES. LIMITS = 1814 NUMBER OF F .GT. MIN = 1798 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 221 152 138 160 155 143 188 191 278 187 FIGURE OF MERIT WITH RESOLUTION DMIN: TOTAL 9.91 6.56 5.22 4.46 3.96 3.60 3.32 3.10 N: 1813 104 150 202 218 247 277 296 319 MEAN FIG MERIT: 0.52 0.46 0.51 0.51 0.50 0.53 0.53 0.55 0.54 COMPOUND 1 SAD data for Pt DMIN: TOTAL 9.91 6.56 5.22 4.46 3.96 3.60 3.32 3.10 ANOM DIFFS: 1555. 72. 115. 171. 189. 211. 244. 263. 290. RMS OBS DIFF: 26.2 36.4 31.9 30.1 28.5 27.3 25.3 21.1 19.8 RMS CALC DIFF: 23.1 33.0 28.5 26.1 24.6 23.6 22.3 18.6 18.1 RMS RESIDUAL: 11.1 14.0 12.5 14.0 13.3 11.6 10.1 8.8 8.0 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 5.3 7.1 5.8 5.8 5.5 3.8 3.5 RMS FPH : 431.6 319.1 343.3 338.2 284.9 240.7 223.1 202.9 RMS FH : 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 RMS SIGMA: 10.8 8.0 8.6 8.5 7.1 6.0 5.6 5.1 PARAMETER SHIFTS FOR DERIV 1 : SAD data for Pt SCALE FACTOR OVERALL B CURRENT VALUES: 1.0000 0.0000 SITE ATOM OCCUP X Y Z B CURRENT VALUES: 1 Se 1.2302 0.1398 0.3600 0.2805 25.2597 CURRENT VALUES: 2 Se 1.0403 0.4400 0.1619 0.3808 16.9368 ************************************************************* ************************************************************* *** Summary of solutions and their relationships to each other and to check solution *** ---------------------------------------------------------- solution # 1 with overall quality = 11.79113 Derivative 1 with 2 sites. Overall scale = 1.000000 and overall b of 0.0000000E+00 0.1397693 0.3600000 0.2804537 1.230202 25.25968 0.4400216 0.1619363 0.3808324 1.040293 16.93677 Best match of solution 1 -> solution 2: -------- solution 1 -------- -------------solution 2 ------ site x y z site x y z DIST (A) Derivative 1 1 0.140 0.360 0.280 1 0.140 0.360 0.280 0.03 2 0.440 0.162 0.381 2 0.440 0.160 0.380 0.06 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