Re: [phenixbb] Only one solution in AutoMR with very negative LLG

*Xtrige log file of P21 * The full list of Patterson peaks is: x y z height p-value(height) ( 0.500, 0.500, 0.000 ) : 56.002 (2.915e-05) ( 0.483, 0.500, 0.034 ) : 6.152 (6.778e-01) If the observed pseudo translationals are crystallographic the following spacegroups and unit cells are possible: space group operator unit cell of reference setting C 1 2 1 (a-1/4,b-1/4,c) x+1/2, y+1/2, z (186.38, 103.16, 295.88, 90.00, 98.79, 90.00) * Xtrige log file of P2* The full list of Patterson peaks is: The Xtrige log is as follows, x y z height p-value(height) ( 0.500, 0.500, 0.000 ) : 56.000 (2.916e-05) ( 0.483, 0.500, 0.034 ) : 6.151 (6.781e-01) If the observed pseudo translationals are crystallographic the following spacegroups and unit cells are possible: space group operator unit cell of reference setting C 1 2 1 x+1/2, y+1/2, z (186.38, 103.16, 295.88, 90.00, 98.79, 90.00) *Results from rotation functions for P2 (Search two monomers in ASU)* ****************************** ******************************************************* *** Phaser Module: MOLECULAR REPLACEMENT FAST ROTATION FUNCTION 2.2.4 *** ************************************************************************************* --------------------- ANISOTROPY CORRECTION --------------------- No refinement of parameters ------------------------------- DATA FOR FAST ROTATION FUNCTION ------------------------------- Outliers with a probability less than 1e-06 will be rejected There were 2 (0.0000%) reflections rejected H K L reso F probability 5 5 62 4.48 42.404 4.049e-07 18 2 -26 8.12 112.092 7.520e-09 Space-Group Name (Number): P 1 2 1 (3) Resolution of All Data (Number): 3.82 49.18 (87989) Resolution of Selected Data (Number): 3.82 49.18 (87985) -------------------------- ENSEMBLE FOR DECOMPOSITION -------------------------- This pdb file contains 1 models The (input) RmsD of this model with respect to the real structure is 0.8 Unit Cell: 394.48 295.80 293.03 90.00 90.00 90.00 Electron Density Calculation 0% 100% |=======| DONE ------------------- WILSON DISTRIBUTION ------------------- Parameters set for Wilson log-likelihood calculation E = 0 and variance 1 for each reflection Without correction for SigF to the variances, Wilson log(likelihood) = - number of acentrics (83981) - half number of centrics (4004/2) = -85983 With correction for SigF, Wilson log(likelihood) = -89650.5 Configuring ensembles --------------------- This pdb file contains 1 models The (input) RmsD of this model with respect to the real structure is 0.8 Unit Cell: 914.73 520.03 508.93 90.00 90.00 90.00 Electron Density Calculation 0% 100% |=======| DONE ------------------------------ FAST ROTATION FUNCTION #1 OF 1 ------------------------------ Search Ensemble: 1 Known MR solutions (empty solution set - no components) Fraction of asymmetric unit modelled: 1.0047 of which the "moving" fraction is 1.0047 Fraction of asymmetric unit modelled (after correction): 0.99 of which the "moving" fraction is 0.99 Spherical Harmonics ------------------- Elmn for Data Elmn Calculation for Data 0% 100% |=========================================================================| DONE Elmn for Search Ensemble Elmn Calculation for Search Ensemble 0% 100% |===========================================================================| DONE Scanning the Range of Beta Angles --------------------------------- Performing a 1.3513 degree search. Clmn Calculation 0% 100% |====================================================================| DONE Top 59 rotations before clustering will be rescored Calculating Likelihood for RF #1 of 1 0% 100% |============================================================| DONE Scoring 500 randomly sampled rotations Generating Statistics for RF #1 of 1 0% 100% |========================================================================| DONE Mean Score (Sigma): -7144.27 (152.138) Highest Score (Z-score): -2269.9 (32.0392) Top Peaks With Clustering ------------------------- # Rank of the peak after rescoring search points (#) Rank of the peak before rescoring search points LLG Log-Likelihood Gain Z-Score Number of standard deviations of LLG above the mean FSS Fast Search Score You requested peaks over 75% of top (i.e. 0.75*(top-mean)+mean) There was 1 site over 75% of top The sites over 75% are: # (#) Euler1 Euler2 Euler3 LLG Z-score Split #Group raw/top 1 1 326.1 62.4 83.0 -2269.90 32.04 0.0 23 100.0/100.0 213.9 117.6 263.0 Fast Rotation Function Table: 1 ------------------------------- #SET Top (Z) Second (Z) Third (Z) 1 -2269.90 32.04 --- --- --- --- ---- ---------- ----- ---------- ----- ---------- ----- --------------- FINAL SELECTION --------------- Mean used for final selection = -7144.27 Cutoff used for final selection = -3488.49 Number of sets stored before final selection = 1 Number of solutions stored before final selection = 1 Number of sets stored (deleted) after final selection = 1 (0) Number of solutions stored (deleted) after final selection = 1 (0) ------------ *Results from rotation functions for P2 (Search one monomer in ASU)* ************************************************************************************* *** Phaser Module: MOLECULAR REPLACEMENT FAST ROTATION FUNCTION 2.2.4 *** ************************************************************************************* --------------------- ANISOTROPY CORRECTION --------------------- No refinement of parameters ------------------------------- DATA FOR FAST ROTATION FUNCTION ------------------------------- Outliers with a probability less than 1e-06 will be rejected There were 2 (0.0000%) reflections rejected H K L reso F probability 5 5 62 4.48 42.404 4.049e-07 18 2 -26 8.12 112.092 7.520e-09 Space-Group Name (Number): P 1 2 1 (3) Resolution of All Data (Number): 3.82 49.18 (87989) Resolution of Selected Data (Number): 3.82 49.18 (87985) -------------------------- ENSEMBLE FOR DECOMPOSITION -------------------------- This pdb file contains 1 models The (input) RmsD of this model with respect to the real structure is 0.8 Unit Cell: 323.84 274.82 261.37 90.00 90.00 90.00 Electron Density Calculation 0% 100% |=======| DONE ------------------- WILSON DISTRIBUTION ------------------- Parameters set for Wilson log-likelihood calculation E = 0 and variance 1 for each reflection Without correction for SigF to the variances, Wilson log(likelihood) = - number of acentrics (83981) - half number of centrics (4004/2) = -85983 With correction for SigF, Wilson log(likelihood) = -89650.5 Configuring ensembles --------------------- - 显示引用文字 - This pdb file contains 1 models The (input) RmsD of this model with respect to the real structure is 0.8 Unit Cell: 714.35 518.29 464.48 90.00 90.00 90.00 Electron Density Calculation 0% 100% |=======| DONE ------------------------------ FAST ROTATION FUNCTION #1 OF 1 ------------------------------ Search Ensemble: 1 Known MR solutions (empty solution set - no components) Fraction of asymmetric unit modelled: 0.831924 of which the "moving" fraction is 0.831924 Spherical Harmonics ------------------- Elmn for Data Elmn Calculation for Data 0% 100% |=========================================================================| DONE Elmn for Search Ensemble Elmn Calculation for Search Ensemble 0% 100% |===========================================================================| DONE Scanning the Range of Beta Angles --------------------------------- Performing a 1.5476 degree search. Clmn Calculation 0% 100% |===========================================================| DONE Top 41 rotations before clustering will be rescored Calculating Likelihood for RF #1 of 1 0% 100% |==========================================| DONE Scoring 500 randomly sampled rotations Generating Statistics for RF #1 of 1 0% 100% |========================================================================| DONE Mean Score (Sigma): -4412.88 (151.158) Highest Score (Z-score): -893.783 (23.2809) Top Peaks With Clustering ------------------------- # Rank of the peak after rescoring search points (#) Rank of the peak before rescoring search points LLG Log-Likelihood Gain Z-Score Number of standard deviations of LLG above the mean FSS Fast Search Score You requested peaks over 75% of top (i.e. 0.75*(top-mean)+mean) There was 1 site over 75% of top The sites over 75% are: # (#) Euler1 Euler2 Euler3 LLG Z-score Split #Group raw/top 1 1 70.6 39.1 10.6 -893.78 23.28 0.0 13 100.0/100.0 109.4 140.9 190.6 Fast Rotation Function Table: 1 ------------------------------- #SET Top (Z) Second (Z) Third (Z) 1 -893.78 23.28 --- --- --- --- ---- ---------- ----- ---------- ----- ---------- ----- --------------- FINAL SELECTION --------------- Mean used for final selection = -4412.88 Cutoff used for final selection = -1773.56 Number of sets stored before final selection = 1 Number of solutions stored before final selection = 1 Number of sets stored (deleted) after final selection = 1 (0) Number of solutions stored (deleted) after final selection = 1 (0) ------------ Results from rotation functions for P21 (Search two monomers in ASU) ************************************************************************************* *** Phaser Module: MOLECULAR REPLACEMENT FAST ROTATION FUNCTION 2.2.4 *** ************************************************************************************* --------------------- ANISOTROPY CORRECTION --------------------- No refinement of parameters ------------------------------- DATA FOR FAST ROTATION FUNCTION ------------------------------- Outliers with a probability less than 1e-06 will be rejected There were 2 (0.0000%) reflections rejected H K L reso F probability 5 5 62 4.48 42.404 4.046e-07 18 2 -26 8.12 112.092 7.516e-09 Space-Group Name (Number): P 1 21 1 (4) Resolution of All Data (Number): 3.82 49.18 (87983) Resolution of Selected Data (Number): 3.82 49.18 (87981) -------------------------- ENSEMBLE FOR DECOMPOSITION -------------------------- This pdb file contains 1 models The (input) RmsD of this model with respect to the real structure is 0.8 Unit Cell: 323.83 274.82 261.37 90.00 90.00 90.00 Electron Density Calculation 0% 100% |=======| DONE ------------------- WILSON DISTRIBUTION ------------------- Parameters set for Wilson log-likelihood calculation E = 0 and variance 1 for each reflection Without correction for SigF to the variances, Wilson log(likelihood) = - number of acentrics (83976) - half number of centrics (4005/2) = -85978 With correction for SigF, Wilson log(likelihood) = -89646.3 Configuring ensembles --------------------- This pdb file contains 1 models The (input) RmsD of this model with respect to the real structure is 0.8 Unit Cell: 714.35 518.29 464.48 90.00 90.00 90.00 Electron Density Calculation 0% 100% |=======| DONE ------------------------------ FAST ROTATION FUNCTION #1 OF 1 ------------------------------ Search Ensemble: 1 Known MR solutions (empty solution set - no components) Fraction of asymmetric unit modelled: 0.737308 of which the "moving" fraction is 0.737308 Spherical Harmonics ------------------- Elmn for Data Elmn Calculation for Data 0% 100% |=========================================================================| DONE Elmn for Search Ensemble Elmn Calculation for Search Ensemble 0% 100% |===========================================================================| DONE Scanning the Range of Beta Angles --------------------------------- Performing a 1.54708 degree search. Clmn Calculation 0% 100% |===========================================================| DONE Top 47 rotations before clustering will be rescored Calculating Likelihood for RF #1 of 1 0% 100% |================================================| DONE Scoring 500 randomly sampled rotations Generating Statistics for RF #1 of 1 0% 100% |========================================================================| DONE Mean Score (Sigma): -3258.27 (128.907) Highest Score (Z-score): -242.259 (23.3968) Top Peaks With Clustering ------------------------- # Rank of the peak after rescoring search points (#) Rank of the peak before rescoring search points LLG Log-Likelihood Gain Z-Score Number of standard deviations of LLG above the mean FSS Fast Search Score You requested peaks over 75% of top (i.e. 0.75*(top-mean)+mean) There was 1 site over 75% of top The sites over 75% are: # (#) Euler1 Euler2 Euler3 LLG Z-score Split #Group raw/top 1 1 70.7 39.1 10.6 -242.26 23.40 0.0 18 100.0/100.0 109.3 140.9 190.6 Fast Rotation Function Table: 1 ------------------------------- #SET Top (Z) Second (Z) Third (Z) 1 -242.26 23.40 --- --- --- --- ---- ---------- ----- ---------- ----- ---------- ----- --------------- FINAL SELECTION --------------- Mean used for final selection = -3258.27 Cutoff used for final selection = -996.261 Number of sets stored before final selection = 1 Number of solutions stored before final selection = 1 Number of sets stored (deleted) after final selection = 1 (0) Number of solutions stored (deleted) after final selection = 1 (0) ------------ Results from rotation functions for P21 (Search One monomers in ASU) ************************************************************************************* *** Phaser Module: MOLECULAR REPLACEMENT FAST ROTATION FUNCTION 2.2.4 *** ************************************************************************************* --------------------- ANISOTROPY CORRECTION --------------------- No refinement of parameters ------------------------------- DATA FOR FAST ROTATION FUNCTION ------------------------------- Outliers with a probability less than 1e-06 will be rejected There were 2 (0.0000%) reflections rejected H K L reso F probability 5 5 62 4.48 42.404 4.046e-07 18 2 -26 8.12 112.092 7.516e-09 Space-Group Name (Number): P 1 21 1 (4) Resolution of All Data (Number): 3.82 49.18 (87983) Resolution of Selected Data (Number): 3.82 49.18 (87981) -------------------------- ENSEMBLE FOR DECOMPOSITION -------------------------- This pdb file contains 1 models The (input) RmsD of this model with respect to the real structure is 0.8 Unit Cell: 323.83 274.82 261.37 90.00 90.00 90.00 Electron Density Calculation 0% 100% |=======| DONE ------------------- WILSON DISTRIBUTION ------------------- Parameters set for Wilson log-likelihood calculation E = 0 and variance 1 for each reflection Without correction for SigF to the variances, Wilson log(likelihood) = - number of acentrics (83976) - half number of centrics (4005/2) = -85978 With correction for SigF, Wilson log(likelihood) = -89646.3 Configuring ensembles --------------------- This pdb file contains 1 models The (input) RmsD of this model with respect to the real structure is 0.8 Unit Cell: 714.35 518.29 464.48 90.00 90.00 90.00 Electron Density Calculation 0% 100% |=======| DONE ------------------------------ FAST ROTATION FUNCTION #1 OF 1 ------------------------------ Search Ensemble: 1 Known MR solutions (empty solution set - no components) Fraction of asymmetric unit modelled: 0.737308 of which the "moving" fraction is 0.737308 Spherical Harmonics ------------------- Elmn for Data Elmn Calculation for Data 0% 100% |=========================================================================| DONE Elmn for Search Ensemble Elmn Calculation for Search Ensemble 0% 100% |===========================================================================| DONE Scanning the Range of Beta Angles --------------------------------- Performing a 1.54708 degree search. Clmn Calculation 0% 100% |===========================================================| DONE Top 47 rotations before clustering will be rescored Calculating Likelihood for RF #1 of 1 0% 100% |================================================| DONE Scoring 500 randomly sampled rotations Generating Statistics for RF #1 of 1 0% 100% |========================================================================| DONE Mean Score (Sigma): -3258.27 (128.907) Highest Score (Z-score): -242.259 (23.3968) Top Peaks With Clustering ------------------------- # Rank of the peak after rescoring search points (#) Rank of the peak before rescoring search points LLG Log-Likelihood Gain Z-Score Number of standard deviations of LLG above the mean FSS Fast Search Score You requested peaks over 75% of top (i.e. 0.75*(top-mean)+mean) There was 1 site over 75% of top The sites over 75% are: # (#) Euler1 Euler2 Euler3 LLG Z-score Split #Group raw/top 1 1 70.7 39.1 10.6 -242.26 23.40 0.0 18 100.0/100.0 109.3 140.9 190.6 Fast Rotation Function Table: 1 ------------------------------- #SET Top (Z) Second (Z) Third (Z) 1 -242.26 23.40 --- --- --- --- ---- ---------- ----- ---------- ----- ---------- ----- --------------- FINAL SELECTION --------------- Mean used for final selection = -3258.27 Cutoff used for final selection = -996.261 Number of sets stored before final selection = 1 Number of solutions stored before final selection = 1 Number of sets stored (deleted) after final selection = 1 (0) Number of solutions stored (deleted) after final selection = 1 (0) ------------ *Thanks a lot. Yu * 2011/3/15 Francis E Reyes

Go back to your xtriage log file... Post the section that looks similar to the one below...

The full list of Patterson peaks is:

x y z height p-value(height) ( 0.500, 0.000, 0.233 ) : 26.198 (2.753e-03) ( 0.000, 0.338, 0.000 ) : 5.699 (7.800e-01)

If the observed pseudo translationals are crystallographic the following spacegroups and unit cells are possible:

space group operator unit cell of reference setting C 2 2 21 (-a,c,2*b) x+1/2, y, z+1/4 (55.47, 73.64, 81.46, 90.00, 90.00, 90.00)

Systematic absences

Also, post the results of the rotation function.. What is the RFZ score and how did it compare to any other rotation solutions.

F

On Mar 15, 2011, at 1:13 PM, Zhang yu wrote:

...

It indicates that pseudo translational symmetry is present in the dataset. I didn't do anything when I first try MR. Is that possible I merged two lattice together during data process, or should I reprocess the data to P1?

I attached the scale log file,

Shell Lower Upper Average Average Norm. Linear Square limit Angstrom I error stat. Chi**2 R-fac R-fac 50.00 10.29 1030.9 76.3 20.0 1.095 0.105 0.118 10.29 8.18 791.3 52.2 18.1 1.108 0.093 0.101 8.18 7.15 350.8 23.5 11.3 1.160 0.108 0.106 7.15 6.49 195.8 17.1 11.4 1.090 0.138 0.131 6.49 6.03 143.7 15.7 12.1 1.029 0.167 0.154 6.03 5.67 130.8 15.6 13.2 1.101 0.187 0.173 5.67 5.39 129.9 16.8 14.6 1.074 0.198 0.184 5.39 5.16 136.0 17.9 15.6 1.078 0.202 0.186 5.16 4.96 138.3 19.2 16.8 1.044 0.207 0.192 4.96 4.79 150.9 20.7 18.0 1.082 0.209 0.191 4.79 4.64 151.3 21.1 18.8 1.140 0.225 0.210 4.64 4.50 143.1 22.4 20.3 1.070 0.236 0.226 4.50 4.39 127.5 22.5 21.1 1.027 0.262 0.251 4.39 4.28 117.7 22.8 22.3 1.051 0.291 0.279 4.28 4.18 105.8 24.2 23.7 0.988 0.322 0.317 4.18 4.09 93.0 25.0 24.9 0.947 0.365 0.371 4.09 4.01 84.9 25.3 25.2 0.884 0.409 0.403 4.01 3.94 76.6 27.4 27.3 0.843 0.457 0.490 3.94 3.87 66.5 27.5 27.5 0.778 0.505 0.559 3.87 3.80 59.3 28.9 28.8 0.766 0.575 0.696 All reflections 222.9 26.7 19.5 1.037 0.165 0.128

2011/3/15 Francis E Reyes This is probably the most revealing to me.. What did you do about this when you did the MR?

On Mar 15, 2011, at 9:45 AM, Zhang yu wrote:

The analyses of the Patterson function reveals a significant off-origin peak that is 56.00 % of the origin peak, indicating pseudo translational symmetry.

--------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

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--------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

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