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Thank you all. My protein has a similar MW to the contaminant, Mass Spec and Edman sequencing will show both protein if the crystals are not washed accurately (and they can dissolve in the process). But now, thanks to all suggestions, I am very convinced it is the contaminant. I will try also SIMBAD. Kind Regards On Fri, Aug 17, 2018 at 4:33 PM zaigham mahmood khan < [log in to unmask]> wrote: > Hey Li > Yes, AcrB is the major contaminant. But this got crystallized rather > easily. hence it is a baby in the bath water. You got a dataset of 6 Ang. > May be that is a positive sign, and it may not be the AcrB. You may grow > more crystals, and try to fish these crystals. You may run the gel of the > crystals only (highly purified protein), and not the whole drop. Subsequent > SDS-PAGE or Western using protein-specific antibody or Edman sequencing or > preferably Mass Spec will give you the definite answer.. > You may also contact Phaser guys, and they might tell you the reliability > of Phaser for the given dataset. > All the best > > > > -Z > > > Zaigham Mahmood Khan, PhD > > Icahn School of Medicine at Mount Sinai > Department of Oncological Sciences > 1470 Madison Avenue > New York > > On Fri, Aug 17, 2018 at 4:17 AM, Li Wei <[log in to unmask]> > wrote: > >> thanks very much, >> now I am more convinced these are crystals of the contaminant. I will not >> optimize these crystals or use data for applications, >> kind regards >> Li Wei >> >> On Thu, Aug 16, 2018 at 4:17 PM, Howard Young <[log in to unmask]> wrote: >> >>> There is a *baby* in the bath water: *AcrB* contamination is a major >>> problem in membrane-protein crystallization >>> >>> Veesler D, Blangy S, Cambillau C, Sciara G. >>> >>> Acta Crystallogr Sect F Struct Biol Cryst Commun. 2008 Oct 1;64(Pt >>> 10):880-5. doi: 10.1107/S1744309108028248. Epub 2008 Sep 30. >>> PMID: 18931428 >>> >>> >>> >>> >>> On Thu, Aug 16, 2018 at 9:11 AM, Christian Roth < >>> [log in to unmask]> wrote: >>> >>>> TFZ score indicates it is solved. With a model refined at high >>>> resolution, a rigid body refinement should lead to spectacular good R >>>> values. >>>> Anyway, why not doing a SDS gel with the crystal or MS to see if the >>>> crystal contains your protein or not. >>>> >>>> Cheers >>>> Christian >>>> >>>> >>>> On Thu, Aug 16, 2018 at 4:50 PM Li Wei <[log in to unmask]> >>>> wrote: >>>> >>>>> Dear All, >>>>> I collected data of crystals at 6A resolution. The space group and the >>>>> unit cell are similar to a very common contaminant (1iwg.pdb) so I did >>>>> molecular replacement with the contaminant and Phaser found a solution with >>>>> good statistics (below I attach the log file). Is it reliable at 6A >>>>> resolution or shall I optimise the crystals hoping it is my protein? >>>>> Thanks for your suggestions >>>>> Li Wei >>>>> >>>>> >>>>> #CCP4I VERSION CCP4Interface 7.0.047 >>>>> #CCP4I SCRIPT LOG phaser_MR >>>>> #CCP4I DATE 14 Aug 2018 22:53:56 >>>>> #CCP4I USER liwei >>>>> #CCP4I PROJECT PROJECT2 >>>>> #CCP4I JOB_ID 1 >>>>> #CCP4I SCRATCH /tmp/liwei >>>>> #CCP4I HOSTNAME MacBook-Pro-of-Li-Wei.local >>>>> #CCP4I PID 52518 >>>>> >>>>> Phaser-2.7.17 (svn exported) >>>>> Enter keyword input: >>>>> <pre> >>>>> <B><FONT COLOR="#FF0000"> >>>>> <html><!-- CCP4 HTML LOGFILE --> >>>>> <!--SUMMARY_BEGIN--> >>>>> >>>>> >>>>> ########################################################################################## >>>>> >>>>> ########################################################################################## >>>>> >>>>> ########################################################################################## >>>>> ### CCP4 PROGRAM SUITE: >>>>> Phaser 2.7.17 ### >>>>> >>>>> ########################################################################################## >>>>> User: liwei >>>>> Run time: Tue Aug 14 22:53:56 2018 >>>>> Version: 2.7.17 >>>>> Release Date: Wed Oct 11 14:49:55 2017 (svn exported) >>>>> >>>>> If you use this software please cite: >>>>> $TEXT:Reference1: $$ $$ >>>>> "Phaser Crystallographic Software" >>>>> A.J. McCoy, R.W. Grosse-Kunstleve, P.D. Adams, M.D. Winn, L.C. Storoni >>>>> & R.J. Read >>>>> J. Appl. Cryst. (2007). 40, 658-674 >>>>> <a href=" >>>>> http://journals.iucr.org/j/issues/2007/04/00/he5368/he5368.pdf >>>>> ">PDF</a> >>>>> >>>>> $$ >>>>> <!--SUMMARY_END--> >>>>> <!--END--></FONT></B> >>>>> <!--SUMMARY_BEGIN--> >>>>> >>>>> >>>>> ****************************************************************************************** >>>>> *** Phaser Module: >>>>> PREPROCESSOR 2.7.17 *** >>>>> >>>>> ****************************************************************************************** >>>>> >>>>> $TEXT:Script: $$ Baubles Markup $$ >>>>> #---PHASER COMMAND SCRIPT GENERATED BY CCP4I--- >>>>> TITLE data_26 model >>>>> MODE MR_AUTO >>>>> ROOT "/Users/liwei/Desktop/Files/PROJECT2_1" >>>>> #---DEFINE DATA--- >>>>> HKLIN "/Users/liwei/Desktop/Files/5945972022_26baedata.mtz" >>>>> LABIN F=FP_ISOB SIGF=SIGFP_ISOB >>>>> SGALTERNATIVE SELECT HAND >>>>> #---DEFINE ENSEMBLES--- >>>>> ENSEMBLE 1iwg & >>>>> PDB "/Users/liwei/Desktop/Files/1iwg.pdb" IDENT 90.0 >>>>> #---DEFINE COMPOSITION--- >>>>> COMPOSITION BY ASU >>>>> COMPOSITION PROTEIN NRES 1000 NUMBER 1 >>>>> #---SEARCH PARAMETERS--- >>>>> SEARCH ENSEMBLE 1iwg NUMBER 1 >>>>> #---EXPERT PARAMETERS--- >>>>> #---OUTPUT CONTROL--- >>>>> #---DEVELOPER PARAMETERS--- >>>>> ## This script run with the command ########## >>>>> # /Applications/ccp4-7.0/bin/phaser >>>>> ################################################ >>>>> >>>>> $$ >>>>> CPU Time: 0 days 0 hrs 0 mins 0.00 secs ( 0.00 secs) >>>>> Finished: Tue Aug 14 22:53:56 2018 >>>>> >>>>> >>>>> ****************************************************************************************** >>>>> *** Phaser Module: READ DATA FROM MTZ >>>>> FILE 2.7.17 *** >>>>> >>>>> ****************************************************************************************** >>>>> >>>>> Read from Mtz File >>>>> ------------------ >>>>> Data read from mtz file: >>>>> /Users/liwei/Desktop/Files/5945972022_26baedata.mtz >>>>> Space-Group Name (Hall Symbol): H 3 2 ( R 3 2") >>>>> Space-Group Number: 155 >>>>> Unit Cell: 148.58 148.58 513.89 90.00 90.00 120.00 >>>>> Column Labels Selected: FP_ISOB SIGFP_ISOB >>>>> Resolution on Mtz file: 6.39 80.31 >>>>> Resolution Selected: 6.42 80.31 >>>>> Number of Reflections in Selected Resolution Range: 4110 >>>>> >>>>> CPU Time: 0 days 0 hrs 0 mins 0.02 secs ( 0.02 secs) >>>>> Finished: Tue Aug 14 22:53:56 2018 >>>>> >>>>> >>>>> ****************************************************************************************** >>>>> *** Phaser Module: AUTOMATED MOLECULAR >>>>> REPLACEMENT 2.7.17 *** >>>>> >>>>> ****************************************************************************************** >>>>> >>>>> ** Steps: >>>>> ** Cell Content Analysis >>>>> ** Anisotropy correction >>>>> ** Translational NCS correction >>>>> ** Rotation Function >>>>> ** Translation Function >>>>> ** Packing >>>>> ** Refinement >>>>> ** Final Refinement (if data higher resolution than search >>>>> resolution) >>>>> ** Number of search ensembles = 1 >>>>> ** Search Method: FAST >>>>> ** Input Search Order: >>>>> ** #1 1iwg >>>>> ** Automatic (best predicted) search order WILL be used >>>>> >>>>> CPU Time: 0 days 0 hrs 0 mins 0.36 secs ( 0.36 secs) >>>>> Finished: Tue Aug 14 22:53:57 2018 >>>>> >>>>> >>>>> ****************************************************************************************** >>>>> *** Phaser Module: CELL CONTENT >>>>> ANALYSIS 2.7.17 *** >>>>> >>>>> ****************************************************************************************** >>>>> >>>>> Space-Group Name (Hall Symbol): H 3 2 ( R 3 2") >>>>> Space-Group Number: 155 >>>>> Unit Cell: 148.58 148.58 513.89 90.00 90.00 120.00 >>>>> >>>>> <!--SUMMARY_END--> >>>>> -------------------- >>>>> SPACE GROUP ANALYSIS >>>>> -------------------- >>>>> >>>>> Input Space Group: H 3 2 >>>>> >>>>> (a) Space groups derived by translation (screw) symmetry >>>>> -------------------------------------------------------- >>>>> Z Space Group Hall Symbol >>>>> ---- >>>>> 18 H 3 2 R 3 2" >>>>> ---- >>>>> >>>>> (b) Subgroups of space group for perfect twinning expansions >>>>> ------------------------------------------------------------ >>>>> R: Reindexing operation required (*) >>>>> Only subgroups related by rotational symmetry are reported >>>>> Z Space Group R Hall Symbol >>>>> ---- >>>>> 3 R 1 * P 1 >>>>> (2/3*x-1/3*y-1/3*z,1/3*x+1/3*y-2/3*z,1/3*x+1/3*y+1/3*z) >>>>> --- >>>>> 6 C 1 2 1 * C 2y (2/3*x,1/3*x+y,-2/3*x+z) >>>>> C 1 2 1 * C 2y (x+y-1/3*z,-x+y+1/3*z,1/3*z) >>>>> C 1 2 1 * C 2y (1/3*x-y,2/3*x,2/3*x+z) >>>>> C 1 2 1 * C 2y (2/3*x,1/3*x+y,-2/3*x+z) >>>>> C 1 2 1 * C 2y (x+y-1/3*z,-x+y+1/3*z,1/3*z) >>>>> C 1 2 1 * C 2y (1/3*x-y,2/3*x,2/3*x+z) >>>>> --- >>>>> 9 H 3 R 3 >>>>> H 3 R 3 >>>>> H 3 R 3 >>>>> H 3 R 3 >>>>> H 3 R 3 >>>>> --- >>>>> 18 H 3 2 R 3 2" >>>>> H 3 2 R 3 2" >>>>> H 3 2 R 3 2" >>>>> H 3 2 R 3 2" >>>>> H 3 2 R 3 2" >>>>> H 3 2 R 3 2" >>>>> H 3 2 R 3 2" >>>>> H 3 2 R 3 2" >>>>> H 3 2 R 3 2" >>>>> ---- >>>>> >>>>> <!--SUMMARY_BEGIN--> >>>>> Composition is of type: PROTEIN >>>>> MW to which Matthews applies: 111000 >>>>> Resolution for Matthews calculation: 6.42 >>>>> >>>>> Z MW VM % solvent rel. freq. >>>>> 1 111000 4.92 74.99 0.014 >>>>> 2 222000 2.46 49.97 1.000 <== most probable >>>>> 3 333000 1.64 24.96 0.008 >>>>> >>>>> Z is the number of multiples of the total composition >>>>> In most cases the most probable Z value should be 1 >>>>> If it is not 1, you may need to consider other compositions >>>>> >>>>> <!--SUMMARY_END--> >>>>> Histogram of relative frequencies of VM values >>>>> ---------------------------------------------- >>>>> Frequency of most common VM value normalized to 1 >>>>> VM values plotted in increments of 1/VM (0.02) >>>>> >>>>> <--- relative frequency ---> >>>>> 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 >>>>> | | | | | | | | | | | >>>>> 10.00 - >>>>> 8.33 - >>>>> 7.14 - >>>>> 6.25 - >>>>> 5.56 - >>>>> 5.00 - >>>>> 4.55 ** (COMPOSITION*1) >>>>> 4.17 -- >>>>> 3.85 ---- >>>>> 3.57 ------ >>>>> 3.33 ---------- >>>>> 3.12 --------------- >>>>> 2.94 --------------------- >>>>> 2.78 ---------------------------- >>>>> 2.63 ----------------------------------- >>>>> 2.50 ------------------------------------------- >>>>> 2.38 ************************************************ >>>>> (COMPOSITION*2) >>>>> 2.27 -------------------------------------------------- >>>>> 2.17 ------------------------------------------------ >>>>> 2.08 ----------------------------------------- >>>>> 2.00 ------------------------------ >>>>> 1.92 ------------------- >>>>> 1.85 ---------- >>>>> 1.79 ----- >>>>> 1.72 -- >>>>> 1.67 - >>>>> 1.61 * (COMPOSITION*3) >>>>> 1.56 - >>>>> 1.52 - >>>>> 1.47 - >>>>> 1.43 - >>>>> 1.39 - >>>>> 1.35 - >>>>> 1.32 - >>>>> 1.28 - >>>>> 1.25 - >>>>> >>>>> $TABLE : Cell Content Analysis: >>>>> $SCATTER >>>>> :N*Composition vs Probability:0|4x0|1:1,2: >>>>> $$ >>>>> N*Composition Probability >>>>> $$ loggraph $$ >>>>> 1 0.0205558 >>>>> 2 0.956573 >>>>> 3 0.00552532 >>>>> $$ >>>>> <!--SUMMARY_BEGIN--> >>>>> >>>>> Most probable VM for resolution = 2.27337 >>>>> Most probable MW of protein in asu for resolution = 240093 >>>>> >>>>> CPU Time: 0 days 0 hrs 0 mins 1.18 secs ( 1.18 secs) >>>>> Finished: Tue Aug 14 22:53:57 2018 >>>>> >>>>> >>>>> ****************************************************************************************** >>>>> *** Phaser Module: ANISOTROPY >>>>> CORRECTION 2.7.17 *** >>>>> >>>>> ****************************************************************************************** >>>>> >>>>> <!--SUMMARY_END--> >>>>> ------------------------------ >>>>> DATA FOR ANISOTROPY CORRECTION >>>>> ------------------------------ >>>>> >>>>> Resolution of All Data (Number): 6.42 80.31 (4110) >>>>> Resolution of Selected Data (Number): 6.42 80.31 (4110) >>>>> >>>>> Outliers with a probability less than 1e-06 will be rejected >>>>> Measurements with fewer bits of information than 0.01 will be >>>>> rejected: >>>>> threshold sigma(Eobs^2) for centrics/acentrics is 11.9664 / >>>>> 8.46225 >>>>> There were 0 (0.0000%) reflections rejected >>>>> >>>>> No reflections are outliers >>>>> >>>>> --------------------- >>>>> ANISOTROPY CORRECTION >>>>> --------------------- >>>>> >>>>> Protocol cycle #1 of 3 >>>>> Refinement protocol for this macrocycle: >>>>> BIN SCALES: REFINE >>>>> ANISOTROPY: REFINE >>>>> SOLVENT K: FIX >>>>> SOLVENT B: FIX >>>>> >>>>> Protocol cycle #2 of 3 >>>>> Refinement protocol for this macrocycle: >>>>> BIN SCALES: REFINE >>>>> ANISOTROPY: REFINE >>>>> SOLVENT K: FIX >>>>> SOLVENT B: FIX >>>>> >>>>> Protocol cycle #3 of 3 >>>>> Refinement protocol for this macrocycle: >>>>> BIN SCALES: REFINE >>>>> ANISOTROPY: REFINE >>>>> SOLVENT K: FIX >>>>> SOLVENT B: FIX >>>>> >>>>> Outliers with a probability less than 1e-06 will be rejected >>>>> Measurements with fewer bits of information than 0.01 will be >>>>> rejected: >>>>> threshold sigma(Eobs^2) for centrics/acentrics is 11.9664 / >>>>> 8.46225 >>>>> There were 0 (0.0000%) reflections rejected >>>>> >>>>> No reflections are outliers >>>>> >>>>> Performing Optimization... >>>>> Done >>>>> --- Convergence before iteration limit (50) at cycle 1 --- >>>>> Start-this-macrocycle End-this-macrocycle Change-this-macrocycle >>>>> -70849.741 -70849.741 -0.000 >>>>> >>>>> Principal components of anisotropic part of B affecting observed >>>>> amplitudes: >>>>> eigenB (A^2) direction cosines (orthogonal coordinates) >>>>> 0.000 0.7082 -0.7039 -0.0550 >>>>> 0.000 -0.0389 0.0389 -0.9985 >>>>> 0.000 0.7050 0.7092 0.0002 >>>>> Anisotropic deltaB (i.e. range of principal components): 0.000 >>>>> Resharpening B (to restore strong direction of diffraction): 0.000 >>>>> Wilson scale applied to get observed intensities: 4.4442e+00 >>>>> >>>>> Outliers with a probability less than 1e-06 will be rejected >>>>> Measurements with fewer bits of information than 0.01 will be >>>>> rejected: >>>>> threshold sigma(Eobs^2) for centrics/acentrics is 11.9664 / >>>>> 8.46225 >>>>> There were 0 (0.0000%) reflections rejected >>>>> >>>>> No reflections are outliers >>>>> >>>>> Performing Optimization... >>>>> Done >>>>> --- Convergence before iteration limit (50) at cycle 1 --- >>>>> Start-this-macrocycle End-this-macrocycle Change-this-macrocycle >>>>> -70849.741 -70849.741 -0.000 >>>>> >>>>> Principal components of anisotropic part of B affecting observed >>>>> amplitudes: >>>>> eigenB (A^2) direction cosines (orthogonal coordinates) >>>>> 0.000 0.7082 -0.7039 -0.0550 >>>>> 0.000 -0.0389 0.0389 -0.9985 >>>>> 0.000 0.7050 0.7092 0.0002 >>>>> Anisotropic deltaB (i.e. range of principal components): 0.000 >>>>> Resharpening B (to restore strong direction of diffraction): 0.000 >>>>> Wilson scale applied to get observed intensities: 4.4442e+00 >>>>> >>>>> Outliers with a probability less than 1e-06 will be rejected >>>>> Measurements with fewer bits of information than 0.01 will be >>>>> rejected: >>>>> threshold sigma(Eobs^2) for centrics/acentrics is 11.9664 / >>>>> 8.46225 >>>>> There were 0 (0.0000%) reflections rejected >>>>> >>>>> No reflections are outliers >>>>> >>>>> Performing Optimization... >>>>> Done >>>>> --- Convergence before iteration limit (50) at cycle 1 --- >>>>> Start-this-macrocycle End-this-macrocycle Change-this-macrocycle >>>>> -70849.741 -70849.741 -0.000 >>>>> >>>>> Principal components of anisotropic part of B affecting observed >>>>> amplitudes: >>>>> eigenB (A^2) direction cosines (orthogonal coordinates) >>>>> 0.000 0.7082 -0.7039 -0.0550 >>>>> 0.000 -0.0389 0.0389 -0.9985 >>>>> 0.000 0.7050 0.7092 0.0002 >>>>> Anisotropic deltaB (i.e. range of principal components): 0.000 >>>>> Resharpening B (to restore strong direction of diffraction): 0.000 >>>>> Wilson scale applied to get observed intensities: 4.4442e+00 >>>>> >>>>> <!--SUMMARY_BEGIN--> >>>>> Refined Anisotropy Parameters >>>>> ----------------------------- >>>>> Principal components of anisotropic part of B affecting observed >>>>> amplitudes: >>>>> eigenB (A^2) direction cosines (orthogonal coordinates) >>>>> 0.000 0.7082 -0.7039 -0.0550 >>>>> 0.000 -0.0389 0.0389 -0.9985 >>>>> 0.000 0.7050 0.7092 0.0002 >>>>> Anisotropic deltaB (i.e. range of principal components): 0.000 >>>>> Resharpening B (to restore strong direction of diffraction): 0.000 >>>>> Wilson scale applied to get observed intensities: 4.4442e+00 >>>>> >>>>> <!--SUMMARY_END--> >>>>> -------------- >>>>> ABSOLUTE SCALE >>>>> -------------- >>>>> >>>>> Scale factor to put input Fs on absolute scale >>>>> Wilson Scale: 0.474353 >>>>> Wilson B-factor: 280.925 >>>>> >>>>> -------------------------------- >>>>> DATA AFTER ANISOTROPY CORRECTION >>>>> -------------------------------- >>>>> >>>>> <!--SUMMARY_BEGIN--> >>>>> Resolution of All Data (Number): 6.42 80.31 (4110) >>>>> Resolution of Selected Data (Number): 6.42 80.31 (4110) >>>>> >>>>> <!--SUMMARY_END--> >>>>> Outliers with a probability less than 1e-06 will be rejected >>>>> Measurements with fewer bits of information than 0.01 will be >>>>> rejected: >>>>> threshold sigma(Eobs^2) for centrics/acentrics is 11.9664 / >>>>> 8.46225 >>>>> There were 0 (0.0000%) reflections rejected >>>>> >>>>> No reflections are outliers >>>>> >>>>> <!--SUMMARY_BEGIN--> >>>>> ------------ >>>>> OUTPUT FILES >>>>> ------------ >>>>> >>>>> No files output >>>>> >>>>> CPU Time: 0 days 0 hrs 0 mins 1.45 secs ( 1.45 secs) >>>>> Finished: Tue Aug 14 22:53:57 2018 >>>>> >>>>> >>>>> ****************************************************************************************** >>>>> *** Phaser Module: TRANSLATIONAL NON-CRYSTALLOGRAPHIC >>>>> SYMMETRY 2.7.17 *** >>>>> >>>>> ****************************************************************************************** >>>>> >>>>> <!--SUMMARY_END--> >>>>> Unit Cell: 148.58 148.58 513.89 90.00 90.00 120.00 >>>>> >>>>> ------------------------------------- >>>>> DATA FOR TRANSLATIONAL NCS CORRECTION >>>>> ------------------------------------- >>>>> >>>>> <!--SUMMARY_BEGIN--> >>>>> Resolution of All Data (Number): 6.42 80.31 (4110) >>>>> Resolution of Selected Data (Number): 6.42 80.31 (4110) >>>>> >>>>> <!--SUMMARY_END--> >>>>> Outliers with a probability less than 1e-06 will be rejected >>>>> Measurements with fewer bits of information than 0.01 will be >>>>> rejected: >>>>> threshold sigma(Eobs^2) for centrics/acentrics is 11.9664 / >>>>> 8.46225 >>>>> There were 0 (0.0000%) reflections rejected >>>>> >>>>> No reflections are outliers >>>>> >>>>> Weighted Intensity Moments for Data >>>>> ----------------------------------- >>>>> Inverse variance-weighted 2nd Moment = <wE^4>/<wE^2>^2 == >>>>> <wJ^2>/<wJ>^2 >>>>> Untwinned Perfect Twin >>>>> 2nd Moment Centric: 3.0 2.0 >>>>> 2nd Moment Acentric: 2.0 1.5 >>>>> Measured >>>>> 2nd Moment Centric: 3.98 >>>>> 2nd Moment Acentric: 2.02 >>>>> >>>>> Resolution for Twin Analysis (85% I/SIGI > 3): 6.42A (HiRes= 6.42A) >>>>> >>>>> $TABLE : Intensity distribution for Data: >>>>> $GRAPHS >>>>> :Cumulative intensity distribution (acentric and >>>>> centric):N:1,2,3,4,5,6: >>>>> $$ >>>>> Z ACent_theor ACent_twin ACent_obser Cent_theor Cent_obser >>>>> $$ loggraph $$ >>>>> 0 0 0 0 0 0 >>>>> 0.04 0.0392106 0.0030343 0.0149701 0.158519 0.116883 >>>>> 0.08 0.0768837 0.0115132 0.0404192 0.222703 0.188312 >>>>> 0.12 0.11308 0.0245815 0.0721557 0.270966 0.244156 >>>>> 0.16 0.147856 0.0414833 0.110479 0.310843 0.3 >>>>> 0.2 0.181269 0.0615519 0.149401 0.345279 0.345455 >>>>> 0.24 0.213372 0.0842006 0.19012 0.375794 0.385714 >>>>> 0.28 0.244216 0.108914 0.227844 0.403299 0.420779 >>>>> 0.32 0.273851 0.13524 0.260479 0.428392 0.453247 >>>>> 0.36 0.302324 0.162786 0.295509 0.451494 0.480519 >>>>> 0.4 0.32968 0.191208 0.32485 0.472911 0.511688 >>>>> 0.44 0.355964 0.220208 0.356886 0.492878 0.528571 >>>>> 0.48 0.381217 0.24953 0.382335 0.511578 0.548052 >>>>> 0.52 0.405479 0.278952 0.407784 0.529158 0.567532 >>>>> 0.56 0.428791 0.308287 0.429042 0.54574 0.590909 >>>>> 0.6 0.451188 0.337373 0.453593 0.561422 0.606494 >>>>> 0.64 0.472708 0.366075 0.47515 0.576289 0.624675 >>>>> 0.68 0.493383 0.394281 0.489521 0.590413 0.638961 >>>>> 0.72 0.513248 0.421896 0.510479 0.603856 0.646753 >>>>> 0.76 0.532334 0.448846 0.533234 0.616672 0.657143 >>>>> 0.8 0.550671 0.475069 0.56018 0.628907 0.663636 >>>>> 0.84 0.56829 0.500518 0.579641 0.640603 0.672727 >>>>> 0.88 0.585217 0.525156 0.597904 0.651798 0.68961 >>>>> 0.92 0.601481 0.548959 0.613473 0.662525 0.703896 >>>>> 0.96 0.617107 0.571908 0.623353 0.672813 0.709091 >>>>> 1 0.632121 0.593994 0.637425 0.682689 0.718182 >>>>> 1.04 0.646545 0.615215 0.648802 0.692179 0.722078 >>>>> 1.08 0.660404 0.635573 0.663174 0.701302 0.731169 >>>>> 1.12 0.67372 0.655074 0.673353 0.710082 0.735065 >>>>> 1.16 0.686514 0.673732 0.684431 0.718534 0.737662 >>>>> 1.2 0.698806 0.691559 0.69521 0.726678 0.74026 >>>>> 1.24 0.710616 0.708574 0.707784 0.734529 0.745455 >>>>> 1.28 0.721963 0.724795 0.718263 0.742101 0.753247 >>>>> 1.32 0.732865 0.740245 0.730838 0.749408 0.757143 >>>>> 1.36 0.743339 0.754946 0.739521 0.756463 0.764935 >>>>> 1.4 0.753403 0.768922 0.750898 0.763276 0.772727 >>>>> 1.44 0.763072 0.782197 0.761377 0.769861 0.777922 >>>>> 1.48 0.772362 0.794797 0.771557 0.776226 0.787013 >>>>> 1.52 0.781288 0.806747 0.780838 0.782381 0.792208 >>>>> 1.56 0.789864 0.818072 0.788323 0.788335 0.797403 >>>>> 1.6 0.798103 0.828799 0.797904 0.794097 0.803896 >>>>> 1.64 0.80602 0.838951 0.80479 0.799674 0.806494 >>>>> 1.68 0.813626 0.848554 0.812874 0.805076 0.814286 >>>>> 1.72 0.820934 0.857633 0.820659 0.810307 0.819481 >>>>> 1.76 0.827955 0.866211 0.829341 0.815376 0.824675 >>>>> 1.8 0.834701 0.874311 0.838623 0.820287 0.833766 >>>>> 1.84 0.841183 0.881957 0.84491 0.825049 0.84026 >>>>> 1.88 0.84741 0.889169 0.848503 0.829666 0.844156 >>>>> 1.92 0.853393 0.895971 0.853593 0.834143 0.846753 >>>>> 1.96 0.859142 0.902382 0.861677 0.838487 0.848052 >>>>> 2 0.864665 0.908422 0.867665 0.842701 0.853247 >>>>> $$ >>>>> $TABLE : Weighted second moments for Data: >>>>> $GRAPHS >>>>> :Weighted second moments vs resolution (acentric only):AUTO:1,2,3,4: >>>>> $$ >>>>> 1/d^2 ACent_theor ACent_twin ACent_obser >>>>> $$ loggraph $$ >>>>> 0.0017 2.00042 1.50042 1.47967 >>>>> 0.0047 2.00085 1.50085 1.71942 >>>>> 0.0077 2.00147 1.50147 2.41165 >>>>> 0.0107 2.00238 1.50238 2.14267 >>>>> 0.0137 2.00971 1.50971 1.93186 >>>>> 0.0168 2.04138 1.54138 1.89608 >>>>> 0.0198 2.15688 1.65688 2.01701 >>>>> 0.0228 2.08427 1.58427 2.14555 >>>>> $$ >>>>> --------------------- >>>>> ANISOTROPY CORRECTION >>>>> --------------------- >>>>> >>>>> Weighted Intensity Moments after Anisotropy Correction >>>>> ------------------------------------------------------ >>>>> Inverse variance-weighted 2nd Moment = <wE^4>/<wE^2>^2 == >>>>> <wJ^2>/<wJ>^2 >>>>> Untwinned Perfect Twin >>>>> 2nd Moment Centric: 3.0 2.0 >>>>> 2nd Moment Acentric: 2.0 1.5 >>>>> Measured >>>>> 2nd Moment Centric: 3.98 >>>>> 2nd Moment Acentric: 2.02 >>>>> >>>>> Resolution for Twin Analysis (85% I/SIGI > 3): 6.42A (HiRes= 6.42A) >>>>> >>>>> $TABLE : Intensity distribution after Anisotropy Correction: >>>>> $GRAPHS >>>>> :Cumulative intensity distribution (acentric and >>>>> centric):N:1,2,3,4,5,6: >>>>> $$ >>>>> Z ACent_theor ACent_twin ACent_obser Cent_theor Cent_obser >>>>> $$ loggraph $$ >>>>> 0 0 0 0 0 0 >>>>> 0.04 0.0392106 0.0030343 0.0149701 0.158519 0.116883 >>>>> 0.08 0.0768837 0.0115132 0.0404192 0.222703 0.188312 >>>>> 0.12 0.11308 0.0245815 0.0721557 0.270966 0.244156 >>>>> 0.16 0.147856 0.0414833 0.110479 0.310843 0.3 >>>>> 0.2 0.181269 0.0615519 0.149401 0.345279 0.345455 >>>>> 0.24 0.213372 0.0842006 0.19012 0.375794 0.385714 >>>>> 0.28 0.244216 0.108914 0.227844 0.403299 0.420779 >>>>> 0.32 0.273851 0.13524 0.260479 0.428392 0.453247 >>>>> 0.36 0.302324 0.162786 0.295509 0.451494 0.480519 >>>>> 0.4 0.32968 0.191208 0.32485 0.472911 0.511688 >>>>> 0.44 0.355964 0.220208 0.356886 0.492878 0.528571 >>>>> 0.48 0.381217 0.24953 0.382335 0.511578 0.548052 >>>>> 0.52 0.405479 0.278952 0.407784 0.529158 0.567532 >>>>> 0.56 0.428791 0.308287 0.429042 0.54574 0.590909 >>>>> 0.6 0.451188 0.337373 0.453593 0.561422 0.606494 >>>>> 0.64 0.472708 0.366075 0.47515 0.576289 0.624675 >>>>> 0.68 0.493383 0.394281 0.489521 0.590413 0.638961 >>>>> 0.72 0.513248 0.421896 0.510479 0.603856 0.646753 >>>>> 0.76 0.532334 0.448846 0.533234 0.616672 0.657143 >>>>> 0.8 0.550671 0.475069 0.56018 0.628907 0.663636 >>>>> 0.84 0.56829 0.500518 0.579641 0.640603 0.672727 >>>>> 0.88 0.585217 0.525156 0.597904 0.651798 0.68961 >>>>> 0.92 0.601481 0.548959 0.613473 0.662525 0.703896 >>>>> 0.96 0.617107 0.571908 0.623353 0.672813 0.709091 >>>>> 1 0.632121 0.593994 0.637425 0.682689 0.718182 >>>>> 1.04 0.646545 0.615215 0.648802 0.692179 0.722078 >>>>> 1.08 0.660404 0.635573 0.663174 0.701302 0.731169 >>>>> 1.12 0.67372 0.655074 0.673353 0.710082 0.735065 >>>>> 1.16 0.686514 0.673732 0.684431 0.718534 0.737662 >>>>> 1.2 0.698806 0.691559 0.69521 0.726678 0.74026 >>>>> 1.24 0.710616 0.708574 0.707784 0.734529 0.745455 >>>>> 1.28 0.721963 0.724795 0.718263 0.742101 0.753247 >>>>> 1.32 0.732865 0.740245 0.730838 0.749408 0.757143 >>>>> 1.36 0.743339 0.754946 0.739521 0.756463 0.764935 >>>>> 1.4 0.753403 0.768922 0.750898 0.763276 0.772727 >>>>> 1.44 0.763072 0.782197 0.761377 0.769861 0.777922 >>>>> 1.48 0.772362 0.794797 0.771557 0.776226 0.787013 >>>>> 1.52 0.781288 0.806747 0.780838 0.782381 0.792208 >>>>> 1.56 0.789864 0.818072 0.788323 0.788335 0.797403 >>>>> 1.6 0.798103 0.828799 0.797904 0.794097 0.803896 >>>>> 1.64 0.80602 0.838951 0.80479 0.799674 0.806494 >>>>> 1.68 0.813626 0.848554 0.812874 0.805076 0.814286 >>>>> 1.72 0.820934 0.857633 0.820659 0.810307 0.819481 >>>>> 1.76 0.827955 0.866211 0.829341 0.815376 0.824675 >>>>> 1.8 0.834701 0.874311 0.838623 0.820287 0.833766 >>>>> 1.84 0.841183 0.881957 0.84491 0.825049 0.84026 >>>>> 1.88 0.84741 0.889169 0.848503 0.829666 0.844156 >>>>> 1.92 0.853393 0.895971 0.853593 0.834143 0.846753 >>>>> 1.96 0.859142 0.902382 0.861677 0.838487 0.848052 >>>>> 2 0.864665 0.908422 0.867665 0.842701 0.853247 >>>>> $$ >>>>> $TABLE : Weighted second moments after Anisotropy Correction: >>>>> $GRAPHS >>>>> :Weighted second moments vs resolution (acentric only):AUTO:1,2,3,4: >>>>> $$ >>>>> 1/d^2 ACent_theor ACent_twin ACent_obser >>>>> $$ loggraph $$ >>>>> 0.0017 2.00042 1.50042 1.47967 >>>>> 0.0047 2.00085 1.50085 1.71942 >>>>> 0.0077 2.00147 1.50147 2.41165 >>>>> 0.0107 2.00238 1.50238 2.14267 >>>>> 0.0137 2.00971 1.50971 1.93186 >>>>> 0.0168 2.04138 1.54138 1.89608 >>>>> 0.0198 2.15688 1.65688 2.01701 >>>>> 0.0228 2.08427 1.58427 2.14555 >>>>> $$ >>>>> ----------------- >>>>> TRANSLATIONAL NCS >>>>> ----------------- >>>>> >>>>> tNCS vector not set >>>>> Space Group : H 3 2 >>>>> Patterson Symmetry: R -3 m :H >>>>> Resolution of All Data (Number): 6.42 80.31 (4110) >>>>> Resolution of Patterson (Number): 6.42 12.80 (3481) >>>>> No large non-origin Patterson peaks >>>>> >>>>> No tNCS found in Patterson >>>>> >>>>> <!--SUMMARY_BEGIN--> >>>>> -------- >>>>> TWINNING >>>>> -------- >>>>> >>>>> tNCS/Twin Detection Table >>>>> ------------------------- >>>>> -Second Moments- >>>>> --P-values-- >>>>> Centric Acentric untwinned >>>>> twin frac <5% >>>>> Theoretical for untwinned 3.00 2.00 >>>>> including measurement error 3.05 2.04 >>>>> Theoretical for perfect twin 2.00 1.50 >>>>> Initial (data as input) 3.98 2.02+/-0.078 1 >>>>> 1 >>>>> After Anisotropy Correction 3.98 2.02+/-0.078 1 >>>>> 1 >>>>> After Anisotropy and tNCS ---n/a--- >>>>> >>>>> P-value < 0.01 for <5% twinned is considered worth investigating >>>>> Resolution for Twin Analysis (85% I/SIGI > 3): 6.42A (HiRes= 6.42A) >>>>> >>>>> <!--SUMMARY_END--> >>>>> --------------------------------------- >>>>> DATA AFTER TRANSLATIONAL NCS CORRECTION >>>>> --------------------------------------- >>>>> >>>>> <!--SUMMARY_BEGIN--> >>>>> Resolution of All Data (Number): 6.42 80.31 (4110) >>>>> Resolution of Selected Data (Number): 6.42 80.31 (4110) >>>>> >>>>> <!--SUMMARY_END--> >>>>> Outliers with a probability less than 1e-06 will be rejected >>>>> Measurements with fewer bits of information than 0.01 will be >>>>> rejected: >>>>> threshold sigma(Eobs^2) for centrics/acentrics is 11.9664 / >>>>> 8.46225 >>>>> There were 0 (0.0000%) reflections rejected >>>>> >>>>> No reflections are outliers >>>>> >>>>> ------------ >>>>> OUTPUT FILES >>>>> ------------ >>>>> >>>>> No files output >>>>> >>>>> <!--SUMMARY_BEGIN--> >>>>> CPU Time: 0 days 0 hrs 0 mins 1.95 secs ( 1.95 secs) >>>>> Finished: Tue Aug 14 22:53:58 2018 >>>>> >>>>> >>>>> ****************************************************************************************** >>>>> *** Phaser Module: AUTOMATED MOLECULAR >>>>> REPLACEMENT 2.7.17 *** >>>>> >>>>> ****************************************************************************************** >>>>> >>>>> ** Z-score test for definite solution is ON >>>>> ** Z-score test for stopping search is OFF >>>>> ** Deep search is ON >>>>> >>>>> CPU Time: 0 days 0 hrs 0 mins 1.95 secs ( 1.95 secs) >>>>> Finished: Tue Aug 14 22:53:58 2018 >>>>> >>>>> >>>>> ****************************************************************************************** >>>>> *** Phaser Module: AUTOMATED MOLECULAR >>>>> REPLACEMENT 2.7.17 *** >>>>> >>>>> ****************************************************************************************** >>>>> >>>>> Composition Table >>>>> ----------------- >>>>> Total Scattering = 361947 >>>>> Search occupancy factor = 1 (default) >>>>> Ensemble Frac.Scat. (Search Frac.Scat.) >>>>> 1iwg 94.04% 94.04% >>>>> >>>>> ** Composition not increased >>>>> <!--SUMMARY_END--> >>>>> >>>>> <!--SUMMARY_BEGIN--> >>>>> CPU Time: 0 days 0 hrs 0 mins 1.95 secs ( 1.95 secs) >>>>> Finished: Tue Aug 14 22:53:58 2018 >>>>> >>>>> >>>>> ****************************************************************************************** >>>>> *** Phaser Module: EXPERIMENTAL ERROR CORRECTION >>>>> PREPARATION 2.7.17 *** >>>>> >>>>> ****************************************************************************************** >>>>> >>>>> <!--SUMMARY_END--> >>>>> ----------------- >>>>> TRANSLATIONAL NCS >>>>> ----------------- >>>>> >>>>> tNCS not present >>>>> >>>>> ----------------------------- >>>>> EXPERIMENTAL ERROR CORRECTION >>>>> ----------------------------- >>>>> >>>>> Calculate Luzzati D factors accounting for observational error... >>>>> >>>>> <!--SUMMARY_BEGIN--> >>>>> Data have been provided as French-Wilson amplitudes >>>>> >>>>> <!--SUMMARY_END--> >>>>> ------------ >>>>> OUTPUT FILES >>>>> ------------ >>>>> >>>>> No files output >>>>> >>>>> <!--SUMMARY_BEGIN--> >>>>> CPU Time: 0 days 0 hrs 0 mins 2.05 secs ( 2.05 secs) >>>>> Finished: Tue Aug 14 22:53:58 2018 >>>>> >>>>> >>>>> ****************************************************************************************** >>>>> *** Phaser Module: EXPECTED LLG OF >>>>> ENSEMBLES 2.7.17 *** >>>>> >>>>> ****************************************************************************************** >>>>> >>>>> <!--SUMMARY_END--> >>>>> ----------------- >>>>> TRANSLATIONAL NCS >>>>> ----------------- >>>>> >>>>> tNCS not present >>>>> >>>>> <!--SUMMARY_BEGIN--> >>>>> Resolution of Data: 6.416 >>>>> Number of Reflections: 4110 >>>>> eLLG Target: 225 >>>>> >>>>> <!--SUMMARY_END--> >>>>> ---------- >>>>> ENSEMBLING >>>>> ---------- >>>>> >>>>> Ensemble: 1iwg >>>>> -------------- >>>>> PDB file # 1: 1iwg.pdb >>>>> This file contains 1 model >>>>> The input RmsD of model #1 with respect to the real structure is >>>>> 0.700 >>>>> <!--SUMMARY_BEGIN--> >>>>> >>>>> eLLG Values Computed for All Data >>>>> --------------------------------- >>>>> Ensemble frac-scat rms >>>>> reso eLLG >>>>> 1iwg 0.94 0.700 >>>>> 6.42 537.0 >>>>> >>>>> Residues/Resolution for eLLG target >>>>> ----------------------------------- >>>>> target-nres: Number of alanine residues to achieve target eLLG >>>>> target-reso: Resolution to achieve target eLLG >>>>> Ensemble eLLG-target target-nres/target-reso >>>>> 1iwg 225.00 975 7.957 >>>>> >>>>> CPU Time: 0 days 0 hrs 0 mins 2.52 secs ( 2.52 secs) >>>>> Finished: Tue Aug 14 22:53:59 2018 >>>>> >>>>> >>>>> ****************************************************************************************** >>>>> *** Phaser Module: AUTOMATED MOLECULAR >>>>> REPLACEMENT 2.7.17 *** >>>>> >>>>> ****************************************************************************************** >>>>> >>>>> ** Search Order (next search *) (placed +): >>>>> ** #1 1iwg * >>>>> >>>>> CPU Time: 0 days 0 hrs 0 mins 2.52 secs ( 2.52 secs) >>>>> Finished: Tue Aug 14 22:53:59 2018 >>>>> >>>>> >>>>> ****************************************************************************************** >>>>> *** Phaser Module: MOLECULAR REPLACEMENT ROTATION >>>>> FUNCTION 2.7.17 *** >>>>> >>>>> ****************************************************************************************** >>>>> >>>>> <!--SUMMARY_END--> >>>>> ----------------- >>>>> TRANSLATIONAL NCS >>>>> ----------------- >>>>> >>>>> tNCS not present >>>>> >>>>> -------------------------- >>>>> DATA FOR ROTATION FUNCTION >>>>> -------------------------- >>>>> >>>>> <!--SUMMARY_BEGIN--> >>>>> High resolution limit unaltered by RMS of ensemble >>>>> High resolution limit lowered by expected LLG = 7.96 >>>>> >>>>> <!--SUMMARY_END--> >>>>> Outliers with a probability less than 1e-06 will be rejected >>>>> Measurements with fewer bits of information than 0.01 will be >>>>> rejected: >>>>> threshold sigma(Eobs^2) for centrics/acentrics is 11.9664 / >>>>> 8.46225 >>>>> There were 0 (0.0000%) reflections rejected >>>>> >>>>> No reflections are outliers >>>>> >>>>> Resolution of All Data (Number): 6.42 80.31 (4110) >>>>> Resolution of Selected Data (Number): 7.96 80.31 (2540) >>>>> >>>>> ------------------- >>>>> 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 (2001) >>>>> - half number of centrics (539/2) >>>>> = -2270 >>>>> With correction for SigF, >>>>> Wilson log(likelihood) = -2257.01 >>>>> >>>>> ---------- >>>>> ENSEMBLING >>>>> ---------- >>>>> >>>>> Ensemble Generation: 1iwg >>>>> ------------------------- >>>>> Ensemble configured for structure factor interpolation >>>>> Ensemble configured to resolution 7.96 >>>>> >>>>> Electron Density Calculation >>>>> 0% 100% >>>>> |=======| DONE >>>>> >>>>> Ensemble Generation Table >>>>> ------------------------- >>>>> Resolution of Ensembles: 7.95683 >>>>> Ensemble Scat% Radius Model# Rel-B Input-RMS >>>>> Initial-Delta-VRMS Initial-RMS >>>>> 1iwg 94.0 47.81 1 201.6 0.700 >>>>> 0.000 0.700 >>>>> >>>>> ----------------- >>>>> ROTATION FUNCTION >>>>> ----------------- >>>>> >>>>> Ensemble configured to resolution 7.96 >>>>> Elmn for Search Ensemble >>>>> Spreading calculation onto 2 threads. >>>>> Elmn Calculation for Search Ensemble >>>>> >>>>> 0% 100% >>>>> >>>>> |====================================================================| DONE >>>>> >>>>> Target Function: FAST LERF1 >>>>> >>>>> ------------------------- >>>>> ROTATION FUNCTION #1 OF 1 >>>>> ------------------------- >>>>> >>>>> Search Ensemble: 1iwg >>>>> >>>>> Sampling: 4.77 degrees >>>>> >>>>> >>>>> Spherical Harmonics >>>>> ------------------- >>>>> Elmn for Data >>>>> Spreading calculation onto 2 threads. >>>>> Elmn Calculation for Data >>>>> >>>>> 0% >>>>> 100% >>>>> >>>>> |==========================================================================| >>>>> DONE >>>>> >>>>> Scanning the Range of Beta Angles >>>>> --------------------------------- >>>>> Spreading calculation onto 2 threads. >>>>> Clmn Calculation >>>>> 0% 100% >>>>> |====================| DONE >>>>> >>>>> Top Peaks Without Clustering >>>>> Select peaks over 67.5% of top (i.e. 0.675*(top-mean)+mean) >>>>> Also store peaks over 54% of top >>>>> There were 71 sites over 67.5% of top >>>>> 71 peaks selected >>>>> The sites over 67.5% are: >>>>> # Euler1 Euler2 Euler3 FSS Z-score >>>>> 1 72.8 0.4 169.6 100.000 6.61 >>>>> 2 81.3 1.2 283.6 96.355 6.37 >>>>> 3 96.9 1.0 27.3 94.975 6.28 >>>>> #Sites = 71: output truncated to 3 sites >>>>> >>>>> Top 71 rotations before clustering will be rescored >>>>> Spreading calculation onto 2 threads >>>>> Calculating Likelihood for RF #1 of 1 >>>>> 0% 100% >>>>> |=====================================| DONE >>>>> >>>>> Mean and Standard Deviation >>>>> --------------------------- >>>>> Scoring 500 randomly sampled rotations >>>>> Spreading calculation onto 2 threads >>>>> Generating Statistics for RF #1 of 1 >>>>> 0% 100% >>>>> |===============================================================| >>>>> DONE >>>>> >>>>> Highest Score (Z-score): 108.746 ( 6.87) >>>>> >>>>> Top Peaks With Clustering >>>>> Select peaks over 75% of top (i.e. 0.75*(top-mean)+mean) >>>>> Also store peaks over 60% of top >>>>> There was 1 site over 75% of top >>>>> The sites over 75% are: >>>>> # Euler1 Euler2 Euler3 LLG Z-score Split #Group >>>>> FSS-this-ang/FSS-top >>>>> 1 72.8 0.4 169.6 108.75 6.87 0.0 37 >>>>> 100.000/ 100.000 >>>>> 192.8 0.4 169.6 >>>>> 312.8 0.4 169.6 >>>>> 47.2 179.6 349.6 >>>>> 167.2 179.6 349.6 >>>>> 287.2 179.6 349.6 >>>>> >>>>> <!--SUMMARY_BEGIN--> >>>>> Rotation Function Table: 1iwg >>>>> ----------------------------- >>>>> (Z-scores from Fast Rotation Function) >>>>> #SET Top (Z) Second (Z) Third (Z) >>>>> 1 108.75 6.87 --- --- --- --- >>>>> >>>>> <!--SUMMARY_END--> >>>>> --------------- >>>>> FINAL SELECTION >>>>> --------------- >>>>> >>>>> <!--SUMMARY_BEGIN--> >>>>> Select by Percentage of Top value: 75% >>>>> Top RF = 108.746 >>>>> Purge RF mean = -42.583 >>>>> 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) >>>>> Percent used for purge = 60.000% >>>>> Includes deep search down percent = 15% >>>>> Number of solutions stored above (below) deep threshold = 1 (0) >>>>> >>>>> Rotation Function Final Selection Table >>>>> --------------------------------------- >>>>> Rotation list length by SET >>>>> SET# Start Final Deleted Set (*) Deep: Start Final Deleted Set >>>>> (*) >>>>> 1 1 1 - 1 1 - >>>>> ALL 1 1 1 1 >>>>> >>>>> <!--SUMMARY_END--> >>>>> $TABLE : Rotation Function Component #1 (1iwg) : >>>>> $GRAPHS >>>>> :RF Number vs LL-gain:AUTO:1,2: :RF Number vs Z-Score:AUTO:1,3: >>>>> $$ >>>>> Number LLG Z-Score >>>>> $$ loggraph $$ >>>>> 1 108.75 6.87 >>>>> $$ >>>>> <!--SUMMARY_BEGIN--> >>>>> ------------ >>>>> OUTPUT FILES >>>>> ------------ >>>>> >>>>> No files output >>>>> >>>>> CPU Time: 0 days 0 hrs 0 mins 35.42 secs ( 35.42 secs) >>>>> Finished: Tue Aug 14 22:54:17 2018 >>>>> >>>>> >>>>> ****************************************************************************************** >>>>> *** Phaser Module: MOLECULAR REPLACEMENT TRANSLATION >>>>> FUNCTION 2.7.17 *** >>>>> >>>>> ****************************************************************************************** >>>>> >>>>> <!--SUMMARY_END--> >>>>> ----------------- >>>>> TRANSLATIONAL NCS >>>>> ----------------- >>>>> >>>>> tNCS not present >>>>> >>>>> ----------------------------- >>>>> DATA FOR TRANSLATION FUNCTION >>>>> ----------------------------- >>>>> >>>>> High Resolution Limit imposed by RF list = 7.96 >>>>> Outliers with a probability less than 1e-06 will be rejected >>>>> Measurements with fewer bits of information than 0.01 will be >>>>> rejected: >>>>> threshold sigma(Eobs^2) for centrics/acentrics is 11.9664 / >>>>> 8.46225 >>>>> There were 0 (0.0000%) reflections rejected >>>>> >>>>> No reflections are outliers >>>>> >>>>> <!--SUMMARY_BEGIN--> >>>>> Resolution of All Data (Number): 6.42 80.31 (4110) >>>>> Resolution of Selected Data (Number): 7.96 80.31 (2540) >>>>> >>>>> <!--SUMMARY_END--> >>>>> ------------------- >>>>> 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 (2001) >>>>> - half number of centrics (539/2) >>>>> = -2270 >>>>> With correction for SigF, >>>>> Wilson log(likelihood) = -2257.01 >>>>> >>>>> <!--SUMMARY_BEGIN--> >>>>> ------------------------ >>>>> ALTERNATIVE SPACE GROUPS >>>>> ------------------------ >>>>> >>>>> Space Group(s) to be tested: >>>>> H 3 2 >>>>> >>>>> <!--SUMMARY_END--> >>>>> ---------- >>>>> ENSEMBLING >>>>> ---------- >>>>> >>>>> Ensemble Generation Table >>>>> ------------------------- >>>>> Resolution of Ensembles: 7.95683 >>>>> Ensemble Scat% Radius Model# Rel-B Input-RMS >>>>> Initial-Delta-VRMS Initial-RMS >>>>> 1iwg 94.0 47.81 1 201.6 0.700 >>>>> 0.000 0.700 >>>>> >>>>> Trace Generation: 1iwg >>>>> ---------------------- >>>>> This trace is from coordinates >>>>> Calculate Hexagonal Grid... >>>>> Sampling #1: 5.73554 Angstroms >>>>> Sampling #2: 11.4711 Angstroms >>>>> Sampling #3: 8.60331 Angstroms >>>>> Sampling #4: 7.16942 Angstroms >>>>> Sampling #5: 6.45248 Angstroms >>>>> Sampling #6: 6.09401 Angstroms >>>>> Done >>>>> >>>>> Trace Generation Table >>>>> ---------------------- >>>>> Ensemble Trace-type Length Sampling Close-contact >>>>> 1iwg 933 6.09 3.52 >>>>> >>>>> --------------------- >>>>> TRANSLATION FUNCTIONS >>>>> --------------------- >>>>> >>>>> Target Function: FAST LETF1 >>>>> Translation Packing Function applied: top peak will pack >>>>> Translation Packing Cutoff: 50% >>>>> Sampling: 1.99 Angstroms >>>>> >>>>> <!--SUMMARY_BEGIN--> >>>>> ---------------------------- >>>>> TRANSLATION FUNCTION #1 OF 1 >>>>> ---------------------------- >>>>> >>>>> <!--SUMMARY_END--> >>>>> SOLU SET >>>>> SOLU SPAC H 3 2 >>>>> SOLU TRIAL ENSEMBLE 1iwg EULER 72.809 0.445 169.630 RFZ 6.87 >>>>> >>>>> <!--SUMMARY_BEGIN--> >>>>> This set has one trial orientation >>>>> >>>>> <!--SUMMARY_END--> >>>>> # Euler Rot-LLG Ensemble >>>>> 1 72.8 0.4 169.6 108.7 1iwg >>>>> >>>>> Scoring 500 randomly sampled orientations and translations >>>>> Spreading calculation onto 2 threads. >>>>> Generating Statistics for TF SET #1 of 1 >>>>> 0% 100% >>>>> |==| DONE >>>>> >>>>> Mean Score (Sigma): -123.71 (25.49) >>>>> >>>>> SET #1 of 1 TRIAL #1 of 1 >>>>> ------------------------- >>>>> Ensemble 1iwg Euler 72.81 0.44 169.63 >>>>> >>>>> Doing Fast Translation Function FFT... >>>>> Done >>>>> >>>>> Packing Fast Search Translations... >>>>> 15190 peaks >>>>> 500 peaks over 166.913 checked for packing >>>>> Translation peak 1 first to be kept >>>>> Done >>>>> >>>>> <!--SUMMARY_BEGIN--> >>>>> New Top Packing Fast Translation Function FSS = 566.01 (TFZ=18.3) >>>>> at Trial #1 >>>>> <!--SUMMARY_END--> >>>>> >>>>> Top Peaks Without Clustering >>>>> Select peaks over 67.5% of top (i.e. 0.675*(top-mean)+mean) >>>>> There were 30 sites over 67.5% of top >>>>> 30 peaks selected >>>>> The sites over 67.5% are: >>>>> # Frac X Frac Y Frac Z FSS Z-score >>>>> 1 0.286 0.631 0.658 566.01 18.30 >>>>> 2 0.285 0.631 0.875 342.97 9.74 >>>>> 3 0.286 0.631 0.649 339.29 9.60 >>>>> #Sites = 30: output truncated to 3 sites >>>>> >>>>> Top 30 translations before clustering will be rescored >>>>> Spreading calculation onto 2 threads. >>>>> Calculating Likelihood for TF SET #1 of 1 TRIAL #1 of 1 >>>>> 0% 100% >>>>> |================| DONE >>>>> >>>>> Packing LLG Translations: pass 1 of 11... >>>>> 30 peaks >>>>> 1 peaks over 388.416 checked for packing >>>>> Translation peak 1 first to be kept >>>>> Done >>>>> Exit: found a peak that packs >>>>> >>>>> <!--SUMMARY_BEGIN--> >>>>> New Top (ML) Translation Function LLG = 388.42 (TFZ=18.3) at Trial >>>>> #1 >>>>> <!--SUMMARY_END--> >>>>> Top Peaks With Clustering >>>>> Select peaks over 75% of top (i.e. 0.75*(top-mean)+mean) >>>>> There were 21 sites over 75% of top >>>>> The sites over 75% are: >>>>> # Frac X Frac Y Frac Z LLG Z-score Split #Group >>>>> FSS-this-xyz/FSS-top >>>>> 1 0.286 0.631 0.658 388.42 18.30 0.0 4 >>>>> 566.01/ 566.01 >>>>> 2 0.285 0.631 0.540 134.76 9.21 60.9 1 >>>>> 329.09/ 329.09 >>>>> 3 0.285 0.631 0.875 128.00 9.74 111.5 1 >>>>> 342.97/ 342.97 >>>>> #SITES = 21: OUTPUT TRUNCATED TO 3 SITES >>>>> >>>>> <!--SUMMARY_BEGIN--> >>>>> Translation Function Table >>>>> -------------------------- >>>>> SET ROT*deep Top (Z) Second (Z) Third (Z) Ensemble >>>>> SpaceGroup >>>>> 1 1 388.4 18.30 134.8 9.21 128.0 9.74 1iwg >>>>> H 3 2 >>>>> --- --- >>>>> >>>>> --------------- >>>>> FINAL SELECTION >>>>> --------------- >>>>> >>>>> LLG will be used for purge, not FSS >>>>> Top TF = 388.42 >>>>> Top TFZ = 18.30 >>>>> Mean TF = -123.71 >>>>> Percent used for purge = 75% >>>>> Cutoff for acceptance = 260.4 >>>>> TFZ used for final selection = 9.15081 >>>>> Number of solutions over TF final cutoff = 1 >>>>> Number of solutions over TFZ final cutoff = 7 >>>>> Number of solutions over TF & TFZ cutoff = 1 >>>>> Number of solutions stored before final selection = 21 >>>>> Number of solutions stored (deleted) after final selection = 7 (14) >>>>> >>>>> <!--SUMMARY_END--> >>>>> $TABLE : Translation Function Component #1 (1iwg): >>>>> $GRAPHS >>>>> :TF Number vs LL-gain:AUTO:1,2: :TF Number vs Z-Score:AUTO:1,3: >>>>> $$ >>>>> Number LLG Z-Score >>>>> $$ loggraph $$ >>>>> 1 388.42 18.30 >>>>> 2 134.76 9.21 >>>>> 3 128.00 9.74 >>>>> 4 119.63 9.40 >>>>> 5 116.37 9.37 >>>>> 6 116.15 9.46 >>>>> 7 116.13 9.16 >>>>> $$ >>>>> <!--SUMMARY_BEGIN--> >>>>> ------------ >>>>> OUTPUT FILES >>>>> ------------ >>>>> >>>>> No files output >>>>> >>>>> CPU Time: 0 days 0 hrs 0 mins 42.29 secs ( 42.29 secs) >>>>> Finished: Tue Aug 14 22:54:22 2018 >>>>> >>>>> >>>>> ****************************************************************************************** >>>>> *** Phaser Module: MOLECULAR REPLACEMENT PACKING >>>>> ANALYSIS 2.7.17 *** >>>>> >>>>> ****************************************************************************************** >>>>> >>>>> <!--SUMMARY_END--> >>>>> --------- >>>>> ENSEMBLES >>>>> --------- >>>>> >>>>> Trace Generation Table >>>>> ---------------------- >>>>> Ensemble Trace-type Length Sampling Close-contact >>>>> 1iwg 933 6.09 3.52 >>>>> >>>>> ----------------- >>>>> ENSEMBLE SYMMETRY >>>>> ----------------- >>>>> >>>>> Ensemble "1iwg" Point Group: 1 >>>>> >>>>> Clash background has been packed at 10.00% >>>>> >>>>> ---------------- >>>>> PACKING FUNCTION >>>>> ---------------- >>>>> >>>>> There are 7 solutions to pack >>>>> Spreading calculation onto 2 threads. >>>>> Packing analysis >>>>> 0% 100% >>>>> |=====| DONE >>>>> >>>>> <!--SUMMARY_BEGIN--> >>>>> Packing Table >>>>> ------------- >>>>> Solutions accepted if pairwise clashes less than 10 % of trace atoms >>>>> #in #out Clash-% Symm TF-SET ROT TFpk# TF TFZ >>>>> SpaceGroup >>>>> 1 Top1 8.039 -- 1 1 1 388.42 18.30 H 3 >>>>> 2 >>>>> 2 --- 17.04 -- 1 1 2 134.76 9.21 H 3 >>>>> 2 >>>>> 3 --- 97.43 -- 1 1 3 128.00 9.74 H 3 >>>>> 2 >>>>> 4 --- 34.08 -- 1 1 4 119.63 9.40 H 3 >>>>> 2 >>>>> 5 --- 45.34 -- 1 1 5 116.37 9.37 H 3 >>>>> 2 >>>>> 6 --- 20.69 -- 1 1 6 116.15 9.46 H 3 >>>>> 2 >>>>> 7 --- 83.17 -- 1 1 7 116.13 9.16 H 3 >>>>> 2 >>>>> >>>>> 1 accepted of 7 solutions >>>>> 1 packs of 1 accepted solution >>>>> >>>>> ------------ >>>>> OUTPUT FILES >>>>> ------------ >>>>> >>>>> No files output >>>>> >>>>> CPU Time: 0 days 0 hrs 0 mins 46.04 secs ( 46.04 secs) >>>>> Finished: Tue Aug 14 22:54:24 2018 >>>>> >>>>> >>>>> ****************************************************************************************** >>>>> *** Phaser Module: MOLECULAR REPLACEMENT REFINEMENT AND >>>>> PHASING 2.7.17 *** >>>>> >>>>> ****************************************************************************************** >>>>> >>>>> <!--SUMMARY_END--> >>>>> ----------------- >>>>> TRANSLATIONAL NCS >>>>> ----------------- >>>>> >>>>> tNCS not present >>>>> >>>>> ------------------------------- >>>>> DATA FOR REFINEMENT AND PHASING >>>>> ------------------------------- >>>>> >>>>> High resolution limit imposed by solution list = 7.96 >>>>> >>>>> Outliers with a probability less than 1e-06 will be rejected >>>>> Measurements with fewer bits of information than 0.01 will be >>>>> rejected: >>>>> threshold sigma(Eobs^2) for centrics/acentrics is 11.9664 / >>>>> 8.46225 >>>>> There were 0 (0.0000%) reflections rejected >>>>> >>>>> No reflections are outliers >>>>> >>>>> <!--SUMMARY_BEGIN--> >>>>> Resolution of All Data (Number): 6.42 80.31 (4110) >>>>> Resolution of Selected Data (Number): 7.96 80.31 (2540) >>>>> >>>>> <!--SUMMARY_END--> >>>>> ------------------- >>>>> 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 (2001) >>>>> - half number of centrics (539/2) >>>>> = -2270 >>>>> With correction for SigF, >>>>> Wilson log(likelihood) = -2257.01 >>>>> >>>>> ---------- >>>>> ENSEMBLING >>>>> ---------- >>>>> >>>>> Ensemble Generation Table >>>>> ------------------------- >>>>> Resolution of Ensembles: 7.95683 >>>>> Ensemble Scat% Radius Model# Rel-B Input-RMS >>>>> Initial-Delta-VRMS Initial-RMS >>>>> 1iwg 94.0 47.81 1 201.6 0.700 >>>>> 0.000 0.700 >>>>> >>>>> ---------- >>>>> REFINEMENT >>>>> ---------- >>>>> >>>>> Protocol cycle #1 of 1 >>>>> Refinement protocol for this macrocycle: >>>>> ROTATION : REFINE >>>>> TRANSLATION : REFINE >>>>> BFACTOR : REFINE >>>>> MODEL VRMS : FIX >>>>> MAP CELL SCALE: FIX >>>>> MAP OFACTOR : FIX >>>>> LAST ONLY : FALSE >>>>> >>>>> There is 1 solution to refine >>>>> Spreading calculation onto 2 threads. >>>>> Refining solutions >>>>> 0% 100% >>>>> |==| DONE >>>>> >>>>> >>>>> REFINING SET #1 OF 1 >>>>> -------------------- >>>>> Initial Parameters: >>>>> SOLU SET >>>>> SOLU 6DIM ENSE 1iwg EULER 47.2 179.6 349.6 FRAC 0.30 -0.38 >>>>> 0.67 BFAC 0.00 >>>>> >>>>> Performing Optimization... >>>>> Done >>>>> --- Convergence before iteration limit (50) at cycle 4 --- >>>>> Start-this-macrocycle End-this-macrocycle Change-this-macrocycle >>>>> 388.816 419.382 30.566 >>>>> >>>>> Final Parameters: >>>>> SOLU SET >>>>> SOLU 6DIM ENSE 1iwg EULER 175.4 179.4 117.6 FRAC 0.34 -0.37 >>>>> 0.67 BFAC -2.34 >>>>> >>>>> --------------- >>>>> TFZ EQUIVALENTS >>>>> --------------- >>>>> >>>>> Refined TFZ equivalents calculated >>>>> 1 top TFZ equivalents calculated >>>>> 1 (Topfiles) >>>>> 0 with TFZ > 6 (TFZ for Possibly Solved) >>>>> >>>>> SOLUTION #1 OF 1 >>>>> ---------------- >>>>> TOPFILE >>>>> TFZ equivalent calculation #1 of 1 >>>>> >>>>> Spreading calculation onto 2 threads. >>>>> Generating Statistics >>>>> 0% 100% >>>>> |===============================================================| >>>>> DONE >>>>> >>>>> Mean Score (Sigma): -132.37 (26.75) >>>>> Refined TF/TFZ equivalent = 419.65/ 20.6 (Unrefined TF/TFZ=388.42/ >>>>> 18.3) >>>>> >>>>> Mean and Sigma after Refinement (for Purge) >>>>> ------------------------------------------- >>>>> Scoring 500 randomly sampled orientations and translations >>>>> >>>>> Spreading calculation onto 2 threads. >>>>> Generating Statistics >>>>> 0% 100% >>>>> |==| DONE >>>>> >>>>> Mean Score for Purge before Refinement: -123.71 >>>>> Mean Score for Purge after Refinement : -132.37 >>>>> >>>>> $TABLE : Refinement After Placing Component #1 (1iwg 7.96A) : >>>>> $GRAPHS >>>>> :Solution Number vs LL-gain:AUTO:1,2,3: :Solution Number vs >>>>> R-value:AUTO:1,4,5: >>>>> $$ >>>>> Number final-LLG initial-LLG final-R initial-R >>>>> $$ loggraph $$ >>>>> 1 419.65 388.42 51.35 52.34 >>>>> $$ >>>>> --------------- >>>>> FIND DUPLICATES >>>>> --------------- >>>>> >>>>> Check for nearly equivalent solutions >>>>> Spreading calculation onto 2 threads. >>>>> Calculating Duplicates for 1 solutions >>>>> 0% 100% >>>>> |==| DONE >>>>> >>>>> No duplicate solutions found >>>>> >>>>> --------------------- >>>>> FIND TEMPLATE MATCHES >>>>> --------------------- >>>>> >>>>> No Template Solution(s) for comparison >>>>> >>>>> <!--SUMMARY_BEGIN--> >>>>> --------------- >>>>> PURGE SELECTION >>>>> --------------- >>>>> >>>>> Purge solutions according to highest LLG from Refinement >>>>> -------------------------------------------------------- >>>>> Top LLG (all) = 419.645 >>>>> Top LLG (packs) = 419.645 >>>>> Mean LLG = -132.366 >>>>> Percent used for purge = 75% >>>>> Cutoff for acceptance = 281.6 >>>>> Overall cutoff for acceptance (excluding high TFZ) = 419.6 >>>>> Number of solutions stored before purge = 1 >>>>> Number of solutions stored (deleted) after purge = 1 (0) >>>>> >>>>> ------- >>>>> RESULTS >>>>> ------- >>>>> >>>>> Refinement Table (Sorted) >>>>> ------------------------- >>>>> #out =#out #in =T (Start LLG Rval TFZ) (Refined LLG Rval TFZ==) >>>>> SpaceGroup Cntrst >>>>> Top1 --- 1 388.4 52.3 18.3 419.6 51.3 20.6 H 3 >>>>> 2 n/a >>>>> >>>>> Refinement Table (Variance Ranges) >>>>> ---------------------------------- >>>>> Range of delta-VRMS and VRMS given over current solution list (1 >>>>> solution(s)) >>>>> Ensemble Model# RMS Delta-VRMS min/max (VRMS min/max) >>>>> 1iwg 1 0.700 +0.000/+0.000 ( 0.700/ 0.700 ) >>>>> >>>>> <!--SUMMARY_END--> >>>>> ------------ >>>>> OUTPUT FILES >>>>> ------------ >>>>> >>>>> Calculation of Map Coefficients >>>>> ------------------------------- >>>>> 1 top map coefficients calculated >>>>> >>>>> Map coefficient calculated for top solution #1 >>>>> SOLU SPAC H 3 2 >>>>> SOLU 6DIM ENSE 1iwg EULER 64.6 0.6 297.6 FRAC -0.00 -0.04 >>>>> -0.01 BFAC -2.34 #TFZ==20.6 >>>>> >>>>> No files output >>>>> >>>>> <!--SUMMARY_BEGIN--> >>>>> CPU Time: 0 days 0 hrs 0 mins 49.59 secs ( 49.59 secs) >>>>> Finished: Tue Aug 14 22:54:26 2018 >>>>> >>>>> >>>>> ****************************************************************************************** >>>>> *** Phaser Module: AUTOMATED MOLECULAR >>>>> REPLACEMENT 2.7.17 *** >>>>> >>>>> ****************************************************************************************** >>>>> >>>>> ** Current is Best Solution (first search) >>>>> ** Current solution has 1 component >>>>> ** New Best LLG = 419.6 (resolution = 7.96) >>>>> ** Best Component so far = 1iwg >>>>> >>>>> CPU Time: 0 days 0 hrs 0 mins 49.59 secs ( 49.59 secs) >>>>> Finished: Tue Aug 14 22:54:26 2018 >>>>> >>>>> >>>>> ****************************************************************************************** >>>>> *** Phaser Module: AUTOMATED MOLECULAR >>>>> REPLACEMENT 2.7.17 *** >>>>> >>>>> ****************************************************************************************** >>>>> >>>>> ** Solutions will be refined to highest resolution >>>>> ** Protocol for MR refinement is DEFAULT >>>>> ** VRMS (variances) of ensemble(s) WILL be refined >>>>> >>>>> CPU Time: 0 days 0 hrs 0 mins 49.61 secs ( 49.61 secs) >>>>> Finished: Tue Aug 14 22:54:26 2018 >>>>> >>>>> >>>>> ****************************************************************************************** >>>>> *** Phaser Module: MOLECULAR REPLACEMENT REFINEMENT AND >>>>> PHASING 2.7.17 *** >>>>> >>>>> ****************************************************************************************** >>>>> >>>>> <!--SUMMARY_END--> >>>>> ----------------- >>>>> TRANSLATIONAL NCS >>>>> ----------------- >>>>> >>>>> tNCS not present >>>>> >>>>> ------------------------------- >>>>> DATA FOR REFINEMENT AND PHASING >>>>> ------------------------------- >>>>> >>>>> Outliers with a probability less than 1e-06 will be rejected >>>>> Measurements with fewer bits of information than 0.01 will be >>>>> rejected: >>>>> threshold sigma(Eobs^2) for centrics/acentrics is 11.9664 / >>>>> 8.46225 >>>>> There were 0 (0.0000%) reflections rejected >>>>> >>>>> No reflections are outliers >>>>> >>>>> <!--SUMMARY_BEGIN--> >>>>> Resolution of All Data (Number): 6.42 80.31 (4110) >>>>> Resolution of Selected Data (Number): 6.42 80.31 (4110) >>>>> >>>>> <!--SUMMARY_END--> >>>>> ------------------- >>>>> 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 (3340) >>>>> - half number of centrics (770/2) >>>>> = -3725 >>>>> With correction for SigF, >>>>> Wilson log(likelihood) = -3732.99 >>>>> >>>>> ---------- >>>>> ENSEMBLING >>>>> ---------- >>>>> >>>>> Ensemble Generation: 1iwg >>>>> ------------------------- >>>>> Ensemble configured for structure factor interpolation >>>>> Ensemble configured to resolution 6.42 >>>>> >>>>> Electron Density Calculation >>>>> 0% 100% >>>>> |=======| DONE >>>>> >>>>> Ensemble Generation Table >>>>> ------------------------- >>>>> Resolution of Ensembles: 6.41564 >>>>> Ensemble Scat% Radius Model# Rel-B Input-RMS >>>>> Initial-Delta-VRMS Initial-RMS >>>>> 1iwg 94.0 47.81 1 87.5 0.700 >>>>> 0.000 0.700 >>>>> >>>>> ---------- >>>>> REFINEMENT >>>>> ---------- >>>>> >>>>> Protocol cycle #1 of 1 >>>>> Refinement protocol for this macrocycle: >>>>> ROTATION : REFINE >>>>> TRANSLATION : REFINE >>>>> BFACTOR : REFINE >>>>> MODEL VRMS : REFINE >>>>> MAP CELL SCALE: FIX >>>>> MAP OFACTOR : FIX >>>>> LAST ONLY : FALSE >>>>> >>>>> There is 1 solution to refine >>>>> Spreading calculation onto 2 threads. >>>>> Refining solutions >>>>> 0% 100% >>>>> |==| DONE >>>>> >>>>> >>>>> REFINING SET #1 OF 1 >>>>> -------------------- >>>>> Initial Parameters: >>>>> SOLU SET >>>>> SOLU 6DIM ENSE 1iwg EULER 64.6 0.6 297.6 FRAC -0.00 -0.04 >>>>> -0.01 BFAC -2.34 #TFZ==20.6 >>>>> >>>>> Performing Optimization... >>>>> Done >>>>> --- Convergence before iteration limit (50) at cycle 4 --- >>>>> Start-this-macrocycle End-this-macrocycle Change-this-macrocycle >>>>> 770.595 788.505 17.911 >>>>> >>>>> Final Parameters: >>>>> SOLU SET >>>>> SOLU 6DIM ENSE 1iwg EULER 61.1 0.3 301.3 FRAC 0.01 -0.03 >>>>> -0.01 BFAC -2.06 #TFZ==20.6 >>>>> SOLU ENSEMBLE 1iwg VRMS DELTA -0.0818 #RMSD 0.70 #VRMS 0.64 >>>>> >>>>> --------------- >>>>> TFZ EQUIVALENTS >>>>> --------------- >>>>> >>>>> Refined TFZ equivalents calculated >>>>> 1 top TFZ equivalents calculated >>>>> 1 (Topfiles) >>>>> 0 with TFZ > 6 (TFZ for Possibly Solved) >>>>> >>>>> SOLUTION #1 OF 1 >>>>> ---------------- >>>>> TOPFILE >>>>> TFZ equivalent calculation #1 of 1 >>>>> >>>>> Spreading calculation onto 2 threads. >>>>> Generating Statistics >>>>> 0% 100% >>>>> |===============================================================| >>>>> DONE >>>>> >>>>> Mean Score (Sigma): -629.68 (55.06) >>>>> Refined TF/TFZ equivalent = 786.72/ 25.7 (Unrefined TF/TFZ=769.93/ >>>>> 20.6) >>>>> >>>>> Mean and Sigma after Refinement (for Purge) >>>>> ------------------------------------------- >>>>> Scoring 500 randomly sampled orientations and translations >>>>> >>>>> Spreading calculation onto 2 threads. >>>>> Generating Statistics >>>>> 0% 100% >>>>> |==| DONE >>>>> >>>>> Mean Score for Purge before Refinement: -132.37 >>>>> Mean Score for Purge after Refinement : -629.68 >>>>> >>>>> $TABLE : Refinement After Placing Component #1 (1iwg 6.42A) : >>>>> $GRAPHS >>>>> :Solution Number vs LL-gain:AUTO:1,2,3: :Solution Number vs >>>>> R-value:AUTO:1,4,5: >>>>> $$ >>>>> Number final-LLG initial-LLG final-R initial-R >>>>> $$ loggraph $$ >>>>> 1 786.72 769.93 50.27 50.69 >>>>> $$ >>>>> --------------- >>>>> FIND DUPLICATES >>>>> --------------- >>>>> >>>>> Check for nearly equivalent solutions >>>>> Spreading calculation onto 2 threads. >>>>> Calculating Duplicates for 1 solutions >>>>> 0% 100% >>>>> |==| DONE >>>>> >>>>> No duplicate solutions found >>>>> >>>>> --------------------- >>>>> FIND TEMPLATE MATCHES >>>>> --------------------- >>>>> >>>>> No Template Solution(s) for comparison >>>>> >>>>> <!--SUMMARY_BEGIN--> >>>>> --------------- >>>>> PURGE SELECTION >>>>> --------------- >>>>> >>>>> Purge solutions according to highest LLG from Refinement >>>>> -------------------------------------------------------- >>>>> Top LLG (all) = 786.716 >>>>> Top LLG (packs) = 786.716 >>>>> Mean LLG = -629.685 >>>>> Percent used for purge = 75% >>>>> Cutoff for acceptance = 432.6 >>>>> Overall cutoff for acceptance (excluding high TFZ) = 786.7 >>>>> Number of solutions stored before purge = 1 >>>>> Number of solutions stored (deleted) after purge = 1 (0) >>>>> >>>>> ------- >>>>> RESULTS >>>>> ------- >>>>> >>>>> Refinement Table (Sorted) >>>>> ------------------------- >>>>> Refinement to full resolution >>>>> #out =#out #in =T (Start LLG Rval TFZ) (Refined LLG Rval TFZ==) >>>>> SpaceGroup Cntrst >>>>> Top1 --- 1 769.9 50.7 20.6 786.7 50.3 25.7 H 3 >>>>> 2 n/a >>>>> >>>>> Refinement Table (Variance Ranges) >>>>> ---------------------------------- >>>>> Range of delta-VRMS and VRMS given over current solution list (1 >>>>> solution(s)) >>>>> Ensemble Model# RMS Delta-VRMS min/max (VRMS min/max) >>>>> 1iwg 1 0.700 -0.082/-0.082 ( 0.638/ 0.638 ) >>>>> >>>>> <!--SUMMARY_END--> >>>>> ------------ >>>>> OUTPUT FILES >>>>> ------------ >>>>> >>>>> Calculation of Map Coefficients >>>>> ------------------------------- >>>>> 1 top map coefficients calculated >>>>> >>>>> Map coefficient calculated for top solution #1 >>>>> SOLU SPAC H 3 2 >>>>> SOLU 6DIM ENSE 1iwg EULER 61.1 0.3 301.3 FRAC 0.01 -0.03 >>>>> -0.01 BFAC -2.06 #TFZ==25.7 >>>>> SOLU ENSEMBLE 1iwg VRMS DELTA -0.0818 #RMSD 0.70 #VRMS 0.64 >>>>> >>>>> No files output >>>>> >>>>> <!--SUMMARY_BEGIN--> >>>>> CPU Time: 0 days 0 hrs 1 mins 1.09 secs ( 61.09 secs) >>>>> Finished: Tue Aug 14 22:54:34 2018 >>>>> >>>>> >>>>> ****************************************************************************************** >>>>> *** Phaser Module: AUTOMATED MOLECULAR >>>>> REPLACEMENT 2.7.17 *** >>>>> >>>>> ****************************************************************************************** >>>>> >>>>> ** Refinement may have introduced clashes >>>>> ** Packing will be checked >>>>> >>>>> CPU Time: 0 days 0 hrs 1 mins 1.09 secs ( 61.09 secs) >>>>> Finished: Tue Aug 14 22:54:34 2018 >>>>> >>>>> >>>>> ****************************************************************************************** >>>>> *** Phaser Module: MOLECULAR REPLACEMENT PACKING >>>>> ANALYSIS 2.7.17 *** >>>>> >>>>> ****************************************************************************************** >>>>> >>>>> <!--SUMMARY_END--> >>>>> --------- >>>>> ENSEMBLES >>>>> --------- >>>>> >>>>> Trace Generation Table >>>>> ---------------------- >>>>> Ensemble Trace-type Length Sampling Close-contact >>>>> 1iwg 933 6.09 3.52 >>>>> >>>>> ----------------- >>>>> ENSEMBLE SYMMETRY >>>>> ----------------- >>>>> >>>>> Ensemble "1iwg" Point Group: 1 >>>>> >>>>> Clash background has been packed at 10.00% >>>>> >>>>> ---------------- >>>>> PACKING FUNCTION >>>>> ---------------- >>>>> >>>>> There is 1 solution to pack >>>>> Spreading calculation onto 2 threads. >>>>> Packing analysis >>>>> 0% 100% >>>>> |==| DONE >>>>> >>>>> <!--SUMMARY_BEGIN--> >>>>> Packing Table >>>>> ------------- >>>>> Solutions accepted if pairwise clashes less than 10 % of trace atoms >>>>> #in #out Clash-% Symm SpaceGroup >>>>> Annotation >>>>> 1 Top1 8.467 -- H 3 2 ... TFZ=18.3 PAK=8 LLG=420 >>>>> TFZ==20.6 LLG=787 TFZ==25.7 PAK=8 >>>>> >>>>> 1 accepted of 1 solutions >>>>> 1 packs of 1 accepted solution >>>>> >>>>> ------------ >>>>> OUTPUT FILES >>>>> ------------ >>>>> >>>>> No files output >>>>> >>>>> CPU Time: 0 days 0 hrs 1 mins 2.18 secs ( 62.18 secs) >>>>> Finished: Tue Aug 14 22:54:35 2018 >>>>> >>>>> >>>>> ****************************************************************************************** >>>>> *** Phaser Module: MOLECULAR REPLACEMENT REFINEMENT AND >>>>> PHASING 2.7.17 *** >>>>> >>>>> ****************************************************************************************** >>>>> >>>>> <!--SUMMARY_END--> >>>>> ----------------- >>>>> TRANSLATIONAL NCS >>>>> ----------------- >>>>> >>>>> tNCS not present >>>>> >>>>> ------------------------------- >>>>> DATA FOR REFINEMENT AND PHASING >>>>> ------------------------------- >>>>> >>>>> Outliers with a probability less than 1e-06 will be rejected >>>>> Measurements with fewer bits of information than 0.01 will be >>>>> rejected: >>>>> threshold sigma(Eobs^2) for centrics/acentrics is 11.9664 / >>>>> 8.46225 >>>>> There were 0 (0.0000%) reflections rejected >>>>> >>>>> No reflections are outliers >>>>> >>>>> <!--SUMMARY_BEGIN--> >>>>> Resolution of All Data (Number): 6.42 80.31 (4110) >>>>> Resolution of Selected Data (Number): 6.42 80.31 (4110) >>>>> >>>>> <!--SUMMARY_END--> >>>>> ------------------- >>>>> 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 (3340) >>>>> - half number of centrics (770/2) >>>>> = -3725 >>>>> With correction for SigF, >>>>> Wilson log(likelihood) = -3732.99 >>>>> >>>>> ---------- >>>>> ENSEMBLING >>>>> ---------- >>>>> >>>>> Ensemble Generation Table >>>>> ------------------------- >>>>> Resolution of Ensembles: 6.41564 >>>>> Ensemble Scat% Radius Model# Rel-B Input-RMS >>>>> Initial-Delta-VRMS Initial-RMS >>>>> 1iwg 94.0 47.81 1 87.5 0.700 >>>>> 0.000 0.700 >>>>> >>>>> ------- >>>>> SCORING >>>>> ------- >>>>> >>>>> There is 1 solution to score >>>>> Spreading calculation onto 2 threads. >>>>> Scoring solutions >>>>> 0% 100% >>>>> |==| DONE >>>>> >>>>> --------------- >>>>> TFZ EQUIVALENTS >>>>> --------------- >>>>> >>>>> Refined TFZ equivalents calculated >>>>> 1 top TFZ equivalents calculated >>>>> 1 (Topfiles) >>>>> 0 with TFZ > 6 (TFZ for Possibly Solved) >>>>> >>>>> SOLUTION #1 OF 1 >>>>> ---------------- >>>>> TOPFILE >>>>> TFZ equivalent calculation #1 of 1 >>>>> >>>>> Spreading calculation onto 2 threads. >>>>> Generating Statistics >>>>> 0% 100% >>>>> |===============================================================| >>>>> DONE >>>>> >>>>> Mean Score (Sigma): -629.68 (55.06) >>>>> Refined TF/TFZ equivalent = 786.72/ 25.7 (Unrefined TF/TFZ=786.72/ >>>>> 25.7) >>>>> >>>>> Mean and Sigma after Refinement (for Purge) >>>>> ------------------------------------------- >>>>> Scoring 500 randomly sampled orientations and translations >>>>> >>>>> Spreading calculation onto 2 threads. >>>>> Generating Statistics >>>>> 0% 100% >>>>> |==| DONE >>>>> >>>>> Mean Score for Purge before Refinement: -629.68 >>>>> Mean Score for Purge after Refinement : -629.68 >>>>> >>>>> $TABLE : Refinement After Placing Component #1 (1iwg 6.42A) : >>>>> $GRAPHS >>>>> :Solution Number vs LL-gain:AUTO:1,2,3: :Solution Number vs >>>>> R-value:AUTO:1,4,5: >>>>> $$ >>>>> Number final-LLG initial-LLG final-R initial-R >>>>> $$ loggraph $$ >>>>> 1 786.72 786.72 50.27 50.27 >>>>> $$ >>>>> --------------- >>>>> FIND DUPLICATES >>>>> --------------- >>>>> >>>>> Check for nearly equivalent solutions >>>>> Spreading calculation onto 2 threads. >>>>> Calculating Duplicates for 1 solutions >>>>> 0% 100% >>>>> |==| DONE >>>>> >>>>> No duplicate solutions found >>>>> >>>>> --------------------- >>>>> FIND TEMPLATE MATCHES >>>>> --------------------- >>>>> >>>>> No Template Solution(s) for comparison >>>>> >>>>> <!--SUMMARY_BEGIN--> >>>>> ------- >>>>> RESULTS >>>>> ------- >>>>> >>>>> Refinement Table (Sorted) >>>>> ------------------------- >>>>> Refinement to full resolution >>>>> #out =#out #in =T (Start LLG Rval TFZ) (Refined LLG Rval TFZ==) >>>>> SpaceGroup Cntrst >>>>> Top1 --- 1 786.7 50.3 n/a 786.7 50.3 25.7 H 3 >>>>> 2 n/a >>>>> >>>>> Refinement Table (Variance Ranges) >>>>> ---------------------------------- >>>>> Range of delta-VRMS and VRMS given over current solution list (1 >>>>> solution(s)) >>>>> Ensemble Model# RMS Delta-VRMS min/max (VRMS min/max) >>>>> 1iwg 1 0.700 -0.082/-0.082 ( 0.638/ 0.638 ) >>>>> >>>>> <!--SUMMARY_END--> >>>>> ------------ >>>>> OUTPUT FILES >>>>> ------------ >>>>> >>>>> Calculation of Map Coefficients >>>>> ------------------------------- >>>>> 1 top map coefficients calculated >>>>> >>>>> Map coefficient calculated for top solution #1 >>>>> SOLU SPAC H 3 2 >>>>> SOLU 6DIM ENSE 1iwg EULER 61.1 0.3 301.3 FRAC 0.01 -0.03 >>>>> -0.01 BFAC -2.06 #TFZ==25.7 >>>>> SOLU ENSEMBLE 1iwg VRMS DELTA -0.0818 #RMSD 0.70 #VRMS 0.64 >>>>> >>>>> No files output >>>>> >>>>> <!--SUMMARY_BEGIN--> >>>>> CPU Time: 0 days 0 hrs 1 mins 6.24 secs ( 66.24 secs) >>>>> Finished: Tue Aug 14 22:54:38 2018 >>>>> >>>>> >>>>> ****************************************************************************************** >>>>> *** Phaser Module: AUTOMATED MOLECULAR >>>>> REPLACEMENT 2.7.17 *** >>>>> >>>>> ****************************************************************************************** >>>>> >>>>> $TEXT:MR Result: $$ Baubles Markup $$ >>>>> >>>>> ** SINGLE solution >>>>> >>>>> ** Solution written to SOL file: >>>>> /Users/liwei/Desktop/Files/PROJECT2_1.sol >>>>> >>>>> ** Solution written to PDB file: >>>>> /Users/liwei/Desktop/Files/PROJECT2_1.1.pdb >>>>> ** Solution written to MTZ file: >>>>> /Users/liwei/Desktop/Files/PROJECT2_1.1.mtz >>>>> Solution annotation (history): >>>>> SOLU SET RFZ=6.9 TFZ=18.3 PAK=8 LLG=420 TFZ==20.6 LLG=787 >>>>> TFZ==25.7 PAK=8 LLG=787 TFZ==25.7 >>>>> SOLU SPAC H 3 2 >>>>> SOLU 6DIM ENSE 1iwg EULER 61.1 0.3 301.3 FRAC 0.01 -0.03 >>>>> -0.01 BFAC -2.06 #TFZ==25.7 >>>>> SOLU ENSEMBLE 1iwg VRMS DELTA -0.0818 #RMSD 0.70 #VRMS 0.64 >>>>> >>>>> $$ >>>>> CPU Time: 0 days 0 hrs 1 mins 6.46 secs ( 66.46 secs) >>>>> Finished: Tue Aug 14 22:54:38 2018 >>>>> >>>>> <!--SUMMARY_END--> >>>>> -------------------- >>>>> EXIT STATUS: SUCCESS >>>>> -------------------- >>>>> >>>>> <!--SUMMARY_BEGIN--> >>>>> CPU Time: 0 days 0 hrs 1 mins 6.47 secs ( 66.47 secs) >>>>> Finished: Tue Aug 14 22:54:38 2018 >>>>> >>>>> <!--SUMMARY_END--> >>>>> </pre> >>>>> </html> >>>>> >>>>> #CCP4I TERMINATION STATUS 1 >>>>> #CCP4I TERMINATION TIME 14 Aug 2018 22:54:39 >>>>> #CCP4I TERMINATION OUTPUT_FILES >>>>> /Users/liwei/Desktop/Files/PROJECT2_1.1.mtz PROJECT2 >>>>> /Users/liwei/Desktop/Files/PROJECT2_1.1.pdb PROJECT2 >>>>> /Users/liwei/Desktop/Files/PROJECT2_1.sol PROJECT2 >>>>> #CCP4I MESSAGE Task completed successfully >>>>> >>>>> >>>>> ------------------------------ >>>>> >>>>> To unsubscribe from the CCP4BB list, click the following link: >>>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 >>>>> >>>> >>>> ------------------------------ >>>> >>>> To unsubscribe from the CCP4BB list, click the following link: >>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 >>>> >>> >>> >>> >>> -- >>> Howard S. Young, PhD >>> Professor >>> Biochemistry, MSB 3-27 >>> University of Alberta >>> Edmonton, Alberta T6G 2H7 >>> (780)492-3931 >>> >>> National Institute for Nanotechnology, >>> National Research Council of Canada >>> >>> Membrane Protein Disease Research Group >>> >>> >>> >>> ------------------------------ >>> >>> To unsubscribe from the CCP4BB list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 >>> >> >> >> ------------------------------ >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 >> > > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1