MODELLER 9.16, 2016/01/07, r10745 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2016 Andrej Sali All Rights Reserved Written by A. Sali with help from B. Webb, M.S. Madhusudhan, M-Y. Shen, G.Q. Dong, M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva, A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov, F. Melo, J.P. Overington, E. Feyfant University of California, San Francisco, USA Rockefeller University, New York, USA Harvard University, Cambridge, USA Imperial Cancer Research Fund, London, UK Birkbeck College, University of London, London, UK Kind, OS, HostName, Kernel, Processor: 4, Linux sunflower.rnet.missouri.edu 2.6.32-431.23.3.el6.x86_64 x86_64 Date and time of compilation : 2016/01/07 10:19:44 MODELLER executable type : i386-intel8 Job starting time (YY/MM/DD HH:MM:SS): 2016/04/05 22:41:58 and have 39 equivalences, and are 54.93% identical Sequence identity comparison (ID_TABLE): Diagonal ... number of residues; Upper triangle ... number of identical residues; Lower triangle ... % sequence identity, id/min(length). 2ctx @22abx @22nbt @11fas @1 2ctx @2 71 39 29 14 2abx @2 55 74 30 23 2nbt @1 44 45 66 16 1fas @1 23 38 26 61 2ctx@2.42abx@2.52nbt@1.01fas@1.8 2ctx@2.4 902.901 676.973 569.107 441.760 2abx@2.5 676.973 901.689 597.640 488.316 2nbt@1.0 569.107 597.640 902.394 478.200 1fas@1.8 441.760 488.316 478.200 901.590 SEQCOMP: Sequence comparison : Residue-residue weights: $(LIB)/as1.sim.mat Residue - gap score : 0.00 Gap - gap score : 1000.00 Number of allowed gaps : 1 Comparison matrix file : toxin.mat Variability file : toxin.var princ___> Principal components clustering Input distance file : toxin.mat Output coordinates file: toxin.princ Reduced number of dimensions : 2 # Eigenvalue Fract.of variance Cumul.fract.var. 1 406930.687500 -1.119622 -1.119622 2 -176299.828125 0.485069 -0.634554 3 -253320.921875 0.696983 0.062429 4 -340763.406250 0.937571 1.000000 Cartesian coords in the lower dimensional space: 1 '2ctx@2.4.4' 318.9555 0.0000 2 '2abx@2.5.5' 318.9555 0.0000 3 '2nbt@1.0.0' 318.9556 0.0000 4 '1fas@1.8.8' 318.9556 0.0000 Eigenvalue, normalized eigenvectors (columns): 1 406930.6875 0.5000 0.6418 -0.4004 -0.4216 2 -176299.8281 0.5000 -0.7618 -0.2622 -0.3177 3 -253320.9219 0.5000 0.0766 0.8564 -0.1037 4 -340763.4062 0.5000 0.0434 -0.1938 0.8430 Original distance matrix: 1 2 3 4 1 902.900 676.970 569.110 441.760 2 676.970 901.690 597.640 488.320 3 569.110 597.640 902.390 478.200 4 441.760 488.320 478.200 901.590 Distance matrix recreated from the lower dim.space: 1 2 3 4 1 0.000 0.000 0.000 0.000 2 0.000 0.000 0.000 0.000 3 0.000 0.000 0.000 0.000 4 0.000 0.000 0.000 0.000 Difference between the two matrices: 1 2 3 4 1-902.900-676.970-569.110-441.760 2-676.970-901.690-597.640-488.320 3-569.110-597.640-902.390-478.200 4-441.760-488.320-478.200-901.590 Weighted pair-group average clustering based on a distance matrix: .--- 2ctx@2.4.4 441.7600 | .--------------------------------- 1fas@1.8.8 523.6550 | .---------------------------------------------------------- 2nbt@1.0.0 590.1425 | .------------------------------------------------------------ 2abx@2.5.5 +----+----+----+----+----+----+----+----+----+----+----+----+ 596.0778 569.3690 542.6601 515.9513 489.2424 462.5336 435.8247 582.7234 556.0145 529.3057 502.5968 475.8880 449.1791 Total CPU time [seconds] : 0.22