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 22:42:11 Multiple dynamic programming alignment (MALIGN): Residue-residue metric : $(LIB)/as1.sim.mat ALIGN_BLOCK : 1 Gap introduction penalty: -500.0000 Gap extension penalty : -300.0000 Length of alignment : 63 # Sequence alignment of the structurally conserved regions # [average distance and standard deviation are with respect # to the framework (i.e., average structure)] # # N av ds st dv 1fdn 5fd1 # =============================== 1 0.846 0.000 * A 1 A 1 2 0.907 0.000 Y 2 F 2 3 0.762 0.000 * V 3 V 3 4 0.462 0.000 I 4 V 4 5 0.518 0.000 N 5 T 5 6 0.576 0.000 E 6 D 6 7 0.441 0.000 A 7 N 7 8 0.340 0.000 * C 8 C 8 # =============================== 9 0.745 0.000 I 9 C 11 10 0.365 0.000 S 10 K 12 11 0.526 0.000 C 11 Y 13 12 0.519 0.000 G 12 T 14 13 0.482 0.000 A 13 D 15 14 0.337 0.000 * C 14 C 16 15 0.720 0.000 E 15 V 17 16 0.950 0.000 P 16 E 18 17 0.749 0.000 E 17 V 19 18 0.702 0.000 * C 18 C 20 19 0.851 0.000 * P 19 P 21 20 0.709 0.000 * V 20 V 22 21 0.442 0.000 N 21 D 23 22 0.554 0.000 A 22 C 24 23 0.517 0.000 I 23 F 25 24 1.092 0.000 S 24 Y 26 25 0.843 0.000 S 25 E 27 26 0.722 0.000 * G 26 G 28 27 1.786 0.000 D 27 P 29 28 1.628 0.000 D 28 N 30 29 0.554 0.000 R 29 F 31 30 0.326 0.000 Y 30 L 32 31 0.318 0.000 * V 31 V 33 32 0.420 0.000 * I 32 I 34 33 0.194 0.000 D 33 H 35 34 0.430 0.000 A 34 P 36 35 0.523 0.000 * D 35 D 37 36 0.428 0.000 T 36 E 38 37 0.681 0.000 * C 37 C 39 38 1.089 0.000 * I 38 I 40 39 1.104 0.000 * D 39 D 41 40 1.211 0.000 * C 40 C 42 41 1.093 0.000 G 41 A 43 42 0.940 0.000 A 42 L 44 43 0.926 0.000 * C 43 C 45 44 0.780 0.000 A 44 E 46 45 0.352 0.000 G 45 P 47 46 0.357 0.000 V 46 E 48 47 0.523 0.000 * C 47 C 49 48 0.726 0.000 * P 48 P 50 49 0.880 0.000 V 49 A 51 50 0.528 0.000 D 50 Q 52 51 0.348 0.000 * A 51 A 53 52 0.603 0.000 P 52 I 54 53 0.840 0.000 V 53 F 55 54 1.032 0.000 Q 54 S 56 55 0.958 0.000 A 55 E 57 # =============================== # Sequence alignment of the structurally conserved regions # [average distance and standard deviation are with respect # to the framework (i.e., average structure)] # # N av ds st dv 1fdn 5fd1 # =============================== 1 0.347 0.000 * A 1 A 1 2 0.389 0.000 Y 2 F 2 3 0.387 0.000 * V 3 V 3 4 0.097 0.000 I 4 V 4 5 0.148 0.000 N 5 T 5 6 0.434 0.000 E 6 D 6 7 0.275 0.000 A 7 N 7 8 0.430 0.000 * C 8 C 8 # =============================== 9 0.740 0.000 I 9 C 11 10 0.187 0.000 S 10 K 12 11 0.440 0.000 C 11 Y 13 12 0.554 0.000 G 12 T 14 13 0.430 0.000 A 13 D 15 14 0.417 0.000 * C 14 C 16 15 0.533 0.000 E 15 V 17 16 1.054 0.000 P 16 E 18 17 0.641 0.000 E 17 V 19 18 0.198 0.000 * C 18 C 20 19 0.355 0.000 * P 19 P 21 20 0.347 0.000 * V 20 V 22 21 0.251 0.000 N 21 D 23 22 0.356 0.000 A 22 C 24 23 0.551 0.000 I 23 F 25 24 1.283 0.000 S 24 Y 26 25 0.936 0.000 S 25 E 27 26 0.796 0.000 * G 26 G 28 27 1.634 0.000 D 27 P 29 28 1.365 0.000 D 28 N 30 29 0.405 0.000 R 29 F 31 30 0.344 0.000 Y 30 L 32 31 0.449 0.000 * V 31 V 33 32 0.195 0.000 * I 32 I 34 33 0.382 0.000 D 33 H 35 34 0.337 0.000 A 34 P 36 35 0.455 0.000 * D 35 D 37 36 0.202 0.000 T 36 E 38 37 0.202 0.000 * C 37 C 39 38 0.552 0.000 * I 38 I 40 39 0.533 0.000 * D 39 D 41 40 0.613 0.000 * C 40 C 42 41 0.556 0.000 G 41 A 43 42 0.486 0.000 A 42 L 44 43 0.494 0.000 * C 43 C 45 44 0.301 0.000 A 44 E 46 45 0.588 0.000 G 45 P 47 46 0.300 0.000 V 46 E 48 47 0.374 0.000 * C 47 C 49 48 0.537 0.000 * P 48 P 50 49 0.788 0.000 V 49 A 51 50 0.507 0.000 D 50 Q 52 51 0.319 0.000 * A 51 A 53 52 0.420 0.000 P 52 I 54 53 0.306 0.000 V 53 F 55 54 0.476 0.000 Q 54 S 56 55 0.428 0.000 A 55 E 57 # =============================== # Sequence alignment of the structurally conserved regions # [average distance and standard deviation are with respect # to the framework (i.e., average structure)] # # N av ds st dv 1fdn 5fd1 # =============================== 1 0.347 0.000 * A 1 A 1 2 0.389 0.000 Y 2 F 2 3 0.387 0.000 * V 3 V 3 4 0.097 0.000 I 4 V 4 5 0.148 0.000 N 5 T 5 6 0.434 0.000 E 6 D 6 7 0.275 0.000 A 7 N 7 8 0.430 0.000 * C 8 C 8 # =============================== 9 0.740 0.000 I 9 C 11 10 0.187 0.000 S 10 K 12 11 0.440 0.000 C 11 Y 13 12 0.554 0.000 G 12 T 14 13 0.430 0.000 A 13 D 15 14 0.417 0.000 * C 14 C 16 15 0.533 0.000 E 15 V 17 16 1.054 0.000 P 16 E 18 17 0.641 0.000 E 17 V 19 18 0.198 0.000 * C 18 C 20 19 0.355 0.000 * P 19 P 21 20 0.347 0.000 * V 20 V 22 21 0.251 0.000 N 21 D 23 22 0.356 0.000 A 22 C 24 23 0.551 0.000 I 23 F 25 24 1.283 0.000 S 24 Y 26 25 0.936 0.000 S 25 E 27 26 0.796 0.000 * G 26 G 28 27 1.634 0.000 D 27 P 29 28 1.365 0.000 D 28 N 30 29 0.405 0.000 R 29 F 31 30 0.344 0.000 Y 30 L 32 31 0.449 0.000 * V 31 V 33 32 0.195 0.000 * I 32 I 34 33 0.382 0.000 D 33 H 35 34 0.337 0.000 A 34 P 36 35 0.455 0.000 * D 35 D 37 36 0.202 0.000 T 36 E 38 37 0.202 0.000 * C 37 C 39 38 0.552 0.000 * I 38 I 40 39 0.533 0.000 * D 39 D 41 40 0.613 0.000 * C 40 C 42 41 0.556 0.000 G 41 A 43 42 0.486 0.000 A 42 L 44 43 0.494 0.000 * C 43 C 45 44 0.301 0.000 A 44 E 46 45 0.588 0.000 G 45 P 47 46 0.300 0.000 V 46 E 48 47 0.374 0.000 * C 47 C 49 48 0.537 0.000 * P 48 P 50 49 0.788 0.000 V 49 A 51 50 0.507 0.000 D 50 Q 52 51 0.319 0.000 * A 51 A 53 52 0.420 0.000 P 52 I 54 53 0.306 0.000 V 53 F 55 54 0.476 0.000 Q 54 S 56 55 0.428 0.000 A 55 E 57 # =============================== Least-squares dynamic programming alignment: FIT_ATOMS atoms for alignment : CA Max dist from frw for equivalence : 4.0000 Gap introduction penalty : 0.0000 Gap extension penalty : 2.0000 Numb of residues in framework : 55 check_ali___> Checking the sequence-structure alignment. Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms: ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST ---------------------------------------------- END OF TABLE Total CPU time [seconds] : 0.18