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 22:38:14 Multiple dynamic programming alignment (MALIGN): Residue-residue metric : $(LIB)/as1.sim.mat ALIGN_BLOCK : 1 Gap introduction penalty: -900.0000 Gap extension penalty : -50.0000 Length of alignment : 56 # 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 1clfA 1durA 1fcaA 2fdnA # ============================================= 1 0.434 0.224 * A 1 A 1 A 1 A 1 2 0.510 0.294 * Y 2 Y 2 Y 2 Y 2 3 0.294 0.173 K 3 V 3 V 3 V 3 4 0.347 0.188 * I 4 I 4 I 4 I 4 5 0.315 0.120 A 5 N 5 N 5 N 5 6 0.423 0.133 D 6 D 6 E 6 E 6 7 0.496 0.276 S 7 S 7 A 7 A 7 8 0.266 0.142 * C 8 C 8 C 8 C 8 9 0.249 0.113 V 9 I 9 I 9 I 9 10 0.300 0.168 S 10 A 10 S 10 S 10 11 0.191 0.100 * C 11 C 11 C 11 C 11 12 0.232 0.129 * G 12 G 12 G 12 G 12 13 0.254 0.152 * A 13 A 13 A 13 A 13 14 0.258 0.145 * C 14 C 14 C 14 C 14 15 0.268 0.129 A 15 K 15 E 15 E 15 16 0.320 0.202 S 16 P 16 P 16 P 16 17 0.325 0.138 * E 17 E 17 E 17 E 17 18 0.165 0.064 * C 18 C 18 C 18 C 18 19 0.301 0.146 * P 19 P 19 P 19 P 19 20 0.336 0.131 * V 20 V 20 V 20 V 20 21 0.408 0.252 N 21 N 21 D 21 N 21 22 0.307 0.117 A 22 C 22 A 22 A 22 23 0.149 0.065 * I 23 I 23 I 23 I 23 24 0.494 0.209 S 24 Q 24 S 24 S 24 25 0.617 0.354 Q 25 E 25 Q 25 S 25 # ============================================= 26 1.222 0.426 S 28 S 27 S 28 D 28 27 0.216 0.101 I 29 I 28 R 29 R 29 28 0.245 0.108 F 30 Y 29 Y 30 Y 30 29 0.245 0.066 V 31 A 30 V 31 V 31 30 0.155 0.098 * I 32 I 31 I 32 I 32 31 0.261 0.159 * D 33 D 32 D 33 D 33 32 0.469 0.246 * A 34 A 33 A 34 A 34 33 0.498 0.154 * D 35 D 34 D 35 D 35 34 0.166 0.029 T 36 S 35 T 36 T 36 35 0.229 0.130 * C 37 C 36 C 37 C 37 36 0.214 0.068 * I 38 I 37 I 38 I 38 37 0.321 0.145 * D 39 D 38 D 39 D 39 38 0.307 0.111 * C 40 C 39 C 40 C 40 39 0.608 0.319 * G 41 G 40 G 41 G 41 40 0.289 0.155 N 42 S 41 A 42 A 42 41 0.314 0.180 * C 43 C 42 C 43 C 43 42 0.466 0.220 * A 44 A 43 A 44 A 44 43 0.324 0.171 N 45 S 44 G 45 G 45 44 0.324 0.164 * V 46 V 45 V 46 V 46 45 0.207 0.116 * C 47 C 46 C 47 C 47 46 0.314 0.149 * P 48 P 47 P 48 P 48 47 0.453 0.260 * V 49 V 48 V 49 V 49 48 0.451 0.293 G 50 G 49 D 50 D 50 49 0.302 0.173 * A 51 A 50 A 51 A 51 50 0.312 0.156 * P 52 P 51 P 52 P 52 51 0.536 0.309 V 53 N 52 V 53 V 53 # ============================================= 52 1.458 0.836 Q 54 E 54 A 55 A 55 # ============================================= # 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 1clfA 1durA 1fcaA 2fdnA # ============================================= 1 0.343 0.160 * A 1 A 1 A 1 A 1 2 0.605 0.350 * Y 2 Y 2 Y 2 Y 2 3 0.371 0.213 K 3 V 3 V 3 V 3 4 0.337 0.184 * I 4 I 4 I 4 I 4 5 0.298 0.115 A 5 N 5 N 5 N 5 6 0.344 0.086 D 6 D 6 E 6 E 6 7 0.399 0.221 S 7 S 7 A 7 A 7 8 0.195 0.096 * C 8 C 8 C 8 C 8 9 0.257 0.137 V 9 I 9 I 9 I 9 10 0.323 0.186 S 10 A 10 S 10 S 10 11 0.184 0.098 * C 11 C 11 C 11 C 11 12 0.222 0.125 * G 12 G 12 G 12 G 12 13 0.236 0.141 * A 13 A 13 A 13 A 13 14 0.237 0.127 * C 14 C 14 C 14 C 14 15 0.263 0.130 A 15 K 15 E 15 E 15 16 0.304 0.202 S 16 P 16 P 16 P 16 17 0.300 0.111 * E 17 E 17 E 17 E 17 18 0.149 0.053 * C 18 C 18 C 18 C 18 19 0.251 0.092 * P 19 P 19 P 19 P 19 20 0.302 0.093 * V 20 V 20 V 20 V 20 21 0.394 0.238 N 21 N 21 D 21 N 21 22 0.293 0.110 A 22 C 22 A 22 A 22 23 0.147 0.048 * I 23 I 23 I 23 I 23 24 0.463 0.208 S 24 Q 24 S 24 S 24 25 0.568 0.331 Q 25 E 25 Q 25 S 25 # ============================================= 26 1.222 0.415 S 28 S 27 S 28 D 28 27 0.277 0.124 I 29 I 28 R 29 R 29 28 0.191 0.076 F 30 Y 29 Y 30 Y 30 29 0.202 0.056 V 31 A 30 V 31 V 31 30 0.148 0.089 * I 32 I 31 I 32 I 32 31 0.248 0.142 * D 33 D 32 D 33 D 33 32 0.419 0.210 * A 34 A 33 A 34 A 34 33 0.459 0.135 * D 35 D 34 D 35 D 35 34 0.173 0.016 T 36 S 35 T 36 T 36 35 0.167 0.104 * C 37 C 36 C 37 C 37 36 0.227 0.103 * I 38 I 37 I 38 I 38 37 0.288 0.126 * D 39 D 38 D 39 D 39 38 0.273 0.110 * C 40 C 39 C 40 C 40 39 0.539 0.275 * G 41 G 40 G 41 G 41 40 0.267 0.151 N 42 S 41 A 42 A 42 41 0.251 0.147 * C 43 C 42 C 43 C 43 42 0.448 0.211 * A 44 A 43 A 44 A 44 43 0.346 0.196 N 45 S 44 G 45 G 45 44 0.352 0.186 * V 46 V 45 V 46 V 46 45 0.187 0.108 * C 47 C 46 C 47 C 47 46 0.268 0.123 * P 48 P 47 P 48 P 48 47 0.382 0.221 * V 49 V 48 V 49 V 49 48 0.392 0.254 G 50 G 49 D 50 D 50 49 0.235 0.133 * A 51 A 50 A 51 A 51 50 0.263 0.116 * P 52 P 51 P 52 P 52 51 0.648 0.381 V 53 N 52 V 53 V 53 # ============================================= 52 1.509 0.879 Q 54 E 54 A 55 A 55 # ============================================= # 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 1clfA 1durA 1fcaA 2fdnA # ============================================= 1 0.343 0.160 * A 1 A 1 A 1 A 1 2 0.605 0.350 * Y 2 Y 2 Y 2 Y 2 3 0.371 0.213 K 3 V 3 V 3 V 3 4 0.337 0.184 * I 4 I 4 I 4 I 4 5 0.298 0.115 A 5 N 5 N 5 N 5 6 0.344 0.086 D 6 D 6 E 6 E 6 7 0.399 0.221 S 7 S 7 A 7 A 7 8 0.195 0.096 * C 8 C 8 C 8 C 8 9 0.257 0.137 V 9 I 9 I 9 I 9 10 0.323 0.186 S 10 A 10 S 10 S 10 11 0.184 0.098 * C 11 C 11 C 11 C 11 12 0.222 0.125 * G 12 G 12 G 12 G 12 13 0.236 0.141 * A 13 A 13 A 13 A 13 14 0.237 0.127 * C 14 C 14 C 14 C 14 15 0.263 0.130 A 15 K 15 E 15 E 15 16 0.304 0.202 S 16 P 16 P 16 P 16 17 0.300 0.111 * E 17 E 17 E 17 E 17 18 0.149 0.053 * C 18 C 18 C 18 C 18 19 0.251 0.092 * P 19 P 19 P 19 P 19 20 0.302 0.093 * V 20 V 20 V 20 V 20 21 0.394 0.238 N 21 N 21 D 21 N 21 22 0.293 0.110 A 22 C 22 A 22 A 22 23 0.147 0.048 * I 23 I 23 I 23 I 23 24 0.463 0.208 S 24 Q 24 S 24 S 24 25 0.568 0.331 Q 25 E 25 Q 25 S 25 # ============================================= 26 1.222 0.415 S 28 S 27 S 28 D 28 27 0.277 0.124 I 29 I 28 R 29 R 29 28 0.191 0.076 F 30 Y 29 Y 30 Y 30 29 0.202 0.056 V 31 A 30 V 31 V 31 30 0.148 0.089 * I 32 I 31 I 32 I 32 31 0.248 0.142 * D 33 D 32 D 33 D 33 32 0.419 0.210 * A 34 A 33 A 34 A 34 33 0.459 0.135 * D 35 D 34 D 35 D 35 34 0.173 0.016 T 36 S 35 T 36 T 36 35 0.167 0.104 * C 37 C 36 C 37 C 37 36 0.227 0.103 * I 38 I 37 I 38 I 38 37 0.288 0.126 * D 39 D 38 D 39 D 39 38 0.273 0.110 * C 40 C 39 C 40 C 40 39 0.539 0.275 * G 41 G 40 G 41 G 41 40 0.267 0.151 N 42 S 41 A 42 A 42 41 0.251 0.147 * C 43 C 42 C 43 C 43 42 0.448 0.211 * A 44 A 43 A 44 A 44 43 0.346 0.196 N 45 S 44 G 45 G 45 44 0.352 0.186 * V 46 V 45 V 46 V 46 45 0.187 0.108 * C 47 C 46 C 47 C 47 46 0.268 0.123 * P 48 P 47 P 48 P 48 47 0.382 0.221 * V 49 V 48 V 49 V 49 48 0.392 0.254 G 50 G 49 D 50 D 50 49 0.235 0.133 * A 51 A 50 A 51 A 51 50 0.263 0.116 * P 52 P 51 P 52 P 52 51 0.648 0.381 V 53 N 52 V 53 V 53 # ============================================= 52 1.509 0.879 Q 54 E 54 A 55 A 55 # ============================================= Least-squares dynamic programming alignment: FIT_ATOMS atoms for alignment : CA Max dist from frw for equivalence : 3.5000 Gap introduction penalty : 0.0000 Gap extension penalty : 1.7500 Numb of residues in framework : 52 COMPARISON OF SEVERAL 3D STRUCTURES: # ALGNMT CODE ATOM FILE 1 1clfA 2 1durA 3 1fcaA 4 2fdnA Variability at a given position is calculated as: VAR = 1/Nij * sum_ij (feat_i - feat_j) sum runs over all pairs of proteins with residues present. >> Least-squares superposition (FIT) : T Atom types for superposition/RMS (FIT_ATOMS): CA Atom type for position average/variability (VARATOM): CA Position comparison (FIT_ATOMS): Cutoff for RMS calculation: 3.5000 Upper = RMS, Lower = numb equiv positions 1clfA 1durA 1fcaA 2fdnA 1clfA 0.000 0.991 0.817 0.875 1durA 52 0.000 0.493 0.513 1fcaA 51 54 0.000 0.270 2fdnA 51 54 55 0.000 Distance comparison (FIT_ATOMS): Cutoff for rms calculation: 3.5000 Upper = Distance RMS, Lower = numb equiv distances 1clfA 1durA 1fcaA 2fdnA 1clfA 0.000 0.723 0.710 0.740 1durA 1324 0.000 0.342 0.347 1fcaA 1314 1431 0.000 0.210 2fdnA 1317 1431 1485 0.000 >> Sequence comparison: Diag=numb res, Upper=numb equiv res, Lower = % seq ID 1clfA 1durA 1fcaA 2fdnA 1clfA 55 36 38 37 1durA 65 55 37 37 1fcaA 69 67 55 51 2fdnA 67 67 93 55 >> Dihedral angle comparison: Alph Cutoff for rms comparison: 60.0000 Upper = RMS Alph, Lower = numb of equiv angles 1clfA 1durA 1fcaA 2fdnA 1clfA 0.000 15.352 17.212 16.087 1durA 48 0.000 11.077 12.209 1fcaA 50 51 0.000 5.544 2fdnA 49 51 52 0.000 >> Dihedral angle comparison: Phi Cutoff for rms comparison: 60.0000 Upper = RMS Phi , Lower = numb of equiv angles 1clfA 1durA 1fcaA 2fdnA 1clfA 0.000 18.362 19.281 19.781 1durA 46 0.000 14.967 12.341 1fcaA 46 52 0.000 7.942 2fdnA 46 51 53 0.000 >> Dihedral angle comparison: Psi Cutoff for rms comparison: 15.0000 Upper = RMS Psi , Lower = numb of equiv angles 1clfA 1durA 1fcaA 2fdnA 1clfA 0.000 7.469 6.725 7.140 1durA 28 0.000 6.844 6.805 1fcaA 28 44 0.000 4.862 2fdnA 27 44 49 0.000 >> Dihedral angle comparison: Omeg Cutoff for rms comparison: 60.0000 Upper = RMS Omeg, Lower = numb of equiv angles 1clfA 1durA 1fcaA 2fdnA 1clfA 0.000 13.125 12.181 13.404 1durA 52 0.000 3.954 5.595 1fcaA 51 53 0.000 4.381 2fdnA 51 53 54 0.000 >> Dihedral angle comparison: chi1 Cutoff for rms comparison: 60.0000 Upper = RMS chi1, Lower = numb of equiv angles 1clfA 1durA 1fcaA 2fdnA 1clfA 0.000 26.795 21.634 22.614 1durA 29 0.000 7.298 9.826 1fcaA 27 32 0.000 10.789 2fdnA 30 33 37 0.000 >> Dihedral angle comparison: chi2 Cutoff for rms comparison: 60.0000 Upper = RMS chi2, Lower = numb of equiv angles 1clfA 1durA 1fcaA 2fdnA 1clfA 0.000 24.163 21.126 11.464 1durA 9 0.000 21.396 25.616 1fcaA 7 17 0.000 14.954 2fdnA 6 19 18 0.000 >> Dihedral angle comparison: chi3 Cutoff for rms comparison: 60.0000 Upper = RMS chi3, Lower = numb of equiv angles 1clfA 1durA 1fcaA 2fdnA 1clfA 0.000 29.040 16.016 5.929 1durA 4 0.000 5.315 23.853 1fcaA 3 6 0.000 26.976 2fdnA 2 5 8 0.000 >> Dihedral angle comparison: chi4 Cutoff for rms comparison: 60.0000 Upper = RMS chi4, Lower = numb of equiv angles 1clfA 1durA 1fcaA 2fdnA 1clfA 0.000 0.000 0.000 0.000 1durA 0 0.000 0.000 0.000 1fcaA 0 0 0.000 23.132 2fdnA 0 0 1 0.000 >> Dihedral angle comparison: chi5 Cutoff for rms comparison: 60.0000 Upper = RMS chi5, Lower = numb of equiv angles 1clfA 1durA 1fcaA 2fdnA 1clfA 0.000 0.000 0.000 0.000 1durA 0 0.000 0.000 0.000 1fcaA 0 0 0.000 0.000 2fdnA 0 0 0 0.000 >> Ramachandran mainchain class substitution prot 1 --> prot 2; class on vert --> class on horiz A P B L E U A 141 0 0 2 0 0 P 7 54 9 6 0 4 B 3 16 36 0 0 0 L 4 0 0 30 0 0 E 0 0 0 0 0 0 U 0 0 0 0 0 7 Summary (% does not count undefined): CODE # ID # NID # TOT % ID % NID % TOT A 141 2 143 45.2 0.6 45.8 P 54 26 80 17.3 8.3 25.6 B 36 19 55 11.5 6.1 17.6 L 30 4 34 9.6 1.3 10.9 E 0 0 0 0.0 0.0 0.0 -------------------------------------------- SUMS 261 51 312 83.7 16.3 100.0 -------------------------------------------- U 7 0 7 2.2 0.0 2.2 >> Dihedral class substitution: Alph prot 1 --> prot 2; class on vert --> class on horiz 1 2 3 4 1 8 0 13 0 2 0 115 5 0 3 0 2 161 2 4 0 0 0 13 Summary (% does not count undefined): CODE # ID # NID # TOT % ID % NID % TOT 1 8 13 21 2.6 4.2 6.9 2 115 5 120 37.6 1.6 39.2 3 161 4 165 52.6 1.3 53.9 -------------------------------------------- SUMS 284 22 306 92.8 7.2 100.0 -------------------------------------------- 4 13 0 13 4.1 0.0 4.1 >> Dihedral class substitution: Phi prot 1 --> prot 2; class on vert --> class on horiz 1 2 3 4 1 144 7 20 0 2 3 30 1 0 3 17 1 90 0 4 0 0 0 6 Summary (% does not count undefined): CODE # ID # NID # TOT % ID % NID % TOT 1 144 27 171 46.0 8.6 54.6 2 30 4 34 9.6 1.3 10.9 3 90 18 108 28.8 5.8 34.5 -------------------------------------------- SUMS 264 49 313 84.3 15.7 100.0 -------------------------------------------- 4 6 0 6 1.9 0.0 1.9 >> Dihedral class substitution: Psi prot 1 --> prot 2; class on vert --> class on horiz 1 2 3 4 1 107 18 0 0 2 8 56 2 0 3 4 6 113 4 4 0 0 0 1 Summary (% does not count undefined): CODE # ID # NID # TOT % ID % NID % TOT 1 107 18 125 33.6 5.7 39.3 2 56 10 66 17.6 3.1 20.8 3 113 14 127 35.5 4.4 39.9 -------------------------------------------- SUMS 276 42 318 86.8 13.2 100.0 -------------------------------------------- 4 1 0 1 0.3 0.0 0.3 >> Dihedral class substitution: Omeg prot 1 --> prot 2; class on vert --> class on horiz 1 2 3 4 1 314 0 0 4 2 0 0 0 0 3 0 0 0 0 4 0 0 0 1 Summary (% does not count undefined): CODE # ID # NID # TOT % ID % NID % TOT 1 314 4 318 98.7 1.3 100.0 2 0 0 0 0.0 0.0 0.0 3 0 0 0 0.0 0.0 0.0 -------------------------------------------- SUMS 314 4 318 98.7 1.3 100.0 -------------------------------------------- 4 1 0 1 0.3 0.0 0.3 >> Dihedral class substitution: chi1 prot 1 --> prot 2; class on vert --> class on horiz 1 2 3 4 1 63 18 3 0 2 10 79 14 16 3 4 4 32 5 4 4 9 5 53 Summary (% does not count undefined): CODE # ID # NID # TOT % ID % NID % TOT 1 63 21 84 25.4 8.5 33.9 2 79 40 119 31.9 16.1 48.0 3 32 13 45 12.9 5.2 18.1 -------------------------------------------- SUMS 174 74 248 70.2 29.8 100.0 -------------------------------------------- 4 53 18 71 16.6 5.6 22.3 >> Dihedral class substitution: chi2 prot 1 --> prot 2; class on vert --> class on horiz 1 2 3 4 1 60 5 7 9 2 19 22 2 8 3 0 0 1 3 4 17 5 0 161 Summary (% does not count undefined): CODE # ID # NID # TOT % ID % NID % TOT 1 60 21 81 44.1 15.4 59.6 2 22 29 51 16.2 21.3 37.5 3 1 3 4 0.7 2.2 2.9 -------------------------------------------- SUMS 83 53 136 61.0 39.0 100.0 -------------------------------------------- 4 161 22 183 50.5 6.9 57.4 >> Dihedral class substitution: chi3 prot 1 --> prot 2; class on vert --> class on horiz 1 2 3 4 1 21 9 0 10 2 1 6 0 2 3 2 0 0 0 4 12 2 1 253 Summary (% does not count undefined): CODE # ID # NID # TOT % ID % NID % TOT 1 21 19 40 41.2 37.3 78.4 2 6 3 9 11.8 5.9 17.6 3 0 2 2 0.0 3.9 3.9 -------------------------------------------- SUMS 27 24 51 52.9 47.1 100.0 -------------------------------------------- 4 253 15 268 79.3 4.7 84.0 >> Dihedral class substitution: chi4 prot 1 --> prot 2; class on vert --> class on horiz 1 2 3 4 1 1 0 0 0 2 0 0 0 3 3 0 0 0 2 4 4 0 1 308 Summary (% does not count undefined): CODE # ID # NID # TOT % ID % NID % TOT 1 1 0 1 16.7 0.0 16.7 2 0 3 3 0.0 50.0 50.0 3 0 2 2 0.0 33.3 33.3 -------------------------------------------- SUMS 1 5 6 16.7 83.3 100.0 -------------------------------------------- 4 308 5 313 96.6 1.6 98.1 >> Dihedral class substitution: chi5 prot 1 --> prot 2; class on vert --> class on horiz 1 2 3 4 1 0 0 0 0 2 0 0 0 0 3 0 0 0 0 4 0 0 0 319 Summary (% does not count undefined): CODE # ID # NID # TOT % ID % NID % TOT 1 0 0 0 0.0 0.0 0.0 2 0 0 0 0.0 0.0 0.0 3 0 0 0 0.0 0.0 0.0 -------------------------------------------- SUMS 0 0 0 0.0 0.0 0.0 -------------------------------------------- 4 319 0 319 100.0 0.0 100.0 >> Detailed comparison: Structure : 2 Structure : 3 Structure : 4 ALN ... alignment position RESID... ... residue numbers 1/2/3 AAA ... amino acid types 1/2/3 MNC ... mainchain classes 1/2/3 ALP... ... dihedral angle classes (alpha,phi,psi,...) ALN RESIDUE_NUMBERS AAA MNC ALP PHI PSI OMG CH1 CH2 CH3 CH4 CH5 --------------------------------------------------------------- 1 1 1 1 AAA UUU 444 444 333 111 444 444 444 444 444 2 2 2 2 YYY PPP 333 331 333 111 111 222 444 444 444 3 3 3 3 VVV BBB 333 333 333 111 333 444 444 444 444 4 4 4 4 III BPP 333 313 333 111 111 111 444 444 444 5 5 5 5 NNN PPP 113 131 333 111 331 121 444 444 444 6 6 6 6 DEE AAA 222 111 111 111 313 113 411 444 444 7 7 7 7 SAA AAA 332 111 111 111 244 444 444 444 444 8 8 8 8 CCC PPP 333 111 333 111 222 444 444 444 444 9 9 9 9 III AAA 333 333 222 111 222 111 444 444 444 10 10 10 10 ASS LLL 333 222 222 111 422 444 444 444 444 11 11 11 11 CCC AAA 333 111 111 111 333 444 444 444 444 12 12 12 12 GGG LLL 333 222 222 111 444 444 444 444 444 13 13 13 13 AAA AAA 222 111 111 111 444 444 444 444 444 14 14 14 14 CCC AAA 222 111 111 111 333 444 444 444 444 15 15 15 15 KEE AAA 222 111 111 111 222 111 311 344 444 16 16 16 16 PPP AAA 222 111 111 111 112 221 112 444 444 17 17 17 17 EEE AAA 222 333 111 111 111 222 111 444 444 18 18 18 18 CCC BPP 333 111 333 111 222 444 444 444 444 19 19 19 19 PPP AAA 222 111 111 111 222 111 222 444 444 20 20 20 20 VVV AAA 333 333 222 111 222 444 444 444 444 21 21 21 21 NDN LLL 333 222 222 111 212 111 444 444 444 22 22 22 22 CAA AAA 222 313 211 111 344 444 444 444 444 23 23 23 23 III PPP 333 333 333 111 111 111 444 444 444 24 24 24 24 QSS BBB 333 333 333 111 111 244 244 444 444 25 25 25 25 EQS PPP 333 111 333 111 323 214 114 444 444 26 26 26 26 GGG BPB 111 333 333 111 444 444 444 444 444 27 ---- 27 27 -GD -PA -11 -11 -31 -11 -41 -41 -44 -44 -44 28 ---- ---- ---- --- --- --- --- --- --- --- --- --- --- --- 29 ---- ---- ---- --- --- --- --- --- --- --- --- --- --- --- 30 27 28 28 SSD ALA 222 123 112 111 413 441 444 444 444 31 28 29 29 IRR BBB 333 333 333 111 233 111 411 411 444 32 29 30 30 YYY PPP 333 111 333 111 111 222 444 444 444 33 30 31 31 AVV BBB 333 333 333 111 413 444 444 444 444 34 31 32 32 III PPP 333 333 333 111 111 111 444 444 444 35 32 33 33 DDD BBB 333 111 333 111 222 111 444 444 444 36 33 34 34 AAA AAA 222 111 111 111 444 444 444 444 444 37 34 35 35 DDD AAA 222 111 121 111 111 111 444 444 444 38 35 36 36 STT AAA 222 333 111 111 211 444 444 444 444 39 36 37 37 CCC PPP 333 111 333 111 222 444 444 444 444 40 37 38 38 III AAA 333 333 222 111 222 133 444 444 444 41 38 39 39 DDD LLL 333 222 222 111 111 111 444 444 444 42 39 40 40 CCC AAA 333 111 111 111 333 444 444 444 444 43 40 41 41 GGG LLL 333 222 222 111 444 444 444 444 444 44 41 42 42 SAA AAA 222 111 111 111 244 444 444 444 444 45 42 43 43 CCC AAA 222 111 111 111 333 444 444 444 444 46 43 44 44 AAA AAA 222 111 111 111 444 444 444 444 444 47 44 45 45 SGG AAA 222 111 112 111 344 444 444 444 444 48 45 46 46 VVV AAA 222 333 122 111 222 444 444 444 444 49 46 47 47 CCC PBB 333 113 333 111 222 444 444 444 444 50 47 48 48 PPP AAA 222 111 111 111 222 111 222 444 444 51 48 49 49 VVV AAA 333 333 222 111 222 444 444 444 444 52 49 50 50 GDD LLL 333 222 222 111 422 411 444 444 444 53 50 51 51 AAA AAA 222 111 111 111 444 444 444 444 444 54 51 52 52 PPP PPP 333 111 222 111 111 222 111 444 444 55 52 53 53 NVV BBB 133 333 333 111 122 244 444 444 444 56 53 54 54 PQQ PPP 344 111 233 111 122 213 121 444 444 57 54 55 55 EAA PUU 444 133 344 144 244 144 144 444 444 58 55 ---- ---- D-- U-- 4-- 3-- 4-- 4-- 1-- 1-- 4-- 4-- 4-- 59 ---- ---- ---- --- --- --- --- --- --- --- --- --- --- --- Sequence identity comparison (ID_TABLE): Diagonal ... number of residues; Upper triangle ... number of identical residues; Lower triangle ... % sequence identity, id/min(length). 1clfA @11durA @21fcaA @12fdnA @0 1clfA @1 55 36 38 37 1durA @2 65 55 37 37 1fcaA @1 69 67 55 51 2fdnA @0 67 67 93 55 Weighted pair-group average clustering based on a distance matrix: .------------------------------------------------------ 1clfA @1.0 32.0000 | | .--- 1fcaA @1.8 7.0000 | | .---------------------------------------------------------- 2fdnA @0.9 34.0000 | .------------------------------------------------------------ 1durA @2.0 +----+----+----+----+----+----+----+----+----+----+----+----+ 35.0800 30.2200 25.3600 20.5000 15.6400 10.7800 5.9200 32.6500 27.7900 22.9300 18.0700 13.2100 8.3500 mkapsa__637W> No residue topology library is in memory. Better radii would be used if topology.read() is called first. iup2crm_280W> No topology library in memory or assigning a BLK residue. Default CHARMM atom type assigned: N --> N This message is written only for the first such atom. iup2crm_280W> No topology library in memory or assigning a BLK residue. Default CHARMM atom type assigned: N --> N This message is written only for the first such atom. iup2crm_280W> No topology library in memory or assigning a BLK residue. Default CHARMM atom type assigned: N --> N This message is written only for the first such atom. iup2crm_280W> No topology library in memory or assigning a BLK residue. Default CHARMM atom type assigned: N --> N This message is written only for the first such atom. Pairwise dynamic programming alignment (ALIGN2D): Residue-residue metric : $(LIB)/as1.sim.mat Diagonal : 100 Overhang : 0 Maximal gap length : 50 Local alignment : F MATRIX_OFFSET (local aln): 0.0000 FIX_OFFSETS : 0.0 -1.0 -2.0 -3.0 -4.0 N_SUBOPT : 0 SUBOPT_OFFSET : 0.0000 Alignment block : 4 Gap introduction penalty : -100.0000 Gap extension penalty : 0.0000 Gap diagonal penalty : 0.0000 Structure gap penalties : 3.500 3.500 3.500 0.200 4.000 6.500 2.000 0.000 Break-break bonus : 10000.0000 Length of alignment : 59 Score : 42593.7695 Total CPU time [seconds] : 0.34