------------------------------------------------------------------------------------------------------------------------- Will print the top 5 alignments (based on backbone shifts) for each pairing of chains, as measured by a combination of score and contiguity. Some relevant parameters: HELIX min length: 5 STRAND min length: 3 shift-tolerance = -10 permissible-violations = 4 max-breaks = NIL retain-m = 100 best-n = 100 anglethresh = 0.5 septhresh = 5 min_length = 4 rmsd-tol = 9.9999999999999E12 Legend: score1 [score2] pairings L2ERR {Xbad/Xsig:Xtot} Breaks (score2 is the score from protein2's perspective, not the minimum of the two perspectives as in some earlier printouts.) Recall that "SIMILARITY" refers to similarities over all alignments not just the top ones. ------------------------------------------------------------------------------------------------------------------------- [2460, 20]: Comparing 1ich_A and 1a1w, based on their crossing files. There are 6 (6 H + 0 S) secondary structure elements in 1ich_A, of which 6 satisfy the size requirements. There are 6 (6 H + 0 S) secondary structure elements in 1a1w, of which 6 satisfy the size requirements. 1.26064 [ 1.26064] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6)) 3.118 {1/9:15} B:0 1.50759 [ 1.50759] ((2 . 1) (4 . 3) (5 . 4) (6 . 5)) 9.070 {0/2:6} B:0 2.06192 [ 2.06192] ((1 . 1) (2 . 2) (4 . 4) (5 . 5) (6 . 6)) 3.235 {1/5:10} B:0 4.00813 [ 4.00813] ((1 . 2) (2 . 4) (4 . 3) (5 . 1) (6 . 5)) 5.481 {2/5:10} B:2 SIMILARITY (1/min{score1}): 0.7932 [and 1/min{score2}: 0.7932] [2460, 706]: Comparing 1ich_A and 1cy5_A, based on their crossing files. There are 6 (6 H + 0 S) secondary structure elements in 1ich_A, of which 6 satisfy the size requirements. There are 7 (7 H + 0 S) secondary structure elements in 1cy5_A, of which 7 satisfy the size requirements. 1.26089 [ 1.35593] ((1 . 2) (2 . 3) (3 . 4) (4 . 5) (5 . 6) (6 . 7)) 3.873 {1/9:15} B:0 1.50790 [ 1.56656] ((1 . 1) (2 . 3) (3 . 4) (4 . 5) (5 . 6) (6 . 7)) 4.265 {1/7:15} B:0 1.58052 [ 1.68223] ((1 . 2) (2 . 3) (3 . 4) (4 . 5) (5 . 6)) 3.259 {1/7:10} B:0 2.57889 [ 2.63962] ((2 . 2) (4 . 4) (5 . 5) (6 . 6)) 9.133 {1/4:6} B:0 2.57922 [ 2.63993] ((3 . 3) (4 . 4) (5 . 5) (6 . 6)) 9.586 {1/4:6} B:0 SIMILARITY (1/min{score1}): 0.7931 [and 1/min{score2}: 0.7375] [2460, 738]: Comparing 1ich_A and 1d2z_A, based on their crossing files. There are 6 (6 H + 0 S) secondary structure elements in 1ich_A, of which 6 satisfy the size requirements. There are 8 (8 H + 0 S) secondary structure elements in 1d2z_A, of which 7 satisfy the size requirements. 1.00059 [ 1.16704] ((1 . 2) (2 . 3) (3 . 4) (4 . 5) (5 . 6) (6 . 7)) 3.531 {0/10:15} B:0 1.51044 [ 1.75660] ((2 . 2) (4 . 4) (5 . 5) (6 . 6)) 9.828 {0/3:6} B:0 3.36704 [ 3.39496] ((1 . 3) (4 . 4) (5 . 2) (6 . 6)) 4.770 {1/3:6} B:1 4.00814 [ 4.01499] ((1 . 3) (2 . 5) (4 . 4) (5 . 2) (6 . 6)) 5.788 {2/5:10} B:2 SIMILARITY (1/min{score1}): 0.9994 [and 1/min{score2}: 0.8569] [2460, 739]: Comparing 1ich_A and 1d2z_B, based on their crossing files. There are 6 (6 H + 0 S) secondary structure elements in 1ich_A, of which 6 satisfy the size requirements. There are 9 (9 H + 0 S) secondary structure elements in 1d2z_B, of which 8 satisfy the size requirements. 1.00021 [ 1.33342] ((1 . 2) (2 . 3) (3 . 6) (4 . 7) (5 . 8) (6 . 9)) 2.727 {0/11:15} B:0 1.50015 [ 2.00006] ((1 . 3) (4 . 6) (5 . 7) (6 . 8)) 3.375 {0/4:6} B:0 1.51316 [ 2.00560] ((2 . 6) (3 . 7) (4 . 8) (5 . 9)) 10.422 {0/4:6} B:0 3.36714 [ 3.43659] ((1 . 8) (2 . 2) (3 . 7) (5 . 9)) 6.247 {1/3:6} B:1 4.00817 [ 4.02545] ((1 . 8) (2 . 2) (3 . 7) (4 . 3) (5 . 9)) 6.252 {2/5:10} B:2 SIMILARITY (1/min{score1}): 0.9998 [and 1/min{score2}: 0.7499] [2460, 804]: Comparing 1ich_A and 1ddf, based on their crossing files. There are 6 (6 H + 0 S) secondary structure elements in 1ich_A, of which 6 satisfy the size requirements. There are 6 (6 H + 0 S) secondary structure elements in 1ddf, of which 6 satisfy the size requirements. 1.00022 [ 1.00022] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6)) 2.767 {0/10:15} B:0 1.20013 [ 1.20013] ((1 . 1) (2 . 2) (4 . 4) (5 . 5) (6 . 6)) 2.772 {0/7:10} B:0 1.50513 [ 1.50513] ((2 . 1) (4 . 3) (5 . 4) (6 . 5)) 8.219 {0/2:6} B:0 1.50929 [ 1.50929] ((2 . 1) (3 . 2) (4 . 3) (6 . 5)) 9.543 {0/3:6} B:0 4.00812 [ 4.00812] ((1 . 2) (2 . 4) (4 . 3) (5 . 1) (6 . 5)) 5.304 {2/5:10} B:2 SIMILARITY (1/min{score1}): 0.9998 [and 1/min{score2}: 0.9998] [2460, 831]: Comparing 1ich_A and 1dgn_A, based on their crossing files. There are 6 (6 H + 0 S) secondary structure elements in 1ich_A, of which 6 satisfy the size requirements. There are 6 (6 H + 0 S) secondary structure elements in 1dgn_A, of which 6 satisfy the size requirements. 1.36220 [ 1.36220] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6)) 3.301 {1/8:15} B:0 2.06193 [ 2.06193] ((1 . 1) (2 . 2) (4 . 4) (5 . 5) (6 . 6)) 3.440 {1/5:10} B:0 2.57839 [ 2.57839] ((1 . 2) (3 . 4) (4 . 5) (5 . 6)) 8.296 {1/4:6} B:0 SIMILARITY (1/min{score1}): 0.7341 [and 1/min{score2}: 0.7341] [2460, 1453]: Comparing 1ich_A and 1fad_A, based on their crossing files. There are 6 (6 H + 0 S) secondary structure elements in 1ich_A, of which 6 satisfy the size requirements. There are 6 (6 H + 0 S) secondary structure elements in 1fad_A, of which 6 satisfy the size requirements. 1.20037 [ 1.20037] ((1 . 1) (2 . 2) (4 . 4) (5 . 5) (6 . 6)) 3.610 {0/7:10} B:0 SIMILARITY (1/min{score1}): 0.8331 [and 1/min{score2}: 0.8331] [2460, 2460]: Comparing 1ich_A and 1ich_A, based on their crossing files. There are 6 (6 H + 0 S) secondary structure elements in 1ich_A, of which 6 satisfy the size requirements. There are 6 (6 H + 0 S) secondary structure elements in 1ich_A, of which 6 satisfy the size requirements. 1.00000 [ 1.00000] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6)) 0.000 {0/12:15} B:0 5.01068 [ 5.01068] ((1 . 3) (2 . 2) (3 . 4) (4 . 5)) 11.776 {2/4:6} B:1 5.01068 [ 5.01068] ((2 . 2) (3 . 1) (4 . 3) (5 . 4)) 11.776 {2/4:6} B:1 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [2460, 4117]: Comparing 1ich_A and 1n3k_A, based on their crossing files. There are 6 (6 H + 0 S) secondary structure elements in 1ich_A, of which 6 satisfy the size requirements. There are 7 (7 H + 0 S) secondary structure elements in 1n3k_A, of which 6 satisfy the size requirements. 1.00039 [ 1.00039] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6)) 3.178 {0/10:15} B:0 1.20026 [ 1.20026] ((1 . 1) (2 . 2) (4 . 4) (5 . 5) (6 . 6)) 3.294 {0/6:10} B:0 1.50961 [ 1.50961] ((2 . 1) (4 . 3) (5 . 4) (6 . 5)) 9.625 {0/3:6} B:0 3.34735 [ 3.34735] ((1 . 2) (2 . 4) (4 . 3) (5 . 1) (6 . 5)) 5.654 {2/6:10} B:2 SIMILARITY (1/min{score1}): 0.9996 [and 1/min{score2}: 0.9996] [2460, 4243]: Comparing 1ich_A and 1ngr, based on their crossing files. There are 6 (6 H + 0 S) secondary structure elements in 1ich_A, of which 6 satisfy the size requirements. There are 6 (6 H + 0 S) secondary structure elements in 1ngr, of which 6 satisfy the size requirements. 1.00021 [ 1.00021] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6)) 2.735 {0/11:15} B:0 1.20008 [ 1.20008] ((2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6)) 2.427 {0/8:10} B:0 1.50009 [ 1.50009] ((1 . 2) (4 . 3) (5 . 4) (6 . 5)) 3.009 {0/4:6} B:0 1.50285 [ 1.50285] ((2 . 1) (4 . 4) (5 . 5) (6 . 6)) 7.090 {0/2:6} B:0 1.50992 [ 1.50992] ((3 . 2) (4 . 3) (5 . 4) (6 . 5)) 9.703 {0/4:6} B:0 SIMILARITY (1/min{score1}): 0.9998 [and 1/min{score2}: 0.9998] [2460, 5971]: Comparing 1ich_A and 1ucp_A, based on their crossing files. There are 6 (6 H + 0 S) secondary structure elements in 1ich_A, of which 6 satisfy the size requirements. There are 6 (6 H + 0 S) secondary structure elements in 1ucp_A, of which 6 satisfy the size requirements. 1.00017 [ 1.00017] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6)) 2.583 {0/10:15} B:0 1.50024 [ 1.50024] ((1 . 2) (4 . 3) (5 . 4) (6 . 5)) 3.817 {0/3:6} B:0 1.50832 [ 1.50832] ((3 . 2) (4 . 3) (5 . 4) (6 . 5)) 9.283 {0/3:6} B:0 1.51181 [ 1.51181] ((2 . 1) (3 . 2) (4 . 3) (6 . 5)) 10.140 {0/3:6} B:0 3.36825 [ 3.36825] ((1 . 2) (2 . 4) (3 . 3) (4 . 5)) 10.589 {1/3:6} B:1 SIMILARITY (1/min{score1}): 0.9998 [and 1/min{score2}: 0.9998] [2460, 6562]: Comparing 1ich_A and 3crd, based on their crossing files. There are 6 (6 H + 0 S) secondary structure elements in 1ich_A, of which 6 satisfy the size requirements. There are 6 (6 H + 0 S) secondary structure elements in 3crd, of which 6 satisfy the size requirements. 1.00164 [ 1.00164] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6)) 4.558 {0/6:15} B:0 SIMILARITY (1/min{score1}): 0.9984 [and 1/min{score2}: 0.9984] [2460, 6605]: Comparing 1ich_A and 3ygs_P, based on their crossing files. There are 6 (6 H + 0 S) secondary structure elements in 1ich_A, of which 6 satisfy the size requirements. There are 7 (7 H + 0 S) secondary structure elements in 3ygs_P, of which 7 satisfy the size requirements. 1.00073 [ 1.16712] ((1 . 2) (2 . 3) (3 . 4) (4 . 5) (5 . 6) (6 . 7)) 3.715 {0/9:15} B:0 1.00126 [ 1.16746] ((1 . 1) (2 . 3) (3 . 4) (4 . 5) (5 . 6) (6 . 7)) 4.261 {0/7:15} B:0 1.20020 [ 1.40012] ((1 . 2) (2 . 3) (3 . 4) (4 . 5) (5 . 6)) 3.074 {0/7:10} B:0 1.50017 [ 1.75011] ((1 . 3) (4 . 4) (5 . 5) (6 . 6)) 3.525 {0/3:6} B:0 1.50970 [ 1.75614] ((3 . 3) (4 . 4) (5 . 5) (6 . 6)) 9.648 {0/3:6} B:0 SIMILARITY (1/min{score1}): 0.9993 [and 1/min{score2}: 0.8568] -------------------------------------------------------------------------------------------------------------------------