------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [106, 106]: Comparing 1ad3_A and 1ad3_A, based on their crossing files. There are 40 (21 H + 19 S) secondary structure elements in 1ad3_A, of which 30 satisfy the size requirements. There are 40 (21 H + 19 S) secondary structure elements in 1ad3_A, of which 30 satisfy the size requirements. 1.00000 [ 1.00000] ((1 . 1) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (8 . 8) (9 . 9) (10 . 10) (11 . 11) (12 . 12) (13 . 13) (14 . 14) (15 . 15) (16 . 16) (17 . 17) (18 . 18) (19 . 19) (20 . 20) (21 . 21) (23 . 23) (24 . 24) (27 . 27) (30 . 30) (31 . 31) (32 . 32) (33 . 33) (34 . 34) (38 . 38) (39 . 39) (40 . 40)) 0.000 {0/362:435} B:0 1.03448 [ 1.03448] ((1 . 1) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (8 . 8) (9 . 9) (10 . 10) (11 . 11) (12 . 12) (13 . 13) (14 . 14) (15 . 15) (16 . 16) (17 . 17) (18 . 18) (19 . 19) (20 . 20) (21 . 21) (23 . 23) (27 . 27) (30 . 30) (31 . 31) (32 . 32) (33 . 33) (34 . 34) (38 . 38) (39 . 39) (40 . 40)) 0.000 {0/334:406} B:0 1.03448 [ 1.03448] ((1 . 1) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (8 . 8) (9 . 9) (10 . 10) (11 . 11) (12 . 12) (13 . 13) (14 . 14) (15 . 15) (16 . 16) (17 . 17) (18 . 18) (19 . 19) (20 . 20) (21 . 21) (23 . 23) (24 . 24) (27 . 27) (30 . 30) (31 . 31) (32 . 32) (33 . 33) (34 . 34) (38 . 38) (39 . 39)) 0.000 {0/335:406} B:0 3.75005 [ 3.75005] ((11 . 9) (13 . 11) (19 . 19) (21 . 21) (30 . 27) (33 . 31) (34 . 32) (39 . 39)) 5.055 {0/21:28} B:0 3.75005 [ 3.75005] ((9 . 11) (11 . 13) (19 . 19) (21 . 21) (27 . 30) (31 . 33) (32 . 34) (39 . 39)) 5.055 {0/21:28} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [106, 1267]: Comparing 1ad3_A and 1euh_A, based on their crossing files. There are 40 (21 H + 19 S) secondary structure elements in 1ad3_A, of which 30 satisfy the size requirements. There are 42 (18 H + 24 S) secondary structure elements in 1euh_A, of which 33 satisfy the size requirements. 1.12300 [ 1.23120] ((1 . 5) (3 . 6) (4 . 7) (6 . 8) (8 . 12) (9 . 13) (10 . 14) (11 . 15) (12 . 16) (13 . 17) (14 . 18) (15 . 19) (16 . 20) (17 . 21) (18 . 22) (19 . 23) (20 . 24) (21 . 25) (23 . 27) (27 . 31) (30 . 33) (31 . 34) (32 . 36) (33 . 37) (34 . 38) (38 . 41) (39 . 42)) 2.855 {14/277:351} B:0 1.37170 [ 1.43561] ((1 . 5) (3 . 6) (4 . 7) (6 . 8) (8 . 12) (9 . 13) (10 . 14) (11 . 15) (12 . 16) (13 . 17) (14 . 18) (15 . 19) (16 . 20) (17 . 21) (18 . 22) (19 . 23) (20 . 24) (21 . 25) (23 . 27) (24 . 31) (27 . 33) (31 . 34) (32 . 36) (33 . 37) (34 . 38) (38 . 41) (39 . 42)) 3.264 {33/277:351} B:0 2.30772 [ 2.53848] ((9 . 15) (13 . 17) (15 . 19) (16 . 20) (19 . 23) (20 . 24) (21 . 25) (31 . 34) (32 . 36) (33 . 37) (34 . 38) (38 . 41) (39 . 42)) 2.428 {1/58:78} B:0 3.00003 [ 3.30002] ((1 . 5) (3 . 6) (4 . 7) (6 . 8) (10 . 14) (11 . 15) (12 . 16) (17 . 19) (33 . 34) (34 . 36)) 3.663 {0/33:45} B:0 3.34971 [ 3.67900] ((9 . 22) (10 . 23) (11 . 24) (12 . 25) (13 . 33) (14 . 34) (15 . 36) (16 . 37) (17 . 38)) 3.858 {2/16:36} B:0 SIMILARITY (1/min{score1}): 0.8905 [and 1/min{score2}: 0.8122] [106, 1320]: Comparing 1ad3_A and 1ez0_A, based on their crossing files. There are 40 (21 H + 19 S) secondary structure elements in 1ad3_A, of which 30 satisfy the size requirements. There are 38 (20 H + 18 S) secondary structure elements in 1ez0_A, of which 34 satisfy the size requirements. 1.11205 [ 1.24280] ((1 . 3) (3 . 4) (4 . 5) (6 . 6) (8 . 8) (9 . 9) (10 . 10) (11 . 11) (12 . 12) (13 . 14) (14 . 15) (15 . 16) (16 . 17) (17 . 18) (18 . 19) (19 . 21) (20 . 22) (21 . 23) (23 . 24) (24 . 25) (27 . 26) (30 . 29) (31 . 30) (32 . 31) (33 . 32) (34 . 33) (38 . 34) (39 . 35)) 3.775 {20/296:378} B:0 2.30776 [ 2.61543] ((1 . 3) (3 . 4) (4 . 5) (6 . 6) (9 . 9) (10 . 10) (11 . 11) (13 . 14) (14 . 15) (15 . 16) (16 . 17) (23 . 24) (34 . 31)) 3.187 {1/48:78} B:0 2.30805 [ 2.61563] ((9 . 11) (13 . 14) (15 . 16) (16 . 17) (19 . 21) (23 . 24) (30 . 29) (31 . 30) (32 . 31) (33 . 32) (34 . 33) (38 . 34) (39 . 35)) 2.919 {2/56:78} B:0 2.50049 [ 2.83367] ((1 . 3) (3 . 4) (4 . 5) (6 . 6) (8 . 8) (9 . 9) (10 . 10) (14 . 15) (16 . 17) (23 . 24) (30 . 26) (34 . 31)) 3.625 {2/49:66} B:0 3.00010 [ 3.40007] ((9 . 11) (11 . 14) (19 . 21) (21 . 23) (23 . 24) (27 . 29) (33 . 32) (34 . 33) (38 . 34) (39 . 35)) 4.273 {1/36:45} B:0 SIMILARITY (1/min{score1}): 0.8992 [and 1/min{score2}: 0.8046] [106, 3197]: Comparing 1ad3_A and 1k75_A, based on their crossing files. There are 40 (21 H + 19 S) secondary structure elements in 1ad3_A, of which 30 satisfy the size requirements. There are 34 (20 H + 14 S) secondary structure elements in 1k75_A, of which 31 satisfy the size requirements. 2.19262 [ 2.20403] ((6 . 7) (8 . 9) (9 . 10) (10 . 11) (11 . 12) (12 . 13) (13 . 14) (14 . 15) (15 . 16) (16 . 17) (18 . 19) (19 . 20) (20 . 21) (21 . 22) (23 . 23) (30 . 24) (31 . 25) (32 . 26) (33 . 27) (34 . 28) (39 . 32) (40 . 33)) 5.229 {36/171:231} B:0 2.33079 [ 2.34223] ((6 . 7) (8 . 9) (9 . 10) (10 . 11) (11 . 12) (12 . 13) (13 . 14) (14 . 15) (15 . 16) (16 . 17) (18 . 19) (19 . 20) (20 . 21) (21 . 22) (23 . 23) (30 . 24) (31 . 25) (32 . 26) (34 . 28) (39 . 32) (40 . 33)) 5.079 {35/156:210} B:0 3.75001 [ 3.87501] ((18 . 10) (19 . 11) (20 . 12) (21 . 13) (30 . 14) (31 . 15) (32 . 16) (33 . 17)) 3.190 {0/9:28} B:0 2.79107 [ 2.79663] ((3 . 6) (5 . 7) (6 . 13) (8 . 9) (9 . 10) (10 . 11) (11 . 12) (13 . 14) (14 . 15) (15 . 16) (16 . 17) (18 . 19) (19 . 20) (20 . 21) (21 . 22) (30 . 24) (31 . 25) (32 . 26) (33 . 27) (34 . 28) (39 . 32) (40 . 34)) 6.980 {44/160:231} B:1 2.84728 [ 2.85494] ((3 . 13) (6 . 7) (8 . 9) (9 . 10) (10 . 11) (11 . 12) (13 . 14) (14 . 15) (15 . 16) (16 . 17) (18 . 19) (19 . 20) (20 . 21) (21 . 22) (30 . 24) (31 . 25) (32 . 26) (33 . 27) (34 . 28) (39 . 32)) 4.838 {36/129:190} B:1 SIMILARITY (1/min{score1}): 0.5660 [and 1/min{score2}: 0.5561] [106, 3474]: Comparing 1ad3_A and 1ky8_A, based on their crossing files. There are 40 (21 H + 19 S) secondary structure elements in 1ad3_A, of which 30 satisfy the size requirements. There are 45 (19 H + 26 S) secondary structure elements in 1ky8_A, of which 38 satisfy the size requirements. 1.06248 [ 1.32446] ((1 . 8) (3 . 10) (4 . 11) (5 . 12) (6 . 13) (8 . 15) (9 . 16) (10 . 17) (11 . 18) (12 . 19) (13 . 20) (14 . 21) (15 . 22) (16 . 23) (17 . 24) (18 . 25) (19 . 26) (20 . 27) (21 . 28) (23 . 29) (24 . 30) (27 . 33) (30 . 36) (31 . 37) (32 . 39) (33 . 40) (34 . 41) (38 . 44) (39 . 45)) 3.825 {19/319:406} B:0 1.08819 [ 1.36551] ((1 . 8) (3 . 10) (4 . 11) (6 . 12) (8 . 15) (9 . 16) (10 . 17) (11 . 18) (12 . 19) (13 . 20) (14 . 21) (15 . 22) (16 . 23) (17 . 24) (18 . 25) (19 . 26) (20 . 27) (21 . 28) (23 . 29) (24 . 30) (27 . 33) (30 . 36) (31 . 37) (32 . 39) (33 . 40) (34 . 41) (38 . 44) (39 . 45)) 3.891 {16/300:378} B:0 1.09223 [ 1.36756] ((1 . 8) (3 . 10) (4 . 11) (5 . 12) (8 . 15) (9 . 16) (10 . 17) (11 . 18) (12 . 19) (13 . 20) (14 . 21) (15 . 22) (16 . 23) (17 . 24) (18 . 25) (19 . 26) (20 . 27) (21 . 28) (23 . 29) (24 . 30) (27 . 33) (30 . 36) (31 . 37) (32 . 39) (33 . 40) (34 . 41) (38 . 44) (39 . 45)) 3.476 {17/300:378} B:0 3.00714 [ 3.80352] ((15 . 24) (19 . 26) (21 . 28) (23 . 29) (31 . 37) (32 . 39) (33 . 40) (34 . 41) (38 . 44) (39 . 45)) 2.861 {3/32:45} B:0 3.33611 [ 4.22359] ((11 . 20) (15 . 24) (23 . 29) (31 . 37) (32 . 39) (33 . 40) (34 . 41) (38 . 44) (39 . 45)) 3.506 {2/25:36} B:0 SIMILARITY (1/min{score1}): 0.9412 [and 1/min{score2}: 0.7550] [106, 4460]: Comparing 1ad3_A and 1o04_A, based on their crossing files. There are 40 (21 H + 19 S) secondary structure elements in 1ad3_A, of which 30 satisfy the size requirements. There are 38 (18 H + 20 S) secondary structure elements in 1o04_A, of which 34 satisfy the size requirements. 1.05717 [ 1.18820] ((1 . 5) (3 . 7) (4 . 8) (5 . 9) (6 . 10) (8 . 12) (9 . 13) (10 . 14) (11 . 15) (12 . 16) (13 . 17) (14 . 18) (15 . 19) (16 . 20) (17 . 21) (18 . 22) (19 . 23) (20 . 24) (21 . 25) (23 . 26) (24 . 27) (27 . 28) (30 . 30) (31 . 31) (32 . 32) (33 . 33) (34 . 34) (38 . 37) (39 . 38)) 2.947 {18/318:406} B:0 1.29753 [ 1.43002] ((1 . 5) (3 . 7) (4 . 9) (6 . 10) (9 . 13) (10 . 14) (11 . 15) (12 . 16) (13 . 17) (14 . 18) (15 . 19) (16 . 20) (17 . 21) (18 . 22) (19 . 23) (20 . 24) (21 . 25) (23 . 26) (27 . 28) (30 . 30) (31 . 31) (32 . 32) (33 . 33) (34 . 34) (38 . 37)) 3.381 {21/225:300} B:0 2.00013 [ 2.26676] ((1 . 5) (4 . 8) (6 . 10) (9 . 13) (10 . 14) (11 . 15) (13 . 17) (14 . 18) (15 . 19) (16 . 20) (19 . 23) (21 . 25) (23 . 26) (34 . 32) (38 . 37)) 2.394 {2/81:105} B:0 2.30798 [ 2.61558] ((11 . 17) (19 . 23) (21 . 25) (23 . 26) (24 . 27) (27 . 28) (30 . 30) (31 . 31) (32 . 32) (33 . 33) (34 . 34) (38 . 37) (39 . 38)) 3.245 {2/60:78} B:0 2.30801 [ 2.61560] ((1 . 5) (6 . 10) (10 . 14) (11 . 15) (13 . 17) (14 . 18) (15 . 19) (16 . 20) (19 . 23) (21 . 25) (23 . 26) (30 . 28) (34 . 32)) 3.568 {2/59:78} B:0 SIMILARITY (1/min{score1}): 0.9459 [and 1/min{score2}: 0.8416] [106, 4476]: Comparing 1ad3_A and 1o20_A, based on their crossing files. There are 40 (21 H + 19 S) secondary structure elements in 1ad3_A, of which 30 satisfy the size requirements. There are 34 (18 H + 16 S) secondary structure elements in 1o20_A, of which 28 satisfy the size requirements. 1.32435 [ 1.24182] ((1 . 1) (3 . 2) (4 . 3) (6 . 5) (8 . 7) (9 . 8) (10 . 9) (11 . 10) (12 . 11) (13 . 13) (14 . 14) (15 . 15) (16 . 16) (18 . 17) (19 . 18) (20 . 19) (21 . 20) (30 . 25) (31 . 26) (32 . 27) (33 . 28) (34 . 29) (39 . 34)) 4.846 {12/186:253} B:0 1.70166 [ 1.67096] ((1 . 1) (3 . 2) (4 . 4) (6 . 5) (8 . 7) (9 . 8) (10 . 9) (11 . 10) (12 . 11) (13 . 13) (14 . 14) (15 . 15) (16 . 16) (18 . 17) (19 . 18) (20 . 19) (21 . 20) (27 . 21) (30 . 25) (31 . 26) (32 . 27) (33 . 28) (34 . 29) (39 . 34)) 4.460 {32/205:276} B:0 2.30790 [ 2.15410] ((1 . 1) (3 . 2) (4 . 3) (6 . 5) (9 . 8) (10 . 9) (11 . 10) (12 . 11) (13 . 13) (14 . 14) (15 . 15) (16 . 16) (32 . 29)) 5.058 {0/45:78} B:0 2.46890 [ 2.45906] ((1 . 1) (3 . 2) (4 . 4) (6 . 5) (8 . 7) (9 . 8) (10 . 9) (11 . 10) (12 . 11) (13 . 13) (14 . 14) (15 . 15) (16 . 16) (18 . 17) (19 . 18) (20 . 19) (21 . 20) (24 . 21) (30 . 25) (31 . 26) (32 . 27) (33 . 28) (34 . 29) (39 . 34)) 4.588 {50/206:276} B:0 2.50721 [ 2.49607] ((1 . 1) (3 . 2) (4 . 4) (6 . 5) (8 . 7) (9 . 8) (10 . 9) (11 . 10) (12 . 11) (13 . 13) (14 . 14) (15 . 15) (18 . 17) (19 . 18) (20 . 19) (21 . 20) (24 . 21) (30 . 25) (31 . 26) (32 . 27) (33 . 28) (34 . 29) (39 . 34)) 4.316 {46/187:253} B:0 SIMILARITY (1/min{score1}): 0.7551 [and 1/min{score2}: 0.8053] [106, 6149]: Comparing 1ad3_A and 1uzb_A, based on their crossing files. There are 40 (21 H + 19 S) secondary structure elements in 1ad3_A, of which 30 satisfy the size requirements. There are 37 (18 H + 19 S) secondary structure elements in 1uzb_A, of which 34 satisfy the size requirements. 1.08162 [ 1.22133] ((1 . 7) (3 . 8) (4 . 9) (6 . 10) (8 . 11) (9 . 12) (10 . 13) (11 . 14) (12 . 15) (13 . 16) (14 . 17) (15 . 18) (16 . 19) (17 . 20) (18 . 21) (19 . 22) (20 . 23) (21 . 24) (23 . 26) (24 . 27) (27 . 28) (30 . 30) (31 . 31) (32 . 32) (33 . 33) (34 . 34) (38 . 36) (39 . 37)) 3.148 {14/297:378} B:0 1.16055 [ 1.31231] ((1 . 7) (3 . 8) (4 . 9) (6 . 10) (8 . 11) (9 . 12) (10 . 13) (11 . 14) (12 . 15) (13 . 16) (14 . 17) (15 . 18) (16 . 19) (17 . 20) (18 . 21) (19 . 22) (20 . 23) (21 . 24) (23 . 26) (30 . 28) (31 . 31) (32 . 32) (33 . 33) (34 . 34) (38 . 36) (39 . 37)) 3.475 {11/247:325} B:0 1.76570 [ 2.00068] ((1 . 7) (6 . 10) (9 . 14) (15 . 18) (16 . 19) (17 . 20) (18 . 21) (19 . 22) (21 . 24) (23 . 26) (24 . 27) (27 . 28) (31 . 31) (32 . 32) (33 . 33) (34 . 34) (38 . 36)) 2.745 {4/105:136} B:0 2.14290 [ 2.42860] ((1 . 7) (9 . 14) (16 . 19) (19 . 22) (20 . 23) (21 . 24) (24 . 27) (27 . 28) (30 . 30) (31 . 31) (32 . 32) (33 . 33) (34 . 34) (38 . 36)) 2.993 {1/71:91} B:0 2.30774 [ 2.61542] ((9 . 14) (11 . 16) (19 . 22) (20 . 23) (21 . 24) (24 . 27) (27 . 28) (30 . 30) (31 . 31) (32 . 32) (33 . 33) (34 . 34) (38 . 36)) 3.069 {1/59:78} B:0 SIMILARITY (1/min{score1}): 0.9245 [and 1/min{score2}: 0.8188] -------------------------------------------------------------------------------------------------------------------------