------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [1965, 320]: Comparing 1gv1_A and 1b8p_A, based on their crossing files. There are 33 (17 H + 16 S) secondary structure elements in 1gv1_A, of which 12 satisfy the size requirements. There are 29 (15 H + 14 S) secondary structure elements in 1b8p_A, of which 12 satisfy the size requirements. 1.69700 [ 1.69700] ((14 . 13) (17 . 16) (19 . 17) (24 . 21) (25 . 23) (26 . 24) (27 . 25) (31 . 27) (32 . 28) (33 . 29)) 4.094 {6/38:45} B:0 1.77523 [ 1.77523] ((14 . 13) (17 . 16) (24 . 22) (25 . 23) (26 . 24) (27 . 25) (31 . 27) (32 . 28) (33 . 29)) 3.876 {5/31:36} B:0 1.87863 [ 1.87863] ((14 . 13) (17 . 16) (19 . 17) (24 . 22) (25 . 23) (26 . 24) (27 . 25) (31 . 27) (32 . 28) (33 . 29)) 3.934 {7/39:45} B:0 2.09232 [ 2.09232] ((14 . 13) (17 . 16) (19 . 17) (24 . 21) (25 . 23) (26 . 24) (27 . 25) (31 . 27) (33 . 29)) 4.198 {6/30:36} B:0 2.27872 [ 2.27872] ((14 . 13) (17 . 16) (19 . 17) (24 . 21) (26 . 23) (33 . 29)) 6.890 {2/11:15} B:0 SIMILARITY (1/min{score1}): 0.5893 [and 1/min{score2}: 0.5893] [1965, 1322]: Comparing 1gv1_A and 1ez4_A, based on their crossing files. There are 33 (17 H + 16 S) secondary structure elements in 1gv1_A, of which 12 satisfy the size requirements. There are 31 (15 H + 16 S) secondary structure elements in 1ez4_A, of which 11 satisfy the size requirements. 1.20814 [ 1.11052] ((14 . 13) (24 . 22) (25 . 23) (26 . 24) (27 . 25) (28 . 26) (30 . 28) (31 . 29) (32 . 30) (33 . 31)) 1.924 {2/41:45} B:0 3.00039 [ 2.75050] ((14 . 13) (25 . 22) (26 . 24) (33 . 31)) 7.235 {0/5:6} B:0 3.06906 [ 2.83845] ((14 . 13) (26 . 24) (30 . 26) (33 . 31)) 4.105 {1/6:6} B:0 3.13876 [ 2.92550] ((14 . 13) (30 . 25) (31 . 26) (32 . 28)) 7.840 {1/5:6} B:0 3.13876 [ 2.92551] ((14 . 13) (27 . 28) (28 . 29) (30 . 30)) 7.860 {1/5:6} B:0 SIMILARITY (1/min{score1}): 0.8277 [and 1/min{score2}: 0.9005] [1965, 1965]: Comparing 1gv1_A and 1gv1_A, based on their crossing files. There are 33 (17 H + 16 S) secondary structure elements in 1gv1_A, of which 12 satisfy the size requirements. There are 33 (17 H + 16 S) secondary structure elements in 1gv1_A, of which 12 satisfy the size requirements. 1.00000 [ 1.00000] ((14 . 14) (17 . 17) (19 . 19) (24 . 24) (25 . 25) (26 . 26) (27 . 27) (28 . 28) (30 . 30) (31 . 31) (32 . 32) (33 . 33)) 0.000 {0/61:66} B:0 3.00035 [ 3.00035] ((14 . 14) (24 . 25) (26 . 26) (33 . 33)) 7.046 {0/5:6} B:0 3.00035 [ 3.00035] ((14 . 14) (25 . 24) (26 . 26) (33 . 33)) 7.046 {0/5:6} B:0 3.06904 [ 3.06904] ((14 . 14) (26 . 26) (30 . 28) (33 . 33)) 3.000 {1/6:6} B:0 3.06904 [ 3.06904] ((14 . 14) (26 . 26) (28 . 30) (33 . 33)) 3.000 {1/6:6} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [1965, 2329]: Comparing 1gv1_A and 1hye_A, based on their crossing files. There are 33 (17 H + 16 S) secondary structure elements in 1gv1_A, of which 12 satisfy the size requirements. There are 29 (13 H + 16 S) secondary structure elements in 1hye_A, of which 12 satisfy the size requirements. 1.09097 [ 1.09097] ((14 . 12) (17 . 15) (19 . 16) (24 . 22) (26 . 23) (27 . 24) (28 . 25) (30 . 26) (31 . 27) (32 . 28) (33 . 29)) 2.090 {0/50:55} B:0 1.09184 [ 1.09184] ((14 . 12) (17 . 15) (19 . 16) (25 . 22) (26 . 23) (27 . 24) (28 . 25) (30 . 26) (31 . 27) (32 . 28) (33 . 29)) 3.773 {1/49:55} B:0 2.01146 [ 2.01146] ((14 . 12) (17 . 15) (19 . 16) (24 . 22) (26 . 23) (30 . 27) (33 . 29)) 5.810 {3/18:21} B:0 2.91541 [ 2.91541] ((14 . 12) (24 . 22) (26 . 23) (28 . 26) (33 . 29)) 3.798 {2/8:10} B:0 3.13831 [ 3.13831] ((14 . 12) (26 . 23) (30 . 25) (33 . 29)) 3.554 {1/5:6} B:0 SIMILARITY (1/min{score1}): 0.9166 [and 1/min{score2}: 0.9166] [1965, 2331]: Comparing 1gv1_A and 1hyh_A, based on their crossing files. There are 33 (17 H + 16 S) secondary structure elements in 1gv1_A, of which 12 satisfy the size requirements. There are 26 (13 H + 13 S) secondary structure elements in 1hyh_A, of which 7 satisfy the size requirements. 1.77229 [ 1.22196] ((14 . 14) (24 . 21) (26 . 22) (27 . 23) (31 . 24) (32 . 25) (33 . 26)) 3.313 {2/19:21} B:0 2.44349 [ 1.58508] ((14 . 14) (24 . 21) (26 . 22) (30 . 25) (33 . 26)) 6.631 {1/8:10} B:0 2.75473 [ 2.30544] ((14 . 14) (24 . 21) (26 . 22) (28 . 24) (33 . 26)) 6.136 {2/9:10} B:0 2.75480 [ 2.30556] ((14 . 14) (24 . 21) (26 . 22) (30 . 24) (33 . 26)) 6.507 {2/9:10} B:0 3.00098 [ 1.75489] ((26 . 21) (31 . 23) (32 . 24) (33 . 26)) 9.116 {0/6:6} B:0 SIMILARITY (1/min{score1}): 0.5642 [and 1/min{score2}: 0.8184] [1965, 3656]: Comparing 1gv1_A and 1lld_A, based on their crossing files. There are 33 (17 H + 16 S) secondary structure elements in 1gv1_A, of which 12 satisfy the size requirements. There are 25 (11 H + 14 S) secondary structure elements in 1lld_A, of which 7 satisfy the size requirements. 1.78544 [ 1.26064] ((14 . 12) (24 . 20) (26 . 21) (27 . 22) (31 . 23) (32 . 24) (33 . 25)) 3.102 {2/18:21} B:0 1.78592 [ 1.26202] ((14 . 12) (25 . 20) (26 . 21) (27 . 22) (31 . 23) (32 . 24) (33 . 25)) 5.351 {2/18:21} B:0 2.01494 [ 1.23628] ((14 . 12) (24 . 20) (26 . 21) (31 . 23) (32 . 24) (33 . 25)) 2.892 {1/12:15} B:0 2.91560 [ 2.55965] ((14 . 12) (24 . 20) (26 . 21) (30 . 23) (33 . 25)) 6.173 {2/8:10} B:0 3.13837 [ 2.24471] ((14 . 12) (26 . 21) (32 . 23) (33 . 25)) 5.053 {1/5:6} B:0 SIMILARITY (1/min{score1}): 0.5601 [and 1/min{score2}: 0.8089] [1965, 4521]: Comparing 1gv1_A and 1o6z_A, based on their crossing files. There are 33 (17 H + 16 S) secondary structure elements in 1gv1_A, of which 12 satisfy the size requirements. There are 27 (13 H + 14 S) secondary structure elements in 1o6z_A, of which 10 satisfy the size requirements. 1.20075 [ 1.00129] ((14 . 13) (17 . 16) (19 . 17) (24 . 20) (26 . 21) (28 . 22) (30 . 24) (31 . 25) (32 . 26) (33 . 27)) 3.010 {1/40:45} B:0 1.33336 [ 1.11116] ((14 . 13) (17 . 16) (19 . 17) (24 . 20) (26 . 21) (30 . 24) (31 . 25) (32 . 26) (33 . 27)) 2.048 {0/33:36} B:0 2.06196 [ 2.03064] ((14 . 13) (17 . 16) (19 . 17) (24 . 20) (26 . 21) (27 . 22) (28 . 24) (31 . 25) (32 . 26) (33 . 27)) 3.792 {8/40:45} B:0 2.41810 [ 2.03091] ((14 . 13) (25 . 20) (26 . 21) (31 . 25) (33 . 27)) 5.329 {1/10:10} B:0 2.75451 [ 2.52097] ((14 . 13) (24 . 20) (26 . 21) (28 . 24) (33 . 27)) 3.825 {2/9:10} B:0 SIMILARITY (1/min{score1}): 0.8328 [and 1/min{score2}: 0.9987] [1965, 4586]: Comparing 1gv1_A and 1obb_A, based on their crossing files. There are 33 (17 H + 16 S) secondary structure elements in 1gv1_A, of which 12 satisfy the size requirements. There are 36 (23 H + 13 S) secondary structure elements in 1obb_A, of which 19 satisfy the size requirements. 1.61511 [ 2.20191] ((14 . 14) (17 . 16) (19 . 17) (24 . 19) (26 . 28) (27 . 29) (31 . 30) (32 . 31) (33 . 32)) 6.342 {4/29:36} B:0 1.89128 [ 2.50774] ((14 . 14) (17 . 16) (19 . 17) (26 . 28) (27 . 29) (31 . 30) (32 . 31) (33 . 32)) 5.696 {4/24:28} B:0 1.89153 [ 2.50785] ((14 . 14) (17 . 16) (19 . 17) (26 . 28) (27 . 29) (31 . 30) (32 . 31) (33 . 33)) 6.203 {4/24:28} B:0 2.03770 [ 2.41373] ((14 . 14) (17 . 16) (19 . 17) (25 . 25) (26 . 28) (27 . 29) (31 . 30) (32 . 31) (33 . 33)) 7.459 {6/31:36} B:0 2.46802 [ 3.32112] ((17 . 16) (26 . 28) (27 . 29) (31 . 30) (32 . 31) (33 . 33)) 5.744 {3/14:15} B:0 SIMILARITY (1/min{score1}): 0.6192 [and 1/min{score2}: 0.4542] [1965, 5878]: Comparing 1gv1_A and 1t2d_A, based on their crossing files. There are 33 (17 H + 16 S) secondary structure elements in 1gv1_A, of which 12 satisfy the size requirements. There are 31 (15 H + 16 S) secondary structure elements in 1t2d_A, of which 11 satisfy the size requirements. 1.20811 [ 1.11049] ((14 . 13) (24 . 22) (25 . 23) (26 . 24) (27 . 25) (28 . 26) (30 . 28) (31 . 29) (32 . 30) (33 . 31)) 1.242 {2/41:45} B:0 3.00034 [ 2.75044] ((14 . 13) (24 . 23) (26 . 24) (33 . 31)) 7.005 {0/5:6} B:0 3.06904 [ 2.83842] ((14 . 13) (26 . 24) (30 . 26) (33 . 31)) 3.191 {1/6:6} B:0 3.13863 [ 2.92535] ((14 . 13) (27 . 28) (28 . 29) (30 . 30)) 7.247 {1/5:6} B:0 3.78141 [ 3.66616] ((14 . 13) (26 . 24) (32 . 29) (33 . 31)) 4.389 {2/6:6} B:0 SIMILARITY (1/min{score1}): 0.8277 [and 1/min{score2}: 0.9005] [1965, 5943]: Comparing 1gv1_A and 1u8x_X, based on their crossing files. There are 33 (17 H + 16 S) secondary structure elements in 1gv1_A, of which 12 satisfy the size requirements. There are 30 (18 H + 12 S) secondary structure elements in 1u8x_X, of which 16 satisfy the size requirements. 1.45578 [ 1.83425] ((14 . 13) (17 . 15) (19 . 16) (24 . 17) (26 . 24) (27 . 25) (31 . 26) (32 . 27) (33 . 28)) 5.411 {3/28:36} B:0 1.68009 [ 2.08519] ((14 . 13) (17 . 15) (19 . 16) (26 . 24) (27 . 25) (31 . 26) (32 . 27) (33 . 28)) 5.149 {3/23:28} B:0 1.92607 [ 2.38620] ((14 . 13) (25 . 23) (26 . 24) (27 . 25) (31 . 26) (32 . 27) (33 . 29)) 8.023 {3/20:21} B:0 1.96327 [ 2.40609] ((14 . 13) (17 . 15) (26 . 24) (27 . 25) (31 . 26) (32 . 27) (33 . 28)) 4.213 {3/19:21} B:0 2.03681 [ 2.21426] ((14 . 13) (17 . 15) (19 . 16) (25 . 22) (26 . 24) (27 . 25) (31 . 26) (32 . 27) (33 . 28)) 5.778 {6/31:36} B:0 SIMILARITY (1/min{score1}): 0.6869 [and 1/min{score2}: 0.5452] [1965, 6421]: Comparing 1gv1_A and 2cmd, based on their crossing files. There are 33 (17 H + 16 S) secondary structure elements in 1gv1_A, of which 12 satisfy the size requirements. There are 25 (14 H + 11 S) secondary structure elements in 2cmd, of which 10 satisfy the size requirements. 1.63448 [ 1.56921] ((14 . 14) (17 . 16) (19 . 17) (24 . 19) (25 . 20) (26 . 21) (27 . 22) (31 . 23) (32 . 24) (33 . 25)) 2.829 {6/40:45} B:0 2.50369 [ 2.42921] ((14 . 14) (17 . 16) (19 . 17) (24 . 19) (26 . 21) (30 . 22) (33 . 25)) 4.522 {4/17:21} B:0 2.77465 [ 2.76200] ((14 . 14) (17 . 16) (19 . 17) (24 . 19) (25 . 20) (26 . 21) (30 . 22) (31 . 23) (32 . 24) (33 . 25)) 4.239 {11/40:45} B:0 3.00036 [ 2.50062] ((14 . 14) (24 . 20) (26 . 21) (33 . 25)) 7.086 {0/4:6} B:0 3.00058 [ 2.50099] ((14 . 14) (25 . 19) (26 . 21) (33 . 25)) 7.991 {0/4:6} B:0 SIMILARITY (1/min{score1}): 0.6118 [and 1/min{score2}: 0.6373] [1965, 6628]: Comparing 1gv1_A and 6ldh, based on their crossing files. There are 33 (17 H + 16 S) secondary structure elements in 1gv1_A, of which 12 satisfy the size requirements. There are 26 (14 H + 12 S) secondary structure elements in 6ldh, of which 7 satisfy the size requirements. 1.77238 [ 1.22221] ((14 . 15) (24 . 21) (26 . 22) (27 . 23) (31 . 24) (32 . 25) (33 . 26)) 3.949 {2/19:21} B:0 1.92402 [ 1.56946] ((14 . 15) (25 . 21) (26 . 22) (27 . 23) (31 . 24) (32 . 25) (33 . 26)) 4.222 {3/20:21} B:0 2.01098 [ 1.21884] ((14 . 15) (24 . 21) (26 . 22) (27 . 23) (32 . 25) (33 . 26)) 4.058 {1/13:15} B:0 2.75484 [ 2.30562] ((14 . 15) (24 . 21) (26 . 22) (30 . 24) (33 . 26)) 6.697 {2/9:10} B:0 3.31054 [ 2.63888] ((14 . 15) (24 . 21) (30 . 25) (33 . 26)) 7.630 {1/4:6} B:0 SIMILARITY (1/min{score1}): 0.5817 [and 1/min{score2}: 0.9766] [1965, 6636]: Comparing 1gv1_A and 7mdh_A, based on their crossing files. There are 33 (17 H + 16 S) secondary structure elements in 1gv1_A, of which 12 satisfy the size requirements. There are 28 (14 H + 14 S) secondary structure elements in 7mdh_A, of which 9 satisfy the size requirements. 2.28811 [ 2.21219] ((14 . 14) (17 . 17) (24 . 22) (25 . 23) (26 . 24) (27 . 25) (31 . 26) (33 . 28)) 5.431 {5/23:28} B:0 2.79564 [ 2.77058] ((14 . 14) (17 . 17) (19 . 18) (24 . 22) (25 . 23) (26 . 24) (27 . 25) (31 . 26) (33 . 28)) 5.205 {8/29:36} B:0 3.31026 [ 2.83617] ((14 . 14) (24 . 23) (26 . 24) (33 . 28)) 5.288 {1/4:6} B:0 4.28465 [ 4.09665] ((14 . 14) (31 . 25) (32 . 26) (33 . 28)) 6.400 {2/5:6} B:0 4.28479 [ 4.09681] ((26 . 14) (31 . 17) (32 . 18) (33 . 22)) 8.154 {2/5:6} B:0 SIMILARITY (1/min{score1}): 0.4370 [and 1/min{score2}: 0.4520] -------------------------------------------------------------------------------------------------------------------------