------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [394, 120]: Comparing 1bi5_A and 1afw_A, based on their crossing files. There are 30 (15 H + 15 S) secondary structure elements in 1bi5_A, of which 15 satisfy the size requirements. There are 31 (19 H + 12 S) secondary structure elements in 1afw_A, of which 15 satisfy the size requirements. 1.66887 [ 1.66887] ((2 . 1) (9 . 3) (11 . 6) (12 . 7) (13 . 8) (14 . 9) (15 . 10) (17 . 15) (18 . 19)) 5.151 {1/24:36} B:0 3.75035 [ 3.75035] ((12 . 3) (13 . 6) (14 . 7) (15 . 8)) 8.326 {0/3:6} B:0 3.75039 [ 3.75039] ((9 . 7) (11 . 8) (12 . 9) (13 . 10)) 8.561 {0/4:6} B:0 3.75048 [ 3.75048] ((9 . 7) (11 . 8) (13 . 10) (17 . 15)) 9.010 {0/4:6} B:0 3.75938 [ 3.75938] ((1 . 3) (7 . 11) (9 . 13) (12 . 15)) 18.993 {0/5:6} B:0 SIMILARITY (1/min{score1}): 0.6428 [and 1/min{score2}: 0.6428] [394, 394]: Comparing 1bi5_A and 1bi5_A, based on their crossing files. There are 30 (15 H + 15 S) secondary structure elements in 1bi5_A, of which 15 satisfy the size requirements. There are 30 (15 H + 15 S) secondary structure elements in 1bi5_A, of which 15 satisfy the size requirements. 1.00000 [ 1.00000] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (9 . 9) (11 . 11) (12 . 12) (13 . 13) (14 . 14) (15 . 15) (17 . 17) (18 . 18)) 0.000 {0/89:105} B:0 3.00008 [ 3.00008] ((9 . 9) (13 . 11) (15 . 13) (17 . 17) (18 . 18)) 4.827 {0/7:10} B:0 3.00139 [ 3.00139] ((7 . 4) (12 . 9) (13 . 11) (14 . 12) (15 . 13)) 9.954 {0/7:10} B:0 3.00139 [ 3.00139] ((4 . 7) (9 . 12) (11 . 13) (12 . 14) (13 . 15)) 9.954 {0/7:10} B:0 3.75197 [ 3.75197] ((4 . 7) (5 . 9) (9 . 12) (11 . 15)) 12.855 {0/4:6} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [394, 395]: Comparing 1bi5_A and 1bi5_A, based on their crossing files. There are 30 (15 H + 15 S) secondary structure elements in 1bi5_A, of which 15 satisfy the size requirements. There are 30 (15 H + 15 S) secondary structure elements in 1bi5_A, of which 8 satisfy the size requirements. 2.14301 [ 1.14388] ((2 . 19) (9 . 24) (11 . 25) (12 . 26) (14 . 28) (15 . 29) (18 . 30)) 4.476 {0/14:21} B:0 2.50010 [ 1.33397] ((9 . 24) (11 . 25) (12 . 26) (14 . 28) (15 . 29) (18 . 30)) 4.453 {0/9:15} B:0 3.06955 [ 1.94566] ((9 . 24) (11 . 25) (12 . 26) (14 . 27) (18 . 30)) 7.957 {1/6:10} B:0 3.75272 [ 2.01770] ((5 . 24) (9 . 26) (12 . 28) (13 . 29)) 13.927 {0/4:6} B:0 3.92360 [ 2.72625] ((12 . 24) (13 . 25) (14 . 26) (17 . 28)) 10.408 {1/4:6} B:0 SIMILARITY (1/min{score1}): 0.4666 [and 1/min{score2}: 0.8742] [394, 1187]: Comparing 1bi5_A and 1ek4_A, based on their crossing files. There are 30 (15 H + 15 S) secondary structure elements in 1bi5_A, of which 15 satisfy the size requirements. There are 32 (18 H + 14 S) secondary structure elements in 1ek4_A, of which 17 satisfy the size requirements. 1.66851 [ 1.89016] ((2 . 1) (7 . 4) (9 . 7) (11 . 9) (12 . 13) (13 . 14) (14 . 15) (15 . 16) (18 . 19)) 4.034 {1/24:36} B:0 1.67337 [ 1.82654] ((2 . 1) (4 . 4) (9 . 7) (11 . 9) (12 . 13) (13 . 14) (14 . 15) (15 . 16) (17 . 17) (18 . 19)) 4.526 {4/31:45} B:0 2.50062 [ 2.83376] ((2 . 1) (9 . 7) (11 . 9) (14 . 13) (15 . 16) (18 . 19)) 7.111 {0/8:15} B:0 3.00092 [ 3.40063] ((7 . 4) (9 . 7) (11 . 9) (14 . 13) (15 . 14)) 8.981 {0/6:10} B:0 3.75021 [ 4.25014] ((7 . 4) (9 . 7) (13 . 9) (15 . 14)) 7.318 {0/4:6} B:0 SIMILARITY (1/min{score1}): 0.5993 [and 1/min{score2}: 0.5475] [394, 1188]: Comparing 1bi5_A and 1ek4_A, based on their crossing files. There are 30 (15 H + 15 S) secondary structure elements in 1bi5_A, of which 15 satisfy the size requirements. There are 32 (18 H + 14 S) secondary structure elements in 1ek4_A, of which 10 satisfy the size requirements. 1.87543 [ 1.25145] ((2 . 21) (9 . 22) (11 . 23) (12 . 24) (13 . 25) (14 . 27) (15 . 31) (18 . 32)) 5.220 {0/14:28} B:0 3.75036 [ 2.50121] ((9 . 22) (14 . 29) (15 . 31) (18 . 32)) 8.396 {0/1:6} B:0 3.75047 [ 2.50157] ((12 . 22) (13 . 23) (14 . 24) (15 . 25)) 8.964 {0/3:6} B:0 3.75059 [ 2.50199] ((6 . 21) (9 . 24) (15 . 31) (18 . 32)) 9.508 {0/3:6} B:0 4.23380 [ 3.57102] ((13 . 21) (14 . 22) (15 . 23) (17 . 26)) 8.967 {1/3:6} B:0 SIMILARITY (1/min{score1}): 0.5332 [and 1/min{score2}: 0.7991] [394, 2247]: Comparing 1bi5_A and 1hnj_A, based on their crossing files. There are 30 (15 H + 15 S) secondary structure elements in 1bi5_A, of which 15 satisfy the size requirements. There are 28 (15 H + 13 S) secondary structure elements in 1hnj_A, of which 14 satisfy the size requirements. 1.23041 [ 1.16852] ((2 . 1) (3 . 2) (4 . 3) (5 . 4) (6 . 5) (9 . 6) (11 . 8) (12 . 9) (13 . 10) (14 . 11) (15 . 12) (17 . 14) (18 . 15)) 3.913 {5/59:78} B:0 1.29629 [ 1.22268] ((2 . 1) (3 . 2) (4 . 3) (5 . 4) (6 . 5) (9 . 6) (11 . 8) (12 . 9) (14 . 11) (15 . 12) (17 . 14) (18 . 15)) 3.974 {4/51:66} B:0 2.50630 [ 2.34107] ((2 . 1) (3 . 2) (4 . 3) (6 . 5) (11 . 10) (12 . 11)) 7.375 {1/13:15} B:0 3.00074 [ 2.80091] ((4 . 3) (5 . 4) (6 . 5) (11 . 10) (12 . 11)) 8.515 {0/10:10} B:0 3.75013 [ 3.50016] ((7 . 3) (12 . 6) (13 . 8) (15 . 10)) 6.494 {0/4:6} B:0 SIMILARITY (1/min{score1}): 0.8127 [and 1/min{score2}: 0.8558] [394, 2248]: Comparing 1bi5_A and 1hnj_A, based on their crossing files. There are 30 (15 H + 15 S) secondary structure elements in 1bi5_A, of which 15 satisfy the size requirements. There are 28 (15 H + 13 S) secondary structure elements in 1hnj_A, of which 8 satisfy the size requirements. 1.87886 [ 1.02458] ((2 . 16) (7 . 17) (9 . 20) (11 . 22) (12 . 23) (14 . 26) (15 . 27) (18 . 28)) 4.585 {1/18:28} B:0 2.07636 [ 1.63963] ((2 . 16) (4 . 17) (9 . 20) (11 . 22) (12 . 23) (14 . 26) (15 . 27) (18 . 28)) 5.302 {3/19:28} B:0 2.14292 [ 1.14326] ((2 . 16) (9 . 20) (11 . 22) (12 . 23) (14 . 26) (15 . 27) (18 . 28)) 3.553 {0/12:21} B:0 2.14298 [ 1.14366] ((7 . 17) (9 . 20) (11 . 22) (12 . 23) (14 . 26) (15 . 27) (18 . 28)) 4.208 {0/14:21} B:0 3.48587 [ 2.92509] ((9 . 20) (11 . 22) (12 . 23) (14 . 26) (15 . 28)) 5.633 {2/7:10} B:0 SIMILARITY (1/min{score1}): 0.5322 [and 1/min{score2}: 0.9760] [394, 2349]: Comparing 1bi5_A and 1hzp_A, based on their crossing files. There are 30 (15 H + 15 S) secondary structure elements in 1bi5_A, of which 15 satisfy the size requirements. There are 28 (14 H + 14 S) secondary structure elements in 1hzp_A, of which 12 satisfy the size requirements. 1.30372 [ 1.09688] ((2 . 1) (3 . 2) (4 . 3) (5 . 4) (6 . 5) (9 . 6) (11 . 8) (12 . 9) (13 . 10) (14 . 11) (15 . 12) (18 . 14)) 3.882 {4/49:66} B:0 3.00073 [ 2.40142] ((4 . 3) (5 . 4) (6 . 5) (11 . 10) (12 . 11)) 8.466 {0/10:10} B:0 3.75015 [ 3.00030] ((12 . 6) (13 . 8) (15 . 10) (18 . 14)) 6.761 {0/4:6} B:0 3.75032 [ 3.00063] ((12 . 6) (13 . 8) (14 . 9) (15 . 10)) 8.179 {0/3:6} B:0 3.75053 [ 3.00103] ((9 . 9) (11 . 10) (12 . 11) (13 . 12)) 9.242 {0/4:6} B:0 SIMILARITY (1/min{score1}): 0.7670 [and 1/min{score2}: 0.9117] [394, 2350]: Comparing 1bi5_A and 1hzp_A, based on their crossing files. There are 30 (15 H + 15 S) secondary structure elements in 1bi5_A, of which 15 satisfy the size requirements. There are 28 (14 H + 14 S) secondary structure elements in 1hzp_A, of which 12 satisfy the size requirements. 2.14307 [ 1.71471] ((2 . 15) (9 . 20) (11 . 22) (12 . 23) (14 . 26) (15 . 27) (18 . 28)) 4.865 {0/12:21} B:0 2.50003 [ 2.00005] ((9 . 20) (11 . 22) (12 . 23) (14 . 26) (15 . 27) (18 . 28)) 3.191 {0/9:15} B:0 2.52912 [ 2.45557] ((2 . 15) (3 . 17) (5 . 18) (9 . 20) (11 . 22) (12 . 23) (14 . 26) (15 . 27) (18 . 28)) 6.071 {6/25:36} B:0 3.75059 [ 3.00116] ((12 . 20) (13 . 22) (14 . 23) (18 . 28)) 9.513 {0/3:6} B:0 3.75064 [ 3.00125] ((2 . 15) (4 . 18) (6 . 19) (9 . 23)) 9.694 {0/5:6} B:0 SIMILARITY (1/min{score1}): 0.5178 [and 1/min{score2}: 0.6237] [394, 3817]: Comparing 1bi5_A and 1m3k_A, based on their crossing files. There are 30 (15 H + 15 S) secondary structure elements in 1bi5_A, of which 15 satisfy the size requirements. There are 29 (15 H + 14 S) secondary structure elements in 1m3k_A, of which 17 satisfy the size requirements. 1.66886 [ 1.89040] ((2 . 1) (9 . 3) (11 . 5) (12 . 6) (13 . 7) (14 . 8) (15 . 9) (17 . 14) (18 . 18)) 5.124 {1/24:36} B:0 1.87512 [ 2.12508] ((2 . 1) (9 . 3) (11 . 5) (12 . 6) (13 . 7) (14 . 8) (15 . 9) (18 . 18)) 3.781 {0/18:28} B:0 3.00054 [ 3.40037] ((6 . 1) (9 . 3) (12 . 6) (13 . 7) (14 . 8)) 7.857 {0/9:10} B:0 3.75036 [ 4.25025] ((12 . 3) (13 . 5) (14 . 6) (15 . 7)) 8.400 {0/3:6} B:0 3.75044 [ 4.25030] ((11 . 1) (12 . 3) (13 . 5) (15 . 7)) 8.823 {0/3:6} B:0 SIMILARITY (1/min{score1}): 0.5992 [and 1/min{score2}: 0.5290] [394, 3818]: Comparing 1bi5_A and 1m3k_A, based on their crossing files. There are 30 (15 H + 15 S) secondary structure elements in 1bi5_A, of which 15 satisfy the size requirements. There are 29 (15 H + 14 S) secondary structure elements in 1m3k_A, of which 7 satisfy the size requirements. 2.14294 [ 1.00082] ((2 . 20) (9 . 21) (11 . 23) (12 . 24) (14 . 27) (15 . 28) (18 . 29)) 3.828 {0/12:21} B:0 2.50006 [ 1.16721] ((9 . 21) (11 . 23) (12 . 24) (14 . 27) (15 . 28) (18 . 29)) 3.875 {0/8:15} B:0 3.48587 [ 2.89761] ((9 . 21) (11 . 23) (12 . 24) (14 . 27) (15 . 29)) 5.542 {2/7:10} B:0 3.75018 [ 1.75175] ((11 . 20) (12 . 21) (13 . 23) (18 . 29)) 7.045 {0/3:6} B:0 6.82768 [ 6.67466] ((13 . 20) (14 . 21) (15 . 23) (17 . 24)) 9.148 {2/3:6} B:0 SIMILARITY (1/min{score1}): 0.4666 [and 1/min{score2}: 0.9992] [394, 4811]: Comparing 1bi5_A and 1ox0_A, based on their crossing files. There are 30 (15 H + 15 S) secondary structure elements in 1bi5_A, of which 15 satisfy the size requirements. There are 32 (17 H + 15 S) secondary structure elements in 1ox0_A, of which 15 satisfy the size requirements. 1.78542 [ 1.78542] ((2 . 1) (3 . 4) (9 . 7) (11 . 9) (12 . 13) (14 . 15) (15 . 16) (17 . 17) (18 . 18)) 4.073 {3/24:36} B:0 1.87517 [ 1.87517] ((2 . 1) (3 . 4) (9 . 7) (11 . 9) (12 . 13) (14 . 15) (15 . 16) (18 . 18)) 4.120 {0/17:28} B:0 1.91198 [ 1.91198] ((2 . 1) (9 . 7) (11 . 9) (12 . 13) (14 . 15) (15 . 16) (17 . 17) (18 . 18)) 4.068 {2/20:28} B:0 2.14290 [ 2.14290] ((2 . 1) (9 . 7) (11 . 9) (12 . 13) (14 . 15) (15 . 16) (18 . 18)) 3.220 {0/14:21} B:0 3.75666 [ 3.75666] ((7 . 10) (9 . 13) (11 . 16) (17 . 19)) 17.433 {0/5:6} B:0 SIMILARITY (1/min{score1}): 0.5601 [and 1/min{score2}: 0.5601] [394, 4812]: Comparing 1bi5_A and 1ox0_A, based on their crossing files. There are 30 (15 H + 15 S) secondary structure elements in 1bi5_A, of which 15 satisfy the size requirements. There are 32 (17 H + 15 S) secondary structure elements in 1ox0_A, of which 8 satisfy the size requirements. 2.14311 [ 1.14455] ((2 . 20) (9 . 21) (12 . 24) (13 . 25) (14 . 27) (15 . 31) (18 . 32)) 5.078 {0/14:21} B:0 3.75037 [ 2.00242] ((9 . 21) (12 . 27) (15 . 31) (18 . 32)) 8.446 {0/3:6} B:0 3.75050 [ 2.00330] ((11 . 20) (12 . 21) (14 . 24) (15 . 25)) 9.127 {0/3:6} B:0 3.75090 [ 2.00591] ((5 . 24) (7 . 26) (9 . 27) (11 . 31)) 10.564 {0/3:6} B:0 3.92464 [ 2.72934] ((2 . 20) (5 . 24) (9 . 27) (11 . 31)) 12.956 {1/4:6} B:0 SIMILARITY (1/min{score1}): 0.4666 [and 1/min{score2}: 0.8737] [394, 5958]: Comparing 1bi5_A and 1ub7_A, based on their crossing files. There are 30 (15 H + 15 S) secondary structure elements in 1bi5_A, of which 15 satisfy the size requirements. There are 28 (14 H + 14 S) secondary structure elements in 1ub7_A, of which 8 satisfy the size requirements. 2.14292 [ 1.14326] ((2 . 16) (9 . 20) (11 . 22) (12 . 23) (14 . 26) (15 . 27) (18 . 28)) 3.548 {0/12:21} B:0 2.37866 [ 2.13181] ((2 . 16) (6 . 18) (9 . 20) (11 . 22) (12 . 23) (14 . 26) (15 . 27) (18 . 28)) 5.000 {4/19:28} B:0 2.50003 [ 1.33355] ((9 . 20) (11 . 22) (12 . 23) (14 . 26) (15 . 27) (18 . 28)) 3.422 {0/9:15} B:0 3.48589 [ 2.92513] ((9 . 20) (11 . 22) (12 . 23) (14 . 26) (15 . 28)) 5.952 {2/7:10} B:0 3.75051 [ 2.00336] ((2 . 16) (9 . 23) (12 . 26) (13 . 27)) 9.170 {0/3:6} B:0 SIMILARITY (1/min{score1}): 0.4667 [and 1/min{score2}: 0.8747] -------------------------------------------------------------------------------------------------------------------------