------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [5748, 2006]: Comparing 1s18_A and 1gyh_A, based on their crossing files. There are 30 (4 H + 26 S) secondary structure elements in 1s18_A, of which 27 satisfy the size requirements. There are 28 (5 H + 23 S) secondary structure elements in 1gyh_A, of which 22 satisfy the size requirements. 3.85725 [ 3.14305] ((2 . 8) (4 . 9) (5 . 10) (16 . 18) (20 . 21) (21 . 22) (24 . 24)) 6.279 {0/16:21} B:0 4.50019 [ 3.66702] ((8 . 9) (9 . 10) (11 . 12) (12 . 13) (17 . 15) (21 . 18)) 8.235 {0/11:15} B:0 4.50020 [ 3.66705] ((4 . 7) (8 . 10) (11 . 13) (12 . 14) (24 . 21) (25 . 22)) 8.365 {0/9:15} B:0 4.50040 [ 3.66741] ((6 . 5) (11 . 9) (12 . 10) (16 . 11) (17 . 12) (30 . 24)) 9.909 {0/9:15} B:0 4.52124 [ 3.70558] ((1 . 10) (4 . 13) (6 . 14) (7 . 15) (8 . 16) (9 . 18)) 8.508 {2/12:15} B:0 SIMILARITY (1/min{score1}): 0.7397 [and 1/min{score2}: 0.9063] [5748, 4834]: Comparing 1s18_A and 1oyg_A, based on their crossing files. There are 30 (4 H + 26 S) secondary structure elements in 1s18_A, of which 27 satisfy the size requirements. There are 40 (16 H + 24 S) secondary structure elements in 1oyg_A, of which 31 satisfy the size requirements. 3.37513 [ 3.87508] ((7 . 13) (8 . 14) (24 . 27) (25 . 28) (26 . 29) (27 . 30) (28 . 32) (29 . 35)) 5.960 {0/19:28} B:0 3.85718 [ 4.42860] ((16 . 27) (17 . 28) (21 . 30) (24 . 32) (25 . 35) (26 . 36) (27 . 37)) 4.836 {0/12:21} B:0 3.85720 [ 4.42861] ((9 . 27) (10 . 28) (11 . 29) (12 . 30) (16 . 32) (21 . 37) (24 . 39)) 5.349 {0/14:21} B:0 3.85732 [ 4.42869] ((4 . 16) (16 . 27) (20 . 29) (21 . 30) (24 . 32) (25 . 35) (27 . 37)) 7.140 {0/15:21} B:0 3.85734 [ 4.42870] ((7 . 13) (8 . 14) (9 . 16) (16 . 21) (26 . 29) (27 . 30) (28 . 32)) 7.363 {0/9:21} B:0 SIMILARITY (1/min{score1}): 0.7400 [and 1/min{score2}: 0.6448] [5748, 5748]: Comparing 1s18_A and 1s18_A, based on their crossing files. There are 30 (4 H + 26 S) secondary structure elements in 1s18_A, of which 27 satisfy the size requirements. There are 30 (4 H + 26 S) secondary structure elements in 1s18_A, of which 27 satisfy the size requirements. 1.00000 [ 1.00000] ((1 . 1) (2 . 2) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (10 . 10) (11 . 11) (12 . 12) (14 . 14) (16 . 16) (17 . 17) (18 . 18) (19 . 19) (20 . 20) (21 . 21) (22 . 22) (23 . 23) (24 . 24) (25 . 25) (26 . 26) (27 . 27) (28 . 28) (29 . 29) (30 . 30)) 0.000 {0/298:351} B:0 1.18325 [ 1.18325] ((1 . 1) (2 . 2) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (10 . 10) (11 . 11) (12 . 12) (16 . 16) (17 . 17) (18 . 18) (19 . 22) (20 . 20) (21 . 21) (23 . 23) (24 . 24) (25 . 25) (26 . 26) (27 . 27) (28 . 28) (29 . 29) (30 . 30)) 1.045 {22/250:300} B:1 1.18325 [ 1.18325] ((1 . 1) (2 . 2) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (10 . 10) (11 . 11) (12 . 12) (16 . 16) (17 . 17) (18 . 18) (20 . 20) (21 . 21) (22 . 19) (23 . 23) (24 . 24) (25 . 25) (26 . 26) (27 . 27) (28 . 28) (29 . 29) (30 . 30)) 1.045 {22/250:300} B:1 1.35371 [ 1.35371] ((2 . 12) (4 . 16) (5 . 17) (7 . 20) (8 . 21) (9 . 24) (10 . 25) (11 . 26) (12 . 27) (16 . 28) (17 . 29) (20 . 30) (21 . 2) (24 . 4) (25 . 6) (26 . 7) (27 . 8) (28 . 9) (29 . 10) (30 . 11)) 7.000 {0/130:190} B:1 1.35371 [ 1.35371] ((2 . 21) (4 . 24) (6 . 25) (7 . 26) (8 . 27) (9 . 28) (10 . 29) (11 . 30) (12 . 2) (16 . 4) (17 . 5) (20 . 7) (21 . 8) (24 . 9) (25 . 10) (26 . 11) (27 . 12) (28 . 16) (29 . 17) (30 . 20)) 7.000 {0/130:190} B:1 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [5748, 5918]: Comparing 1s18_A and 1tl2_A, based on their crossing files. There are 30 (4 H + 26 S) secondary structure elements in 1s18_A, of which 27 satisfy the size requirements. There are 29 (9 H + 20 S) secondary structure elements in 1tl2_A, of which 20 satisfy the size requirements. 1.35141 [ 1.00346] ((2 . 1) (4 . 2) (6 . 4) (7 . 5) (8 . 6) (9 . 7) (10 . 9) (11 . 11) (12 . 12) (16 . 13) (17 . 15) (20 . 17) (21 . 18) (24 . 19) (25 . 21) (26 . 23) (27 . 24) (28 . 25) (29 . 27) (30 . 29)) 5.494 {0/127:190} B:0 1.35177 [ 1.00434] ((2 . 1) (4 . 2) (5 . 4) (7 . 5) (8 . 6) (9 . 7) (10 . 9) (11 . 11) (12 . 12) (16 . 13) (17 . 15) (20 . 17) (21 . 18) (24 . 19) (25 . 21) (26 . 23) (27 . 24) (28 . 25) (29 . 27) (30 . 29)) 5.817 {0/126:190} B:0 1.42190 [ 1.05471] ((2 . 1) (4 . 2) (7 . 5) (8 . 6) (9 . 7) (10 . 9) (11 . 11) (12 . 12) (16 . 13) (17 . 15) (20 . 17) (21 . 18) (24 . 19) (25 . 21) (26 . 23) (27 . 24) (28 . 25) (29 . 27) (30 . 29)) 5.027 {0/108:171} B:0 3.85716 [ 2.85717] ((24 . 2) (25 . 4) (26 . 5) (27 . 6) (28 . 7) (29 . 9) (30 . 11)) 3.713 {0/11:21} B:0 4.50001 [ 3.33335] ((16 . 5) (24 . 13) (25 . 15) (26 . 17) (29 . 21) (30 . 23)) 3.466 {0/10:15} B:0 SIMILARITY (1/min{score1}): 0.7400 [and 1/min{score2}: 0.9966] [5748, 6142]: Comparing 1s18_A and 1uyp_A, based on their crossing files. There are 30 (4 H + 26 S) secondary structure elements in 1s18_A, of which 27 satisfy the size requirements. There are 38 (3 H + 35 S) secondary structure elements in 1uyp_A, of which 23 satisfy the size requirements. 3.37501 [ 2.87502] ((19 . 1) (20 . 2) (21 . 3) (25 . 5) (26 . 6) (27 . 7) (28 . 8) (30 . 10)) 3.405 {0/16:28} B:0 3.85716 [ 3.28575] ((7 . 2) (8 . 3) (9 . 4) (10 . 5) (12 . 7) (16 . 8) (21 . 11)) 4.185 {0/9:21} B:0 3.85719 [ 3.28579] ((2 . 7) (4 . 8) (9 . 12) (10 . 13) (11 . 14) (12 . 15) (18 . 21)) 5.161 {0/17:21} B:0 3.85720 [ 3.28580] ((7 . 2) (8 . 3) (11 . 6) (12 . 7) (16 . 8) (20 . 10) (21 . 11)) 5.313 {0/3:21} B:0 3.85721 [ 3.28582] ((2 . 3) (4 . 4) (5 . 5) (11 . 10) (12 . 11) (16 . 12) (17 . 13)) 5.562 {0/14:21} B:0 SIMILARITY (1/min{score1}): 0.7399 [and 1/min{score2}: 0.8676] -------------------------------------------------------------------------------------------------------------------------