------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [2949, 461]: Comparing 1jkw and 1bu2_A, based on their crossing files. There are 13 (13 H + 0 S) secondary structure elements in 1jkw, of which 6 satisfy the size requirements. There are 13 (13 H + 0 S) secondary structure elements in 1bu2_A, of which 6 satisfy the size requirements. 1.02838 [ 1.02838] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6)) 9.386 {0/13:15} B:0 1.50379 [ 1.50379] ((2 . 3) (3 . 4) (4 . 5) (5 . 6)) 7.617 {0/5:6} B:0 1.50625 [ 1.50625] ((3 . 2) (4 . 3) (5 . 4) (6 . 5)) 8.636 {0/6:6} B:0 1.51051 [ 1.51051] ((1 . 1) (2 . 2) (4 . 4) (6 . 6)) 9.846 {0/6:6} B:0 1.51737 [ 1.51737] ((3 . 1) (4 . 2) (5 . 3) (6 . 4)) 11.182 {0/5:6} B:0 SIMILARITY (1/min{score1}): 0.9724 [and 1/min{score2}: 0.9724] [2949, 462]: Comparing 1jkw and 1bu2_A, based on their crossing files. There are 13 (13 H + 0 S) secondary structure elements in 1jkw, of which 6 satisfy the size requirements. There are 13 (13 H + 0 S) secondary structure elements in 1bu2_A, of which 6 satisfy the size requirements. 1.20139 [ 1.20139] ((2 . 7) (3 . 8) (4 . 10) (5 . 11) (6 . 12)) 5.011 {0/8:10} B:0 1.50499 [ 1.50499] ((3 . 7) (4 . 8) (5 . 10) (6 . 11)) 8.160 {0/5:6} B:0 SIMILARITY (1/min{score1}): 0.8324 [and 1/min{score2}: 0.8324] [2949, 1405]: Comparing 1jkw and 1f5q_B, based on their crossing files. There are 13 (13 H + 0 S) secondary structure elements in 1jkw, of which 6 satisfy the size requirements. There are 14 (14 H + 0 S) secondary structure elements in 1f5q_B, of which 7 satisfy the size requirements. 1.01474 [ 1.17604] ((1 . 1) (2 . 3) (3 . 4) (4 . 5) (5 . 6) (6 . 7)) 7.928 {0/13:15} B:0 2.57963 [ 2.64031] ((2 . 1) (4 . 3) (5 . 4) (6 . 5)) 10.072 {1/4:6} B:0 2.58068 [ 2.64130] ((3 . 1) (4 . 3) (5 . 4) (6 . 5)) 11.075 {1/4:6} B:0 3.36825 [ 3.39614] ((2 . 1) (3 . 3) (4 . 4) (5 . 5)) 10.588 {1/3:6} B:0 SIMILARITY (1/min{score1}): 0.9855 [and 1/min{score2}: 0.8503] [2949, 1406]: Comparing 1jkw and 1f5q_B, based on their crossing files. There are 13 (13 H + 0 S) secondary structure elements in 1jkw, of which 6 satisfy the size requirements. There are 14 (14 H + 0 S) secondary structure elements in 1f5q_B, of which 7 satisfy the size requirements. 1.20235 [ 1.40148] ((2 . 8) (3 . 9) (4 . 11) (5 . 12) (6 . 13)) 5.715 {0/8:10} B:0 1.50658 [ 1.75416] ((3 . 8) (4 . 9) (5 . 11) (6 . 12)) 8.749 {0/5:6} B:0 1.50147 [ 1.75093] ((2 . 9) (3 . 8) (4 . 12) (5 . 13)) 6.011 {0/5:6} B:1 1.50372 [ 1.75235] ((2 . 9) (3 . 8) (4 . 12) (5 . 11)) 7.581 {0/4:6} B:2 SIMILARITY (1/min{score1}): 0.8317 [and 1/min{score2}: 0.7135] [2949, 1710]: Comparing 1jkw and 1g3n_C, based on their crossing files. There are 13 (13 H + 0 S) secondary structure elements in 1jkw, of which 6 satisfy the size requirements. There are 14 (14 H + 0 S) secondary structure elements in 1g3n_C, of which 7 satisfy the size requirements. 1.00244 [ 1.16820] ((1 . 2) (2 . 3) (3 . 4) (4 . 5) (5 . 6) (6 . 7)) 5.033 {0/14:15} B:0 1.20072 [ 1.40045] ((2 . 3) (3 . 4) (4 . 5) (5 . 6) (6 . 7)) 4.251 {0/9:10} B:0 1.50581 [ 1.75367] ((3 . 3) (4 . 4) (5 . 5) (6 . 6)) 8.481 {0/5:6} B:0 2.58021 [ 2.64086] ((2 . 1) (4 . 3) (5 . 4) (6 . 5)) 10.662 {1/4:6} B:0 2.58106 [ 2.64165] ((3 . 1) (4 . 3) (5 . 4) (6 . 5)) 11.375 {1/4:6} B:0 SIMILARITY (1/min{score1}): 0.9976 [and 1/min{score2}: 0.8560] [2949, 1963]: Comparing 1jkw and 1gux_A, based on their crossing files. There are 13 (13 H + 0 S) secondary structure elements in 1jkw, of which 6 satisfy the size requirements. There are 10 (10 H + 0 S) secondary structure elements in 1gux_A, of which 10 satisfy the size requirements. 1.00300 [ 1.66732] ((1 . 2) (2 . 3) (3 . 4) (4 . 6) (5 . 7) (6 . 8)) 5.301 {0/13:15} B:0 1.51135 [ 2.50247] ((2 . 1) (4 . 3) (5 . 4) (6 . 6)) 10.038 {0/6:6} B:0 1.89848 [ 2.61820] ((1 . 3) (3 . 6) (4 . 7) (6 . 9)) 10.856 {1/6:6} B:0 2.57956 [ 2.97447] ((1 . 4) (2 . 6) (3 . 8) (5 . 10)) 9.999 {1/4:6} B:0 6.00607 [ 6.04493] ((2 . 1) (3 . 3) (4 . 4) (6 . 6)) 10.622 {3/5:6} B:0 SIMILARITY (1/min{score1}): 0.9970 [and 1/min{score2}: 0.5998] [2949, 1964]: Comparing 1jkw and 1gux_B, based on their crossing files. There are 13 (13 H + 0 S) secondary structure elements in 1jkw, of which 6 satisfy the size requirements. There are 11 (9 H + 2 S) secondary structure elements in 1gux_B, of which 8 satisfy the size requirements. 1.20201 [ 1.60085] ((2 . 1) (3 . 2) (4 . 4) (5 . 5) (6 . 6)) 5.499 {0/8:10} B:0 1.50307 [ 2.00130] ((2 . 2) (3 . 4) (4 . 5) (5 . 9)) 7.225 {0/5:6} B:0 1.50316 [ 2.00134] ((2 . 2) (3 . 4) (4 . 5) (5 . 6)) 7.279 {0/4:6} B:0 1.50490 [ 2.00207] ((3 . 1) (4 . 2) (5 . 4) (6 . 5)) 8.125 {0/6:6} B:0 4.01982 [ 4.06127] ((2 . 11) (3 . 4) (4 . 5) (5 . 9)) 7.539 {2/5:6} B:1 SIMILARITY (1/min{score1}): 0.8319 [and 1/min{score2}: 0.6247] [2949, 2077]: Comparing 1jkw and 1h4l_D, based on their crossing files. There are 13 (13 H + 0 S) secondary structure elements in 1jkw, of which 6 satisfy the size requirements. There are 7 (7 H + 0 S) secondary structure elements in 1h4l_D, of which 7 satisfy the size requirements. 1.20544 [ 1.40343] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (6 . 5)) 7.056 {0/8:10} B:0 1.50086 [ 1.75054] ((2 . 2) (3 . 3) (4 . 4) (6 . 5)) 5.256 {0/5:6} B:0 2.14506 [ 2.24690] ((1 . 2) (2 . 3) (3 . 4) (5 . 6)) 9.199 {1/5:6} B:0 SIMILARITY (1/min{score1}): 0.8296 [and 1/min{score2}: 0.7125] [2949, 2949]: Comparing 1jkw and 1jkw, based on their crossing files. There are 13 (13 H + 0 S) secondary structure elements in 1jkw, of which 6 satisfy the size requirements. There are 13 (13 H + 0 S) secondary structure elements in 1jkw, 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 {0/14:15} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [2949, 2950]: Comparing 1jkw and 1jkw, based on their crossing files. There are 13 (13 H + 0 S) secondary structure elements in 1jkw, of which 6 satisfy the size requirements. There are 13 (13 H + 0 S) secondary structure elements in 1jkw, of which 7 satisfy the size requirements. 1.20092 [ 1.40058] ((2 . 7) (3 . 8) (4 . 10) (5 . 11) (6 . 12)) 4.515 {0/8:10} B:0 1.50566 [ 1.75357] ((3 . 7) (4 . 8) (5 . 10) (6 . 11)) 8.425 {0/5:6} B:0 SIMILARITY (1/min{score1}): 0.8327 [and 1/min{score2}: 0.7140] [2949, 6267]: Comparing 1jkw and 1vin, based on their crossing files. There are 13 (13 H + 0 S) secondary structure elements in 1jkw, of which 6 satisfy the size requirements. There are 16 (16 H + 0 S) secondary structure elements in 1vin, of which 7 satisfy the size requirements. 1.01784 [ 1.17804] ((1 . 1) (2 . 3) (3 . 4) (4 . 5) (5 . 6) (6 . 7)) 8.325 {0/13:15} B:0 2.14754 [ 2.24907] ((3 . 1) (4 . 3) (5 . 4) (6 . 5)) 10.800 {1/5:6} B:0 2.57997 [ 2.64064] ((2 . 1) (3 . 3) (4 . 4) (5 . 5)) 10.434 {1/4:6} B:0 SIMILARITY (1/min{score1}): 0.9825 [and 1/min{score2}: 0.8489] [2949, 6268]: Comparing 1jkw and 1vin, based on their crossing files. There are 13 (13 H + 0 S) secondary structure elements in 1jkw, of which 6 satisfy the size requirements. There are 16 (16 H + 0 S) secondary structure elements in 1vin, of which 7 satisfy the size requirements. 1.20222 [ 1.40140] ((2 . 8) (3 . 9) (4 . 11) (5 . 12) (6 . 13)) 5.637 {0/8:10} B:0 1.50669 [ 1.75423] ((3 . 8) (4 . 9) (5 . 11) (6 . 12)) 8.786 {0/4:6} B:0 SIMILARITY (1/min{score1}): 0.8318 [and 1/min{score2}: 0.7136] -------------------------------------------------------------------------------------------------------------------------