------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [2449, 275]: Comparing 1ib8_A and 1b34_A, based on their crossing files. There are 11 (3 H + 8 S) secondary structure elements in 1ib8_A, of which 6 satisfy the size requirements. There are 9 (3 H + 6 S) secondary structure elements in 1b34_A, of which 8 satisfy the size requirements. 1.00042 [ 1.33351] ((6 . 1) (7 . 2) (8 . 3) (9 . 4) (10 . 6) (11 . 8)) 3.232 {0/11:15} B:0 1.20016 [ 1.60007] ((6 . 1) (7 . 2) (8 . 3) (10 . 6) (11 . 8)) 2.922 {0/8:10} B:0 2.14248 [ 2.37856] ((6 . 1) (7 . 2) (8 . 3) (10 . 5)) 4.751 {1/5:6} B:0 SIMILARITY (1/min{score1}): 0.9996 [and 1/min{score2}: 0.7499] [2449, 276]: Comparing 1ib8_A and 1b34_B, based on their crossing files. There are 11 (3 H + 8 S) secondary structure elements in 1ib8_A, of which 6 satisfy the size requirements. There are 7 (2 H + 5 S) secondary structure elements in 1b34_B, of which 6 satisfy the size requirements. 1.00030 [ 1.00030] ((6 . 1) (7 . 2) (8 . 3) (9 . 4) (10 . 5) (11 . 7)) 2.975 {0/11:15} B:0 SIMILARITY (1/min{score1}): 0.9997 [and 1/min{score2}: 0.9997] [2449, 740]: Comparing 1ib8_A and 1d3b_A, based on their crossing files. There are 11 (3 H + 8 S) secondary structure elements in 1ib8_A, of which 6 satisfy the size requirements. There are 9 (2 H + 7 S) secondary structure elements in 1d3b_A, of which 8 satisfy the size requirements. 1.00054 [ 1.33356] ((6 . 1) (7 . 2) (8 . 3) (9 . 4) (10 . 7) (11 . 9)) 3.446 {0/10:15} B:0 SIMILARITY (1/min{score1}): 0.9995 [and 1/min{score2}: 0.7499] [2449, 741]: Comparing 1ib8_A and 1d3b_B, based on their crossing files. There are 11 (3 H + 8 S) secondary structure elements in 1ib8_A, of which 6 satisfy the size requirements. There are 8 (2 H + 6 S) secondary structure elements in 1d3b_B, of which 7 satisfy the size requirements. 1.00242 [ 1.16819] ((6 . 1) (7 . 2) (8 . 3) (9 . 5) (10 . 6) (11 . 8)) 5.023 {0/10:15} B:0 1.00369 [ 1.16900] ((6 . 1) (7 . 2) (8 . 3) (9 . 4) (10 . 6) (11 . 8)) 5.585 {0/10:15} B:0 1.50196 [ 1.75123] ((6 . 1) (8 . 4) (9 . 5) (10 . 6)) 6.454 {0/4:6} B:0 SIMILARITY (1/min{score1}): 0.9976 [and 1/min{score2}: 0.8560] [2449, 2220]: Comparing 1ib8_A and 1hk9_A, based on their crossing files. There are 11 (3 H + 8 S) secondary structure elements in 1ib8_A, of which 6 satisfy the size requirements. There are 7 (2 H + 5 S) secondary structure elements in 1hk9_A, of which 6 satisfy the size requirements. 1.00102 [ 1.00102] ((6 . 1) (7 . 2) (8 . 3) (9 . 4) (10 . 5) (11 . 7)) 4.045 {0/10:15} B:0 1.20031 [ 1.20031] ((7 . 2) (8 . 3) (9 . 4) (10 . 5) (11 . 7)) 3.431 {0/8:10} B:0 SIMILARITY (1/min{score1}): 0.9990 [and 1/min{score2}: 0.9990] [2449, 2449]: Comparing 1ib8_A and 1ib8_A, based on their crossing files. There are 11 (3 H + 8 S) secondary structure elements in 1ib8_A, of which 6 satisfy the size requirements. There are 11 (3 H + 8 S) secondary structure elements in 1ib8_A, of which 6 satisfy the size requirements. 1.00000 [ 1.00000] ((6 . 6) (7 . 7) (8 . 8) (9 . 9) (10 . 10) (11 . 11)) 0.000 {0/13:15} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [2449, 3394]: Comparing 1ib8_A and 1kq1_A, based on their crossing files. There are 11 (3 H + 8 S) secondary structure elements in 1ib8_A, of which 6 satisfy the size requirements. There are 7 (2 H + 5 S) secondary structure elements in 1kq1_A, of which 6 satisfy the size requirements. 1.00078 [ 1.00078] ((6 . 1) (7 . 2) (8 . 3) (9 . 4) (10 . 5) (11 . 7)) 3.781 {0/11:15} B:0 1.89782 [ 1.89782] ((6 . 1) (7 . 3) (8 . 4) (9 . 7)) 10.616 {1/6:6} B:0 SIMILARITY (1/min{score1}): 0.9992 [and 1/min{score2}: 0.9992] [2449, 3640]: Comparing 1ib8_A and 1ljo_A, based on their crossing files. There are 11 (3 H + 8 S) secondary structure elements in 1ib8_A, of which 6 satisfy the size requirements. There are 8 (2 H + 6 S) secondary structure elements in 1ljo_A, of which 7 satisfy the size requirements. 1.00130 [ 1.16749] ((6 . 1) (7 . 2) (8 . 3) (9 . 4) (10 . 6) (11 . 8)) 4.301 {0/10:15} B:0 1.14001 [ 1.26264] ((6 . 1) (7 . 2) (8 . 3) (9 . 5) (10 . 6) (11 . 8)) 4.459 {1/11:15} B:0 1.20038 [ 1.40024] ((6 . 1) (7 . 2) (8 . 3) (10 . 6) (11 . 8)) 3.617 {0/7:10} B:0 1.45812 [ 1.58356] ((6 . 1) (7 . 2) (8 . 3) (9 . 5) (10 . 6)) 4.322 {1/8:10} B:0 SIMILARITY (1/min{score1}): 0.9987 [and 1/min{score2}: 0.8565] [2449, 3843]: Comparing 1ib8_A and 1m5q_1, based on their crossing files. There are 11 (3 H + 8 S) secondary structure elements in 1ib8_A, of which 6 satisfy the size requirements. There are 13 (4 H + 9 S) secondary structure elements in 1m5q_1, of which 12 satisfy the size requirements. 1.00023 [ 2.00003] ((6 . 1) (7 . 2) (8 . 3) (9 . 4) (10 . 5) (11 . 7)) 2.799 {0/10:15} B:0 1.50019 [ 3.00002] ((7 . 9) (8 . 10) (9 . 11) (10 . 12)) 3.613 {0/3:6} B:0 1.50187 [ 3.00023] ((6 . 8) (8 . 10) (9 . 11) (10 . 12)) 6.381 {0/3:6} B:0 SIMILARITY (1/min{score1}): 0.9998 [and 1/min{score2}: 0.5000] [2449, 3924]: Comparing 1ib8_A and 1mgq_A, based on their crossing files. There are 11 (3 H + 8 S) secondary structure elements in 1ib8_A, of which 6 satisfy the size requirements. There are 9 (2 H + 7 S) secondary structure elements in 1mgq_A, of which 8 satisfy the size requirements. 1.00163 [ 1.33402] ((6 . 1) (7 . 2) (8 . 3) (9 . 6) (10 . 7) (11 . 9)) 4.549 {0/11:15} B:0 4.02032 [ 4.06175] ((6 . 1) (8 . 3) (9 . 4) (11 . 7)) 10.410 {2/5:6} B:0 1.20027 [ 1.60012] ((7 . 6) (8 . 3) (9 . 2) (10 . 9) (11 . 7)) 3.334 {0/8:10} B:3 SIMILARITY (1/min{score1}): 0.9984 [and 1/min{score2}: 0.7496] [2449, 4179]: Comparing 1ib8_A and 1n9r_A, based on their crossing files. There are 11 (3 H + 8 S) secondary structure elements in 1ib8_A, of which 6 satisfy the size requirements. There are 9 (2 H + 7 S) secondary structure elements in 1n9r_A, of which 8 satisfy the size requirements. 1.20057 [ 1.60024] ((7 . 2) (8 . 3) (9 . 4) (10 . 7) (11 . 9)) 4.004 {0/8:10} B:0 1.50016 [ 2.00007] ((7 . 2) (8 . 3) (9 . 4) (11 . 9)) 3.458 {0/5:6} B:0 3.00939 [ 3.02901] ((6 . 1) (7 . 2) (8 . 3) (9 . 4) (10 . 5) (11 . 9)) 5.921 {3/10:15} B:0 SIMILARITY (1/min{score1}): 0.8329 [and 1/min{score2}: 0.6249] -------------------------------------------------------------------------------------------------------------------------