------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [2713, 2532]: Comparing 1j2r_A and 1im5_A, based on their crossing files. There are 16 (9 H + 7 S) secondary structure elements in 1j2r_A, of which 13 satisfy the size requirements. There are 14 (7 H + 7 S) secondary structure elements in 1im5_A, of which 10 satisfy the size requirements. 1.30004 [ 1.00008] ((2 . 1) (4 . 3) (5 . 4) (7 . 7) (8 . 8) (9 . 9) (10 . 10) (11 . 11) (13 . 13) (15 . 14)) 2.142 {0/29:45} B:0 1.30007 [ 1.00016] ((2 . 1) (4 . 3) (5 . 4) (7 . 7) (8 . 8) (9 . 9) (10 . 10) (11 . 11) (14 . 13) (15 . 14)) 2.562 {0/28:45} B:0 2.16691 [ 1.66720] ((2 . 1) (4 . 3) (5 . 4) (7 . 7) (10 . 8) (15 . 11)) 5.037 {0/9:15} B:0 2.16779 [ 1.66912] ((2 . 1) (4 . 3) (5 . 4) (7 . 7) (15 . 11) (16 . 13)) 7.392 {0/9:15} B:0 3.25009 [ 2.50019] ((7 . 9) (8 . 10) (9 . 11) (11 . 14)) 5.276 {0/4:6} B:0 SIMILARITY (1/min{score1}): 0.7692 [and 1/min{score2}: 0.9999] [2713, 2713]: Comparing 1j2r_A and 1j2r_A, based on their crossing files. There are 16 (9 H + 7 S) secondary structure elements in 1j2r_A, of which 13 satisfy the size requirements. There are 16 (9 H + 7 S) secondary structure elements in 1j2r_A, of which 13 satisfy the size requirements. 1.00000 [ 1.00000] ((2 . 2) (3 . 3) (4 . 4) (5 . 5) (7 . 7) (8 . 8) (9 . 9) (10 . 10) (11 . 11) (13 . 13) (14 . 14) (15 . 15) (16 . 16)) 0.000 {0/58:78} B:0 1.08354 [ 1.08354] ((2 . 2) (3 . 3) (4 . 4) (5 . 5) (7 . 7) (8 . 8) (9 . 9) (10 . 10) (11 . 11) (14 . 13) (15 . 15) (16 . 16)) 2.877 {0/50:66} B:0 1.18200 [ 1.18200] ((2 . 2) (3 . 3) (4 . 4) (5 . 5) (7 . 7) (8 . 8) (9 . 9) (10 . 10) (11 . 11) (13 . 14) (15 . 15)) 2.991 {0/41:55} B:0 2.16784 [ 2.16784] ((2 . 2) (3 . 3) (4 . 4) (5 . 5) (10 . 8) (14 . 13)) 7.477 {0/8:15} B:0 3.25016 [ 3.25016] ((2 . 2) (5 . 5) (8 . 10) (14 . 14)) 6.207 {0/1:6} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [2713, 4186]: Comparing 1j2r_A and 1nba_A, based on their crossing files. There are 16 (9 H + 7 S) secondary structure elements in 1j2r_A, of which 13 satisfy the size requirements. There are 20 (13 H + 7 S) secondary structure elements in 1nba_A, of which 13 satisfy the size requirements. 1.18184 [ 1.18184] ((2 . 2) (4 . 4) (5 . 5) (7 . 10) (8 . 11) (9 . 12) (10 . 13) (11 . 14) (13 . 17) (15 . 18) (16 . 19)) 1.811 {0/38:55} B:0 1.30002 [ 1.30002] ((2 . 2) (4 . 4) (5 . 5) (7 . 10) (8 . 11) (9 . 12) (10 . 13) (11 . 14) (13 . 17) (16 . 19)) 1.789 {0/29:45} B:0 2.16692 [ 2.16692] ((2 . 2) (4 . 4) (5 . 5) (10 . 11) (13 . 13) (15 . 14)) 5.077 {0/8:15} B:0 3.03464 [ 3.03464] ((2 . 2) (4 . 4) (5 . 5) (10 . 11) (16 . 17)) 7.433 {1/4:10} B:0 3.25008 [ 3.25008] ((7 . 12) (8 . 13) (9 . 14) (11 . 18)) 5.143 {0/4:6} B:0 SIMILARITY (1/min{score1}): 0.9219 [and 1/min{score2}: 0.9219] [2713, 4229]: Comparing 1j2r_A and 1nf9_A, based on their crossing files. There are 16 (9 H + 7 S) secondary structure elements in 1j2r_A, of which 13 satisfy the size requirements. There are 19 (12 H + 7 S) secondary structure elements in 1nf9_A, of which 14 satisfy the size requirements. 1.08379 [ 1.16703] ((2 . 3) (3 . 4) (4 . 5) (5 . 6) (7 . 11) (8 . 12) (9 . 13) (10 . 14) (11 . 15) (13 . 17) (15 . 18) (16 . 19)) 2.062 {1/47:66} B:0 1.08393 [ 1.16715] ((2 . 3) (3 . 4) (4 . 5) (5 . 6) (7 . 11) (8 . 12) (9 . 13) (10 . 14) (11 . 15) (14 . 17) (15 . 18) (16 . 19)) 2.517 {1/45:66} B:0 1.18186 [ 1.27276] ((2 . 3) (3 . 4) (4 . 5) (5 . 6) (7 . 11) (8 . 12) (9 . 13) (10 . 14) (11 . 15) (13 . 17) (15 . 18)) 2.072 {0/39:55} B:0 2.16691 [ 2.33353] ((2 . 3) (9 . 6) (10 . 12) (11 . 13) (14 . 14) (15 . 15)) 5.032 {0/4:15} B:0 2.60018 [ 2.80015] ((2 . 3) (3 . 4) (4 . 5) (5 . 6) (8 . 14)) 5.390 {0/6:10} B:0 SIMILARITY (1/min{score1}): 0.9227 [and 1/min{score2}: 0.8569] [2713, 6356]: Comparing 1j2r_A and 1yac_A, based on their crossing files. There are 16 (9 H + 7 S) secondary structure elements in 1j2r_A, of which 13 satisfy the size requirements. There are 17 (11 H + 6 S) secondary structure elements in 1yac_A, of which 15 satisfy the size requirements. 1.08341 [ 1.25005] ((2 . 1) (3 . 2) (4 . 3) (5 . 4) (7 . 6) (8 . 8) (9 . 9) (10 . 10) (11 . 11) (13 . 12) (15 . 13) (16 . 14)) 2.262 {0/46:66} B:0 1.08346 [ 1.25008] ((2 . 1) (3 . 2) (4 . 3) (5 . 4) (7 . 6) (8 . 8) (9 . 9) (10 . 10) (11 . 11) (14 . 12) (15 . 13) (16 . 14)) 2.551 {0/44:66} B:0 1.18188 [ 1.36368] ((2 . 1) (3 . 2) (4 . 3) (5 . 4) (7 . 6) (8 . 8) (9 . 9) (10 . 10) (11 . 11) (13 . 12) (15 . 13)) 2.304 {0/39:55} B:0 1.18193 [ 1.36371] ((2 . 1) (3 . 2) (4 . 3) (5 . 4) (7 . 6) (8 . 8) (9 . 9) (10 . 10) (11 . 11) (14 . 12) (16 . 14)) 2.661 {0/34:55} B:0 1.85723 [ 2.14292] ((5 . 1) (7 . 6) (8 . 8) (9 . 9) (10 . 10) (11 . 11) (15 . 13)) 3.526 {0/13:21} B:0 SIMILARITY (1/min{score1}): 0.9230 [and 1/min{score2}: 0.8000] -------------------------------------------------------------------------------------------------------------------------