------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [4354, 4354]: Comparing 1nqj_A and 1nqj_A, based on their crossing files. There are 10 (0 H + 10 S) secondary structure elements in 1nqj_A, of which 8 satisfy the size requirements. There are 10 (0 H + 10 S) secondary structure elements in 1nqj_A, of which 8 satisfy the size requirements. 1.00000 [ 1.00000] ((2 . 2) (3 . 3) (4 . 4) (5 . 5) (7 . 7) (8 . 8) (9 . 9) (10 . 10)) 0.000 {0/14:28} B:0 1.34098 [ 1.34098] ((4 . 3) (5 . 4) (7 . 5) (8 . 7) (9 . 8) (10 . 9)) 8.321 {0/1:15} B:0 1.34098 [ 1.34098] ((3 . 4) (4 . 5) (5 . 7) (7 . 8) (8 . 9) (9 . 10)) 8.321 {0/1:15} B:0 2.00146 [ 2.00146] ((7 . 3) (8 . 4) (9 . 5) (10 . 7)) 7.434 {0/2:6} B:0 2.00146 [ 2.00146] ((3 . 7) (4 . 8) (5 . 9) (7 . 10)) 7.434 {0/2:6} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [4354, 4381]: Comparing 1nqj_A and 1nt0_A, based on their crossing files. There are 10 (0 H + 10 S) secondary structure elements in 1nqj_A, of which 8 satisfy the size requirements. There are 22 (1 H + 21 S) secondary structure elements in 1nt0_A, of which 8 satisfy the size requirements. 1.00295 [ 1.00295] ((2 . 1) (3 . 2) (4 . 3) (5 . 5) (7 . 6) (8 . 7) (9 . 8) (10 . 9)) 5.278 {0/9:28} B:0 2.00040 [ 2.00040] ((2 . 1) (3 . 2) (4 . 3) (8 . 5)) 5.387 {0/3:6} B:0 2.00070 [ 2.00070] ((7 . 2) (8 . 3) (9 . 5) (10 . 6)) 6.184 {0/3:6} B:0 2.00074 [ 2.00074] ((3 . 6) (4 . 7) (5 . 8) (7 . 9)) 6.282 {0/3:6} B:0 2.00084 [ 2.00084] ((4 . 2) (5 . 3) (7 . 5) (8 . 6)) 6.488 {0/1:6} B:0 SIMILARITY (1/min{score1}): 0.9978 [and 1/min{score2}: 0.9978] [4354, 4383]: Comparing 1nqj_A and 1nt0_A, based on their crossing files. There are 10 (0 H + 10 S) secondary structure elements in 1nqj_A, of which 8 satisfy the size requirements. There are 22 (1 H + 21 S) secondary structure elements in 1nt0_A, of which 8 satisfy the size requirements. 1.33414 [ 1.33414] ((2 . 15) (3 . 16) (4 . 17) (5 . 18) (9 . 21) (10 . 22)) 4.730 {0/3:15} B:0 1.33554 [ 1.33554] ((2 . 15) (3 . 16) (4 . 17) (8 . 18) (9 . 21) (10 . 22)) 6.087 {0/3:15} B:0 1.60115 [ 1.60115] ((2 . 14) (3 . 15) (4 . 16) (5 . 17) (10 . 21)) 5.927 {0/3:10} B:0 1.60238 [ 1.60238] ((4 . 16) (5 . 17) (7 . 18) (8 . 19) (10 . 21)) 7.115 {0/0:10} B:0 1.60315 [ 1.60315] ((2 . 16) (3 . 17) (4 . 18) (8 . 21) (9 . 22)) 7.632 {0/0:10} B:0 SIMILARITY (1/min{score1}): 0.8712 [and 1/min{score2}: 0.8712] [4354, 4453]: Comparing 1nqj_A and 1nzi_A, based on their crossing files. There are 10 (0 H + 10 S) secondary structure elements in 1nqj_A, of which 8 satisfy the size requirements. There are 14 (1 H + 13 S) secondary structure elements in 1nzi_A, of which 8 satisfy the size requirements. 1.60184 [ 1.60184] ((4 . 2) (5 . 3) (8 . 6) (9 . 8) (10 . 9)) 6.671 {0/0:10} B:0 2.00052 [ 2.00052] ((4 . 5) (7 . 8) (8 . 9) (9 . 10)) 5.742 {0/2:6} B:0 2.00072 [ 2.00072] ((3 . 6) (4 . 8) (5 . 9) (7 . 10)) 6.227 {0/2:6} B:0 2.00079 [ 2.00079] ((2 . 1) (3 . 2) (4 . 3) (8 . 5)) 6.372 {0/3:6} B:0 2.00082 [ 2.00082] ((3 . 6) (4 . 8) (5 . 9) (8 . 10)) 6.445 {0/1:6} B:0 SIMILARITY (1/min{score1}): 0.9976 [and 1/min{score2}: 0.9976] [4354, 5808]: Comparing 1nqj_A and 1sfp, based on their crossing files. There are 10 (0 H + 10 S) secondary structure elements in 1nqj_A, of which 8 satisfy the size requirements. There are 10 (0 H + 10 S) secondary structure elements in 1sfp, of which 9 satisfy the size requirements. 1.33453 [ 1.50084] ((2 . 3) (3 . 4) (4 . 5) (8 . 8) (9 . 9) (10 . 10)) 5.225 {0/3:15} B:0 1.33481 [ 1.50103] ((2 . 2) (3 . 3) (5 . 5) (8 . 7) (9 . 8) (10 . 9)) 5.502 {0/6:15} B:0 1.33512 [ 1.50125] ((2 . 2) (3 . 3) (4 . 4) (5 . 5) (8 . 7) (10 . 9)) 5.772 {0/5:15} B:0 1.60297 [ 1.80209] ((2 . 4) (4 . 6) (5 . 7) (8 . 9) (9 . 10)) 7.522 {0/1:10} B:0 1.60416 [ 1.80292] ((3 . 2) (4 . 3) (5 . 4) (7 . 5) (8 . 6)) 8.181 {0/3:10} B:0 SIMILARITY (1/min{score1}): 0.9938 [and 1/min{score2}: 0.8854] [4354, 5836]: Comparing 1nqj_A and 1spp_B, based on their crossing files. There are 10 (0 H + 10 S) secondary structure elements in 1nqj_A, of which 8 satisfy the size requirements. There are 11 (1 H + 10 S) secondary structure elements in 1spp_B, of which 11 satisfy the size requirements. 1.33460 [ 1.83382] ((2 . 4) (3 . 5) (4 . 6) (8 . 9) (9 . 10) (10 . 11)) 5.302 {0/3:15} B:0 1.33523 [ 1.83407] ((2 . 3) (3 . 4) (4 . 5) (5 . 6) (8 . 8) (10 . 10)) 5.866 {0/6:15} B:0 1.60054 [ 2.20021] ((2 . 3) (5 . 6) (8 . 8) (9 . 9) (10 . 10)) 4.904 {0/4:10} B:0 1.60143 [ 2.20055] ((2 . 1) (3 . 3) (4 . 4) (5 . 5) (7 . 6)) 6.261 {0/5:10} B:0 1.60166 [ 2.20064] ((3 . 4) (4 . 5) (5 . 6) (9 . 9) (10 . 10)) 6.495 {0/1:10} B:0 SIMILARITY (1/min{score1}): 0.9974 [and 1/min{score2}: 0.7267] -------------------------------------------------------------------------------------------------------------------------