------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [5723, 481]: Comparing 1rxx_A and 1bwd_A, based on their crossing files. There are 39 (19 H + 20 S) secondary structure elements in 1rxx_A, of which 32 satisfy the size requirements. There are 34 (15 H + 19 S) secondary structure elements in 1bwd_A, of which 24 satisfy the size requirements. 1.62446 [ 1.25536] ((2 . 1) (5 . 6) (6 . 7) (17 . 11) (18 . 12) (19 . 14) (20 . 15) (21 . 16) (23 . 19) (24 . 20) (25 . 21) (26 . 22) (28 . 24) (29 . 25) (34 . 27) (35 . 29) (36 . 30) (37 . 31) (38 . 32) (39 . 34)) 2.197 {6/75:190} B:0 1.68675 [ 1.26914] ((2 . 1) (5 . 6) (6 . 7) (17 . 11) (18 . 12) (19 . 14) (21 . 16) (23 . 19) (24 . 20) (25 . 21) (26 . 22) (28 . 24) (29 . 25) (34 . 27) (35 . 29) (36 . 30) (37 . 31) (38 . 32) (39 . 34)) 2.099 {3/64:171} B:0 2.04159 [ 1.92344] ((2 . 1) (5 . 6) (6 . 7) (17 . 11) (18 . 12) (19 . 14) (20 . 15) (21 . 16) (23 . 19) (24 . 20) (25 . 21) (26 . 22) (28 . 24) (29 . 25) (33 . 26) (34 . 27) (35 . 29) (36 . 30) (37 . 31) (38 . 32) (39 . 34)) 2.410 {16/86:210} B:0 3.55558 [ 2.66672] ((19 . 6) (21 . 7) (26 . 16) (33 . 21) (34 . 22) (35 . 24) (36 . 25) (38 . 27) (39 . 29)) 4.003 {0/14:36} B:0 4.00188 [ 3.00446] ((6 . 1) (21 . 16) (23 . 19) (24 . 20) (25 . 21) (26 . 22) (28 . 24) (29 . 25)) 2.512 {1/12:28} B:0 SIMILARITY (1/min{score1}): 0.6546 [and 1/min{score2}: 0.8681] [5723, 1738]: Comparing 1rxx_A and 1g61_A, based on their crossing files. There are 39 (19 H + 20 S) secondary structure elements in 1rxx_A, of which 32 satisfy the size requirements. There are 25 (10 H + 15 S) secondary structure elements in 1g61_A, of which 19 satisfy the size requirements. 4.57143 [ 2.71430] ((21 . 6) (24 . 9) (25 . 10) (26 . 11) (28 . 13) (29 . 14) (30 . 15)) 2.728 {0/7:21} B:0 5.33334 [ 3.16668] ((33 . 5) (34 . 6) (36 . 9) (37 . 10) (38 . 11) (39 . 13)) 2.922 {0/4:15} B:0 5.33335 [ 3.16674] ((24 . 4) (26 . 6) (34 . 17) (35 . 18) (36 . 19) (38 . 21)) 4.999 {0/2:15} B:0 5.34021 [ 3.19906] ((21 . 6) (24 . 9) (25 . 10) (26 . 11) (30 . 15) (34 . 19)) 5.402 {1/7:15} B:0 6.43693 [ 3.96669] ((24 . 9) (25 . 10) (30 . 15) (33 . 16) (36 . 21)) 3.013 {1/4:10} B:0 SIMILARITY (1/min{score1}): 0.5558 [and 1/min{score2}: 0.8937] [5723, 1739]: Comparing 1rxx_A and 1g62_A, based on their crossing files. There are 39 (19 H + 20 S) secondary structure elements in 1rxx_A, of which 32 satisfy the size requirements. There are 25 (10 H + 15 S) secondary structure elements in 1g62_A, of which 19 satisfy the size requirements. 5.33334 [ 3.16668] ((33 . 10) (34 . 11) (35 . 13) (36 . 14) (38 . 16) (39 . 18)) 3.512 {0/2:15} B:0 5.33335 [ 3.16674] ((23 . 3) (24 . 4) (25 . 5) (26 . 6) (34 . 16) (38 . 21)) 4.995 {0/4:15} B:0 5.33335 [ 3.16675] ((23 . 3) (24 . 4) (26 . 6) (34 . 14) (38 . 21) (39 . 23)) 5.076 {0/4:15} B:0 5.33337 [ 3.16686] ((24 . 9) (25 . 10) (26 . 11) (30 . 15) (35 . 23) (37 . 25)) 6.341 {0/6:15} B:0 5.71277 [ 4.34543] ((21 . 4) (24 . 9) (25 . 10) (26 . 11) (28 . 13) (29 . 14)) 3.860 {2/5:15} B:0 SIMILARITY (1/min{score1}): 0.5923 [and 1/min{score2}: 0.9809] [5723, 2117]: Comparing 1rxx_A and 1h70_A, based on their crossing files. There are 39 (19 H + 20 S) secondary structure elements in 1rxx_A, of which 32 satisfy the size requirements. There are 27 (12 H + 15 S) secondary structure elements in 1h70_A, of which 22 satisfy the size requirements. 1.91049 [ 1.69389] ((2 . 1) (3 . 2) (5 . 3) (6 . 4) (17 . 5) (18 . 6) (19 . 8) (21 . 9) (23 . 11) (24 . 12) (25 . 13) (26 . 14) (28 . 16) (29 . 17) (33 . 19) (34 . 20) (35 . 22) (36 . 23) (37 . 24) (38 . 25)) 2.860 {10/62:190} B:0 2.13353 [ 1.95043] ((2 . 1) (5 . 3) (6 . 4) (17 . 5) (18 . 6) (19 . 8) (21 . 9) (23 . 11) (24 . 12) (25 . 13) (26 . 14) (28 . 16) (29 . 17) (33 . 19) (34 . 20) (35 . 22) (36 . 23) (37 . 24) (38 . 25)) 2.714 {10/53:171} B:0 1.68443 [ 1.15857] ((2 . 12) (5 . 13) (6 . 14) (17 . 16) (18 . 17) (20 . 19) (21 . 20) (23 . 22) (24 . 23) (25 . 24) (26 . 25) (29 . 1) (33 . 3) (34 . 4) (35 . 5) (36 . 6) (37 . 8) (38 . 9) (39 . 11)) 4.071 {0/57:171} B:1 1.69397 [ 1.18707] ((2 . 1) (5 . 3) (6 . 4) (11 . 2) (17 . 5) (18 . 6) (19 . 8) (21 . 9) (23 . 11) (24 . 12) (25 . 13) (26 . 14) (28 . 16) (29 . 17) (34 . 20) (35 . 22) (36 . 23) (37 . 24) (38 . 25)) 3.812 {4/61:171} B:1 1.71635 [ 1.24848] ((2 . 6) (5 . 8) (6 . 9) (17 . 11) (18 . 12) (19 . 13) (21 . 14) (23 . 16) (24 . 17) (25 . 19) (26 . 20) (28 . 22) (29 . 23) (33 . 24) (34 . 25) (36 . 1) (37 . 3) (38 . 4) (39 . 5)) 4.744 {4/45:171} B:1 SIMILARITY (1/min{score1}): 0.5937 [and 1/min{score2}: 0.8631] [5723, 2833]: Comparing 1rxx_A and 1jdw, based on their crossing files. There are 39 (19 H + 20 S) secondary structure elements in 1rxx_A, of which 32 satisfy the size requirements. There are 31 (14 H + 17 S) secondary structure elements in 1jdw, of which 27 satisfy the size requirements. 1.60123 [ 1.35205] ((2 . 1) (5 . 4) (6 . 5) (17 . 9) (18 . 10) (19 . 12) (21 . 13) (23 . 17) (24 . 18) (25 . 19) (26 . 20) (28 . 21) (29 . 22) (33 . 23) (34 . 24) (35 . 26) (36 . 27) (37 . 28) (38 . 29) (39 . 31)) 3.087 {2/54:190} B:0 1.68596 [ 1.48381] ((2 . 1) (5 . 4) (6 . 5) (17 . 9) (18 . 10) (20 . 12) (21 . 13) (23 . 17) (24 . 18) (25 . 19) (26 . 20) (28 . 21) (29 . 22) (33 . 23) (34 . 24) (35 . 26) (36 . 27) (37 . 28) (38 . 29) (39 . 31)) 3.286 {6/54:190} B:0 3.20002 [ 2.70003] ((6 . 1) (17 . 9) (18 . 10) (19 . 12) (21 . 13) (25 . 19) (34 . 24) (37 . 28) (38 . 29) (39 . 31)) 3.400 {0/15:45} B:0 3.55556 [ 3.00001] ((23 . 9) (24 . 10) (26 . 13) (34 . 20) (35 . 21) (36 . 22) (37 . 23) (38 . 24) (39 . 26)) 3.124 {0/10:36} B:0 4.57144 [ 3.85717] ((5 . 12) (6 . 13) (21 . 24) (23 . 26) (24 . 27) (25 . 28) (26 . 29)) 4.502 {0/10:21} B:0 SIMILARITY (1/min{score1}): 0.6534 [and 1/min{score2}: 0.7712] [5723, 5723]: Comparing 1rxx_A and 1rxx_A, based on their crossing files. There are 39 (19 H + 20 S) secondary structure elements in 1rxx_A, of which 32 satisfy the size requirements. There are 39 (19 H + 20 S) secondary structure elements in 1rxx_A, of which 32 satisfy the size requirements. 1.00000 [ 1.00000] ((2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (10 . 10) (11 . 11) (14 . 14) (15 . 15) (17 . 17) (18 . 18) (19 . 19) (20 . 20) (21 . 21) (23 . 23) (24 . 24) (25 . 25) (26 . 26) (28 . 28) (29 . 29) (30 . 30) (31 . 31) (32 . 32) (33 . 33) (34 . 34) (35 . 35) (36 . 36) (37 . 37) (38 . 38) (39 . 39)) 0.000 {0/354:496} B:0 5.33334 [ 5.33334] ((21 . 26) (23 . 28) (24 . 29) (33 . 37) (34 . 38) (35 . 39)) 3.731 {0/6:15} B:0 1.39633 [ 1.39633] ((2 . 2) (5 . 3) (7 . 7) (8 . 8) (18 . 18) (19 . 19) (21 . 21) (23 . 23) (24 . 24) (25 . 25) (26 . 26) (28 . 28) (29 . 29) (30 . 30) (31 . 31) (32 . 32) (33 . 33) (34 . 34) (35 . 35) (36 . 36) (37 . 37) (38 . 6) (39 . 17)) 5.383 {7/155:253} B:1 1.60211 [ 1.60211] ((2 . 24) (5 . 25) (6 . 26) (17 . 28) (18 . 29) (19 . 33) (21 . 34) (23 . 35) (24 . 36) (25 . 37) (26 . 38) (28 . 39) (29 . 2) (33 . 5) (34 . 6) (35 . 17) (36 . 18) (37 . 19) (38 . 21) (39 . 23)) 5.545 {2/53:190} B:1 1.60211 [ 1.60211] ((2 . 29) (5 . 33) (6 . 34) (17 . 35) (18 . 36) (19 . 37) (21 . 38) (23 . 39) (24 . 2) (25 . 5) (26 . 6) (28 . 17) (29 . 18) (33 . 19) (34 . 21) (35 . 23) (36 . 24) (37 . 25) (38 . 26) (39 . 28)) 5.545 {2/53:190} B:1 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [5723, 5782]: Comparing 1rxx_A and 1s9r_A, based on their crossing files. There are 39 (19 H + 20 S) secondary structure elements in 1rxx_A, of which 32 satisfy the size requirements. There are 39 (20 H + 19 S) secondary structure elements in 1s9r_A, of which 33 satisfy the size requirements. 1.09060 [ 1.12191] ((2 . 1) (3 . 2) (4 . 3) (5 . 4) (6 . 5) (7 . 6) (8 . 7) (10 . 8) (11 . 9) (15 . 12) (17 . 14) (18 . 15) (19 . 17) (21 . 18) (23 . 21) (24 . 22) (25 . 23) (26 . 24) (28 . 26) (29 . 27) (30 . 28) (31 . 29) (32 . 30) (33 . 31) (34 . 32) (35 . 34) (36 . 35) (37 . 36) (38 . 37) (39 . 39)) 2.298 {16/272:435} B:0 1.39115 [ 1.40476] ((2 . 1) (3 . 2) (4 . 3) (5 . 4) (6 . 5) (7 . 6) (8 . 7) (10 . 8) (11 . 9) (14 . 11) (15 . 12) (17 . 14) (18 . 15) (19 . 17) (21 . 18) (23 . 21) (24 . 22) (25 . 23) (26 . 24) (28 . 26) (29 . 27) (30 . 28) (31 . 29) (32 . 30) (33 . 31) (34 . 32) (35 . 34) (36 . 35) (37 . 36) (38 . 37) (39 . 39)) 2.926 {38/299:465} B:0 1.47392 [ 1.48698] ((2 . 1) (3 . 2) (4 . 3) (5 . 4) (6 . 5) (7 . 6) (8 . 7) (10 . 8) (11 . 9) (14 . 11) (15 . 12) (17 . 14) (18 . 15) (19 . 17) (21 . 18) (23 . 21) (24 . 22) (25 . 23) (26 . 24) (28 . 26) (29 . 27) (30 . 28) (31 . 29) (33 . 31) (34 . 32) (35 . 34) (36 . 35) (37 . 36) (38 . 37) (39 . 39)) 2.818 {37/272:435} B:0 1.51357 [ 1.52943] ((2 . 1) (3 . 3) (5 . 4) (6 . 5) (8 . 7) (10 . 8) (11 . 9) (15 . 12) (17 . 14) (18 . 15) (20 . 17) (21 . 18) (23 . 21) (24 . 22) (25 . 23) (26 . 24) (28 . 26) (29 . 27) (30 . 28) (31 . 29) (32 . 30) (33 . 31) (34 . 32) (35 . 34) (36 . 35) (37 . 36) (38 . 37) (39 . 39)) 3.473 {31/226:378} B:0 1.64724 [ 1.65960] ((2 . 1) (3 . 3) (5 . 4) (6 . 5) (8 . 7) (10 . 8) (11 . 11) (15 . 12) (17 . 14) (18 . 15) (19 . 17) (21 . 18) (23 . 21) (24 . 22) (25 . 23) (26 . 24) (28 . 26) (29 . 27) (30 . 28) (31 . 29) (32 . 30) (33 . 31) (34 . 32) (35 . 34) (36 . 35) (37 . 36) (38 . 37) (39 . 39)) 4.257 {35/227:378} B:0 SIMILARITY (1/min{score1}): 0.9169 [and 1/min{score2}: 0.8913] -------------------------------------------------------------------------------------------------------------------------