------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [2036, 2036]: Comparing 1h16_A and 1h16_A, based on their crossing files. There are 53 (36 H + 17 S) secondary structure elements in 1h16_A, of which 44 satisfy the size requirements. There are 53 (36 H + 17 S) secondary structure elements in 1h16_A, of which 44 satisfy the size requirements. 1.00000 [ 1.00000] ((1 . 1) (3 . 3) (5 . 5) (6 . 6) (7 . 7) (9 . 9) (10 . 10) (11 . 11) (12 . 12) (13 . 13) (14 . 14) (15 . 15) (16 . 16) (17 . 17) (18 . 18) (19 . 19) (20 . 20) (21 . 21) (22 . 22) (23 . 23) (24 . 24) (25 . 25) (26 . 26) (27 . 27) (28 . 28) (29 . 29) (30 . 30) (31 . 31) (32 . 32) (33 . 33) (34 . 34) (35 . 35) (36 . 36) (37 . 37) (39 . 39) (40 . 40) (41 . 41) (44 . 44) (46 . 46) (47 . 47) (48 . 48) (50 . 50) (51 . 51) (53 . 53)) 0.000 {0/821:946} B:0 1.07509 [ 1.07509] ((1 . 1) (3 . 3) (5 . 5) (6 . 6) (10 . 9) (11 . 11) (12 . 12) (13 . 13) (14 . 14) (16 . 16) (17 . 17) (18 . 18) (19 . 19) (20 . 20) (21 . 21) (22 . 22) (23 . 23) (24 . 24) (25 . 25) (26 . 26) (27 . 27) (28 . 28) (29 . 29) (30 . 30) (31 . 31) (32 . 32) (33 . 33) (34 . 34) (35 . 35) (36 . 36) (37 . 37) (39 . 39) (40 . 40) (41 . 41) (44 . 44) (46 . 46) (47 . 47) (48 . 48) (50 . 50) (51 . 51) (53 . 53)) 2.245 {22/712:820} B:0 1.15982 [ 1.15982] ((1 . 1) (3 . 3) (5 . 5) (9 . 10) (12 . 12) (13 . 13) (14 . 14) (16 . 16) (17 . 17) (18 . 18) (19 . 19) (20 . 20) (21 . 21) (22 . 22) (23 . 23) (24 . 24) (25 . 25) (26 . 26) (27 . 27) (28 . 28) (29 . 29) (30 . 30) (31 . 31) (32 . 32) (33 . 33) (34 . 34) (35 . 35) (36 . 36) (37 . 37) (39 . 39) (40 . 40) (41 . 41) (44 . 44) (46 . 46) (47 . 47) (50 . 50) (51 . 51) (53 . 53)) 2.326 {20/610:703} B:0 1.15982 [ 1.15982] ((1 . 1) (3 . 3) (5 . 5) (10 . 9) (12 . 12) (13 . 13) (14 . 14) (16 . 16) (17 . 17) (18 . 18) (19 . 19) (20 . 20) (21 . 21) (22 . 22) (23 . 23) (24 . 24) (25 . 25) (26 . 26) (27 . 27) (28 . 28) (29 . 29) (30 . 30) (31 . 31) (32 . 32) (33 . 33) (34 . 34) (35 . 35) (36 . 36) (37 . 37) (39 . 39) (40 . 40) (41 . 41) (44 . 44) (46 . 46) (47 . 47) (50 . 50) (51 . 51) (53 . 53)) 2.326 {20/610:703} B:0 1.17184 [ 1.17184] ((5 . 5) (6 . 6) (7 . 7) (9 . 9) (11 . 11) (12 . 12) (13 . 13) (16 . 14) (17 . 17) (18 . 18) (19 . 19) (20 . 20) (21 . 21) (22 . 22) (23 . 23) (24 . 24) (25 . 25) (26 . 26) (27 . 27) (28 . 28) (29 . 29) (30 . 30) (31 . 31) (33 . 33) (34 . 34) (35 . 35) (36 . 36) (37 . 37) (39 . 39) (40 . 40) (41 . 41) (44 . 44) (46 . 46) (47 . 47) (48 . 48) (50 . 50) (51 . 51) (53 . 53)) 2.003 {33/606:703} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [2036, 2219]: Comparing 1h16_A and 1hk8_A, based on their crossing files. There are 53 (36 H + 17 S) secondary structure elements in 1h16_A, of which 44 satisfy the size requirements. There are 39 (20 H + 19 S) secondary structure elements in 1hk8_A, of which 32 satisfy the size requirements. 1.76230 [ 1.28594] ((11 . 1) (12 . 2) (13 . 5) (17 . 8) (18 . 10) (19 . 11) (21 . 12) (22 . 13) (23 . 14) (24 . 15) (25 . 16) (26 . 17) (29 . 18) (30 . 19) (31 . 22) (32 . 24) (33 . 26) (34 . 27) (37 . 28) (39 . 29) (40 . 30) (41 . 31) (44 . 32) (46 . 33) (47 . 34)) 4.459 {11/240:300} B:0 1.80023 [ 1.37670] ((9 . 1) (12 . 2) (13 . 5) (17 . 8) (18 . 10) (19 . 11) (21 . 12) (22 . 13) (23 . 14) (24 . 15) (25 . 16) (26 . 17) (29 . 18) (30 . 19) (31 . 22) (32 . 24) (33 . 26) (34 . 27) (37 . 28) (39 . 29) (40 . 30) (41 . 31) (44 . 32) (46 . 33) (47 . 34)) 4.394 {23/236:300} B:0 1.93918 [ 1.56535] ((5 . 8) (9 . 1) (12 . 2) (17 . 5) (18 . 10) (19 . 11) (21 . 12) (22 . 13) (23 . 14) (24 . 15) (25 . 16) (26 . 17) (29 . 18) (30 . 19) (31 . 22) (33 . 26) (34 . 27) (37 . 28) (39 . 29) (40 . 30) (41 . 31) (44 . 32) (46 . 33) (47 . 34)) 6.013 {28/216:276} B:1 1.96442 [ 1.73128] ((9 . 1) (12 . 2) (13 . 5) (17 . 8) (18 . 10) (19 . 11) (21 . 12) (22 . 13) (23 . 14) (24 . 15) (25 . 16) (26 . 17) (27 . 9) (29 . 18) (30 . 19) (31 . 22) (32 . 24) (33 . 26) (34 . 27) (37 . 28) (39 . 29) (40 . 30) (41 . 31) (44 . 32) (46 . 33) (47 . 34)) 4.522 {41/255:325} B:1 2.02859 [ 1.77934] ((9 . 1) (12 . 2) (13 . 5) (17 . 8) (18 . 10) (19 . 11) (21 . 12) (22 . 13) (23 . 14) (24 . 15) (25 . 16) (26 . 17) (27 . 9) (29 . 18) (30 . 19) (31 . 22) (33 . 26) (34 . 27) (37 . 28) (39 . 29) (40 . 30) (41 . 31) (44 . 32) (46 . 33) (47 . 34)) 4.592 {39/237:300} B:1 SIMILARITY (1/min{score1}): 0.5674 [and 1/min{score2}: 0.7776] [2036, 3514]: Comparing 1h16_A and 1l1l_A, based on their crossing files. There are 53 (36 H + 17 S) secondary structure elements in 1h16_A, of which 44 satisfy the size requirements. There are 56 (30 H + 26 S) secondary structure elements in 1l1l_A, of which 48 satisfy the size requirements. 3.16667 [ 3.25700] ((12 . 7) (13 . 16) (17 . 24) (19 . 26) (21 . 25) (22 . 29) (23 . 28) (24 . 52) (27 . 30) (29 . 35) (30 . 36) (31 . 37) (33 . 39) (34 . 40) (37 . 43) (40 . 45) (41 . 50) (50 . 51) (51 . 53)) 7.319 {39/134:171} B:3 3.17632 [ 3.21239] ((12 . 7) (17 . 20) (19 . 27) (21 . 25) (22 . 26) (23 . 28) (24 . 29) (25 . 30) (26 . 31) (27 . 33) (28 . 34) (29 . 8) (30 . 36) (31 . 37) (32 . 14) (33 . 35) (34 . 40) (37 . 43) (39 . 39) (40 . 45) (41 . 50) (44 . 51) (46 . 52) (47 . 53)) 5.790 {66/214:276} B:4 3.36939 [ 3.39520] ((12 . 7) (13 . 14) (17 . 20) (19 . 24) (20 . 2) (21 . 25) (22 . 26) (23 . 28) (24 . 29) (25 . 30) (26 . 31) (27 . 33) (28 . 34) (29 . 8) (30 . 36) (31 . 37) (33 . 35) (34 . 40) (37 . 43) (39 . 39) (40 . 45) (41 . 50) (44 . 51) (46 . 52) (47 . 53)) 5.936 {77/233:300} B:4 3.41306 [ 3.43433] ((12 . 7) (16 . 20) (17 . 23) (18 . 24) (19 . 27) (21 . 25) (22 . 26) (23 . 28) (24 . 29) (25 . 30) (26 . 31) (27 . 33) (28 . 34) (29 . 8) (30 . 36) (31 . 37) (32 . 14) (33 . 35) (34 . 40) (37 . 43) (39 . 39) (40 . 45) (41 . 50) (44 . 51) (46 . 52) (47 . 53)) 7.249 {84/250:325} B:4 3.47743 [ 3.50094] ((12 . 7) (13 . 14) (17 . 20) (19 . 27) (20 . 2) (21 . 25) (22 . 26) (23 . 28) (24 . 29) (25 . 30) (26 . 31) (27 . 33) (28 . 34) (29 . 8) (30 . 36) (31 . 37) (33 . 35) (34 . 40) (37 . 43) (39 . 39) (40 . 45) (41 . 50) (44 . 51) (46 . 52) (47 . 53)) 5.948 {80/234:300} B:4 SIMILARITY (1/min{score1}): 0.3780 [and 1/min{score2}: 0.3695] [2036, 5676]: Comparing 1h16_A and 1rlr, based on their crossing files. There are 53 (36 H + 17 S) secondary structure elements in 1h16_A, of which 44 satisfy the size requirements. There are 54 (38 H + 16 S) secondary structure elements in 1rlr, of which 34 satisfy the size requirements. 2.25691 [ 1.81583] ((3 . 24) (17 . 15) (19 . 17) (21 . 18) (22 . 19) (23 . 21) (24 . 27) (25 . 28) (26 . 29) (29 . 31) (31 . 32) (32 . 33) (33 . 34) (34 . 35) (37 . 36) (40 . 42) (41 . 47) (44 . 48) (46 . 51) (47 . 53)) 5.404 {19/151:190} B:1 2.66851 [ 2.38215] ((13 . 15) (17 . 17) (21 . 18) (22 . 19) (23 . 21) (24 . 27) (25 . 28) (26 . 29) (27 . 16) (29 . 31) (31 . 32) (33 . 34) (34 . 35) (37 . 36) (40 . 42) (41 . 47) (44 . 48) (46 . 51) (47 . 53)) 5.104 {29/134:171} B:1 2.37106 [ 1.90246] ((17 . 15) (19 . 17) (21 . 18) (22 . 19) (23 . 21) (24 . 27) (25 . 28) (26 . 29) (27 . 14) (29 . 31) (31 . 32) (34 . 35) (37 . 36) (39 . 34) (40 . 42) (41 . 47) (44 . 48) (46 . 51) (47 . 53)) 5.005 {17/131:171} B:2 2.39507 [ 2.05496] ((16 . 33) (17 . 15) (18 . 24) (19 . 17) (21 . 18) (22 . 19) (23 . 21) (24 . 27) (25 . 28) (26 . 29) (29 . 31) (31 . 32) (33 . 34) (34 . 35) (37 . 36) (40 . 42) (41 . 47) (44 . 48) (46 . 51) (47 . 53)) 6.756 {27/154:190} B:2 2.40461 [ 2.14152] ((3 . 24) (17 . 15) (19 . 17) (21 . 18) (22 . 19) (23 . 21) (24 . 27) (25 . 28) (26 . 29) (27 . 16) (29 . 31) (31 . 32) (32 . 33) (33 . 34) (34 . 35) (37 . 36) (40 . 42) (41 . 47) (44 . 48) (46 . 51) (47 . 53)) 5.515 {32/165:210} B:2 SIMILARITY (1/min{score1}): 0.4431 [and 1/min{score2}: 0.5507] -------------------------------------------------------------------------------------------------------------------------