------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [2758, 24]: Comparing 1j7n_A and 1a26, based on their crossing files. There are 60 (41 H + 19 S) secondary structure elements in 1j7n_A, of which 19 satisfy the size requirements. There are 28 (14 H + 14 S) secondary structure elements in 1a26, of which 20 satisfy the size requirements. 3.80101 [ 4.00087] ((29 . 7) (32 . 12) (41 . 22) (43 . 24) (44 . 25)) 10.983 {0/9:10} B:0 4.75010 [ 5.00008] ((31 . 9) (35 . 14) (37 . 16) (39 . 19)) 7.210 {0/4:6} B:0 4.75017 [ 5.00014] ((25 . 7) (27 . 9) (29 . 10) (31 . 14)) 8.280 {0/4:6} B:0 4.75028 [ 5.00024] ((30 . 7) (33 . 13) (39 . 18) (40 . 19)) 9.404 {0/3:6} B:0 4.75036 [ 5.00031] ((32 . 7) (35 . 10) (38 . 13) (44 . 18)) 10.002 {0/2:6} B:0 SIMILARITY (1/min{score1}): 0.2909 [and 1/min{score2}: 0.2828] [2758, 1349]: Comparing 1j7n_A and 1f0l_A, based on their crossing files. There are 60 (41 H + 19 S) secondary structure elements in 1j7n_A, of which 19 satisfy the size requirements. There are 49 (23 H + 26 S) secondary structure elements in 1f0l_A, of which 15 satisfy the size requirements. 3.80036 [ 3.00073] ((33 . 3) (35 . 5) (37 . 7) (39 . 9) (44 . 14)) 8.486 {0/6:10} B:0 3.81912 [ 3.03841] ((35 . 5) (37 . 7) (38 . 9) (39 . 10) (44 . 14)) 8.032 {1/7:10} B:0 4.75023 [ 3.75046] ((33 . 4) (37 . 7) (39 . 10) (44 . 14)) 8.918 {0/4:6} B:0 4.75059 [ 3.75119] ((32 . 5) (33 . 7) (41 . 14) (43 . 15)) 11.327 {0/3:6} B:0 4.75113 [ 3.75230] ((29 . 5) (35 . 13) (37 . 15) (38 . 17)) 13.354 {0/4:6} B:0 SIMILARITY (1/min{score1}): 0.3446 [and 1/min{score2}: 0.4000] [2758, 1694]: Comparing 1j7n_A and 1g24_A, based on their crossing files. There are 60 (41 H + 19 S) secondary structure elements in 1j7n_A, of which 19 satisfy the size requirements. There are 14 (6 H + 8 S) secondary structure elements in 1g24_A, of which 12 satisfy the size requirements. 1.58948 [ 1.02368] ((24 . 1) (25 . 2) (31 . 3) (32 . 4) (33 . 5) (36 . 7) (37 . 8) (38 . 9) (39 . 10) (41 . 12) (42 . 13) (44 . 14)) 3.711 {3/54:66} B:0 1.63142 [ 1.15814] ((24 . 1) (25 . 2) (31 . 3) (32 . 4) (33 . 5) (36 . 7) (37 . 8) (38 . 9) (39 . 10) (41 . 12) (43 . 13) (44 . 14)) 4.623 {5/53:66} B:0 2.37570 [ 1.50276] ((31 . 3) (32 . 4) (33 . 5) (36 . 7) (37 . 8) (38 . 9) (39 . 10) (44 . 14)) 3.207 {1/23:28} B:0 2.47338 [ 2.26816] ((24 . 1) (25 . 2) (32 . 4) (33 . 5) (35 . 7) (37 . 8) (38 . 9) (39 . 10) (41 . 12) (44 . 14)) 4.511 {8/36:45} B:0 3.15037 [ 2.91040] ((24 . 1) (25 . 2) (26 . 3) (32 . 4) (33 . 5) (35 . 7) (39 . 10) (41 . 12)) 7.431 {6/21:28} B:0 SIMILARITY (1/min{score1}): 0.6291 [and 1/min{score2}: 0.9769] [2758, 1834]: Comparing 1j7n_A and 1giq_A, based on their crossing files. There are 60 (41 H + 19 S) secondary structure elements in 1j7n_A, of which 19 satisfy the size requirements. There are 33 (17 H + 16 S) secondary structure elements in 1giq_A, of which 14 satisfy the size requirements. 1.67848 [ 1.36827] ((24 . 1) (25 . 2) (31 . 3) (32 . 5) (33 . 6) (36 . 8) (37 . 9) (39 . 10) (40 . 11) (41 . 12) (42 . 13) (44 . 14)) 5.041 {6/53:66} B:0 1.75904 [ 1.50586] ((24 . 1) (25 . 2) (31 . 3) (32 . 5) (33 . 6) (36 . 8) (37 . 9) (39 . 10) (40 . 11) (41 . 12) (43 . 13) (44 . 14)) 4.383 {7/52:66} B:0 1.80330 [ 1.43982] ((24 . 1) (25 . 2) (31 . 3) (32 . 5) (33 . 6) (36 . 8) (37 . 9) (39 . 10) (41 . 12) (43 . 13) (44 . 14)) 4.505 {5/44:55} B:0 2.71458 [ 2.00074] ((32 . 5) (33 . 6) (36 . 8) (38 . 9) (39 . 10) (43 . 13) (44 . 14)) 6.268 {0/15:21} B:0 4.20657 [ 4.15871] ((25 . 1) (31 . 3) (32 . 5) (33 . 6) (37 . 9) (39 . 10) (40 . 12) (41 . 13) (44 . 14)) 8.492 {12/29:36} B:0 SIMILARITY (1/min{score1}): 0.5958 [and 1/min{score2}: 0.7309] [2758, 2002]: Comparing 1j7n_A and 1gxy_A, based on their crossing files. There are 60 (41 H + 19 S) secondary structure elements in 1j7n_A, of which 19 satisfy the size requirements. There are 18 (9 H + 9 S) secondary structure elements in 1gxy_A, of which 10 satisfy the size requirements. 2.71764 [ 1.45109] ((25 . 4) (31 . 5) (32 . 7) (33 . 8) (39 . 12) (42 . 17) (44 . 18)) 4.875 {1/14:21} B:0 3.80021 [ 2.00146] ((30 . 3) (33 . 8) (39 . 12) (42 . 17) (44 . 18)) 7.434 {0/6:10} B:0 4.75022 [ 2.50149] ((29 . 3) (31 . 5) (32 . 7) (33 . 8)) 8.842 {0/4:6} B:0 4.75027 [ 2.50185] ((31 . 4) (32 . 5) (36 . 11) (43 . 18)) 9.338 {0/5:6} B:0 4.75076 [ 2.50521] ((30 . 2) (35 . 5) (37 . 8) (44 . 17)) 12.097 {0/4:6} B:0 SIMILARITY (1/min{score1}): 0.4168 [and 1/min{score2}: 0.7178] [2758, 2525]: Comparing 1j7n_A and 1ikp_A, based on their crossing files. There are 60 (41 H + 19 S) secondary structure elements in 1j7n_A, of which 19 satisfy the size requirements. There are 52 (27 H + 25 S) secondary structure elements in 1ikp_A, of which 14 satisfy the size requirements. 4.75005 [ 3.50011] ((33 . 38) (35 . 39) (37 . 41) (39 . 43)) 5.983 {0/3:6} B:0 4.75023 [ 3.50057] ((31 . 39) (35 . 44) (36 . 46) (39 . 48)) 8.953 {0/4:6} B:0 4.78692 [ 3.58985] ((33 . 38) (37 . 41) (39 . 43) (40 . 45)) 5.464 {1/5:6} B:0 4.78704 [ 3.59014] ((25 . 39) (29 . 44) (30 . 46) (35 . 52)) 8.119 {1/5:6} B:0 4.78751 [ 3.59124] ((27 . 37) (29 . 39) (32 . 44) (35 . 46)) 11.542 {1/5:6} B:0 SIMILARITY (1/min{score1}): 0.2830 [and 1/min{score2}: 0.3293] [2758, 2758]: Comparing 1j7n_A and 1j7n_A, based on their crossing files. There are 60 (41 H + 19 S) secondary structure elements in 1j7n_A, of which 19 satisfy the size requirements. There are 60 (41 H + 19 S) secondary structure elements in 1j7n_A, of which 19 satisfy the size requirements. 1.00000 [ 1.00000] ((24 . 24) (25 . 25) (26 . 26) (27 . 27) (29 . 29) (30 . 30) (31 . 31) (32 . 32) (33 . 33) (35 . 35) (36 . 36) (37 . 37) (38 . 38) (39 . 39) (40 . 40) (41 . 41) (42 . 42) (43 . 43) (44 . 44)) 0.000 {0/150:171} B:0 3.17207 [ 3.17207] ((24 . 24) (29 . 30) (32 . 32) (33 . 33) (35 . 35) (36 . 36)) 4.300 {1/11:15} B:0 3.96688 [ 3.96688] ((24 . 24) (25 . 25) (32 . 32) (33 . 33) (42 . 41)) 7.526 {2/8:10} B:0 4.75046 [ 4.75046] ((32 . 30) (35 . 32) (41 . 37) (42 . 38)) 10.660 {0/4:6} B:0 4.75046 [ 4.75046] ((30 . 32) (32 . 35) (37 . 41) (38 . 42)) 10.660 {0/4:6} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [2758, 4678]: Comparing 1j7n_A and 1ojq_A, based on their crossing files. There are 60 (41 H + 19 S) secondary structure elements in 1j7n_A, of which 19 satisfy the size requirements. There are 16 (8 H + 8 S) secondary structure elements in 1ojq_A, of which 14 satisfy the size requirements. 1.46247 [ 1.07925] ((24 . 1) (25 . 2) (31 . 3) (32 . 5) (33 . 6) (35 . 8) (36 . 9) (37 . 10) (38 . 11) (39 . 12) (41 . 14) (42 . 15) (44 . 16)) 3.642 {2/65:78} B:0 1.58443 [ 1.16941] ((24 . 1) (25 . 2) (31 . 3) (32 . 5) (33 . 6) (36 . 9) (37 . 10) (38 . 11) (39 . 12) (41 . 14) (42 . 15) (44 . 16)) 3.508 {2/57:66} B:0 1.69436 [ 1.49714] ((24 . 1) (25 . 2) (31 . 3) (32 . 5) (33 . 6) (35 . 7) (36 . 9) (37 . 10) (38 . 11) (39 . 12) (41 . 14) (42 . 15) (44 . 16)) 3.885 {9/65:78} B:0 3.10832 [ 2.72414] ((24 . 1) (33 . 6) (35 . 9) (38 . 11) (39 . 12) (41 . 14) (44 . 16)) 4.712 {4/16:21} B:0 3.96688 [ 3.16685] ((31 . 2) (32 . 5) (33 . 6) (35 . 8) (36 . 9)) 7.609 {2/8:10} B:0 SIMILARITY (1/min{score1}): 0.6838 [and 1/min{score2}: 0.9266] [2758, 5085]: Comparing 1j7n_A and 1prt_A, based on their crossing files. There are 60 (41 H + 19 S) secondary structure elements in 1j7n_A, of which 19 satisfy the size requirements. There are 22 (10 H + 12 S) secondary structure elements in 1prt_A, of which 15 satisfy the size requirements. 4.75038 [ 3.75077] ((31 . 2) (35 . 7) (41 . 13) (42 . 16)) 10.150 {0/3:6} B:0 4.75045 [ 3.75092] ((35 . 7) (38 . 9) (43 . 16) (44 . 17)) 10.625 {0/3:6} B:0 4.75073 [ 3.75148] ((35 . 7) (37 . 8) (38 . 9) (43 . 16)) 11.967 {0/3:6} B:0 4.78700 [ 3.82388] ((36 . 10) (39 . 13) (40 . 16) (41 . 17)) 7.554 {1/5:6} B:0 5.25972 [ 4.61604] ((31 . 2) (35 . 7) (36 . 10) (39 . 13)) 11.526 {2/5:6} B:0 SIMILARITY (1/min{score1}): 0.2937 [and 1/min{score2}: 0.3055] [2758, 5439]: Comparing 1j7n_A and 1qs1_A, based on their crossing files. There are 60 (41 H + 19 S) secondary structure elements in 1j7n_A, of which 19 satisfy the size requirements. There are 32 (13 H + 19 S) secondary structure elements in 1qs1_A, of which 14 satisfy the size requirements. 1.47366 [ 1.10638] ((24 . 1) (25 . 2) (31 . 3) (32 . 4) (33 . 5) (36 . 9) (38 . 11) (39 . 12) (40 . 13) (41 . 14) (42 . 15) (43 . 16) (44 . 17)) 2.640 {4/64:78} B:0 1.71000 [ 1.57529] ((24 . 1) (25 . 2) (31 . 3) (32 . 4) (33 . 5) (35 . 6) (36 . 9) (38 . 11) (39 . 12) (40 . 13) (41 . 14) (42 . 15) (43 . 16) (44 . 17)) 3.565 {11/73:91} B:0 3.16683 [ 2.33374] ((31 . 2) (32 . 4) (33 . 5) (36 . 9) (38 . 11) (39 . 12)) 6.052 {0/11:15} B:0 3.17074 [ 2.34346] ((32 . 4) (33 . 5) (36 . 9) (38 . 11) (39 . 12) (43 . 15)) 6.945 {1/12:15} B:0 4.75036 [ 3.50091] ((31 . 1) (41 . 12) (43 . 13) (44 . 14)) 10.058 {0/4:6} B:0 SIMILARITY (1/min{score1}): 0.6786 [and 1/min{score2}: 0.9038] [2758, 5440]: Comparing 1j7n_A and 1qs1_A, based on their crossing files. There are 60 (41 H + 19 S) secondary structure elements in 1j7n_A, of which 19 satisfy the size requirements. There are 32 (13 H + 19 S) secondary structure elements in 1qs1_A, of which 14 satisfy the size requirements. 1.46596 [ 1.08785] ((24 . 18) (25 . 19) (31 . 20) (32 . 21) (33 . 22) (36 . 24) (37 . 25) (38 . 26) (39 . 27) (40 . 28) (41 . 30) (42 . 31) (44 . 32)) 4.651 {3/64:78} B:0 1.46628 [ 1.08864] ((24 . 18) (25 . 19) (31 . 20) (32 . 21) (33 . 22) (36 . 24) (37 . 25) (38 . 26) (39 . 27) (40 . 28) (41 . 30) (43 . 31) (44 . 32)) 4.186 {3/62:78} B:0 1.58372 [ 1.16764] ((24 . 18) (31 . 20) (32 . 21) (33 . 22) (36 . 24) (37 . 25) (38 . 26) (39 . 27) (40 . 28) (41 . 30) (43 . 31) (44 . 32)) 4.234 {1/53:66} B:0 1.58918 [ 1.18110] ((24 . 18) (25 . 19) (31 . 20) (32 . 21) (33 . 22) (37 . 25) (38 . 26) (39 . 27) (40 . 28) (41 . 30) (42 . 31) (44 . 32)) 4.228 {3/55:66} B:0 2.11165 [ 1.55690] ((32 . 21) (33 . 22) (36 . 24) (37 . 25) (38 . 26) (39 . 27) (41 . 30) (43 . 31) (44 . 32)) 4.014 {1/28:36} B:0 SIMILARITY (1/min{score1}): 0.6821 [and 1/min{score2}: 0.9192] [2758, 5770]: Comparing 1j7n_A and 1s5d_A, based on their crossing files. There are 60 (41 H + 19 S) secondary structure elements in 1j7n_A, of which 19 satisfy the size requirements. There are 22 (12 H + 10 S) secondary structure elements in 1s5d_A, of which 14 satisfy the size requirements. 3.96685 [ 3.16679] ((33 . 1) (37 . 6) (39 . 8) (40 . 9) (42 . 12)) 7.298 {2/8:10} B:0 4.75012 [ 3.50029] ((31 . 2) (35 . 7) (36 . 10) (37 . 12)) 7.588 {0/5:6} B:0 4.75072 [ 3.50181] ((29 . 5) (30 . 7) (33 . 15) (35 . 18)) 11.939 {0/4:6} B:0 4.75175 [ 3.50438] ((30 . 2) (32 . 7) (33 . 8) (35 . 10)) 14.899 {0/3:6} B:0 4.75185 [ 3.50462] ((31 . 2) (32 . 5) (35 . 7) (36 . 10)) 15.100 {0/4:6} B:0 SIMILARITY (1/min{score1}): 0.3152 [and 1/min{score2}: 0.4260] -------------------------------------------------------------------------------------------------------------------------