------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [129, 129]: Comparing 1ahs_A and 1ahs_A, based on their crossing files. There are 12 (1 H + 11 S) secondary structure elements in 1ahs_A, of which 9 satisfy the size requirements. There are 12 (1 H + 11 S) secondary structure elements in 1ahs_A, of which 9 satisfy the size requirements. 1.00000 [ 1.00000] ((1 . 1) (2 . 2) (3 . 3) (5 . 5) (8 . 8) (9 . 9) (10 . 10) (11 . 11) (12 . 12)) 0.000 {0/25:36} B:0 2.25029 [ 2.25029] ((2 . 1) (3 . 2) (5 . 3) (8 . 5)) 5.439 {0/2:6} B:0 2.25029 [ 2.25029] ((1 . 2) (2 . 3) (3 . 5) (5 . 8)) 5.439 {0/2:6} B:0 2.25063 [ 2.25063] ((2 . 1) (3 . 2) (9 . 8) (12 . 11)) 6.582 {0/2:6} B:0 2.25063 [ 2.25063] ((1 . 2) (2 . 3) (8 . 9) (11 . 12)) 6.582 {0/2:6} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [129, 474]: Comparing 1ahs_A and 1bvp_1, based on their crossing files. There are 12 (1 H + 11 S) secondary structure elements in 1ahs_A, of which 9 satisfy the size requirements. There are 22 (10 H + 12 S) secondary structure elements in 1bvp_1, of which 12 satisfy the size requirements. 1.00011 [ 1.33338] ((1 . 8) (2 . 9) (3 . 10) (5 . 12) (8 . 14) (9 . 15) (10 . 16) (11 . 17) (12 . 18)) 2.294 {0/25:36} B:0 2.25070 [ 3.00030] ((1 . 9) (2 . 10) (8 . 15) (11 . 18)) 6.769 {0/3:6} B:0 2.25082 [ 3.00035] ((1 . 9) (2 . 10) (3 . 12) (11 . 18)) 7.033 {0/3:6} B:0 2.25096 [ 3.00040] ((3 . 8) (5 . 10) (8 . 12) (12 . 17)) 7.310 {0/0:6} B:0 2.25096 [ 3.00041] ((2 . 10) (3 . 12) (5 . 14) (8 . 17)) 7.319 {0/2:6} B:0 SIMILARITY (1/min{score1}): 0.9999 [and 1/min{score2}: 0.7500] [129, 1548]: Comparing 1ahs_A and 1flc_A, based on their crossing files. There are 12 (1 H + 11 S) secondary structure elements in 1ahs_A, of which 9 satisfy the size requirements. There are 39 (9 H + 30 S) secondary structure elements in 1flc_A, of which 9 satisfy the size requirements. 1.50058 [ 1.50058] ((2 . 18) (3 . 21) (5 . 23) (8 . 24) (11 . 25) (12 . 26)) 4.765 {0/3:15} B:0 2.25023 [ 2.25023] ((3 . 18) (5 . 21) (8 . 23) (12 . 25)) 5.125 {0/0:6} B:0 2.25029 [ 2.25029] ((1 . 23) (2 . 24) (3 . 25) (5 . 26)) 5.432 {0/0:6} B:0 2.25082 [ 2.25082] ((1 . 24) (3 . 25) (5 . 26) (8 . 27)) 7.040 {0/0:6} B:0 2.25097 [ 2.25097] ((1 . 24) (2 . 25) (3 . 26) (5 . 27)) 7.334 {0/0:6} B:0 SIMILARITY (1/min{score1}): 0.7760 [and 1/min{score2}: 0.7760] [129, 3047]: Comparing 1ahs_A and 1jsd_A, based on their crossing files. There are 12 (1 H + 11 S) secondary structure elements in 1ahs_A, of which 9 satisfy the size requirements. There are 33 (6 H + 27 S) secondary structure elements in 1jsd_A, of which 24 satisfy the size requirements. 1.13024 [ 3.00028] ((2 . 16) (3 . 17) (5 . 18) (8 . 20) (9 . 21) (10 . 22) (11 . 23) (12 . 25)) 6.662 {0/4:28} B:0 1.80042 [ 4.80002] ((2 . 16) (3 . 17) (5 . 18) (8 . 20) (12 . 22)) 5.029 {0/0:10} B:0 1.80331 [ 4.80017] ((1 . 13) (3 . 16) (5 . 17) (8 . 18) (10 . 21)) 8.439 {0/4:10} B:0 2.25037 [ 6.00002] ((1 . 20) (2 . 21) (3 . 22) (5 . 23)) 5.753 {0/0:6} B:0 2.25156 [ 6.00008] ((3 . 16) (5 . 18) (10 . 21) (12 . 22)) 8.265 {0/0:6} B:0 SIMILARITY (1/min{score1}): 0.8848 [and 1/min{score2}: 0.3333] [129, 5333]: Comparing 1ahs_A and 1qhd_A, based on their crossing files. There are 12 (1 H + 11 S) secondary structure elements in 1ahs_A, of which 9 satisfy the size requirements. There are 30 (13 H + 17 S) secondary structure elements in 1qhd_A, of which 16 satisfy the size requirements. 1.22272 [ 1.83036] ((1 . 11) (2 . 12) (3 . 14) (5 . 16) (8 . 21) (9 . 22) (10 . 23) (11 . 24) (12 . 26)) 4.700 {2/19:36} B:0 1.28687 [ 2.28592] ((1 . 12) (2 . 14) (3 . 16) (5 . 21) (8 . 22) (11 . 23) (12 . 24)) 5.038 {0/7:21} B:0 1.80124 [ 3.20022] ((1 . 14) (8 . 21) (9 . 22) (11 . 24) (12 . 26)) 6.601 {0/4:10} B:0 2.25034 [ 4.00006] ((1 . 10) (2 . 11) (5 . 14) (11 . 21)) 5.660 {0/2:6} B:0 2.25072 [ 4.00013] ((2 . 11) (3 . 12) (5 . 14) (8 . 16)) 6.815 {0/1:6} B:0 SIMILARITY (1/min{score1}): 0.8839 [and 1/min{score2}: 0.5463] [129, 5997]: Comparing 1ahs_A and 1uf2_C, based on their crossing files. There are 12 (1 H + 11 S) secondary structure elements in 1ahs_A, of which 9 satisfy the size requirements. There are 27 (16 H + 11 S) secondary structure elements in 1uf2_C, of which 12 satisfy the size requirements. 1.00684 [ 1.33624] ((1 . 11) (2 . 12) (3 . 13) (5 . 15) (8 . 16) (9 . 17) (10 . 18) (11 . 20) (12 . 21)) 3.403 {1/25:36} B:0 2.25017 [ 3.00007] ((1 . 11) (2 . 12) (3 . 13) (11 . 17)) 4.736 {0/4:6} B:0 2.25029 [ 3.00012] ((2 . 11) (3 . 12) (5 . 13) (8 . 15)) 5.409 {0/2:6} B:0 2.25058 [ 3.00024] ((3 . 15) (9 . 18) (11 . 21) (12 . 22)) 6.438 {0/2:6} B:0 2.25168 [ 3.00071] ((1 . 13) (2 . 14) (8 . 18) (12 . 22)) 8.416 {0/2:6} B:0 SIMILARITY (1/min{score1}): 0.9932 [and 1/min{score2}: 0.7484] [129, 6555]: Comparing 1ahs_A and 2viu_A, based on their crossing files. There are 12 (1 H + 11 S) secondary structure elements in 1ahs_A, of which 9 satisfy the size requirements. There are 35 (4 H + 31 S) secondary structure elements in 2viu_A, of which 29 satisfy the size requirements. 1.33110 [ 3.63304] ((2 . 17) (3 . 19) (5 . 20) (8 . 22) (9 . 23) (10 . 24) (11 . 25) (12 . 26)) 5.441 {1/9:28} B:0 1.50056 [ 4.83335] ((2 . 19) (3 . 20) (5 . 22) (8 . 23) (11 . 24) (12 . 25)) 4.720 {0/2:15} B:0 1.80030 [ 5.80001] ((2 . 19) (3 . 20) (5 . 22) (8 . 23) (12 . 25)) 4.612 {0/1:10} B:0 1.80051 [ 5.80002] ((2 . 17) (3 . 19) (5 . 20) (8 . 22) (12 . 24)) 5.286 {0/2:10} B:0 2.25022 [ 7.25001] ((1 . 17) (8 . 23) (11 . 24) (12 . 25)) 5.081 {0/2:6} B:0 SIMILARITY (1/min{score1}): 0.7513 [and 1/min{score2}: 0.2753] -------------------------------------------------------------------------------------------------------------------------