------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [1990, 194]: Comparing 1gwu_A and 1aru, based on their crossing files. There are 18 (16 H + 2 S) secondary structure elements in 1gwu_A, of which 15 satisfy the size requirements. There are 25 (17 H + 8 S) secondary structure elements in 1aru, of which 13 satisfy the size requirements. 1.50007 [ 1.30011] ((1 . 1) (2 . 2) (5 . 6) (6 . 7) (8 . 9) (9 . 10) (15 . 14) (16 . 17) (17 . 18) (18 . 19)) 2.827 {0/40:45} B:0 2.14497 [ 1.86039] ((1 . 1) (2 . 2) (5 . 6) (6 . 7) (8 . 9) (9 . 10) (16 . 18)) 4.580 {1/19:21} B:0 2.28599 [ 2.06316] ((1 . 1) (2 . 2) (5 . 6) (6 . 7) (8 . 9) (9 . 10) (11 . 12)) 4.783 {3/19:21} B:0 2.56456 [ 2.26311] ((1 . 1) (2 . 2) (13 . 14) (16 . 17) (17 . 18) (18 . 19)) 6.594 {2/14:15} B:0 3.20421 [ 2.89363] ((9 . 9) (15 . 14) (16 . 17) (17 . 18) (18 . 19)) 6.314 {2/9:10} B:0 SIMILARITY (1/min{score1}): 0.6666 [and 1/min{score2}: 0.7692] [1990, 1990]: Comparing 1gwu_A and 1gwu_A, based on their crossing files. There are 18 (16 H + 2 S) secondary structure elements in 1gwu_A, of which 15 satisfy the size requirements. There are 18 (16 H + 2 S) secondary structure elements in 1gwu_A, of which 15 satisfy the size requirements. 1.00000 [ 1.00000] ((1 . 1) (2 . 2) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (10 . 10) (11 . 11) (13 . 13) (14 . 14) (15 . 15) (16 . 16) (17 . 17) (18 . 18)) 0.000 {0/97:105} B:0 2.50008 [ 2.50008] ((5 . 5) (6 . 6) (10 . 10) (13 . 13) (14 . 14) (16 . 17)) 4.192 {0/12:15} B:0 2.50008 [ 2.50008] ((5 . 5) (6 . 6) (10 . 10) (13 . 13) (14 . 14) (17 . 16)) 4.192 {0/12:15} B:0 3.75033 [ 3.75033] ((1 . 5) (2 . 6) (11 . 15) (13 . 17)) 8.222 {0/5:6} B:0 3.75033 [ 3.75033] ((5 . 1) (6 . 2) (15 . 11) (17 . 13)) 8.222 {0/5:6} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [1990, 2832]: Comparing 1gwu_A and 1jdr_A, based on their crossing files. There are 18 (16 H + 2 S) secondary structure elements in 1gwu_A, of which 15 satisfy the size requirements. There are 24 (17 H + 7 S) secondary structure elements in 1jdr_A, of which 14 satisfy the size requirements. 1.50003 [ 1.40003] ((1 . 2) (2 . 4) (5 . 8) (6 . 9) (8 . 11) (9 . 12) (15 . 16) (16 . 20) (17 . 21) (18 . 22)) 2.217 {0/41:45} B:0 1.78578 [ 1.69780] ((1 . 2) (2 . 4) (5 . 8) (6 . 9) (8 . 11) (9 . 12) (11 . 16) (17 . 21) (18 . 22)) 5.328 {4/32:36} B:0 2.14454 [ 2.00207] ((1 . 2) (2 . 4) (5 . 8) (6 . 9) (8 . 11) (9 . 12) (16 . 21)) 4.007 {1/20:21} B:0 3.01445 [ 2.81774] ((5 . 4) (15 . 16) (16 . 20) (17 . 21) (18 . 22)) 7.493 {1/9:10} B:0 3.75043 [ 3.50052] ((5 . 2) (6 . 4) (13 . 11) (16 . 16)) 8.763 {0/5:6} B:0 SIMILARITY (1/min{score1}): 0.7073 [and 1/min{score2}: 0.7499] [1990, 4061]: Comparing 1gwu_A and 1mwv_A, based on their crossing files. There are 18 (16 H + 2 S) secondary structure elements in 1gwu_A, of which 15 satisfy the size requirements. There are 54 (42 H + 12 S) secondary structure elements in 1mwv_A, of which 14 satisfy the size requirements. 1.50002 [ 1.40003] ((1 . 5) (2 . 7) (5 . 11) (6 . 12) (8 . 16) (9 . 17) (15 . 22) (16 . 28) (17 . 29) (18 . 30)) 2.076 {0/41:45} B:0 3.75350 [ 3.50430] ((5 . 5) (6 . 7) (8 . 11) (18 . 17)) 14.832 {0/4:6} B:0 3.82397 [ 3.59017] ((2 . 11) (8 . 12) (15 . 16) (17 . 17)) 8.270 {1/5:6} B:0 3.82413 [ 3.59036] ((5 . 12) (8 . 16) (9 . 17) (18 . 28)) 9.143 {1/5:6} B:0 4.23380 [ 4.06711] ((8 . 16) (9 . 17) (15 . 22) (18 . 28)) 8.951 {2/6:6} B:0 SIMILARITY (1/min{score1}): 0.6667 [and 1/min{score2}: 0.7143] [1990, 4062]: Comparing 1gwu_A and 1mwv_A, based on their crossing files. There are 18 (16 H + 2 S) secondary structure elements in 1gwu_A, of which 15 satisfy the size requirements. There are 54 (42 H + 12 S) secondary structure elements in 1mwv_A, of which 14 satisfy the size requirements. 1.36380 [ 1.27293] ((1 . 33) (2 . 34) (5 . 38) (6 . 39) (7 . 40) (8 . 44) (9 . 45) (15 . 47) (16 . 51) (17 . 52) (18 . 53)) 3.236 {0/49:55} B:0 2.50017 [ 2.33354] ((1 . 33) (2 . 34) (5 . 38) (6 . 39) (15 . 47) (17 . 51)) 5.103 {0/14:15} B:0 2.50432 [ 2.33865] ((1 . 33) (2 . 34) (5 . 38) (6 . 39) (17 . 51) (18 . 53)) 5.131 {1/14:15} B:0 3.75117 [ 3.50144] ((1 . 38) (2 . 39) (6 . 44) (8 . 47)) 11.289 {0/3:6} B:0 3.75293 [ 3.50360] ((7 . 39) (9 . 40) (11 . 44) (16 . 47)) 14.191 {0/3:6} B:0 SIMILARITY (1/min{score1}): 0.7332 [and 1/min{score2}: 0.7856] [1990, 4578]: Comparing 1gwu_A and 1oaf_A, based on their crossing files. There are 18 (16 H + 2 S) secondary structure elements in 1gwu_A, of which 15 satisfy the size requirements. There are 15 (13 H + 2 S) secondary structure elements in 1oaf_A, of which 10 satisfy the size requirements. 1.50466 [ 1.01543] ((1 . 1) (2 . 2) (5 . 6) (6 . 7) (8 . 8) (9 . 9) (15 . 12) (16 . 13) (17 . 14) (18 . 15)) 2.561 {2/40:45} B:0 1.78446 [ 1.57010] ((1 . 1) (2 . 2) (5 . 6) (6 . 7) (8 . 8) (9 . 9) (11 . 12) (16 . 13) (17 . 14) (18 . 15)) 5.581 {6/40:45} B:0 3.01443 [ 2.04733] ((5 . 2) (15 . 12) (16 . 13) (17 . 14) (18 . 15)) 7.373 {1/9:10} B:0 3.02257 [ 2.07296] ((6 . 6) (15 . 12) (16 . 13) (17 . 14) (18 . 15)) 6.308 {1/8:10} B:0 3.31080 [ 2.72515] ((2 . 1) (5 . 6) (6 . 7) (8 . 8) (9 . 9)) 8.749 {2/8:10} B:0 SIMILARITY (1/min{score1}): 0.6646 [and 1/min{score2}: 0.9848] [1990, 5206]: Comparing 1gwu_A and 1q4g_A, based on their crossing files. There are 18 (16 H + 2 S) secondary structure elements in 1gwu_A, of which 15 satisfy the size requirements. There are 42 (32 H + 10 S) secondary structure elements in 1q4g_A, of which 29 satisfy the size requirements. 3.75045 [ 7.25006] ((5 . 32) (6 . 33) (9 . 38) (13 . 42)) 8.889 {0/6:6} B:0 3.75070 [ 7.25010] ((5 . 22) (6 . 23) (8 . 29) (18 . 38)) 9.915 {0/0:6} B:0 3.75110 [ 7.25015] ((1 . 22) (6 . 29) (11 . 35) (13 . 37)) 11.110 {0/5:6} B:0 3.75182 [ 7.25025] ((8 . 20) (13 . 23) (17 . 29) (18 . 31)) 12.595 {0/4:6} B:0 3.75607 [ 7.25084] ((1 . 22) (7 . 32) (11 . 35) (15 . 41)) 17.029 {0/3:6} B:0 SIMILARITY (1/min{score1}): 0.5324 [and 1/min{score2}: 0.2758] -------------------------------------------------------------------------------------------------------------------------