------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [5265, 748]: Comparing 1qad_A and 1d4t_A, based on their crossing files. There are 11 (5 H + 6 S) secondary structure elements in 1qad_A, of which 7 satisfy the size requirements. There are 7 (2 H + 5 S) secondary structure elements in 1d4t_A, of which 6 satisfy the size requirements. 1.16667 [ 1.00001] ((4 . 1) (5 . 2) (6 . 3) (7 . 4) (8 . 5) (9 . 6)) 1.281 {0/8:15} B:0 1.75068 [ 1.50108] ((3 . 2) (5 . 4) (6 . 5) (9 . 6)) 5.557 {0/2:6} B:0 SIMILARITY (1/min{score1}): 0.8571 [and 1/min{score2}: 0.9999] [5265, 2381]: Comparing 1qad_A and 1i3z_A, based on their crossing files. There are 11 (5 H + 6 S) secondary structure elements in 1qad_A, of which 7 satisfy the size requirements. There are 9 (2 H + 7 S) secondary structure elements in 1i3z_A, of which 6 satisfy the size requirements. 1.16668 [ 1.00003] ((4 . 2) (5 . 3) (6 . 4) (7 . 5) (8 . 6) (9 . 8)) 1.648 {0/8:15} B:0 1.75061 [ 1.50096] ((3 . 3) (5 . 5) (6 . 6) (9 . 8)) 5.405 {0/1:6} B:0 5.01866 [ 5.01010] ((4 . 2) (5 . 3) (7 . 4) (9 . 8)) 4.304 {1/2:6} B:0 SIMILARITY (1/min{score1}): 0.8571 [and 1/min{score2}: 0.9999] [5265, 3064]: Comparing 1qad_A and 1ju5_A, based on their crossing files. There are 11 (5 H + 6 S) secondary structure elements in 1qad_A, of which 7 satisfy the size requirements. There are 9 (2 H + 7 S) secondary structure elements in 1ju5_A, of which 7 satisfy the size requirements. 1.16669 [ 1.16669] ((4 . 2) (5 . 3) (6 . 4) (7 . 5) (8 . 6) (9 . 8)) 1.791 {0/6:15} B:0 1.40002 [ 1.40002] ((4 . 2) (5 . 3) (6 . 4) (7 . 5) (9 . 8)) 1.822 {0/4:10} B:0 1.75073 [ 1.75073] ((5 . 5) (6 . 6) (7 . 7) (9 . 8)) 5.661 {0/2:6} B:0 5.01875 [ 5.01875] ((3 . 4) (5 . 5) (7 . 6) (8 . 7)) 7.567 {2/4:6} B:0 6.00448 [ 6.00448] ((3 . 4) (5 . 5) (6 . 6) (7 . 7) (9 . 8)) 6.881 {3/5:10} B:0 SIMILARITY (1/min{score1}): 0.8571 [and 1/min{score2}: 0.8571] [5265, 3230]: Comparing 1qad_A and 1k9a_A, based on their crossing files. There are 11 (5 H + 6 S) secondary structure elements in 1qad_A, of which 7 satisfy the size requirements. There are 36 (15 H + 21 S) secondary structure elements in 1k9a_A, of which 6 satisfy the size requirements. 1.16668 [ 1.00002] ((4 . 8) (5 . 9) (6 . 10) (7 . 11) (8 . 12) (9 . 13)) 1.413 {0/8:15} B:0 1.40001 [ 1.20001] ((4 . 8) (5 . 9) (6 . 10) (7 . 11) (9 . 13)) 1.476 {0/5:10} B:0 1.75106 [ 1.50168] ((3 . 9) (5 . 11) (6 . 12) (9 . 13)) 6.208 {0/1:6} B:0 1.75183 [ 1.50291] ((3 . 9) (5 . 10) (6 . 12) (9 . 13)) 7.127 {0/1:6} B:0 1.75274 [ 1.50434] ((4 . 8) (7 . 9) (8 . 10) (9 . 13)) 7.881 {0/3:6} B:0 SIMILARITY (1/min{score1}): 0.8571 [and 1/min{score2}: 0.9999] [5265, 3850]: Comparing 1qad_A and 1m61_A, based on their crossing files. There are 11 (5 H + 6 S) secondary structure elements in 1qad_A, of which 7 satisfy the size requirements. There are 17 (8 H + 9 S) secondary structure elements in 1m61_A, of which 7 satisfy the size requirements. 1.16667 [ 1.16667] ((3 . 1) (4 . 2) (5 . 3) (6 . 4) (7 . 5) (9 . 7)) 1.244 {0/8:15} B:0 3.39493 [ 3.39493] ((3 . 1) (4 . 2) (6 . 3) (9 . 7)) 3.684 {1/3:6} B:0 5.01867 [ 5.01867] ((3 . 1) (4 . 2) (7 . 4) (9 . 7)) 4.673 {2/4:6} B:0 1.40494 [ 1.40494] ((4 . 2) (5 . 1) (7 . 3) (8 . 4) (9 . 7)) 7.732 {0/4:10} B:1 6.67457 [ 6.67457] ((3 . 3) (4 . 2) (6 . 5) (9 . 7)) 4.843 {2/3:6} B:1 SIMILARITY (1/min{score1}): 0.8571 [and 1/min{score2}: 0.8571] [5265, 3851]: Comparing 1qad_A and 1m61_A, based on their crossing files. There are 11 (5 H + 6 S) secondary structure elements in 1qad_A, of which 7 satisfy the size requirements. There are 17 (8 H + 9 S) secondary structure elements in 1m61_A, of which 7 satisfy the size requirements. 1.40000 [ 1.40000] ((4 . 12) (5 . 13) (6 . 14) (7 . 15) (9 . 17)) 1.261 {0/5:10} B:0 5.01877 [ 5.01877] ((4 . 10) (7 . 13) (8 . 14) (9 . 17)) 7.831 {2/4:6} B:0 5.01867 [ 5.01867] ((3 . 13) (4 . 12) (6 . 15) (9 . 17)) 4.724 {2/4:6} B:1 SIMILARITY (1/min{score1}): 0.7143 [and 1/min{score2}: 0.7143] [5265, 3935]: Comparing 1qad_A and 1mil, based on their crossing files. There are 11 (5 H + 6 S) secondary structure elements in 1qad_A, of which 7 satisfy the size requirements. There are 10 (2 H + 8 S) secondary structure elements in 1mil, of which 7 satisfy the size requirements. 1.40005 [ 1.40005] ((4 . 1) (5 . 2) (6 . 3) (7 . 4) (9 . 7)) 2.409 {0/4:10} B:0 1.75332 [ 1.75332] ((4 . 1) (7 . 2) (8 . 3) (9 . 7)) 8.271 {0/1:6} B:0 5.01878 [ 5.01878] ((3 . 3) (5 . 4) (7 . 8) (8 . 9)) 8.057 {2/4:6} B:0 1.75211 [ 1.75211] ((3 . 2) (5 . 4) (7 . 9) (8 . 8)) 7.379 {0/4:6} B:1 3.39509 [ 3.39509] ((3 . 2) (5 . 4) (8 . 8) (9 . 7)) 6.566 {1/3:6} B:1 SIMILARITY (1/min{score1}): 0.7143 [and 1/min{score2}: 0.7143] [5265, 5265]: Comparing 1qad_A and 1qad_A, based on their crossing files. There are 11 (5 H + 6 S) secondary structure elements in 1qad_A, of which 7 satisfy the size requirements. There are 11 (5 H + 6 S) secondary structure elements in 1qad_A, of which 7 satisfy the size requirements. 1.00000 [ 1.00000] ((3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (9 . 9)) 0.000 {0/12:21} B:0 5.01866 [ 5.01866] ((3 . 3) (4 . 4) (6 . 7) (9 . 9)) 4.368 {2/4:6} B:0 1.40496 [ 1.40496] ((3 . 5) (4 . 4) (5 . 7) (6 . 8) (9 . 9)) 7.739 {0/3:10} B:1 1.40496 [ 1.40496] ((4 . 4) (5 . 3) (7 . 5) (8 . 6) (9 . 9)) 7.739 {0/3:10} B:1 6.67458 [ 6.67458] ((3 . 5) (4 . 4) (6 . 7) (9 . 9)) 5.643 {2/3:6} B:1 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [5265, 5688]: Comparing 1qad_A and 1rpy_A, based on their crossing files. There are 11 (5 H + 6 S) secondary structure elements in 1qad_A, of which 7 satisfy the size requirements. There are 7 (4 H + 3 S) secondary structure elements in 1rpy_A, of which 6 satisfy the size requirements. 1.75010 [ 1.50016] ((4 . 2) (5 . 4) (6 . 5) (7 . 6)) 3.431 {0/3:6} B:0 1.75075 [ 1.50120] ((4 . 3) (5 . 4) (6 . 5) (7 . 6)) 5.704 {0/3:6} B:0 2.55939 [ 2.53260] ((4 . 2) (5 . 4) (6 . 5) (7 . 6) (9 . 7)) 4.115 {1/4:10} B:0 10.00234 [10.00127] ((3 . 4) (4 . 2) (5 . 5) (6 . 6)) 3.136 {2/2:6} B:1 10.00235 [10.00127] ((4 . 2) (5 . 4) (6 . 6) (7 . 5)) 4.434 {2/2:6} B:1 SIMILARITY (1/min{score1}): 0.5714 [and 1/min{score2}: 0.6666] [5265, 6120]: Comparing 1qad_A and 1uur_A, based on their crossing files. There are 11 (5 H + 6 S) secondary structure elements in 1qad_A, of which 7 satisfy the size requirements. There are 31 (12 H + 19 S) secondary structure elements in 1uur_A, of which 9 satisfy the size requirements. 1.40014 [ 1.80006] ((4 . 23) (5 . 24) (6 . 25) (7 . 26) (9 . 28)) 3.147 {0/5:10} B:0 1.75294 [ 2.25138] ((3 . 26) (4 . 28) (5 . 29) (6 . 30)) 8.020 {0/2:6} B:0 5.01867 [ 5.05051] ((4 . 23) (5 . 24) (7 . 25) (9 . 28)) 4.942 {1/2:6} B:0 5.01876 [ 5.05059] ((4 . 22) (7 . 24) (8 . 25) (9 . 28)) 7.656 {2/4:6} B:0 7.50558 [ 7.51517] ((3 . 26) (4 . 28) (6 . 29) (7 . 30)) 7.739 {3/4:6} B:0 SIMILARITY (1/min{score1}): 0.7142 [and 1/min{score2}: 0.5555] [5265, 6513]: Comparing 1qad_A and 2pld_A, based on their crossing files. There are 11 (5 H + 6 S) secondary structure elements in 1qad_A, of which 7 satisfy the size requirements. There are 9 (2 H + 7 S) secondary structure elements in 2pld_A, of which 6 satisfy the size requirements. 1.40024 [ 1.20038] ((4 . 2) (5 . 3) (6 . 4) (7 . 6) (9 . 9)) 3.618 {0/4:10} B:0 1.40137 [ 1.20217] ((4 . 2) (5 . 3) (6 . 4) (7 . 5) (9 . 9)) 5.606 {0/4:10} B:0 1.75364 [ 1.50576] ((4 . 2) (7 . 3) (8 . 4) (9 . 9)) 8.461 {0/1:6} B:0 1.75141 [ 1.50224] ((3 . 3) (4 . 2) (7 . 5) (9 . 9)) 6.678 {0/4:6} B:1 3.34592 [ 3.34021] ((3 . 3) (4 . 2) (5 . 4) (6 . 5) (7 . 6) (9 . 9)) 6.163 {2/6:15} B:1 SIMILARITY (1/min{score1}): 0.7142 [and 1/min{score2}: 0.8331] -------------------------------------------------------------------------------------------------------------------------