------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [6336, 1399]: Comparing 1wot_A and 1f5a_A, based on their crossing files. There are 8 (4 H + 4 S) secondary structure elements in 1wot_A, of which 6 satisfy the size requirements. There are 30 (20 H + 10 S) secondary structure elements in 1f5a_A, of which 12 satisfy the size requirements. 1.00155 [ 2.00019] ((1 . 2) (3 . 5) (4 . 6) (5 . 8) (6 . 11) (7 . 13)) 4.494 {0/11:15} B:0 1.20187 [ 2.40023] ((1 . 2) (3 . 5) (4 . 6) (5 . 8) (6 . 9)) 5.401 {0/7:10} B:0 2.57881 [ 3.31088] ((1 . 3) (3 . 5) (4 . 6) (5 . 8)) 9.016 {1/4:6} B:0 2.73975 [ 2.90629] ((1 . 2) (3 . 5) (4 . 11) (5 . 8) (6 . 10) (7 . 13)) 5.952 {3/11:15} B:1 SIMILARITY (1/min{score1}): 0.9985 [and 1/min{score2}: 0.5000] [6336, 2782]: Comparing 1wot_A and 1jaj_A, based on their crossing files. There are 8 (4 H + 4 S) secondary structure elements in 1wot_A, of which 6 satisfy the size requirements. There are 20 (7 H + 13 S) secondary structure elements in 1jaj_A, of which 17 satisfy the size requirements. 1.50263 [ 4.25012] ((1 . 2) (3 . 6) (4 . 8) (5 . 9)) 6.949 {0/4:6} B:0 5.01017 [ 5.55365] ((3 . 15) (4 . 16) (6 . 18) (7 . 19)) 7.038 {2/4:6} B:0 5.01018 [ 5.55366] ((3 . 14) (4 . 16) (6 . 18) (7 . 19)) 7.351 {2/4:6} B:0 2.57777 [ 4.37196] ((1 . 2) (3 . 6) (4 . 5) (5 . 9)) 6.629 {1/4:6} B:1 7.14438 [ 7.23291] ((1 . 2) (4 . 5) (5 . 9) (6 . 8) (7 . 19)) 9.872 {5/7:10} B:1 SIMILARITY (1/min{score1}): 0.6655 [and 1/min{score2}: 0.2353] [6336, 2980]: Comparing 1wot_A and 1jms_A, based on their crossing files. There are 8 (4 H + 4 S) secondary structure elements in 1wot_A, of which 6 satisfy the size requirements. There are 26 (18 H + 8 S) secondary structure elements in 1jms_A, of which 13 satisfy the size requirements. 1.20231 [ 2.60023] ((1 . 11) (3 . 13) (4 . 14) (5 . 15) (6 . 16)) 5.692 {0/7:10} B:0 1.50027 [ 3.25003] ((1 . 11) (3 . 13) (4 . 14) (5 . 15)) 3.936 {0/4:6} B:0 1.50153 [ 3.25015] ((1 . 11) (3 . 13) (5 . 15) (6 . 16)) 6.069 {0/4:6} B:0 3.34729 [ 3.60641] ((1 . 11) (3 . 13) (4 . 12) (5 . 15) (6 . 14)) 4.553 {2/6:10} B:2 SIMILARITY (1/min{score1}): 0.8317 [and 1/min{score2}: 0.3846] [6336, 2990]: Comparing 1wot_A and 1jn3_A, based on their crossing files. There are 8 (4 H + 4 S) secondary structure elements in 1wot_A, of which 6 satisfy the size requirements. There are 22 (13 H + 9 S) secondary structure elements in 1jn3_A, of which 13 satisfy the size requirements. 2.51593 [ 2.79589] ((1 . 8) (3 . 10) (4 . 12) (5 . 13) (6 . 16) (7 . 17)) 4.240 {2/8:15} B:0 SIMILARITY (1/min{score1}): 0.3975 [and 1/min{score2}: 0.3577] [6336, 3370]: Comparing 1wot_A and 1kny_A, based on their crossing files. There are 8 (4 H + 4 S) secondary structure elements in 1wot_A, of which 6 satisfy the size requirements. There are 16 (11 H + 5 S) secondary structure elements in 1kny_A, of which 10 satisfy the size requirements. 1.20088 [ 2.00019] ((1 . 1) (3 . 3) (4 . 4) (6 . 6) (7 . 8)) 4.468 {0/7:10} B:0 1.50010 [ 2.50002] ((1 . 1) (3 . 3) (4 . 4) (6 . 6)) 3.052 {0/4:6} B:0 1.50490 [ 2.50106] ((1 . 7) (3 . 8) (4 . 9) (5 . 10)) 8.125 {0/3:6} B:0 2.87919 [ 3.01513] ((1 . 1) (3 . 3) (4 . 4) (6 . 6) (7 . 7)) 4.630 {2/7:10} B:0 6.67100 [ 6.69945] ((1 . 1) (3 . 3) (5 . 7) (6 . 9)) 8.527 {2/3:6} B:0 SIMILARITY (1/min{score1}): 0.8327 [and 1/min{score2}: 0.5000] [6336, 3938]: Comparing 1wot_A and 1miw_A, based on their crossing files. There are 8 (4 H + 4 S) secondary structure elements in 1wot_A, of which 6 satisfy the size requirements. There are 37 (26 H + 11 S) secondary structure elements in 1miw_A, of which 10 satisfy the size requirements. 1.20098 [ 2.00021] ((1 . 1) (3 . 3) (4 . 4) (5 . 5) (6 . 9)) 4.589 {0/8:10} B:0 2.57764 [ 2.97322] ((1 . 1) (3 . 3) (5 . 5) (6 . 6)) 6.078 {1/4:6} B:0 5.01025 [ 5.07650] ((1 . 1) (4 . 6) (6 . 9) (7 . 12)) 8.399 {3/6:6} B:0 6.00587 [ 6.04473] ((1 . 1) (3 . 3) (4 . 4) (6 . 8)) 6.045 {3/5:6} B:0 1.46079 [ 2.07336] ((1 . 1) (3 . 3) (4 . 6) (5 . 5) (6 . 9)) 7.092 {1/8:10} B:1 SIMILARITY (1/min{score1}): 0.8327 [and 1/min{score2}: 0.4999] [6336, 4332]: Comparing 1wot_A and 1no5_A, based on their crossing files. There are 8 (4 H + 4 S) secondary structure elements in 1wot_A, of which 6 satisfy the size requirements. There are 9 (5 H + 4 S) secondary structure elements in 1no5_A, of which 8 satisfy the size requirements. 1.00006 [ 1.33336] ((1 . 1) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 8)) 1.968 {0/10:15} B:0 3.34008 [ 3.35448] ((1 . 1) (3 . 3) (4 . 2) (5 . 5) (6 . 6) (7 . 8)) 3.364 {4/12:15} B:1 SIMILARITY (1/min{score1}): 0.9999 [and 1/min{score2}: 0.7500] [6336, 4788]: Comparing 1wot_A and 1ou5_A, based on their crossing files. There are 8 (4 H + 4 S) secondary structure elements in 1wot_A, of which 6 satisfy the size requirements. There are 26 (20 H + 6 S) secondary structure elements in 1ou5_A, of which 9 satisfy the size requirements. 1.20083 [ 1.80024] ((1 . 2) (3 . 4) (4 . 5) (5 . 6) (6 . 8)) 4.399 {0/8:10} B:0 7.50304 [ 7.51518] ((1 . 1) (3 . 2) (5 . 4) (6 . 5)) 8.206 {3/4:6} B:0 SIMILARITY (1/min{score1}): 0.8328 [and 1/min{score2}: 0.5555] [6336, 5141]: Comparing 1wot_A and 1px5_A, based on their crossing files. There are 8 (4 H + 4 S) secondary structure elements in 1wot_A, of which 6 satisfy the size requirements. There are 21 (14 H + 7 S) secondary structure elements in 1px5_A, of which 12 satisfy the size requirements. 2.57809 [ 3.31054] ((1 . 3) (4 . 5) (5 . 7) (6 . 8)) 7.626 {1/4:6} B:0 6.67098 [ 6.73403] ((1 . 3) (4 . 9) (5 . 7) (6 . 8)) 7.702 {2/3:6} B:1 SIMILARITY (1/min{score1}): 0.3879 [and 1/min{score2}: 0.3021] [6336, 5589]: Comparing 1wot_A and 1r89_A, based on their crossing files. There are 8 (4 H + 4 S) secondary structure elements in 1wot_A, of which 6 satisfy the size requirements. There are 35 (19 H + 16 S) secondary structure elements in 1r89_A, of which 10 satisfy the size requirements. 1.20161 [ 2.00035] ((1 . 2) (3 . 4) (4 . 5) (5 . 6) (7 . 10)) 5.197 {0/7:10} B:0 1.20487 [ 2.00106] ((1 . 2) (3 . 4) (4 . 5) (5 . 6) (6 . 7)) 6.863 {0/8:10} B:0 2.73967 [ 2.81790] ((1 . 2) (3 . 4) (4 . 3) (5 . 6) (6 . 9) (7 . 10)) 5.372 {3/11:15} B:1 2.73995 [ 2.81816] ((1 . 2) (3 . 4) (4 . 9) (5 . 6) (6 . 8) (7 . 10)) 6.945 {3/11:15} B:1 SIMILARITY (1/min{score1}): 0.8322 [and 1/min{score2}: 0.4999] [6336, 5740]: Comparing 1wot_A and 1rzt_A, based on their crossing files. There are 8 (4 H + 4 S) secondary structure elements in 1wot_A, of which 6 satisfy the size requirements. There are 28 (16 H + 12 S) secondary structure elements in 1rzt_A, of which 15 satisfy the size requirements. 4.44733 [ 4.55177] ((1 . 11) (3 . 13) (4 . 15) (5 . 16) (6 . 19) (7 . 21)) 5.627 {4/9:15} B:0 1.51245 [ 3.75081] ((3 . 21) (4 . 23) (5 . 22) (7 . 27)) 10.276 {0/3:6} B:1 3.34735 [ 3.78145] ((1 . 11) (3 . 13) (4 . 20) (5 . 16) (6 . 19)) 5.661 {2/6:10} B:1 SIMILARITY (1/min{score1}): 0.6612 [and 1/min{score2}: 0.2666] [6336, 6281]: Comparing 1wot_A and 1vj7_A, based on their crossing files. There are 8 (4 H + 4 S) secondary structure elements in 1wot_A, of which 6 satisfy the size requirements. There are 23 (18 H + 5 S) secondary structure elements in 1vj7_A, of which 10 satisfy the size requirements. 1.50040 [ 2.50009] ((1 . 13) (4 . 17) (5 . 18) (6 . 21)) 4.342 {0/2:6} B:0 7.50303 [ 7.52307] ((1 . 13) (3 . 15) (4 . 17) (5 . 18)) 7.661 {3/4:6} B:0 7.50303 [ 7.52308] ((1 . 13) (3 . 15) (5 . 18) (6 . 17)) 7.882 {3/4:6} B:1 SIMILARITY (1/min{score1}): 0.6665 [and 1/min{score2}: 0.4000] [6336, 6336]: Comparing 1wot_A and 1wot_A, based on their crossing files. There are 8 (4 H + 4 S) secondary structure elements in 1wot_A, of which 6 satisfy the size requirements. There are 8 (4 H + 4 S) secondary structure elements in 1wot_A, of which 6 satisfy the size requirements. 1.00000 [ 1.00000] ((1 . 1) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7)) 0.000 {0/13:15} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] -------------------------------------------------------------------------------------------------------------------------