------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [5108, 3274]: Comparing 1pu6_A and 1kea_A, based on their crossing files. There are 13 (13 H + 0 S) secondary structure elements in 1pu6_A, of which 13 satisfy the size requirements. There are 15 (15 H + 0 S) secondary structure elements in 1kea_A, of which 13 satisfy the size requirements. 1.18202 [ 1.18202] ((1 . 1) (2 . 3) (3 . 4) (4 . 5) (5 . 6) (6 . 7) (8 . 8) (9 . 9) (10 . 10) (11 . 12) (13 . 13)) 3.072 {0/44:55} B:0 2.29350 [ 2.29350] ((1 . 1) (2 . 3) (3 . 4) (4 . 6) (6 . 7) (11 . 12)) 6.605 {2/13:15} B:0 2.62171 [ 2.62171] ((5 . 3) (6 . 4) (7 . 5) (8 . 6) (9 . 7)) 6.098 {1/9:10} B:0 2.62277 [ 2.62277] ((6 . 4) (7 . 5) (8 . 6) (9 . 7) (11 . 9)) 8.948 {1/9:10} B:0 2.70375 [ 2.70375] ((3 . 3) (6 . 7) (9 . 9) (10 . 10) (13 . 13)) 6.442 {1/6:10} B:0 SIMILARITY (1/min{score1}): 0.8460 [and 1/min{score2}: 0.8460] [5108, 3672]: Comparing 1pu6_A and 1lmz_A, based on their crossing files. There are 13 (13 H + 0 S) secondary structure elements in 1pu6_A, of which 13 satisfy the size requirements. There are 11 (9 H + 2 S) secondary structure elements in 1lmz_A, of which 9 satisfy the size requirements. 1.65772 [ 1.21518] ((2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 9) (9 . 10)) 4.624 {2/23:28} B:0 2.62185 [ 1.86328] ((5 . 2) (6 . 3) (7 . 4) (8 . 5) (9 . 6)) 6.753 {1/9:10} B:0 3.03541 [ 2.65505] ((2 . 2) (5 . 3) (6 . 4) (11 . 9) (13 . 10)) 9.653 {2/8:10} B:0 3.25053 [ 2.25159] ((4 . 1) (10 . 6) (11 . 7) (13 . 9)) 8.307 {0/4:6} B:0 3.25127 [ 2.25382] ((8 . 4) (10 . 6) (11 . 7) (13 . 9)) 10.344 {0/5:6} B:0 SIMILARITY (1/min{score1}): 0.6032 [and 1/min{score2}: 0.8229] [5108, 3820]: Comparing 1pu6_A and 1m3q_A, based on their crossing files. There are 13 (13 H + 0 S) secondary structure elements in 1pu6_A, of which 13 satisfy the size requirements. There are 23 (16 H + 7 S) secondary structure elements in 1m3q_A, of which 13 satisfy the size requirements. 1.18790 [ 1.18790] ((2 . 11) (3 . 12) (4 . 15) (5 . 16) (6 . 17) (7 . 18) (8 . 19) (9 . 20) (10 . 21) (11 . 22) (13 . 23)) 3.132 {2/45:55} B:0 2.05730 [ 2.05730] ((2 . 11) (3 . 12) (4 . 15) (5 . 16) (6 . 17) (9 . 19) (10 . 22) (13 . 23)) 5.386 {4/22:28} B:0 2.63421 [ 2.63421] ((2 . 11) (3 . 12) (6 . 17) (11 . 21) (13 . 23)) 5.229 {1/8:10} B:0 2.80961 [ 2.80961] ((2 . 11) (5 . 12) (6 . 18) (8 . 19) (9 . 20) (10 . 21) (11 . 22) (13 . 23)) 5.740 {6/22:28} B:0 3.25021 [ 3.25021] ((3 . 17) (5 . 19) (6 . 20) (8 . 21)) 6.591 {0/6:6} B:0 SIMILARITY (1/min{score1}): 0.8418 [and 1/min{score2}: 0.8418] [5108, 4003]: Comparing 1pu6_A and 1mpg_A, based on their crossing files. There are 13 (13 H + 0 S) secondary structure elements in 1pu6_A, of which 13 satisfy the size requirements. There are 20 (15 H + 5 S) secondary structure elements in 1mpg_A, of which 11 satisfy the size requirements. 1.18776 [ 1.00973] ((1 . 10) (2 . 11) (3 . 12) (4 . 13) (5 . 14) (6 . 15) (8 . 16) (9 . 17) (10 . 18) (11 . 19) (13 . 20)) 3.965 {2/46:55} B:0 2.66511 [ 2.51028] ((2 . 11) (6 . 12) (7 . 13) (8 . 14) (9 . 15) (13 . 18)) 7.622 {3/13:15} B:0 2.89355 [ 2.62981] ((1 . 10) (4 . 13) (5 . 14) (6 . 15) (11 . 20)) 5.798 {2/9:10} B:0 3.25040 [ 2.75066] ((3 . 15) (5 . 16) (6 . 17) (7 . 18)) 7.748 {0/5:6} B:0 3.25223 [ 2.75368] ((3 . 11) (6 . 14) (10 . 17) (11 . 18)) 11.905 {0/5:6} B:0 SIMILARITY (1/min{score1}): 0.8419 [and 1/min{score2}: 0.9904] [5108, 4042]: Comparing 1pu6_A and 1mun, based on their crossing files. There are 13 (13 H + 0 S) secondary structure elements in 1pu6_A, of which 13 satisfy the size requirements. There are 15 (15 H + 0 S) secondary structure elements in 1mun, of which 12 satisfy the size requirements. 1.18249 [ 1.09177] ((1 . 1) (2 . 3) (3 . 4) (4 . 5) (5 . 6) (6 . 7) (8 . 8) (9 . 9) (10 . 10) (11 . 11) (13 . 12)) 3.291 {1/44:55} B:0 1.30094 [ 1.20120] ((1 . 1) (2 . 3) (3 . 4) (4 . 5) (5 . 6) (6 . 7) (9 . 9) (10 . 10) (11 . 11) (13 . 12)) 3.216 {1/35:45} B:0 2.63432 [ 2.44332] ((5 . 3) (6 . 4) (7 . 5) (8 . 6) (9 . 7)) 5.984 {1/8:10} B:0 2.70371 [ 2.52915] ((3 . 3) (6 . 7) (9 . 9) (10 . 10) (13 . 12)) 6.237 {1/6:10} B:0 3.03440 [ 2.91557] ((3 . 3) (8 . 8) (9 . 9) (10 . 10) (13 . 12)) 5.992 {2/8:10} B:0 SIMILARITY (1/min{score1}): 0.8457 [and 1/min{score2}: 0.9159] [5108, 4242]: Comparing 1pu6_A and 1ngn_A, based on their crossing files. There are 13 (13 H + 0 S) secondary structure elements in 1pu6_A, of which 13 satisfy the size requirements. There are 10 (10 H + 0 S) secondary structure elements in 1ngn_A, of which 8 satisfy the size requirements. 1.86757 [ 1.18553] ((2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (9 . 8) (13 . 10)) 4.941 {1/14:21} B:0 2.63438 [ 1.73298] ((5 . 2) (6 . 3) (7 . 4) (8 . 5) (9 . 6)) 6.319 {1/8:10} B:0 3.25008 [ 2.00035] ((2 . 1) (3 . 2) (4 . 3) (5 . 6)) 5.197 {0/3:6} B:0 3.25044 [ 2.00190] ((2 . 1) (3 . 2) (4 . 3) (6 . 5)) 7.949 {0/3:6} B:0 3.36107 [ 2.37935] ((5 . 1) (6 . 2) (8 . 4) (9 . 5)) 7.579 {1/5:6} B:0 SIMILARITY (1/min{score1}): 0.5355 [and 1/min{score2}: 0.8435] [5108, 4764]: Comparing 1pu6_A and 1orn_A, based on their crossing files. There are 13 (13 H + 0 S) secondary structure elements in 1pu6_A, of which 13 satisfy the size requirements. There are 14 (14 H + 0 S) secondary structure elements in 1orn_A, of which 12 satisfy the size requirements. 1.20635 [ 1.12175] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (8 . 7) (9 . 8) (10 . 9) (11 . 10) (13 . 11)) 2.890 {3/47:55} B:0 1.33822 [ 1.24785] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (9 . 8) (10 . 9) (11 . 10) (13 . 11)) 2.770 {3/39:45} B:0 2.60029 [ 2.40037] ((5 . 2) (6 . 3) (7 . 4) (8 . 5) (9 . 6)) 6.069 {0/10:10} B:0 2.80307 [ 2.64865] ((1 . 1) (2 . 2) (3 . 3) (4 . 5) (6 . 6)) 7.046 {2/10:10} B:0 3.25055 [ 3.00070] ((3 . 6) (5 . 7) (6 . 8) (7 . 9)) 8.385 {0/5:6} B:0 SIMILARITY (1/min{score1}): 0.8289 [and 1/min{score2}: 0.8915] [5108, 5108]: Comparing 1pu6_A and 1pu6_A, based on their crossing files. There are 13 (13 H + 0 S) secondary structure elements in 1pu6_A, of which 13 satisfy the size requirements. There are 13 (13 H + 0 S) secondary structure elements in 1pu6_A, of which 13 satisfy the size requirements. 1.00000 [ 1.00000] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (10 . 10) (11 . 11) (12 . 12) (13 . 13)) 0.000 {0/68:78} B:0 2.61446 [ 2.61446] ((2 . 5) (3 . 6) (4 . 7) (5 . 8) (6 . 9)) 6.373 {1/10:10} B:0 2.61446 [ 2.61446] ((5 . 2) (6 . 3) (7 . 4) (8 . 5) (9 . 6)) 6.373 {1/10:10} B:0 3.36381 [ 3.36381] ((3 . 9) (4 . 10) (6 . 12) (7 . 13)) 13.229 {1/5:6} B:0 3.36381 [ 3.36381] ((9 . 3) (10 . 4) (12 . 6) (13 . 7)) 13.229 {1/5:6} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] -------------------------------------------------------------------------------------------------------------------------