------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [593, 248]: Comparing 1chm_A and 1az9, based on their crossing files. There are 35 (14 H + 21 S) secondary structure elements in 1chm_A, of which 14 satisfy the size requirements. There are 35 (17 H + 18 S) secondary structure elements in 1az9, of which 16 satisfy the size requirements. 1.22492 [ 1.33757] ((15 . 17) (16 . 18) (17 . 19) (18 . 20) (20 . 21) (23 . 24) (24 . 25) (25 . 26) (29 . 29) (30 . 30) (31 . 32) (32 . 33) (33 . 34)) 2.102 {4/41:78} B:0 3.50022 [ 4.00014] ((16 . 17) (17 . 19) (24 . 25) (25 . 26)) 7.015 {0/1:6} B:0 3.50031 [ 4.00021] ((24 . 17) (25 . 18) (29 . 21) (31 . 24)) 7.665 {0/1:6} B:0 3.50045 [ 4.00030] ((24 . 17) (25 . 18) (30 . 21) (32 . 24)) 8.411 {0/2:6} B:0 3.50096 [ 4.00064] ((25 . 17) (29 . 19) (31 . 21) (32 . 24)) 10.185 {0/0:6} B:0 SIMILARITY (1/min{score1}): 0.8164 [and 1/min{score2}: 0.7476] [593, 300]: Comparing 1chm_A and 1b6a, based on their crossing files. There are 35 (14 H + 21 S) secondary structure elements in 1chm_A, of which 14 satisfy the size requirements. There are 28 (9 H + 19 S) secondary structure elements in 1b6a, of which 16 satisfy the size requirements. 2.33356 [ 2.66682] ((15 . 4) (16 . 5) (20 . 9) (24 . 11) (25 . 12) (29 . 18)) 5.264 {0/4:15} B:0 2.80070 [ 3.20047] ((16 . 5) (17 . 6) (20 . 8) (24 . 11) (25 . 12)) 7.955 {0/2:10} B:0 3.16685 [ 3.46393] ((20 . 2) (24 . 4) (25 . 5) (30 . 9) (31 . 10)) 7.636 {1/4:10} B:0 3.50019 [ 4.00012] ((24 . 4) (25 . 5) (29 . 8) (32 . 10)) 6.753 {0/1:6} B:0 3.50123 [ 4.00083] ((15 . 3) (20 . 8) (24 . 11) (25 . 12)) 10.849 {0/1:6} B:0 SIMILARITY (1/min{score1}): 0.5618 [and 1/min{score2}: 0.5154] [593, 510]: Comparing 1chm_A and 1c22_A, based on their crossing files. There are 35 (14 H + 21 S) secondary structure elements in 1chm_A, of which 14 satisfy the size requirements. There are 21 (5 H + 16 S) secondary structure elements in 1c22_A, of which 19 satisfy the size requirements. 1.27326 [ 1.63007] ((15 . 1) (16 . 2) (17 . 5) (20 . 7) (23 . 8) (24 . 9) (25 . 10) (29 . 14) (30 . 15) (31 . 18) (32 . 19) (33 . 20)) 3.781 {3/32:66} B:0 1.67213 [ 1.87083] ((15 . 1) (16 . 2) (17 . 5) (20 . 7) (23 . 8) (24 . 9) (25 . 10) (29 . 12) (30 . 15) (31 . 18) (32 . 19) (33 . 20)) 4.188 {5/32:66} B:0 1.75221 [ 2.37589] ((15 . 1) (16 . 2) (17 . 5) (20 . 7) (23 . 8) (24 . 9) (25 . 10) (29 . 15)) 7.468 {0/7:28} B:0 1.76137 [ 2.37958] ((15 . 1) (16 . 2) (17 . 5) (20 . 7) (23 . 8) (24 . 9) (25 . 10) (33 . 17)) 11.271 {0/13:28} B:0 2.80287 [ 3.80115] ((20 . 5) (23 . 7) (25 . 9) (29 . 12) (32 . 14)) 11.344 {0/0:10} B:0 SIMILARITY (1/min{score1}): 0.7854 [and 1/min{score2}: 0.6135] [593, 593]: Comparing 1chm_A and 1chm_A, based on their crossing files. There are 35 (14 H + 21 S) secondary structure elements in 1chm_A, of which 14 satisfy the size requirements. There are 35 (14 H + 21 S) secondary structure elements in 1chm_A, of which 14 satisfy the size requirements. 1.00000 [ 1.00000] ((14 . 14) (15 . 15) (16 . 16) (17 . 17) (18 . 18) (20 . 20) (23 . 23) (24 . 24) (25 . 25) (29 . 29) (30 . 30) (31 . 31) (32 . 32) (33 . 33)) 0.000 {0/61:91} B:0 2.88413 [ 2.88413] ((14 . 14) (15 . 15) (16 . 16) (18 . 18) (25 . 24)) 5.196 {1/6:10} B:0 2.88413 [ 2.88413] ((14 . 14) (15 . 15) (16 . 16) (18 . 18) (24 . 25)) 5.196 {1/6:10} B:0 3.50031 [ 3.50031] ((15 . 24) (16 . 25) (20 . 30) (23 . 31)) 7.660 {0/1:6} B:0 3.50031 [ 3.50031] ((24 . 15) (25 . 16) (30 . 20) (31 . 23)) 7.660 {0/1:6} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [593, 5121]: Comparing 1chm_A and 1pv9_A, based on their crossing files. There are 35 (14 H + 21 S) secondary structure elements in 1chm_A, of which 14 satisfy the size requirements. There are 31 (12 H + 19 S) secondary structure elements in 1pv9_A, of which 16 satisfy the size requirements. 1.12152 [ 1.26139] ((15 . 13) (16 . 14) (17 . 16) (18 . 17) (20 . 18) (23 . 21) (24 . 22) (25 . 23) (29 . 27) (30 . 28) (31 . 29) (32 . 30) (33 . 31)) 1.699 {3/43:78} B:0 1.22355 [ 1.37255] ((15 . 13) (16 . 14) (17 . 16) (18 . 17) (20 . 18) (24 . 22) (25 . 23) (29 . 27) (30 . 28) (31 . 29) (32 . 30) (33 . 31)) 1.642 {3/38:66} B:0 2.80061 [ 3.20041] ((24 . 13) (25 . 14) (29 . 18) (30 . 19) (31 . 21)) 7.704 {0/1:10} B:0 2.80078 [ 3.20053] ((15 . 22) (16 . 23) (17 . 25) (20 . 27) (23 . 29)) 8.197 {0/4:10} B:0 3.16687 [ 3.46395] ((15 . 22) (16 . 23) (17 . 25) (20 . 28) (23 . 30)) 7.730 {1/4:10} B:0 SIMILARITY (1/min{score1}): 0.8916 [and 1/min{score2}: 0.7928] [593, 5490]: Comparing 1chm_A and 1qxy_A, based on their crossing files. There are 35 (14 H + 21 S) secondary structure elements in 1chm_A, of which 14 satisfy the size requirements. There are 19 (5 H + 14 S) secondary structure elements in 1qxy_A, of which 14 satisfy the size requirements. 1.75023 [ 1.75023] ((15 . 1) (16 . 2) (17 . 5) (20 . 7) (23 . 8) (24 . 9) (25 . 10) (29 . 14)) 4.243 {0/7:28} B:0 1.75045 [ 1.75045] ((15 . 1) (16 . 2) (17 . 5) (20 . 7) (23 . 8) (24 . 9) (25 . 10) (29 . 13)) 5.027 {0/7:28} B:0 2.80012 [ 2.80012] ((15 . 1) (16 . 2) (24 . 9) (25 . 10) (32 . 18)) 5.171 {0/3:10} B:0 2.80286 [ 2.80286] ((20 . 5) (23 . 7) (25 . 9) (29 . 12) (32 . 14)) 11.328 {0/0:10} B:0 3.50004 [ 3.50004] ((15 . 9) (16 . 10) (20 . 14) (23 . 18)) 4.530 {0/2:6} B:0 SIMILARITY (1/min{score1}): 0.7004 [and 1/min{score2}: 0.7004] [593, 6345]: Comparing 1chm_A and 1xgs_A, based on their crossing files. There are 35 (14 H + 21 S) secondary structure elements in 1chm_A, of which 14 satisfy the size requirements. There are 24 (7 H + 17 S) secondary structure elements in 1xgs_A, of which 14 satisfy the size requirements. 1.27333 [ 1.27333] ((15 . 1) (16 . 2) (17 . 4) (20 . 6) (23 . 7) (24 . 8) (25 . 9) (29 . 13) (30 . 14) (31 . 22) (32 . 23) (33 . 24)) 3.950 {3/32:66} B:0 1.75264 [ 1.75264] ((15 . 1) (16 . 2) (17 . 4) (20 . 6) (23 . 7) (24 . 8) (25 . 9) (29 . 14)) 7.812 {0/6:28} B:0 2.33425 [ 2.33425] ((15 . 8) (16 . 9) (17 . 11) (20 . 13) (23 . 23) (29 . 24)) 7.431 {0/4:15} B:0 2.80051 [ 2.80051] ((15 . 8) (16 . 9) (17 . 11) (20 . 13) (29 . 24)) 7.370 {0/1:10} B:0 2.80056 [ 2.80056] ((15 . 8) (16 . 9) (17 . 11) (20 . 13) (29 . 23)) 7.548 {0/1:10} B:0 SIMILARITY (1/min{score1}): 0.7853 [and 1/min{score2}: 0.7853] -------------------------------------------------------------------------------------------------------------------------