------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [155, 2]: Comparing 1am7_A and 153l, based on their crossing files. There are 8 (6 H + 2 S) secondary structure elements in 1am7_A, of which 8 satisfy the size requirements. There are 12 (10 H + 2 S) secondary structure elements in 153l, of which 7 satisfy the size requirements. 2.00019 [ 1.75029] ((1 . 5) (5 . 8) (7 . 9) (8 . 12)) 4.486 {0/5:6} B:0 2.20742 [ 2.03418] ((5 . 3) (6 . 4) (7 . 5) (8 . 8)) 6.502 {1/6:6} B:0 2.38440 [ 2.25161] ((4 . 5) (5 . 8) (7 . 9) (8 . 12)) 12.065 {1/5:6} B:0 5.03186 [ 5.01882] ((1 . 3) (5 . 8) (7 . 9) (8 . 12)) 8.581 {3/6:6} B:0 5.01318 [ 5.00779] ((1 . 12) (5 . 3) (6 . 4) (7 . 5) (8 . 8)) 7.938 {5/10:10} B:1 SIMILARITY (1/min{score1}): 0.5000 [and 1/min{score2}: 0.5713] [155, 155]: Comparing 1am7_A and 1am7_A, based on their crossing files. There are 8 (6 H + 2 S) secondary structure elements in 1am7_A, of which 8 satisfy the size requirements. There are 8 (6 H + 2 S) secondary structure elements in 1am7_A, of which 8 satisfy the size requirements. 1.00000 [ 1.00000] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (7 . 7) (8 . 8)) 0.000 {0/25:28} B:0 1.14286 [ 1.14286] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (7 . 7) (8 . 8)) 0.000 {0/18:21} B:0 2.00263 [ 2.00263] ((1 . 1) (5 . 4) (6 . 5) (8 . 8)) 8.624 {0/5:6} B:0 2.00263 [ 2.00263] ((1 . 1) (4 . 5) (5 . 6) (8 . 8)) 8.624 {0/5:6} B:0 3.37680 [ 3.37680] ((1 . 1) (4 . 4) (5 . 5) (6 . 7) (8 . 8)) 5.418 {3/9:10} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [155, 329]: Comparing 1am7_A and 1b9o_A, based on their crossing files. There are 8 (6 H + 2 S) secondary structure elements in 1am7_A, of which 8 satisfy the size requirements. There are 10 (7 H + 3 S) secondary structure elements in 1b9o_A, of which 7 satisfy the size requirements. 2.72552 [ 2.63981] ((2 . 4) (3 . 5) (4 . 7) (6 . 9)) 9.409 {1/4:6} B:0 5.03215 [ 5.01911] ((2 . 5) (3 . 4) (4 . 7) (6 . 9)) 11.113 {2/4:6} B:1 6.01865 [ 6.01104] ((3 . 4) (4 . 7) (5 . 1) (6 . 9)) 10.560 {3/5:6} B:1 SIMILARITY (1/min{score1}): 0.3669 [and 1/min{score2}: 0.3788] [155, 591]: Comparing 1am7_A and 1chk_A, based on their crossing files. There are 8 (6 H + 2 S) secondary structure elements in 1am7_A, of which 8 satisfy the size requirements. There are 19 (14 H + 5 S) secondary structure elements in 1chk_A, of which 15 satisfy the size requirements. 2.00972 [ 3.75149] ((1 . 3) (5 . 10) (7 . 12) (8 . 13)) 11.972 {0/5:6} B:0 3.34501 [ 3.46756] ((1 . 2) (2 . 4) (3 . 5) (4 . 7) (5 . 10) (7 . 12) (8 . 15)) 6.852 {5/15:21} B:0 4.06152 [ 4.61565] ((5 . 7) (6 . 8) (7 . 9) (8 . 10)) 9.327 {2/5:6} B:0 4.09467 [ 4.13543] ((1 . 2) (2 . 4) (3 . 5) (4 . 7) (5 . 10) (6 . 11) (7 . 12) (8 . 15)) 6.780 {9/22:28} B:0 4.46321 [ 4.65925] ((1 . 12) (3 . 4) (5 . 10) (6 . 11) (7 . 13)) 8.442 {4/9:10} B:1 SIMILARITY (1/min{score1}): 0.4976 [and 1/min{score2}: 0.2884] [155, 967]: Comparing 1am7_A and 1dxj_A, based on their crossing files. There are 8 (6 H + 2 S) secondary structure elements in 1am7_A, of which 8 satisfy the size requirements. There are 13 (13 H + 0 S) secondary structure elements in 1dxj_A, of which 11 satisfy the size requirements. 1.33368 [ 1.83347] ((1 . 4) (4 . 6) (5 . 8) (6 . 9) (7 . 11) (8 . 13)) 3.822 {0/13:15} B:0 2.00064 [ 2.75025] ((1 . 4) (4 . 8) (7 . 11) (8 . 13)) 6.048 {0/5:6} B:0 2.00180 [ 2.75069] ((4 . 8) (5 . 9) (7 . 11) (8 . 13)) 7.838 {0/5:6} B:0 2.20766 [ 2.83881] ((4 . 7) (5 . 8) (6 . 9) (8 . 12)) 7.048 {1/6:6} B:0 3.43775 [ 3.66721] ((1 . 4) (5 . 6) (7 . 8) (8 . 9)) 10.853 {2/6:6} B:0 SIMILARITY (1/min{score1}): 0.7498 [and 1/min{score2}: 0.5454] [155, 3137]: Comparing 1am7_A and 1k28_A, based on their crossing files. There are 8 (6 H + 2 S) secondary structure elements in 1am7_A, of which 8 satisfy the size requirements. There are 33 (16 H + 17 S) secondary structure elements in 1k28_A, of which 15 satisfy the size requirements. 1.68778 [ 3.01435] ((4 . 19) (5 . 21) (6 . 22) (7 . 25) (8 . 26)) 7.007 {1/9:10} B:0 2.20838 [ 3.78637] ((1 . 14) (5 . 21) (6 . 22) (8 . 26)) 8.189 {1/6:6} B:0 2.37910 [ 3.82382] ((4 . 19) (6 . 22) (7 . 25) (8 . 26)) 7.005 {1/5:6} B:0 2.37952 [ 3.82392] ((1 . 14) (4 . 19) (5 . 21) (6 . 22)) 7.900 {1/5:6} B:0 2.72465 [ 3.92306] ((1 . 14) (6 . 23) (7 . 24) (8 . 26)) 7.533 {1/4:6} B:0 SIMILARITY (1/min{score1}): 0.5925 [and 1/min{score2}: 0.3317] [155, 5080]: Comparing 1am7_A and 1pqm_A, based on their crossing files. There are 8 (6 H + 2 S) secondary structure elements in 1am7_A, of which 8 satisfy the size requirements. There are 14 (11 H + 3 S) secondary structure elements in 1pqm_A, of which 13 satisfy the size requirements. 1.68676 [ 2.62165] ((1 . 1) (4 . 5) (5 . 6) (6 . 7) (7 . 8)) 5.785 {1/9:10} B:0 2.00103 [ 3.25024] ((4 . 6) (5 . 8) (6 . 9) (8 . 13)) 6.815 {0/5:6} B:0 2.00279 [ 3.25065] ((4 . 8) (5 . 9) (6 . 10) (7 . 11)) 8.748 {0/3:6} B:0 2.00299 [ 3.25070] ((5 . 10) (6 . 11) (7 . 12) (8 . 14)) 8.902 {0/4:6} B:0 2.54950 [ 2.79614] ((1 . 1) (4 . 5) (5 . 6) (6 . 7) (7 . 8) (8 . 13)) 6.464 {3/12:15} B:0 SIMILARITY (1/min{score1}): 0.5929 [and 1/min{score2}: 0.3814] [155, 5323]: Comparing 1am7_A and 1qgi_A, based on their crossing files. There are 8 (6 H + 2 S) secondary structure elements in 1am7_A, of which 8 satisfy the size requirements. There are 19 (14 H + 5 S) secondary structure elements in 1qgi_A, of which 15 satisfy the size requirements. 2.00144 [ 3.75022] ((4 . 14) (5 . 15) (6 . 16) (8 . 18)) 7.410 {0/4:6} B:0 2.72699 [ 3.92385] ((1 . 3) (4 . 8) (5 . 9) (7 . 12)) 11.182 {1/4:6} B:0 3.43822 [ 4.23443] ((1 . 4) (5 . 13) (7 . 15) (8 . 16)) 11.711 {2/6:6} B:0 4.06172 [ 4.61579] ((2 . 11) (5 . 15) (7 . 16) (8 . 17)) 10.289 {2/5:6} B:0 4.06219 [ 4.61611] ((1 . 3) (4 . 8) (6 . 13) (8 . 14)) 11.805 {2/5:6} B:0 SIMILARITY (1/min{score1}): 0.6239 [and 1/min{score2}: 0.3333] [155, 5442]: Comparing 1am7_A and 1qsa_A, based on their crossing files. There are 8 (6 H + 2 S) secondary structure elements in 1am7_A, of which 8 satisfy the size requirements. There are 40 (40 H + 0 S) secondary structure elements in 1qsa_A, of which 10 satisfy the size requirements. 1.60010 [ 2.00005] ((1 . 32) (4 . 33) (5 . 35) (7 . 36) (8 . 39)) 3.185 {0/9:10} B:0 1.73244 [ 2.07265] ((1 . 32) (4 . 33) (5 . 35) (7 . 38) (8 . 39)) 5.409 {1/8:10} B:0 2.00005 [ 2.50002] ((1 . 32) (4 . 33) (5 . 35) (8 . 39)) 3.125 {0/5:6} B:0 2.00587 [ 2.50301] ((1 . 32) (4 . 35) (5 . 37) (7 . 38)) 10.546 {0/3:6} B:0 2.00593 [ 2.50305] ((5 . 33) (6 . 34) (7 . 35) (8 . 37)) 10.573 {0/5:6} B:0 SIMILARITY (1/min{score1}): 0.6250 [and 1/min{score2}: 0.5000] [155, 5462]: Comparing 1am7_A and 1qus_A, based on their crossing files. There are 8 (6 H + 2 S) secondary structure elements in 1am7_A, of which 8 satisfy the size requirements. There are 22 (15 H + 7 S) secondary structure elements in 1qus_A, of which 18 satisfy the size requirements. 1.73202 [ 3.61303] ((1 . 7) (4 . 13) (5 . 14) (7 . 21) (8 . 22)) 4.099 {1/8:10} B:0 2.00102 [ 4.50009] ((2 . 19) (3 . 20) (4 . 21) (5 . 22)) 6.798 {0/4:6} B:0 2.00399 [ 4.50035] ((1 . 6) (4 . 10) (5 . 13) (7 . 14)) 9.572 {0/4:6} B:0 2.20690 [ 4.52103] ((4 . 13) (5 . 14) (7 . 21) (8 . 22)) 4.201 {1/6:6} B:0 2.38237 [ 4.54384] ((1 . 7) (4 . 13) (5 . 14) (8 . 17)) 10.875 {1/5:6} B:0 SIMILARITY (1/min{score1}): 0.5774 [and 1/min{score2}: 0.2768] [155, 6580]: Comparing 1am7_A and 3lzt, based on their crossing files. There are 8 (6 H + 2 S) secondary structure elements in 1am7_A, of which 8 satisfy the size requirements. There are 10 (7 H + 3 S) secondary structure elements in 3lzt, of which 8 satisfy the size requirements. 2.38009 [ 2.38009] ((1 . 2) (4 . 7) (5 . 9) (6 . 10)) 8.773 {1/5:6} B:0 3.35477 [ 3.35477] ((1 . 2) (2 . 3) (3 . 4) (4 . 7) (7 . 9) (8 . 10)) 7.389 {4/12:15} B:0 3.43677 [ 3.43677] ((1 . 2) (3 . 4) (7 . 9) (8 . 10)) 7.651 {2/6:6} B:0 4.02548 [ 4.02548] ((1 . 2) (3 . 4) (5 . 7) (7 . 9) (8 . 10)) 6.744 {4/10:10} B:0 4.06115 [ 4.06115] ((2 . 3) (3 . 4) (5 . 7) (8 . 10)) 5.715 {2/5:6} B:0 SIMILARITY (1/min{score1}): 0.4998 [and 1/min{score2}: 0.4998] -------------------------------------------------------------------------------------------------------------------------