------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [810, 566]: Comparing 1de4_A and 1cd1_A, based on their crossing files. There are 24 (8 H + 16 S) secondary structure elements in 1de4_A, of which 13 satisfy the size requirements. There are 21 (4 H + 17 S) secondary structure elements in 1cd1_A, of which 11 satisfy the size requirements. 1.18240 [ 1.00096] ((1 . 1) (2 . 2) (3 . 3) (6 . 5) (7 . 6) (8 . 7) (9 . 8) (11 . 9) (12 . 10) (13 . 11) (14 . 12)) 2.798 {1/43:55} B:0 2.89390 [ 2.63027] ((1 . 1) (6 . 5) (7 . 6) (12 . 11) (14 . 12)) 7.595 {2/9:10} B:0 3.25018 [ 2.75030] ((3 . 2) (8 . 6) (9 . 7) (11 . 8)) 6.365 {0/2:6} B:0 3.25019 [ 2.75031] ((2 . 1) (8 . 6) (9 . 7) (11 . 8)) 6.412 {0/2:6} B:0 3.25021 [ 2.75034] ((2 . 1) (3 . 2) (4 . 3) (8 . 6)) 6.583 {0/2:6} B:0 SIMILARITY (1/min{score1}): 0.8457 [and 1/min{score2}: 0.9990] [810, 810]: Comparing 1de4_A and 1de4_A, based on their crossing files. There are 24 (8 H + 16 S) secondary structure elements in 1de4_A, of which 13 satisfy the size requirements. There are 24 (8 H + 16 S) secondary structure elements in 1de4_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) (11 . 11) (12 . 12) (13 . 13) (14 . 14)) 0.000 {0/63:78} B:0 1.08333 [ 1.08333] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (11 . 11) (12 . 12) (13 . 13) (14 . 14)) 0.000 {0/53:66} B:0 2.65812 [ 2.65812] ((7 . 1) (8 . 2) (9 . 3) (11 . 4) (13 . 5)) 7.925 {1/7:10} B:0 3.25008 [ 3.25008] ((1 . 2) (2 . 3) (3 . 4) (7 . 8)) 5.133 {0/2:6} B:0 3.25008 [ 3.25008] ((2 . 1) (3 . 2) (4 . 3) (8 . 7)) 5.133 {0/2:6} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [810, 2021]: Comparing 1de4_A and 1gzq_A, based on their crossing files. There are 24 (8 H + 16 S) secondary structure elements in 1de4_A, of which 13 satisfy the size requirements. There are 24 (7 H + 17 S) secondary structure elements in 1gzq_A, of which 13 satisfy the size requirements. 1.08365 [ 1.08365] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (6 . 5) (7 . 6) (8 . 7) (9 . 8) (11 . 9) (12 . 11) (13 . 12) (14 . 13)) 3.204 {0/50:66} B:0 3.25013 [ 3.25013] ((1 . 2) (2 . 3) (3 . 4) (7 . 7)) 5.844 {0/2:6} B:0 3.25018 [ 3.25018] ((3 . 2) (8 . 6) (9 . 7) (11 . 8)) 6.372 {0/2:6} B:0 3.25019 [ 3.25019] ((2 . 1) (8 . 6) (9 . 7) (11 . 8)) 6.388 {0/2:6} B:0 3.25019 [ 3.25019] ((2 . 1) (3 . 2) (4 . 3) (8 . 6)) 6.466 {0/2:6} B:0 SIMILARITY (1/min{score1}): 0.9228 [and 1/min{score2}: 0.9228] [810, 2185]: Comparing 1de4_A and 1hdm_A, based on their crossing files. There are 24 (8 H + 16 S) secondary structure elements in 1de4_A, of which 13 satisfy the size requirements. There are 14 (2 H + 12 S) secondary structure elements in 1hdm_A, of which 6 satisfy the size requirements. 2.16676 [ 1.00097] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6)) 3.995 {0/11:15} B:0 2.16680 [ 1.00136] ((7 . 1) (8 . 2) (9 . 3) (11 . 4) (12 . 5) (13 . 6)) 4.350 {0/10:15} B:0 2.16736 [ 1.00697] ((7 . 1) (8 . 2) (9 . 3) (11 . 4) (13 . 5) (14 . 6)) 6.555 {0/10:15} B:0 5.20970 [ 5.01022] ((7 . 2) (8 . 3) (9 . 4) (12 . 6)) 8.063 {2/4:6} B:0 5.20976 [ 5.01030] ((7 . 1) (8 . 3) (9 . 4) (12 . 6)) 9.052 {2/4:6} B:0 SIMILARITY (1/min{score1}): 0.4615 [and 1/min{score2}: 0.9990] [810, 2187]: Comparing 1de4_A and 1hdm_B, based on their crossing files. There are 24 (8 H + 16 S) secondary structure elements in 1de4_A, of which 13 satisfy the size requirements. There are 16 (4 H + 12 S) secondary structure elements in 1hdm_B, of which 8 satisfy the size requirements. 1.96992 [ 1.48550] ((7 . 1) (8 . 2) (9 . 3) (11 . 4) (12 . 5) (13 . 6) (14 . 8)) 3.768 {2/15:21} B:0 2.18329 [ 1.40029] ((7 . 1) (8 . 2) (9 . 3) (11 . 4) (12 . 5) (14 . 8)) 3.010 {1/11:15} B:0 2.60106 [ 1.60454] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (6 . 5)) 8.365 {0/6:10} B:0 3.36167 [ 2.38104] ((7 . 2) (8 . 3) (9 . 4) (13 . 7)) 9.814 {1/5:6} B:0 3.50418 [ 2.72591] ((1 . 2) (2 . 3) (3 . 4) (6 . 7)) 9.977 {1/4:6} B:0 SIMILARITY (1/min{score1}): 0.5076 [and 1/min{score2}: 0.7141] [810, 2337]: Comparing 1de4_A and 1hyr_C, based on their crossing files. There are 24 (8 H + 16 S) secondary structure elements in 1de4_A, of which 13 satisfy the size requirements. There are 22 (4 H + 18 S) secondary structure elements in 1hyr_C, of which 12 satisfy the size requirements. 1.18223 [ 1.09144] ((1 . 1) (2 . 3) (3 . 4) (4 . 5) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (11 . 10) (12 . 11) (14 . 12)) 3.662 {0/44:55} B:0 1.18298 [ 1.09238] ((1 . 1) (2 . 3) (3 . 4) (4 . 5) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (11 . 10) (12 . 11) (13 . 12)) 4.195 {1/43:55} B:0 1.30037 [ 1.20047] ((1 . 1) (2 . 3) (3 . 4) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (11 . 10) (12 . 11) (14 . 12)) 3.813 {0/35:45} B:0 3.25022 [ 3.00028] ((3 . 2) (8 . 7) (9 . 8) (11 . 9)) 6.691 {0/4:6} B:0 3.25075 [ 3.00095] ((1 . 1) (2 . 9) (3 . 10) (13 . 12)) 9.061 {0/4:6} B:0 SIMILARITY (1/min{score1}): 0.8459 [and 1/min{score2}: 0.9162] [810, 2854]: Comparing 1de4_A and 1jfm_A, based on their crossing files. There are 24 (8 H + 16 S) secondary structure elements in 1de4_A, of which 13 satisfy the size requirements. There are 11 (4 H + 7 S) secondary structure elements in 1jfm_A, of which 11 satisfy the size requirements. 1.18241 [ 1.00098] ((1 . 1) (2 . 2) (3 . 3) (6 . 4) (7 . 5) (8 . 6) (9 . 7) (11 . 8) (12 . 9) (13 . 10) (14 . 11)) 4.001 {0/41:55} B:0 1.30042 [ 1.10069] ((1 . 1) (2 . 2) (3 . 3) (6 . 4) (7 . 5) (8 . 6) (9 . 7) (11 . 8) (12 . 9) (13 . 10)) 3.939 {0/32:45} B:0 1.62801 [ 1.37995] ((1 . 1) (2 . 2) (6 . 4) (7 . 5) (8 . 6) (9 . 7) (12 . 10) (13 . 11)) 7.631 {0/19:28} B:0 1.83489 [ 1.79515] ((1 . 1) (2 . 2) (4 . 3) (6 . 4) (7 . 5) (8 . 6) (9 . 7) (11 . 8) (12 . 9) (13 . 10) (14 . 11)) 4.434 {7/40:55} B:0 3.25013 [ 2.75021] ((3 . 2) (8 . 5) (9 . 6) (11 . 7)) 5.832 {0/3:6} B:0 SIMILARITY (1/min{score1}): 0.8457 [and 1/min{score2}: 0.9990] [810, 3184]: Comparing 1de4_A and 1k5n_A, based on their crossing files. There are 24 (8 H + 16 S) secondary structure elements in 1de4_A, of which 13 satisfy the size requirements. There are 24 (7 H + 17 S) secondary structure elements in 1k5n_A, of which 11 satisfy the size requirements. 1.18238 [ 1.00093] ((1 . 1) (2 . 2) (3 . 3) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (11 . 10) (12 . 11) (13 . 12) (14 . 13)) 1.871 {1/41:55} B:0 1.30078 [ 1.10128] ((1 . 1) (2 . 2) (3 . 3) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (12 . 11) (13 . 12) (14 . 13)) 1.834 {1/35:45} B:0 1.44761 [ 1.22743] ((1 . 1) (2 . 2) (3 . 3) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (13 . 11) (14 . 12)) 5.726 {1/26:36} B:0 2.05839 [ 2.03058] ((1 . 1) (2 . 2) (4 . 3) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (11 . 10) (12 . 11) (13 . 12) (14 . 13)) 3.014 {8/40:55} B:0 2.60235 [ 2.20387] ((3 . 1) (4 . 2) (6 . 6) (9 . 7) (11 . 8)) 10.204 {0/4:10} B:0 SIMILARITY (1/min{score1}): 0.8458 [and 1/min{score2}: 0.9991] [810, 3261]: Comparing 1de4_A and 1kcg_C, based on their crossing files. There are 24 (8 H + 16 S) secondary structure elements in 1de4_A, of which 13 satisfy the size requirements. There are 12 (4 H + 8 S) secondary structure elements in 1kcg_C, of which 11 satisfy the size requirements. 1.18189 [ 1.00011] ((1 . 1) (2 . 2) (3 . 3) (6 . 5) (7 . 6) (8 . 7) (9 . 8) (11 . 9) (12 . 10) (13 . 11) (14 . 12)) 2.323 {0/41:55} B:0 1.62652 [ 1.37750] ((1 . 1) (2 . 2) (3 . 3) (6 . 5) (7 . 6) (8 . 7) (9 . 8) (13 . 12)) 6.430 {0/19:28} B:0 3.25008 [ 2.75014] ((2 . 1) (3 . 2) (4 . 3) (8 . 6)) 5.241 {0/2:6} B:0 3.25023 [ 2.75038] ((3 . 1) (4 . 2) (6 . 5) (14 . 11)) 6.763 {0/4:6} B:0 3.25051 [ 2.75084] ((4 . 2) (6 . 5) (11 . 7) (13 . 11)) 8.238 {0/4:6} B:0 SIMILARITY (1/min{score1}): 0.8461 [and 1/min{score2}: 0.9999] [810, 3703]: Comparing 1de4_A and 1lqv_A, based on their crossing files. There are 24 (8 H + 16 S) secondary structure elements in 1de4_A, of which 13 satisfy the size requirements. There are 12 (4 H + 8 S) secondary structure elements in 1lqv_A, of which 12 satisfy the size requirements. 1.08349 [ 1.00019] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (6 . 5) (7 . 6) (8 . 7) (9 . 8) (11 . 9) (12 . 10) (13 . 11) (14 . 12)) 2.674 {0/48:66} B:0 1.18192 [ 1.09104] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (6 . 5) (7 . 6) (8 . 7) (9 . 8) (11 . 9) (12 . 10) (13 . 11)) 2.561 {0/38:55} B:0 2.60281 [ 2.40357] ((3 . 1) (4 . 2) (6 . 5) (9 . 6) (11 . 7)) 10.669 {0/5:10} B:0 3.25018 [ 3.00023] ((2 . 1) (8 . 6) (9 . 7) (11 . 8)) 6.364 {0/2:6} B:0 3.25193 [ 3.00246] ((1 . 8) (2 . 9) (5 . 11) (6 . 12)) 11.486 {0/4:6} B:0 SIMILARITY (1/min{score1}): 0.9229 [and 1/min{score2}: 0.9998] [810, 6123]: Comparing 1de4_A and 1uvq_A, based on their crossing files. There are 24 (8 H + 16 S) secondary structure elements in 1de4_A, of which 13 satisfy the size requirements. There are 16 (2 H + 14 S) secondary structure elements in 1uvq_A, of which 7 satisfy the size requirements. 2.04613 [ 1.60479] ((1 . 1) (7 . 2) (8 . 3) (9 . 4) (11 . 5) (12 . 6) (14 . 7)) 6.679 {2/13:21} B:0 2.51980 [ 2.32894] ((1 . 1) (7 . 2) (8 . 3) (9 . 4) (11 . 5) (12 . 6) (13 . 7)) 7.890 {3/13:21} B:0 3.25263 [ 1.76665] ((9 . 2) (11 . 3) (13 . 6) (14 . 7)) 12.410 {0/4:6} B:0 3.50377 [ 2.63928] ((2 . 1) (3 . 2) (4 . 3) (6 . 7)) 8.528 {1/4:6} B:0 6.75894 [ 6.67464] ((7 . 3) (8 . 4) (9 . 5) (12 . 7)) 8.567 {2/3:6} B:0 SIMILARITY (1/min{score1}): 0.4887 [and 1/min{score2}: 0.6231] [810, 6125]: Comparing 1de4_A and 1uvq_B, based on their crossing files. There are 24 (8 H + 16 S) secondary structure elements in 1de4_A, of which 13 satisfy the size requirements. There are 17 (4 H + 13 S) secondary structure elements in 1uvq_B, of which 8 satisfy the size requirements. 1.85716 [ 1.14292] ((7 . 1) (8 . 2) (9 . 3) (11 . 4) (12 . 5) (13 . 6) (14 . 7)) 2.223 {0/16:21} B:0 1.86310 [ 1.16772] ((7 . 1) (8 . 2) (9 . 3) (11 . 4) (12 . 5) (13 . 6) (14 . 8)) 2.651 {1/16:21} B:0 2.16693 [ 1.33444] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6)) 5.127 {0/10:15} B:0 3.25194 [ 2.00826] ((7 . 3) (8 . 4) (12 . 7) (13 . 8)) 11.491 {0/5:6} B:0 3.25418 [ 2.01772] ((1 . 3) (2 . 4) (5 . 7) (6 . 8)) 13.930 {0/5:6} B:0 SIMILARITY (1/min{score1}): 0.5385 [and 1/min{score2}: 0.8750] [810, 6366]: Comparing 1de4_A and 1zag_A, based on their crossing files. There are 24 (8 H + 16 S) secondary structure elements in 1de4_A, of which 13 satisfy the size requirements. There are 22 (6 H + 16 S) secondary structure elements in 1zag_A, of which 13 satisfy the size requirements. 1.08373 [ 1.08373] ((1 . 1) (2 . 2) (3 . 3) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (11 . 10) (12 . 11) (13 . 12) (14 . 13)) 2.551 {1/52:66} B:0 1.85773 [ 1.85773] ((1 . 1) (2 . 2) (7 . 7) (8 . 8) (9 . 9) (12 . 12) (13 . 13)) 5.610 {0/13:21} B:0 2.60040 [ 2.60040] ((7 . 1) (8 . 2) (9 . 3) (12 . 5) (13 . 6)) 6.540 {0/6:10} B:0 2.60091 [ 2.60091] ((1 . 1) (5 . 5) (6 . 6) (12 . 11) (14 . 12)) 8.059 {0/9:10} B:0 2.60230 [ 2.60230] ((2 . 7) (8 . 8) (9 . 9) (12 . 12) (13 . 14)) 10.148 {0/8:10} B:0 SIMILARITY (1/min{score1}): 0.9227 [and 1/min{score2}: 0.9227] [810, 6569]: Comparing 1de4_A and 3fru_A, based on their crossing files. There are 24 (8 H + 16 S) secondary structure elements in 1de4_A, of which 13 satisfy the size requirements. There are 23 (7 H + 16 S) secondary structure elements in 3fru_A, of which 13 satisfy the size requirements. 1.08368 [ 1.08368] ((1 . 1) (2 . 2) (3 . 3) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (11 . 10) (12 . 11) (13 . 12) (14 . 13)) 2.111 {1/51:66} B:0 1.82432 [ 1.82432] ((1 . 1) (2 . 2) (4 . 3) (5 . 5) (6 . 6) (7 . 7) (8 . 8) (9 . 9) (11 . 10) (12 . 11) (13 . 12) (14 . 13)) 2.840 {9/51:66} B:0 3.25013 [ 3.25013] ((3 . 1) (4 . 2) (6 . 6) (14 . 12)) 5.882 {0/4:6} B:0 3.25015 [ 3.25015] ((2 . 1) (8 . 7) (9 . 8) (11 . 9)) 6.024 {0/2:6} B:0 3.25070 [ 3.25070] ((1 . 1) (9 . 2) (11 . 3) (14 . 11)) 8.898 {0/4:6} B:0 SIMILARITY (1/min{score1}): 0.9228 [and 1/min{score2}: 0.9228] -------------------------------------------------------------------------------------------------------------------------