------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [5722, 834]: Comparing 1rxw_A and 1dgs_A, based on their crossing files. There are 23 (16 H + 7 S) secondary structure elements in 1rxw_A, of which 6 satisfy the size requirements. There are 44 (25 H + 19 S) secondary structure elements in 1dgs_A, of which 13 satisfy the size requirements. 1.50165 [ 3.25016] ((18 . 39) (19 . 40) (20 . 42) (21 . 43)) 6.188 {0/6:6} B:0 4.02132 [ 4.37990] ((18 . 34) (19 . 35) (20 . 36) (23 . 40)) 13.028 {2/5:6} B:0 SIMILARITY (1/min{score1}): 0.6659 [and 1/min{score2}: 0.3077] [5722, 1552]: Comparing 1rxw_A and 1flo_A, based on their crossing files. There are 23 (16 H + 7 S) secondary structure elements in 1rxw_A, of which 6 satisfy the size requirements. There are 30 (20 H + 10 S) secondary structure elements in 1flo_A, of which 9 satisfy the size requirements. NO SIMILARITY! [5722, 1887]: Comparing 1rxw_A and 1go3_F, based on their crossing files. There are 23 (16 H + 7 S) secondary structure elements in 1rxw_A, of which 6 satisfy the size requirements. There are 7 (6 H + 1 S) secondary structure element in 1go3_F, of which 7 satisfy the size requirements. 1.50078 [ 1.75049] ((18 . 4) (19 . 5) (20 . 6) (21 . 7)) 5.132 {0/5:6} B:0 3.36840 [ 3.39629] ((18 . 3) (19 . 4) (20 . 5) (21 . 6)) 10.899 {2/6:6} B:0 1.50024 [ 1.75015] ((18 . 5) (19 . 4) (20 . 7) (21 . 6)) 3.809 {0/5:6} B:2 SIMILARITY (1/min{score1}): 0.6666 [and 1/min{score2}: 0.5714] [5722, 3866]: Comparing 1rxw_A and 1m6y_A, based on their crossing files. There are 23 (16 H + 7 S) secondary structure elements in 1rxw_A, of which 6 satisfy the size requirements. There are 23 (15 H + 8 S) secondary structure elements in 1m6y_A, of which 6 satisfy the size requirements. 1.50073 [ 1.50073] ((18 . 11) (19 . 12) (20 . 13) (21 . 15)) 5.037 {0/6:6} B:0 1.50844 [ 1.50844] ((18 . 11) (19 . 12) (20 . 13) (21 . 14)) 9.314 {0/6:6} B:0 3.38777 [ 3.38777] ((19 . 10) (21 . 12) (22 . 13) (23 . 15)) 21.402 {2/6:6} B:0 4.02023 [ 4.02023] ((18 . 10) (19 . 12) (20 . 13) (21 . 14)) 10.044 {2/5:6} B:0 5.01025 [ 5.01025] ((18 . 11) (19 . 13) (20 . 14) (21 . 15)) 8.486 {3/6:6} B:0 SIMILARITY (1/min{score1}): 0.6663 [and 1/min{score2}: 0.6663] [5722, 5722]: Comparing 1rxw_A and 1rxw_A, based on their crossing files. There are 23 (16 H + 7 S) secondary structure elements in 1rxw_A, of which 6 satisfy the size requirements. There are 23 (16 H + 7 S) secondary structure elements in 1rxw_A, of which 6 satisfy the size requirements. 1.00000 [ 1.00000] ((18 . 18) (19 . 19) (20 . 20) (21 . 21) (22 . 22) (23 . 23)) 0.000 {0/12:15} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [5722, 5905]: Comparing 1rxw_A and 1tfr, based on their crossing files. There are 23 (16 H + 7 S) secondary structure elements in 1rxw_A, of which 6 satisfy the size requirements. There are 24 (16 H + 8 S) secondary structure elements in 1tfr, of which 8 satisfy the size requirements. 1.50059 [ 2.00025] ((18 . 13) (19 . 18) (20 . 19) (21 . 20)) 4.782 {0/6:6} B:0 2.26934 [ 2.35964] ((18 . 13) (19 . 18) (20 . 19) (21 . 20) (23 . 23)) 7.966 {2/9:10} B:0 3.36744 [ 3.43687] ((19 . 18) (20 . 19) (21 . 20) (23 . 23)) 8.167 {2/6:6} B:0 3.36750 [ 3.43693] ((18 . 17) (19 . 18) (22 . 23) (23 . 24)) 8.455 {1/3:6} B:0 5.01026 [ 5.03186] ((18 . 17) (20 . 20) (22 . 23) (23 . 24)) 8.540 {1/2:6} B:0 SIMILARITY (1/min{score1}): 0.6664 [and 1/min{score2}: 0.4999] [5722, 6349]: Comparing 1rxw_A and 1xo1_A, based on their crossing files. There are 23 (16 H + 7 S) secondary structure elements in 1rxw_A, of which 6 satisfy the size requirements. There are 21 (15 H + 6 S) secondary structure elements in 1xo1_A, of which 7 satisfy the size requirements. 1.50028 [ 1.75018] ((18 . 14) (19 . 16) (20 . 17) (21 . 19)) 3.982 {0/5:6} B:0 1.52632 [ 1.76677] ((18 . 14) (19 . 16) (22 . 20) (23 . 21)) 12.435 {0/4:6} B:0 4.01984 [ 4.03635] ((18 . 14) (19 . 16) (21 . 17) (23 . 21)) 7.749 {2/5:6} B:0 SIMILARITY (1/min{score1}): 0.6665 [and 1/min{score2}: 0.5714] -------------------------------------------------------------------------------------------------------------------------