------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [2564, 1763]: Comparing 1iq8_A and 1g8f_A, based on their crossing files. There are 52 (27 H + 25 S) secondary structure elements in 1iq8_A, of which 7 satisfy the size requirements. There are 40 (22 H + 18 S) secondary structure elements in 1g8f_A, of which 12 satisfy the size requirements. 1.17186 [ 2.00104] ((44 . 3) (45 . 4) (49 . 9) (50 . 10) (51 . 11) (52 . 13)) 6.830 {0/14:15} B:0 1.40016 [ 2.40003] ((44 . 3) (45 . 4) (49 . 9) (50 . 10) (52 . 13)) 3.276 {0/10:10} B:0 1.75112 [ 3.00022] ((48 . 7) (49 . 9) (50 . 10) (51 . 11)) 6.302 {0/5:6} B:0 1.76545 [ 3.00310] ((45 . 1) (48 . 3) (51 . 6) (52 . 7)) 12.179 {0/3:6} B:0 2.03605 [ 3.06980] ((44 . 3) (45 . 4) (50 . 7) (52 . 9)) 8.765 {1/6:6} B:0 SIMILARITY (1/min{score1}): 0.8533 [and 1/min{score2}: 0.4997] [2564, 2564]: Comparing 1iq8_A and 1iq8_A, based on their crossing files. There are 52 (27 H + 25 S) secondary structure elements in 1iq8_A, of which 7 satisfy the size requirements. There are 52 (27 H + 25 S) secondary structure elements in 1iq8_A, of which 7 satisfy the size requirements. 1.00000 [ 1.00000] ((44 . 44) (45 . 45) (48 . 48) (49 . 49) (50 . 50) (51 . 51) (52 . 52)) 0.000 {0/18:21} B:0 4.45535 [ 4.45535] ((44 . 44) (45 . 45) (50 . 49) (51 . 51) (52 . 52)) 3.260 {4/9:10} B:0 4.45535 [ 4.45535] ((44 . 44) (45 . 45) (49 . 50) (51 . 51) (52 . 52)) 3.260 {4/9:10} B:0 2.24559 [ 2.24559] ((44 . 49) (45 . 51) (48 . 50) (49 . 52)) 7.550 {1/5:6} B:1 2.24559 [ 2.24559] ((49 . 44) (50 . 48) (51 . 45) (52 . 49)) 7.550 {1/5:6} B:1 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [2564, 2867]: Comparing 1iq8_A and 1jhd_A, based on their crossing files. There are 52 (27 H + 25 S) secondary structure elements in 1iq8_A, of which 7 satisfy the size requirements. There are 30 (15 H + 15 S) secondary structure elements in 1jhd_A, of which 11 satisfy the size requirements. 3.39581 [ 3.66685] ((44 . 7) (48 . 8) (51 . 11) (52 . 12)) 9.794 {1/3:6} B:0 4.03674 [ 4.20733] ((44 . 8) (45 . 10) (48 . 9) (50 . 12)) 10.077 {2/5:6} B:1 SIMILARITY (1/min{score1}): 0.2945 [and 1/min{score2}: 0.2727] [2564, 5231]: Comparing 1iq8_A and 1q7h_A, based on their crossing files. There are 52 (27 H + 25 S) secondary structure elements in 1iq8_A, of which 7 satisfy the size requirements. There are 17 (6 H + 11 S) secondary structure elements in 1q7h_A, of which 8 satisfy the size requirements. 1.00002 [ 1.14287] ((44 . 8) (45 . 9) (48 . 12) (49 . 13) (50 . 14) (51 . 15) (52 . 16)) 1.559 {0/18:21} B:0 1.75115 [ 2.00077] ((44 . 8) (45 . 9) (48 . 13) (51 . 15)) 6.338 {0/3:6} B:0 4.45535 [ 4.46300] ((44 . 8) (45 . 9) (50 . 13) (51 . 15) (52 . 16)) 3.967 {4/9:10} B:0 2.24543 [ 2.37920] ((49 . 8) (50 . 12) (51 . 9) (52 . 13)) 7.263 {1/5:6} B:1 2.24608 [ 2.37975] ((44 . 13) (45 . 15) (48 . 14) (49 . 16)) 8.280 {1/5:6} B:1 SIMILARITY (1/min{score1}): 0.9999 [and 1/min{score2}: 0.8750] [2564, 6168]: Comparing 1iq8_A and 1v47_A, based on their crossing files. There are 52 (27 H + 25 S) secondary structure elements in 1iq8_A, of which 7 satisfy the size requirements. There are 28 (13 H + 15 S) secondary structure elements in 1v47_A, of which 11 satisfy the size requirements. 2.03876 [ 2.84039] ((45 . 3) (49 . 4) (50 . 5) (52 . 7)) 10.448 {1/6:6} B:0 4.03654 [ 4.20716] ((48 . 4) (49 . 6) (50 . 7) (51 . 8)) 9.098 {2/5:6} B:0 1.75088 [ 2.75023] ((44 . 4) (49 . 7) (50 . 10) (51 . 9)) 5.928 {0/4:6} B:1 1.75275 [ 2.75071] ((44 . 4) (48 . 7) (50 . 10) (51 . 9)) 7.890 {0/2:6} B:1 2.64308 [ 3.13517] ((45 . 2) (48 . 1) (51 . 3) (52 . 4)) 12.404 {1/4:6} B:1 SIMILARITY (1/min{score1}): 0.7141 [and 1/min{score2}: 0.4545] [2564, 6236]: Comparing 1iq8_A and 1vhk_A, based on their crossing files. There are 52 (27 H + 25 S) secondary structure elements in 1iq8_A, of which 7 satisfy the size requirements. There are 19 (8 H + 11 S) secondary structure elements in 1vhk_A, of which 7 satisfy the size requirements. 1.40076 [ 1.40076] ((44 . 1) (48 . 3) (49 . 5) (50 . 6) (52 . 7)) 4.837 {0/9:10} B:0 1.75026 [ 1.75026] ((44 . 3) (45 . 4) (49 . 6) (50 . 7)) 4.369 {0/6:6} B:0 1.75104 [ 1.75104] ((48 . 1) (49 . 3) (50 . 5) (52 . 6)) 6.180 {0/6:6} B:0 1.75116 [ 1.75116] ((45 . 4) (48 . 5) (49 . 6) (50 . 7)) 6.351 {0/5:6} B:0 1.75012 [ 1.75012] ((48 . 1) (49 . 3) (50 . 7) (52 . 6)) 3.605 {0/6:6} B:1 SIMILARITY (1/min{score1}): 0.7139 [and 1/min{score2}: 0.7139] [2564, 6250]: Comparing 1iq8_A and 1vhy_A, based on their crossing files. There are 52 (27 H + 25 S) secondary structure elements in 1iq8_A, of which 7 satisfy the size requirements. There are 21 (8 H + 13 S) secondary structure elements in 1vhy_A, of which 6 satisfy the size requirements. 1.75136 [ 1.50216] ((48 . 1) (49 . 2) (50 . 4) (52 . 5)) 6.618 {0/6:6} B:0 1.75149 [ 1.50236] ((45 . 3) (48 . 4) (49 . 5) (50 . 6)) 6.765 {0/5:6} B:0 1.75284 [ 1.50449] ((48 . 1) (49 . 2) (51 . 3) (52 . 5)) 7.950 {0/5:6} B:0 1.75013 [ 1.50021] ((48 . 1) (49 . 2) (50 . 6) (52 . 5)) 3.690 {0/5:6} B:1 1.75024 [ 1.50039] ((44 . 2) (48 . 6) (49 . 5) (50 . 4)) 4.302 {0/5:6} B:2 SIMILARITY (1/min{score1}): 0.5714 [and 1/min{score2}: 0.6666] -------------------------------------------------------------------------------------------------------------------------