------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [2591, 1051]: Comparing 1is2_A and 1e6i_A, based on their crossing files. There are 44 (33 H + 11 S) secondary structure elements in 1is2_A, of which 10 satisfy the size requirements. There are 7 (7 H + 0 S) secondary structure elements in 1e6i_A, of which 6 satisfy the size requirements. 2.50305 [ 1.51394] ((34 . 1) (36 . 4) (37 . 5) (38 . 6)) 10.574 {0/2:6} B:0 2.50739 [ 1.53322] ((34 . 1) (35 . 3) (36 . 4) (37 . 5)) 13.203 {0/3:6} B:0 2.97395 [ 2.57876] ((35 . 4) (36 . 5) (37 . 6) (38 . 7)) 8.943 {1/4:6} B:0 2.97908 [ 2.58662] ((34 . 1) (35 . 3) (36 . 4) (37 . 6)) 14.307 {1/4:6} B:0 10.00985 [10.00136] ((34 . 1) (36 . 4) (37 . 5) (39 . 6)) 12.710 {2/2:6} B:0 SIMILARITY (1/min{score1}): 0.3995 [and 1/min{score2}: 0.6605] [2591, 1246]: Comparing 1is2_A and 1eqf_A, based on their crossing files. There are 44 (33 H + 11 S) secondary structure elements in 1is2_A, of which 10 satisfy the size requirements. There are 15 (15 H + 0 S) secondary structure elements in 1eqf_A, of which 6 satisfy the size requirements. 2.50138 [ 1.50633] ((34 . 1) (35 . 3) (36 . 4) (39 . 7)) 8.665 {0/5:6} B:0 2.98594 [ 2.59708] ((36 . 1) (37 . 3) (38 . 4) (42 . 7)) 17.302 {1/4:6} B:0 10.00986 [10.00138] ((34 . 1) (36 . 4) (37 . 5) (39 . 6)) 13.134 {2/2:6} B:0 2.07542 [ 1.46666] ((34 . 6) (35 . 3) (36 . 4) (37 . 1) (39 . 7)) 9.260 {1/8:10} B:2 SIMILARITY (1/min{score1}): 0.4818 [and 1/min{score2}: 0.6818] [2591, 1247]: Comparing 1is2_A and 1eqf_A, based on their crossing files. There are 44 (33 H + 11 S) secondary structure elements in 1is2_A, of which 10 satisfy the size requirements. There are 15 (15 H + 0 S) secondary structure elements in 1eqf_A, of which 6 satisfy the size requirements. 2.50145 [ 1.50666] ((34 . 9) (35 . 11) (36 . 12) (39 . 15)) 8.774 {0/5:6} B:0 10.00987 [10.00138] ((34 . 9) (36 . 12) (37 . 13) (39 . 14)) 13.153 {1/1:6} B:0 2.72482 [ 2.14387] ((34 . 14) (35 . 11) (36 . 12) (39 . 15)) 7.998 {1/5:6} B:1 SIMILARITY (1/min{score1}): 0.3998 [and 1/min{score2}: 0.6637] [2591, 1415]: Comparing 1is2_A and 1f68_A, based on their crossing files. There are 44 (33 H + 11 S) secondary structure elements in 1is2_A, of which 10 satisfy the size requirements. There are 6 (6 H + 0 S) secondary structure elements in 1f68_A, of which 6 satisfy the size requirements. 10.00984 [10.00136] ((34 . 1) (36 . 4) (37 . 5) (39 . 6)) 12.512 {2/2:6} B:0 SIMILARITY (1/min{score1}): 0.0999 [and 1/min{score2}: 0.0999] [2591, 2590]: Comparing 1is2_A and 1is2_A, based on their crossing files. There are 44 (33 H + 11 S) secondary structure elements in 1is2_A, of which 10 satisfy the size requirements. There are 44 (33 H + 11 S) secondary structure elements in 1is2_A, of which 8 satisfy the size requirements. 2.00163 [ 1.60317] ((34 . 26) (36 . 28) (37 . 29) (39 . 31) (40 . 32)) 7.644 {0/5:10} B:0 2.37937 [ 2.18048] ((34 . 26) (36 . 28) (37 . 29) (38 . 31) (39 . 32)) 7.624 {1/5:10} B:0 2.50078 [ 2.00152] ((34 . 26) (36 . 28) (37 . 29) (38 . 30)) 7.512 {0/3:6} B:0 2.50085 [ 2.00167] ((34 . 26) (36 . 28) (37 . 29) (39 . 31)) 7.690 {0/1:6} B:0 2.50426 [ 2.00829] ((36 . 26) (37 . 28) (39 . 29) (41 . 30)) 11.501 {0/1:6} B:0 SIMILARITY (1/min{score1}): 0.4996 [and 1/min{score2}: 0.6238] [2591, 2591]: Comparing 1is2_A and 1is2_A, based on their crossing files. There are 44 (33 H + 11 S) secondary structure elements in 1is2_A, of which 10 satisfy the size requirements. There are 44 (33 H + 11 S) secondary structure elements in 1is2_A, of which 10 satisfy the size requirements. 1.00000 [ 1.00000] ((34 . 34) (35 . 35) (36 . 36) (37 . 37) (38 . 38) (39 . 39) (40 . 40) (41 . 41) (42 . 42) (44 . 44)) 0.000 {0/39:45} B:0 2.97517 [ 2.97517] ((36 . 34) (37 . 36) (39 . 37) (40 . 38)) 11.043 {1/4:6} B:0 2.97517 [ 2.97517] ((34 . 36) (36 . 37) (37 . 39) (38 . 40)) 11.043 {1/4:6} B:0 7.52355 [ 7.52355] ((34 . 36) (36 . 37) (37 . 39) (39 . 42)) 15.411 {3/4:6} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [2591, 2967]: Comparing 1is2_A and 1jm6_A, based on their crossing files. There are 44 (33 H + 11 S) secondary structure elements in 1is2_A, of which 10 satisfy the size requirements. There are 20 (13 H + 7 S) secondary structure elements in 1jm6_A, of which 7 satisfy the size requirements. 2.50318 [ 1.75922] ((34 . 3) (36 . 5) (37 . 6) (39 . 8)) 10.688 {0/3:6} B:0 2.50860 [ 1.77468] ((34 . 3) (36 . 5) (37 . 7) (39 . 8)) 13.718 {0/1:6} B:0 SIMILARITY (1/min{score1}): 0.3995 [and 1/min{score2}: 0.5684] [2591, 5016]: Comparing 1is2_A and 1pi1_A, based on their crossing files. There are 44 (33 H + 11 S) secondary structure elements in 1is2_A, of which 10 satisfy the size requirements. There are 10 (8 H + 2 S) secondary structure elements in 1pi1_A, of which 8 satisfy the size requirements. 2.00259 [ 1.60505] ((34 . 2) (36 . 5) (37 . 6) (38 . 7) (39 . 8)) 8.590 {0/6:10} B:0 2.50315 [ 2.00613] ((34 . 5) (36 . 6) (37 . 8) (39 . 10)) 10.659 {0/4:6} B:0 3.58449 [ 3.45215] ((34 . 1) (36 . 2) (37 . 5) (42 . 8)) 20.251 {1/3:6} B:0 5.07675 [ 5.03210] ((34 . 5) (36 . 6) (37 . 8) (38 . 9)) 10.786 {1/2:6} B:0 6.70002 [ 6.68077] ((34 . 2) (36 . 5) (37 . 6) (39 . 7)) 14.989 {2/3:6} B:0 SIMILARITY (1/min{score1}): 0.4994 [and 1/min{score2}: 0.6230] [2591, 5648]: Comparing 1is2_A and 1rj1_A, based on their crossing files. There are 44 (33 H + 11 S) secondary structure elements in 1is2_A, of which 10 satisfy the size requirements. There are 8 (8 H + 0 S) secondary structure elements in 1rj1_A, of which 8 satisfy the size requirements. 2.50236 [ 2.00460] ((34 . 4) (36 . 5) (37 . 7) (39 . 8)) 9.919 {0/0:6} B:0 2.50238 [ 2.00464] ((34 . 4) (36 . 6) (37 . 7) (39 . 8)) 9.938 {0/0:6} B:0 2.50319 [ 2.00622] ((34 . 4) (36 . 6) (37 . 7) (38 . 8)) 10.699 {0/0:6} B:0 SIMILARITY (1/min{score1}): 0.3996 [and 1/min{score2}: 0.4989] -------------------------------------------------------------------------------------------------------------------------