------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [6337, 1169]: Comparing 1wub_A and 1ei5_A, based on their crossing files. There are 16 (3 H + 13 S) secondary structure elements in 1wub_A, of which 13 satisfy the size requirements. There are 47 (16 H + 31 S) secondary structure elements in 1ei5_A, of which 8 satisfy the size requirements. 2.60066 [ 1.60282] ((10 . 32) (11 . 33) (12 . 34) (14 . 35) (16 . 37)) 7.421 {0/5:10} B:0 3.25013 [ 2.00055] ((10 . 33) (11 . 34) (12 . 35) (14 . 37)) 5.823 {0/2:6} B:0 3.25016 [ 2.00067] ((6 . 29) (10 . 34) (11 . 35) (12 . 37)) 6.132 {0/3:6} B:0 3.25016 [ 2.00071] ((5 . 29) (6 . 30) (10 . 35) (11 . 37)) 6.206 {0/4:6} B:0 3.25024 [ 2.00103] ((10 . 31) (11 . 32) (12 . 33) (14 . 37)) 6.818 {0/3:6} B:0 SIMILARITY (1/min{score1}): 0.6149 [and 1/min{score2}: 0.9943] [6337, 1170]: Comparing 1wub_A and 1ei5_A, based on their crossing files. There are 16 (3 H + 13 S) secondary structure elements in 1wub_A, of which 13 satisfy the size requirements. There are 47 (16 H + 31 S) secondary structure elements in 1ei5_A, of which 8 satisfy the size requirements. 1.62546 [ 1.00196] ((1 . 38) (5 . 39) (6 . 40) (10 . 43) (11 . 44) (12 . 45) (14 . 46) (16 . 47)) 4.767 {0/20:28} B:0 2.60015 [ 1.60065] ((6 . 38) (10 . 43) (11 . 44) (12 . 45) (14 . 46)) 5.136 {0/6:10} B:0 2.60026 [ 1.60113] ((5 . 39) (6 . 40) (10 . 45) (11 . 46) (12 . 47)) 5.899 {0/6:10} B:0 2.60027 [ 1.60117] ((5 . 39) (6 . 40) (9 . 45) (11 . 46) (12 . 47)) 5.956 {0/5:10} B:0 3.25015 [ 2.00066] ((3 . 38) (4 . 39) (9 . 45) (11 . 46)) 6.097 {0/4:6} B:0 SIMILARITY (1/min{score1}): 0.6152 [and 1/min{score2}: 0.9980] [6337, 2895]: Comparing 1wub_A and 1jiw_I, based on their crossing files. There are 16 (3 H + 13 S) secondary structure elements in 1wub_A, of which 13 satisfy the size requirements. There are 11 (3 H + 8 S) secondary structure elements in 1jiw_I, of which 9 satisfy the size requirements. 1.62734 [ 1.13201] ((1 . 2) (5 . 3) (6 . 5) (10 . 7) (11 . 8) (12 . 9) (14 . 10) (16 . 11)) 7.169 {0/20:28} B:0 3.25033 [ 2.25101] ((3 . 5) (5 . 7) (6 . 8) (9 . 11)) 7.408 {0/3:6} B:0 3.25037 [ 2.25112] ((10 . 2) (11 . 3) (12 . 5) (14 . 7)) 7.604 {0/3:6} B:0 3.25041 [ 2.25124] ((3 . 5) (4 . 7) (6 . 8) (9 . 11)) 7.804 {0/3:6} B:0 3.25061 [ 2.25183] ((11 . 2) (14 . 5) (15 . 6) (16 . 9)) 8.598 {0/4:6} B:0 SIMILARITY (1/min{score1}): 0.6150 [and 1/min{score2}: 0.8866] [6337, 2986]: Comparing 1wub_A and 1jmx_A, based on their crossing files. There are 16 (3 H + 13 S) secondary structure elements in 1wub_A, of which 13 satisfy the size requirements. There are 46 (16 H + 30 S) secondary structure elements in 1jmx_A, of which 9 satisfy the size requirements. 1.62617 [ 1.12852] ((1 . 18) (5 . 19) (6 . 20) (9 . 21) (11 . 22) (12 . 23) (14 . 24) (16 . 25)) 6.028 {0/19:28} B:0 2.60094 [ 1.80283] ((10 . 19) (11 . 20) (12 . 21) (14 . 22) (16 . 25)) 8.117 {0/6:10} B:0 2.60106 [ 1.80319] ((10 . 18) (11 . 19) (12 . 20) (14 . 21) (16 . 24)) 8.361 {0/6:10} B:0 3.25008 [ 2.25024] ((6 . 18) (9 . 21) (11 . 22) (12 . 23)) 5.177 {0/4:6} B:0 3.25009 [ 2.25028] ((11 . 18) (12 . 19) (14 . 20) (16 . 23)) 5.362 {0/3:6} B:0 SIMILARITY (1/min{score1}): 0.6150 [and 1/min{score2}: 0.8865] [6337, 3153]: Comparing 1wub_A and 1k3b_A, based on their crossing files. There are 16 (3 H + 13 S) secondary structure elements in 1wub_A, of which 13 satisfy the size requirements. There are 11 (1 H + 10 S) secondary structure elements in 1k3b_A, of which 9 satisfy the size requirements. 2.60212 [ 1.80636] ((4 . 2) (9 . 6) (11 . 7) (12 . 10) (14 . 11)) 9.944 {0/7:10} B:0 2.60237 [ 1.80712] ((5 . 2) (6 . 3) (10 . 6) (11 . 7) (14 . 11)) 10.229 {0/8:10} B:0 3.25013 [ 2.25040] ((6 . 2) (11 . 4) (12 . 5) (16 . 11)) 5.866 {0/5:6} B:0 3.25041 [ 2.25122] ((11 . 2) (12 . 3) (14 . 4) (16 . 7)) 7.778 {0/4:6} B:0 3.25047 [ 2.25143] ((5 . 4) (6 . 5) (9 . 8) (10 . 10)) 8.083 {0/3:6} B:0 SIMILARITY (1/min{score1}): 0.6150 [and 1/min{score2}: 0.8864] [6337, 3740]: Comparing 1wub_A and 1luq_A, based on their crossing files. There are 16 (3 H + 13 S) secondary structure elements in 1wub_A, of which 13 satisfy the size requirements. There are 9 (1 H + 8 S) secondary structure elements in 1luq_A, of which 9 satisfy the size requirements. 1.62547 [ 1.12641] ((1 . 1) (5 . 2) (6 . 3) (9 . 4) (11 . 5) (12 . 6) (14 . 7) (16 . 9)) 4.790 {0/18:28} B:0 2.16709 [ 1.50126] ((6 . 1) (9 . 4) (11 . 5) (12 . 6) (14 . 7) (16 . 9)) 5.780 {0/10:15} B:0 2.17022 [ 1.51063] ((5 . 1) (6 . 2) (10 . 5) (11 . 6) (12 . 7) (14 . 9)) 9.874 {0/11:15} B:0 2.60015 [ 1.80045] ((10 . 3) (11 . 4) (12 . 5) (14 . 6) (16 . 7)) 5.136 {0/5:10} B:0 2.60055 [ 1.80165] ((3 . 1) (4 . 2) (9 . 6) (11 . 7) (12 . 9)) 7.094 {0/7:10} B:0 SIMILARITY (1/min{score1}): 0.6152 [and 1/min{score2}: 0.8878] [6337, 4356]: Comparing 1wub_A and 1nqn_A, based on their crossing files. There are 16 (3 H + 13 S) secondary structure elements in 1wub_A, of which 13 satisfy the size requirements. There are 9 (1 H + 8 S) secondary structure elements in 1nqn_A, of which 9 satisfy the size requirements. 1.62541 [ 1.12624] ((1 . 1) (5 . 2) (6 . 3) (9 . 4) (11 . 5) (12 . 6) (14 . 7) (16 . 9)) 4.643 {0/19:28} B:0 2.16694 [ 1.50082] ((6 . 1) (9 . 4) (11 . 5) (12 . 6) (14 . 7) (16 . 9)) 5.199 {0/11:15} B:0 2.16804 [ 1.50413] ((6 . 1) (10 . 4) (11 . 5) (12 . 6) (14 . 7) (16 . 9)) 7.781 {0/10:15} B:0 2.17078 [ 1.51227] ((5 . 1) (6 . 2) (10 . 5) (11 . 6) (12 . 7) (14 . 9)) 10.238 {0/10:15} B:0 2.60047 [ 1.80142] ((3 . 1) (4 . 2) (9 . 6) (11 . 7) (12 . 9)) 6.832 {0/7:10} B:0 SIMILARITY (1/min{score1}): 0.6152 [and 1/min{score2}: 0.8879] [6337, 4438]: Comparing 1wub_A and 1nyc_A, based on their crossing files. There are 16 (3 H + 13 S) secondary structure elements in 1wub_A, of which 13 satisfy the size requirements. There are 10 (2 H + 8 S) secondary structure elements in 1nyc_A, of which 9 satisfy the size requirements. 2.60037 [ 1.80113] ((9 . 5) (10 . 6) (11 . 7) (12 . 8) (14 . 9)) 6.443 {0/6:10} B:0 3.25011 [ 2.25034] ((3 . 4) (4 . 5) (5 . 6) (6 . 7)) 5.632 {0/4:6} B:0 3.25015 [ 2.25044] ((5 . 1) (10 . 6) (11 . 7) (12 . 8)) 6.017 {0/3:6} B:0 3.25032 [ 2.25096] ((6 . 1) (9 . 4) (11 . 5) (14 . 8)) 7.327 {0/3:6} B:0 3.25032 [ 2.25097] ((10 . 7) (11 . 8) (12 . 9) (14 . 10)) 7.341 {0/3:6} B:0 SIMILARITY (1/min{score1}): 0.6148 [and 1/min{score2}: 0.8853] [6337, 4653]: Comparing 1wub_A and 1oh1_A, based on their crossing files. There are 16 (3 H + 13 S) secondary structure elements in 1wub_A, of which 13 satisfy the size requirements. There are 9 (1 H + 8 S) secondary structure elements in 1oh1_A, of which 9 satisfy the size requirements. 3.25030 [ 2.25091] ((5 . 1) (9 . 5) (11 . 6) (12 . 7)) 7.224 {0/3:6} B:0 3.25035 [ 2.25106] ((6 . 1) (9 . 3) (11 . 4) (14 . 7)) 7.511 {0/3:6} B:0 3.25041 [ 2.25124] ((3 . 1) (4 . 3) (10 . 8) (11 . 9)) 7.796 {0/4:6} B:0 3.25045 [ 2.25136] ((3 . 3) (4 . 4) (6 . 6) (10 . 9)) 7.992 {0/5:6} B:0 3.25046 [ 2.25137] ((3 . 3) (4 . 4) (6 . 6) (9 . 9)) 8.000 {0/4:6} B:0 SIMILARITY (1/min{score1}): 0.4614 [and 1/min{score2}: 0.6661] [6337, 4966]: Comparing 1wub_A and 1pby_A, based on their crossing files. There are 16 (3 H + 13 S) secondary structure elements in 1wub_A, of which 13 satisfy the size requirements. There are 43 (15 H + 28 S) secondary structure elements in 1pby_A, of which 8 satisfy the size requirements. 1.62607 [ 1.00458] ((1 . 16) (5 . 17) (6 . 18) (9 . 19) (11 . 20) (12 . 21) (14 . 22) (16 . 23)) 5.896 {0/19:28} B:0 2.60086 [ 1.60367] ((10 . 16) (11 . 17) (12 . 18) (14 . 19) (16 . 22)) 7.931 {0/6:10} B:0 2.60092 [ 1.60394] ((10 . 17) (11 . 18) (12 . 19) (14 . 20) (16 . 23)) 8.071 {0/6:10} B:0 3.25008 [ 2.00036] ((6 . 18) (9 . 21) (11 . 22) (12 . 23)) 5.239 {0/3:6} B:0 3.25009 [ 2.00039] ((11 . 16) (12 . 17) (14 . 18) (16 . 21)) 5.351 {0/3:6} B:0 SIMILARITY (1/min{score1}): 0.6150 [and 1/min{score2}: 0.9961] [6337, 5828]: Comparing 1wub_A and 1smp_I, based on their crossing files. There are 16 (3 H + 13 S) secondary structure elements in 1wub_A, of which 13 satisfy the size requirements. There are 10 (2 H + 8 S) secondary structure elements in 1smp_I, of which 9 satisfy the size requirements. 2.60138 [ 1.80414] ((10 . 3) (11 . 4) (12 . 6) (14 . 7) (16 . 10)) 8.925 {0/5:10} B:0 2.60207 [ 1.80621] ((5 . 2) (10 . 7) (11 . 8) (12 . 9) (14 . 10)) 9.883 {0/5:10} B:0 3.25015 [ 2.25046] ((6 . 2) (10 . 6) (11 . 7) (12 . 8)) 6.073 {0/3:6} B:0 3.25016 [ 2.25048] ((10 . 4) (11 . 6) (12 . 7) (14 . 8)) 6.163 {0/2:6} B:0 3.25018 [ 2.25055] ((5 . 3) (10 . 8) (11 . 9) (12 . 10)) 6.356 {0/3:6} B:0 SIMILARITY (1/min{score1}): 0.6148 [and 1/min{score2}: 0.8853] [6337, 6337]: Comparing 1wub_A and 1wub_A, based on their crossing files. There are 16 (3 H + 13 S) secondary structure elements in 1wub_A, of which 13 satisfy the size requirements. There are 16 (3 H + 13 S) secondary structure elements in 1wub_A, of which 13 satisfy the size requirements. 1.00000 [ 1.00000] ((1 . 1) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (8 . 8) (9 . 9) (10 . 10) (11 . 11) (12 . 12) (14 . 14) (15 . 15) (16 . 16)) 0.000 {0/64:78} B:0 2.60054 [ 2.60054] ((8 . 8) (10 . 9) (14 . 14) (15 . 15) (16 . 16)) 7.075 {0/8:10} B:0 2.60054 [ 2.60054] ((8 . 8) (9 . 10) (14 . 14) (15 . 15) (16 . 16)) 7.075 {0/8:10} B:0 2.60054 [ 2.60054] ((1 . 6) (5 . 9) (6 . 11) (9 . 12) (12 . 16)) 7.078 {0/4:10} B:0 2.60099 [ 2.60099] ((6 . 1) (9 . 4) (10 . 5) (11 . 6) (16 . 12)) 8.227 {0/6:10} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] -------------------------------------------------------------------------------------------------------------------------