------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [798, 226]: Comparing 1dcq_A and 1awc_B, based on their crossing files. There are 16 (13 H + 3 S) secondary structure elements in 1dcq_A, of which 8 satisfy the size requirements. There are 10 (10 H + 0 S) secondary structure elements in 1awc_B, of which 10 satisfy the size requirements. 1.33352 [ 1.66676] ((9 . 5) (10 . 6) (11 . 7) (12 . 8) (13 . 9) (14 . 10)) 3.286 {0/2:15} B:0 1.36206 [ 1.48654] ((9 . 1) (10 . 2) (11 . 3) (12 . 4) (13 . 5) (14 . 6) (15 . 7) (16 . 8)) 2.297 {1/8:28} B:0 1.60038 [ 2.00020] ((9 . 5) (10 . 6) (11 . 7) (12 . 8) (13 . 10)) 4.502 {0/1:10} B:0 1.60090 [ 2.00046] ((10 . 5) (11 . 7) (12 . 8) (13 . 9) (14 . 10)) 5.575 {0/0:10} B:0 1.60106 [ 2.00054] ((9 . 2) (11 . 4) (13 . 6) (14 . 7) (15 . 8)) 5.812 {0/1:10} B:0 SIMILARITY (1/min{score1}): 0.9981 [and 1/min{score2}: 0.7994] [798, 351]: Comparing 1dcq_A and 1bd8, based on their crossing files. There are 16 (13 H + 3 S) secondary structure elements in 1dcq_A, of which 8 satisfy the size requirements. There are 10 (10 H + 0 S) secondary structure elements in 1bd8, of which 9 satisfy the size requirements. 1.14625 [ 1.28810] ((9 . 1) (11 . 2) (12 . 4) (13 . 5) (14 . 6) (15 . 7) (16 . 8)) 6.042 {0/6:21} B:0 1.14775 [ 1.28916] ((10 . 1) (11 . 4) (12 . 5) (13 . 6) (14 . 7) (15 . 8) (16 . 9)) 6.626 {0/1:21} B:0 1.33341 [ 1.50006] ((9 . 5) (10 . 6) (11 . 7) (12 . 8) (13 . 9) (14 . 10)) 2.652 {0/3:15} B:0 1.60002 [ 1.80001] ((12 . 4) (13 . 5) (14 . 6) (15 . 7) (16 . 8)) 2.102 {0/1:10} B:0 1.60062 [ 1.80043] ((10 . 5) (11 . 7) (12 . 8) (13 . 9) (14 . 10)) 5.072 {0/1:10} B:0 SIMILARITY (1/min{score1}): 0.9983 [and 1/min{score2}: 0.8879] [798, 798]: Comparing 1dcq_A and 1dcq_A, based on their crossing files. There are 16 (13 H + 3 S) secondary structure elements in 1dcq_A, of which 8 satisfy the size requirements. There are 16 (13 H + 3 S) secondary structure elements in 1dcq_A, of which 8 satisfy the size requirements. 1.00000 [ 1.00000] ((9 . 9) (10 . 10) (11 . 11) (12 . 12) (13 . 13) (14 . 14) (15 . 15) (16 . 16)) 0.000 {0/9:28} B:0 1.60207 [ 1.60207] ((10 . 9) (12 . 11) (13 . 12) (14 . 13) (16 . 15)) 6.868 {0/1:10} B:0 1.60207 [ 1.60207] ((9 . 10) (11 . 12) (12 . 13) (13 . 14) (15 . 16)) 6.868 {0/1:10} B:0 2.00007 [ 2.00007] ((13 . 9) (14 . 10) (15 . 11) (16 . 12)) 3.474 {0/1:6} B:0 2.00007 [ 2.00007] ((9 . 13) (10 . 14) (11 . 15) (12 . 16)) 3.474 {0/1:6} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [798, 2521]: Comparing 1dcq_A and 1ikn_D, based on their crossing files. There are 16 (13 H + 3 S) secondary structure elements in 1dcq_A, of which 8 satisfy the size requirements. There are 13 (13 H + 0 S) secondary structure elements in 1ikn_D, of which 10 satisfy the size requirements. 1.14318 [ 1.42874] ((9 . 4) (10 . 5) (11 . 7) (12 . 8) (13 . 9) (14 . 10) (16 . 12)) 3.359 {0/7:21} B:0 1.33658 [ 1.66833] ((11 . 1) (12 . 2) (13 . 3) (14 . 4) (15 . 5) (16 . 7)) 6.710 {0/0:15} B:0 1.60002 [ 2.00001] ((11 . 1) (13 . 2) (14 . 3) (15 . 4) (16 . 5)) 2.265 {0/2:10} B:0 1.60066 [ 2.00034] ((10 . 1) (11 . 2) (12 . 3) (13 . 4) (14 . 5)) 5.164 {0/0:10} B:0 1.60110 [ 2.00057] ((12 . 2) (13 . 3) (14 . 4) (15 . 5) (16 . 7)) 5.870 {0/0:10} B:0 SIMILARITY (1/min{score1}): 0.9985 [and 1/min{score2}: 0.7995] [798, 2656]: Comparing 1dcq_A and 1ixv_A, based on their crossing files. There are 16 (13 H + 3 S) secondary structure elements in 1dcq_A, of which 8 satisfy the size requirements. There are 16 (16 H + 0 S) secondary structure elements in 1ixv_A, of which 14 satisfy the size requirements. 1.00036 [ 1.75007] ((9 . 1) (10 . 2) (11 . 4) (12 . 5) (13 . 7) (14 . 8) (15 . 9) (16 . 10)) 3.123 {0/8:28} B:0 1.55679 [ 2.11916] ((9 . 9) (10 . 10) (11 . 11) (12 . 12) (13 . 13) (14 . 14) (16 . 16)) 3.707 {1/7:21} B:0 1.60103 [ 2.80019] ((9 . 5) (11 . 8) (13 . 10) (14 . 11) (15 . 12)) 5.762 {0/1:10} B:0 1.60105 [ 2.80020] ((9 . 2) (11 . 5) (13 . 8) (14 . 9) (15 . 10)) 5.794 {0/1:10} B:0 1.60109 [ 2.80020] ((9 . 2) (11 . 5) (13 . 8) (15 . 10) (16 . 11)) 5.844 {0/1:10} B:0 SIMILARITY (1/min{score1}): 0.9996 [and 1/min{score2}: 0.5714] [798, 3126]: Comparing 1dcq_A and 1k1a_A, based on their crossing files. There are 16 (13 H + 3 S) secondary structure elements in 1dcq_A, of which 8 satisfy the size requirements. There are 13 (13 H + 0 S) secondary structure elements in 1k1a_A, of which 13 satisfy the size requirements. 1.00026 [ 1.62506] ((9 . 5) (10 . 6) (11 . 7) (12 . 8) (13 . 9) (14 . 10) (15 . 11) (16 . 12)) 2.869 {0/7:28} B:0 1.36215 [ 1.75171] ((9 . 1) (10 . 2) (11 . 3) (12 . 4) (13 . 5) (14 . 6) (15 . 7) (16 . 8)) 3.013 {1/8:28} B:0 1.60008 [ 2.60002] ((9 . 9) (10 . 10) (11 . 11) (12 . 12) (14 . 13)) 2.998 {0/2:10} B:0 1.60034 [ 2.60008] ((9 . 9) (10 . 10) (11 . 11) (12 . 12) (13 . 13)) 4.363 {0/0:10} B:0 1.60045 [ 2.60011] ((9 . 5) (10 . 6) (11 . 7) (12 . 8) (13 . 10)) 4.693 {0/1:10} B:0 SIMILARITY (1/min{score1}): 0.9997 [and 1/min{score2}: 0.6154] [798, 3660]: Comparing 1dcq_A and 1lm5_A, based on their crossing files. There are 16 (13 H + 3 S) secondary structure elements in 1dcq_A, of which 8 satisfy the size requirements. There are 19 (11 H + 8 S) secondary structure elements in 1lm5_A, of which 12 satisfy the size requirements. 2.00028 [ 3.00008] ((11 . 9) (12 . 10) (13 . 12) (14 . 13)) 4.928 {0/1:6} B:0 2.00104 [ 3.00031] ((10 . 3) (11 . 4) (14 . 9) (16 . 12)) 6.830 {0/3:6} B:0 2.00168 [ 3.00050] ((11 . 4) (13 . 8) (14 . 9) (15 . 10)) 7.701 {0/1:6} B:0 10.00400 [10.02019] ((13 . 3) (14 . 4) (15 . 7) (16 . 8)) 5.012 {2/2:6} B:0 10.00400 [10.02019] ((9 . 9) (10 . 10) (11 . 12) (12 . 13)) 6.206 {1/1:6} B:0 SIMILARITY (1/min{score1}): 0.4999 [and 1/min{score2}: 0.3333] [798, 3661]: Comparing 1dcq_A and 1lm7_A, based on their crossing files. There are 16 (13 H + 3 S) secondary structure elements in 1dcq_A, of which 8 satisfy the size requirements. There are 26 (13 H + 13 S) secondary structure elements in 1lm7_A, of which 20 satisfy the size requirements. 2.00053 [ 5.00003] ((12 . 9) (13 . 10) (14 . 13) (15 . 14)) 5.781 {0/0:6} B:0 2.00055 [ 5.00004] ((10 . 9) (11 . 10) (12 . 13) (13 . 14)) 5.825 {0/0:6} B:0 2.00133 [ 5.00009] ((11 . 9) (12 . 10) (15 . 17) (16 . 18)) 7.275 {0/1:6} B:0 2.00141 [ 5.00009] ((12 . 9) (13 . 10) (14 . 13) (16 . 14)) 7.373 {0/0:6} B:0 2.00208 [ 5.00013] ((9 . 9) (10 . 10) (11 . 13) (12 . 14)) 8.126 {0/0:6} B:0 SIMILARITY (1/min{score1}): 0.6245 [and 1/min{score2}: 0.2500] [798, 4081]: Comparing 1dcq_A and 1myo, based on their crossing files. There are 16 (13 H + 3 S) secondary structure elements in 1dcq_A, of which 8 satisfy the size requirements. There are 8 (8 H + 0 S) secondary structure elements in 1myo, of which 8 satisfy the size requirements. 1.00056 [ 1.00056] ((9 . 1) (10 . 2) (11 . 3) (12 . 4) (13 . 5) (14 . 6) (15 . 7) (16 . 8)) 3.483 {0/9:28} B:0 1.60110 [ 1.60110] ((12 . 1) (13 . 2) (14 . 3) (15 . 4) (16 . 5)) 5.861 {0/0:10} B:0 1.60111 [ 1.60111] ((10 . 1) (12 . 3) (14 . 5) (15 . 6) (16 . 7)) 5.880 {0/1:10} B:0 1.60135 [ 1.60135] ((10 . 1) (12 . 3) (13 . 4) (14 . 5) (16 . 7)) 6.176 {0/1:10} B:0 1.60200 [ 1.60200] ((9 . 2) (11 . 4) (12 . 5) (13 . 6) (15 . 8)) 6.812 {0/1:10} B:0 SIMILARITY (1/min{score1}): 0.9994 [and 1/min{score2}: 0.9994] [798, 4097]: Comparing 1dcq_A and 1n11_A, based on their crossing files. There are 16 (13 H + 3 S) secondary structure elements in 1dcq_A, of which 8 satisfy the size requirements. There are 24 (24 H + 0 S) secondary structure elements in 1n11_A, of which 24 satisfy the size requirements. 1.00024 [ 3.00001] ((9 . 5) (10 . 6) (11 . 7) (12 . 8) (13 . 9) (14 . 10) (15 . 11) (16 . 12)) 2.805 {0/8:28} B:0 1.00025 [ 3.00001] ((9 . 9) (10 . 10) (11 . 11) (12 . 12) (13 . 13) (14 . 14) (15 . 15) (16 . 16)) 2.859 {0/5:28} B:0 1.00050 [ 3.00002] ((9 . 17) (10 . 18) (11 . 19) (12 . 20) (13 . 21) (14 . 22) (15 . 23) (16 . 24)) 3.378 {0/9:28} B:0 1.36213 [ 3.02236] ((9 . 13) (10 . 14) (11 . 15) (12 . 16) (13 . 17) (14 . 18) (15 . 19) (16 . 20)) 2.944 {1/8:28} B:0 1.36214 [ 3.02237] ((9 . 1) (10 . 2) (11 . 3) (12 . 4) (13 . 5) (14 . 6) (15 . 7) (16 . 8)) 2.967 {1/8:28} B:0 SIMILARITY (1/min{score1}): 0.9998 [and 1/min{score2}: 0.3333] [798, 4778]: Comparing 1dcq_A and 1ot8_A, based on their crossing files. There are 16 (13 H + 3 S) secondary structure elements in 1dcq_A, of which 8 satisfy the size requirements. There are 14 (14 H + 0 S) secondary structure elements in 1ot8_A, of which 14 satisfy the size requirements. 1.00018 [ 1.75003] ((9 . 3) (10 . 4) (11 . 5) (12 . 6) (13 . 7) (14 . 8) (15 . 9) (16 . 10)) 2.620 {0/9:28} B:0 1.14288 [ 2.00001] ((10 . 4) (11 . 5) (12 . 6) (13 . 7) (14 . 8) (15 . 9) (16 . 10)) 1.810 {0/5:21} B:0 1.36232 [ 1.85432] ((9 . 7) (10 . 8) (11 . 9) (12 . 10) (13 . 11) (14 . 12) (15 . 13) (16 . 14)) 3.747 {1/8:28} B:0 1.60054 [ 2.80010] ((12 . 1) (13 . 3) (14 . 4) (15 . 5) (16 . 6)) 4.899 {0/2:10} B:0 1.60077 [ 2.80014] ((9 . 6) (11 . 8) (13 . 10) (14 . 11) (15 . 12)) 5.360 {0/1:10} B:0 SIMILARITY (1/min{score1}): 0.9998 [and 1/min{score2}: 0.5714] [798, 4823]: Comparing 1dcq_A and 1oy3_D, based on their crossing files. There are 16 (13 H + 3 S) secondary structure elements in 1dcq_A, of which 8 satisfy the size requirements. There are 14 (14 H + 0 S) secondary structure elements in 1oy3_D, of which 13 satisfy the size requirements. 1.00030 [ 1.62507] ((9 . 1) (10 . 2) (11 . 4) (12 . 5) (13 . 6) (14 . 7) (15 . 9) (16 . 10)) 2.981 {0/5:28} B:0 1.33343 [ 2.16669] ((9 . 9) (10 . 10) (11 . 11) (12 . 12) (13 . 13) (14 . 14)) 2.750 {0/3:15} B:0 1.60002 [ 2.60000] ((10 . 10) (11 . 11) (12 . 12) (13 . 13) (14 . 14)) 2.145 {0/1:10} B:0 1.60043 [ 2.60010] ((11 . 4) (12 . 5) (13 . 6) (14 . 7) (16 . 9)) 4.642 {0/1:10} B:0 1.60044 [ 2.60010] ((9 . 9) (10 . 10) (11 . 11) (12 . 12) (13 . 14)) 4.661 {0/1:10} B:0 SIMILARITY (1/min{score1}): 0.9997 [and 1/min{score2}: 0.6154] [798, 5866]: Comparing 1dcq_A and 1sw6_A, based on their crossing files. There are 16 (13 H + 3 S) secondary structure elements in 1dcq_A, of which 8 satisfy the size requirements. There are 19 (15 H + 4 S) secondary structure elements in 1sw6_A, of which 17 satisfy the size requirements. 1.00084 [ 2.12509] ((9 . 5) (10 . 6) (11 . 7) (12 . 9) (13 . 12) (14 . 13) (15 . 17) (16 . 18)) 3.858 {0/6:28} B:0 1.33473 [ 2.83348] ((10 . 7) (11 . 12) (12 . 13) (13 . 17) (14 . 18) (15 . 19)) 5.431 {0/0:15} B:0 1.60009 [ 3.40001] ((11 . 3) (13 . 5) (14 . 6) (15 . 7) (16 . 9)) 3.094 {0/2:10} B:0 1.60031 [ 3.40003] ((11 . 3) (12 . 4) (13 . 5) (14 . 6) (15 . 7)) 4.264 {0/1:10} B:0 1.60171 [ 3.40018] ((9 . 9) (10 . 13) (11 . 17) (12 . 18) (13 . 19)) 6.548 {0/1:10} B:0 SIMILARITY (1/min{score1}): 0.9992 [and 1/min{score2}: 0.4706] [798, 6065]: Comparing 1dcq_A and 1uoh_A, based on their crossing files. There are 16 (13 H + 3 S) secondary structure elements in 1dcq_A, of which 8 satisfy the size requirements. There are 15 (15 H + 0 S) secondary structure elements in 1uoh_A, of which 14 satisfy the size requirements. 1.00023 [ 1.75004] ((9 . 6) (10 . 7) (11 . 8) (12 . 9) (13 . 10) (14 . 11) (15 . 12) (16 . 13)) 2.799 {0/8:28} B:0 1.26063 [ 1.81719] ((9 . 1) (10 . 2) (11 . 4) (12 . 5) (13 . 6) (14 . 7) (15 . 8) (16 . 9)) 3.060 {1/9:28} B:0 1.60006 [ 2.80001] ((9 . 10) (10 . 11) (11 . 12) (12 . 13) (14 . 15)) 2.882 {0/3:10} B:0 1.60041 [ 2.80008] ((9 . 10) (10 . 11) (11 . 12) (12 . 13) (13 . 15)) 4.578 {0/1:10} B:0 1.60043 [ 2.80008] ((9 . 1) (10 . 2) (11 . 4) (12 . 5) (13 . 7)) 4.645 {0/1:10} B:0 SIMILARITY (1/min{score1}): 0.9998 [and 1/min{score2}: 0.5714] [798, 6359]: Comparing 1dcq_A and 1ycs_B, based on their crossing files. There are 16 (13 H + 3 S) secondary structure elements in 1dcq_A, of which 8 satisfy the size requirements. There are 15 (10 H + 5 S) secondary structure elements in 1ycs_B, of which 7 satisfy the size requirements. 1.14299 [ 1.00020] ((9 . 1) (10 . 2) (11 . 3) (12 . 4) (13 . 5) (14 . 6) (16 . 8)) 2.696 {0/6:21} B:0 1.60098 [ 1.40147] ((12 . 1) (13 . 2) (14 . 3) (15 . 4) (16 . 5)) 5.702 {0/0:10} B:0 1.60101 [ 1.40151] ((11 . 2) (12 . 3) (13 . 4) (14 . 5) (15 . 6)) 5.740 {0/0:10} B:0 1.60148 [ 1.40220] ((9 . 2) (11 . 4) (12 . 5) (13 . 6) (15 . 8)) 6.314 {0/1:10} B:0 1.60189 [ 1.40282] ((10 . 1) (11 . 2) (12 . 3) (13 . 4) (14 . 5)) 6.716 {0/0:10} B:0 SIMILARITY (1/min{score1}): 0.8749 [and 1/min{score2}: 0.9998] -------------------------------------------------------------------------------------------------------------------------