------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [1947, 41]: Comparing 1gtm_A and 1a4i_A, based on their crossing files. There are 32 (18 H + 14 S) secondary structure elements in 1gtm_A, of which 9 satisfy the size requirements. There are 21 (12 H + 9 S) secondary structure elements in 1a4i_A, of which 7 satisfy the size requirements. 1.80114 [ 1.40242] ((6 . 3) (7 . 4) (8 . 5) (10 . 6) (12 . 8)) 6.465 {0/1:10} B:0 2.25028 [ 1.75059] ((6 . 3) (8 . 5) (10 . 6) (12 . 8)) 5.375 {0/1:6} B:0 2.25957 [ 1.77013] ((2 . 4) (3 . 5) (6 . 7) (7 . 8)) 13.024 {0/2:6} B:0 1.50471 [ 1.17659] ((3 . 5) (4 . 3) (7 . 4) (8 . 7) (10 . 6) (12 . 8)) 8.044 {0/2:15} B:2 1.80388 [ 1.40820] ((2 . 4) (3 . 5) (4 . 3) (8 . 7) (10 . 6)) 8.784 {0/1:10} B:2 SIMILARITY (1/min{score1}): 0.6646 [and 1/min{score2}: 0.8499] [1947, 258]: Comparing 1gtm_A and 1b0a_A, based on their crossing files. There are 32 (18 H + 14 S) secondary structure elements in 1gtm_A, of which 9 satisfy the size requirements. There are 22 (10 H + 12 S) secondary structure elements in 1b0a_A, of which 7 satisfy the size requirements. 2.25867 [ 1.76826] ((2 . 4) (3 . 6) (6 . 8) (7 . 9)) 12.705 {0/0:6} B:0 2.25081 [ 1.75172] ((2 . 2) (3 . 6) (4 . 3) (8 . 8)) 7.014 {0/0:6} B:1 1.80154 [ 1.40326] ((2 . 2) (3 . 6) (4 . 3) (8 . 8) (10 . 7)) 6.964 {0/1:10} B:2 SIMILARITY (1/min{score1}): 0.5551 [and 1/min{score2}: 0.7126] [1947, 505]: Comparing 1gtm_A and 1c1d_A, based on their crossing files. There are 32 (18 H + 14 S) secondary structure elements in 1gtm_A, of which 9 satisfy the size requirements. There are 27 (16 H + 11 S) secondary structure elements in 1c1d_A, of which 9 satisfy the size requirements. 1.13209 [ 1.13209] ((1 . 1) (3 . 2) (4 . 3) (6 . 4) (7 . 5) (8 . 6) (10 . 8) (12 . 10)) 7.188 {0/17:28} B:0 1.28613 [ 1.28613] ((3 . 2) (4 . 3) (6 . 4) (7 . 5) (8 . 6) (10 . 8) (12 . 10)) 3.913 {0/14:21} B:0 1.80103 [ 1.80103] ((1 . 1) (7 . 5) (8 . 6) (10 . 8) (12 . 10)) 6.307 {0/7:10} B:0 2.25548 [ 2.25548] ((6 . 2) (8 . 4) (10 . 5) (12 . 8)) 11.318 {0/4:6} B:0 2.25640 [ 2.25640] ((3 . 4) (6 . 6) (7 . 8) (10 . 10)) 11.769 {0/4:6} B:0 SIMILARITY (1/min{score1}): 0.8833 [and 1/min{score2}: 0.8833] [1947, 1116]: Comparing 1gtm_A and 1edz_A, based on their crossing files. There are 32 (18 H + 14 S) secondary structure elements in 1gtm_A, of which 9 satisfy the size requirements. There are 21 (10 H + 11 S) secondary structure elements in 1edz_A, of which 8 satisfy the size requirements. 1.80161 [ 1.60230] ((6 . 3) (7 . 4) (8 . 5) (10 . 6) (12 . 8)) 7.051 {0/2:10} B:0 2.25054 [ 2.00077] ((6 . 3) (7 . 4) (8 . 5) (10 . 6)) 6.347 {0/1:6} B:0 2.26109 [ 2.01573] ((2 . 4) (3 . 5) (6 . 7) (7 . 8)) 13.516 {0/2:6} B:0 2.25068 [ 2.00097] ((3 . 5) (4 . 3) (8 . 7) (10 . 6)) 6.721 {0/2:6} B:2 10.00128 [10.00081] ((4 . 5) (6 . 7) (7 . 4) (8 . 3) (10 . 6) (12 . 8)) 8.245 {3/3:15} B:2 SIMILARITY (1/min{score1}): 0.5551 [and 1/min{score2}: 0.6241] [1947, 1947]: Comparing 1gtm_A and 1gtm_A, based on their crossing files. There are 32 (18 H + 14 S) secondary structure elements in 1gtm_A, of which 9 satisfy the size requirements. There are 32 (18 H + 14 S) secondary structure elements in 1gtm_A, of which 9 satisfy the size requirements. 1.00000 [ 1.00000] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (6 . 6) (7 . 7) (8 . 8) (10 . 10) (12 . 12)) 0.000 {0/26:36} B:0 2.43038 [ 2.43038] ((2 . 1) (7 . 7) (8 . 8) (10 . 10) (12 . 12)) 4.319 {2/9:10} B:0 2.43038 [ 2.43038] ((1 . 2) (7 . 7) (8 . 8) (10 . 10) (12 . 12)) 4.319 {2/9:10} B:0 3.40205 [ 3.40205] ((4 . 3) (7 . 7) (8 . 8) (10 . 10) (12 . 12)) 3.177 {3/9:10} B:0 3.40205 [ 3.40205] ((3 . 4) (7 . 7) (8 . 8) (10 . 10) (12 . 12)) 3.177 {3/9:10} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [1947, 2015]: Comparing 1gtm_A and 1gz3_A, based on their crossing files. There are 32 (18 H + 14 S) secondary structure elements in 1gtm_A, of which 9 satisfy the size requirements. There are 42 (28 H + 14 S) secondary structure elements in 1gz3_A, of which 17 satisfy the size requirements. 1.80064 [ 3.40010] ((3 . 9) (7 . 13) (8 . 15) (10 . 17) (12 . 19)) 5.600 {0/7:10} B:0 2.25111 [ 4.25016] ((1 . 7) (2 . 8) (7 . 13) (8 . 15)) 7.586 {0/1:6} B:0 2.25188 [ 4.25028] ((1 . 1) (2 . 3) (10 . 11) (12 . 13)) 8.662 {0/5:6} B:0 2.25260 [ 4.25039] ((1 . 1) (2 . 3) (7 . 6) (12 . 13)) 9.387 {0/3:6} B:0 3.49674 [ 4.60611] ((2 . 13) (3 . 15) (7 . 17) (8 . 18)) 12.865 {1/3:6} B:0 SIMILARITY (1/min{score1}): 0.7749 [and 1/min{score2}: 0.4116] [1947, 2269]: Comparing 1gtm_A and 1hrd_A, based on their crossing files. There are 32 (18 H + 14 S) secondary structure elements in 1gtm_A, of which 9 satisfy the size requirements. There are 32 (20 H + 12 S) secondary structure elements in 1hrd_A, of which 13 satisfy the size requirements. 1.00035 [ 1.44456] ((1 . 2) (2 . 5) (3 . 6) (4 . 7) (6 . 8) (7 . 9) (8 . 10) (10 . 11) (12 . 13)) 3.092 {0/23:36} B:0 2.25369 [ 3.25123] ((6 . 10) (7 . 11) (8 . 12) (10 . 13)) 10.254 {0/4:6} B:0 2.25452 [ 3.25150] ((1 . 1) (2 . 2) (4 . 6) (6 . 7)) 10.789 {0/0:6} B:0 2.54705 [ 3.36375] ((1 . 9) (3 . 10) (6 . 12) (7 . 13)) 13.164 {1/5:6} B:0 3.40205 [ 3.60638] ((4 . 6) (7 . 9) (8 . 10) (10 . 11) (12 . 13)) 3.271 {3/9:10} B:0 SIMILARITY (1/min{score1}): 0.9997 [and 1/min{score2}: 0.6923] [1947, 2308]: Comparing 1gtm_A and 1hwx_A, based on their crossing files. There are 32 (18 H + 14 S) secondary structure elements in 1gtm_A, of which 9 satisfy the size requirements. There are 34 (23 H + 11 S) secondary structure elements in 1hwx_A, of which 12 satisfy the size requirements. 1.00063 [ 1.33360] ((1 . 1) (2 . 3) (3 . 4) (4 . 5) (6 . 6) (7 . 7) (8 . 8) (10 . 10) (12 . 12)) 3.582 {0/25:36} B:0 1.12554 [ 1.50023] ((2 . 3) (3 . 4) (4 . 5) (6 . 6) (7 . 7) (8 . 8) (10 . 10) (12 . 12)) 3.762 {0/21:28} B:0 2.54026 [ 3.13838] ((1 . 3) (7 . 7) (8 . 8) (10 . 10)) 5.203 {1/5:6} B:0 2.54666 [ 3.14178] ((1 . 7) (3 . 8) (6 . 11) (7 . 12)) 12.973 {1/5:6} B:0 4.09815 [ 4.28597] ((2 . 7) (3 . 8) (6 . 11) (7 . 12)) 13.020 {2/5:6} B:0 SIMILARITY (1/min{score1}): 0.9994 [and 1/min{score2}: 0.7499] [1947, 3609]: Comparing 1gtm_A and 1leh_A, based on their crossing files. There are 32 (18 H + 14 S) secondary structure elements in 1gtm_A, of which 9 satisfy the size requirements. There are 27 (15 H + 12 S) secondary structure elements in 1leh_A, of which 8 satisfy the size requirements. 1.12731 [ 1.00328] ((1 . 1) (3 . 2) (4 . 3) (6 . 5) (7 . 6) (8 . 7) (10 . 8) (12 . 10)) 5.420 {0/19:28} B:0 1.28597 [ 1.14323] ((3 . 2) (4 . 3) (6 . 5) (7 . 6) (8 . 7) (10 . 8) (12 . 10)) 3.469 {0/16:21} B:0 1.67270 [ 1.63958] ((2 . 1) (3 . 2) (4 . 3) (6 . 5) (7 . 6) (8 . 7) (10 . 8) (12 . 10)) 5.194 {3/19:28} B:0 2.25024 [ 2.00033] ((1 . 1) (7 . 6) (8 . 7) (10 . 10)) 5.148 {0/4:6} B:0 2.25381 [ 2.00542] ((6 . 2) (8 . 5) (10 . 6) (12 . 8)) 10.334 {0/4:6} B:0 SIMILARITY (1/min{score1}): 0.8871 [and 1/min{score2}: 0.9967] [1947, 3733]: Comparing 1gtm_A and 1lu9_A, based on their crossing files. There are 32 (18 H + 14 S) secondary structure elements in 1gtm_A, of which 9 satisfy the size requirements. There are 23 (11 H + 12 S) secondary structure elements in 1lu9_A, of which 9 satisfy the size requirements. 1.80081 [ 1.80081] ((6 . 1) (7 . 2) (8 . 3) (10 . 4) (12 . 7)) 5.937 {0/4:10} B:0 1.95988 [ 1.95988] ((6 . 1) (7 . 2) (8 . 3) (10 . 7) (12 . 9)) 8.809 {1/7:10} B:0 2.25134 [ 2.25134] ((6 . 3) (7 . 4) (8 . 6) (12 . 9)) 7.952 {0/3:6} B:0 2.25150 [ 2.25150] ((6 . 3) (7 . 4) (8 . 6) (10 . 7)) 8.186 {0/2:6} B:0 2.25249 [ 2.25249] ((3 . 3) (6 . 6) (7 . 7) (8 . 8)) 9.291 {0/3:6} B:0 SIMILARITY (1/min{score1}): 0.6641 [and 1/min{score2}: 0.6641] [1947, 4350]: Comparing 1gtm_A and 1npy_A, based on their crossing files. There are 32 (18 H + 14 S) secondary structure elements in 1gtm_A, of which 9 satisfy the size requirements. There are 23 (11 H + 12 S) secondary structure elements in 1npy_A, of which 10 satisfy the size requirements. 2.25019 [ 2.50014] ((6 . 1) (7 . 2) (8 . 3) (10 . 4)) 4.903 {0/0:6} B:0 2.25075 [ 2.50054] ((6 . 1) (7 . 2) (8 . 3) (10 . 6)) 6.871 {0/3:6} B:0 2.25192 [ 2.50140] ((6 . 3) (7 . 4) (8 . 5) (10 . 8)) 8.702 {0/0:6} B:0 2.25255 [ 2.50186] ((3 . 1) (6 . 3) (7 . 4) (8 . 5)) 9.349 {0/0:6} B:0 3.49541 [ 3.57153] ((2 . 2) (3 . 3) (6 . 5) (8 . 10)) 10.582 {1/3:6} B:0 SIMILARITY (1/min{score1}): 0.6655 [and 1/min{score2}: 0.5993] [1947, 4446]: Comparing 1gtm_A and 1nyt_A, based on their crossing files. There are 32 (18 H + 14 S) secondary structure elements in 1gtm_A, of which 9 satisfy the size requirements. There are 25 (13 H + 12 S) secondary structure elements in 1nyt_A, of which 9 satisfy the size requirements. 2.25013 [ 2.25013] ((6 . 1) (7 . 2) (8 . 3) (10 . 4)) 4.476 {0/1:6} B:0 2.25132 [ 2.25132] ((3 . 1) (6 . 3) (7 . 4) (8 . 5)) 7.922 {0/1:6} B:0 2.25175 [ 2.25175] ((6 . 3) (7 . 4) (8 . 5) (10 . 8)) 8.500 {0/2:6} B:0 3.49502 [ 3.49502] ((2 . 2) (3 . 3) (6 . 5) (8 . 10)) 9.504 {1/3:6} B:0 4.01990 [ 4.01990] ((3 . 5) (4 . 1) (6 . 3) (7 . 4) (8 . 9) (10 . 2)) 8.214 {2/5:15} B:2 SIMILARITY (1/min{score1}): 0.4444 [and 1/min{score2}: 0.4444] [1947, 6256]: Comparing 1gtm_A and 1vi2_A, based on their crossing files. There are 32 (18 H + 14 S) secondary structure elements in 1gtm_A, of which 9 satisfy the size requirements. There are 24 (12 H + 12 S) secondary structure elements in 1vi2_A, of which 10 satisfy the size requirements. 1.80085 [ 2.00062] ((6 . 1) (7 . 2) (8 . 3) (10 . 4) (12 . 6)) 6.013 {0/4:10} B:0 2.25021 [ 2.50015] ((6 . 1) (7 . 2) (8 . 3) (10 . 4)) 5.016 {0/0:6} B:0 2.25027 [ 2.50020] ((7 . 2) (8 . 3) (10 . 4) (12 . 6)) 5.349 {0/3:6} B:0 2.25206 [ 2.50150] ((6 . 3) (7 . 4) (8 . 5) (10 . 8)) 8.855 {0/1:6} B:0 2.25243 [ 2.50177] ((3 . 1) (6 . 3) (7 . 4) (8 . 5)) 9.230 {0/0:6} B:0 SIMILARITY (1/min{score1}): 0.6651 [and 1/min{score2}: 0.5991] -------------------------------------------------------------------------------------------------------------------------