------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [4688, 989]: Comparing 1okg_A and 1e0c_A, based on their crossing files. There are 32 (14 H + 18 S) secondary structure elements in 1okg_A, of which 8 satisfy the size requirements. There are 25 (14 H + 11 S) secondary structure elements in 1e0c_A, of which 9 satisfy the size requirements. 1.00003 [ 1.12502] ((2 . 3) (4 . 4) (5 . 5) (8 . 8) (9 . 9) (10 . 10) (11 . 11) (12 . 12)) 1.699 {0/21:28} B:0 1.14288 [ 1.28573] ((2 . 3) (4 . 4) (5 . 5) (9 . 9) (10 . 10) (11 . 11) (12 . 12)) 1.726 {0/16:21} B:0 1.80967 [ 1.95705] ((2 . 3) (4 . 4) (5 . 5) (8 . 10) (9 . 11)) 4.558 {1/7:10} B:0 2.00158 [ 2.25111] ((4 . 4) (5 . 8) (8 . 10) (9 . 11)) 7.586 {0/3:6} B:0 5.03186 [ 5.05065] ((2 . 5) (5 . 8) (9 . 11) (10 . 12)) 8.628 {2/4:6} B:0 SIMILARITY (1/min{score1}): 0.9999 [and 1/min{score2}: 0.8889] [4688, 990]: Comparing 1okg_A and 1e0c_A, based on their crossing files. There are 32 (14 H + 18 S) secondary structure elements in 1okg_A, of which 8 satisfy the size requirements. There are 25 (14 H + 11 S) secondary structure elements in 1e0c_A, of which 9 satisfy the size requirements. 1.00012 [ 1.12508] ((2 . 13) (4 . 14) (5 . 15) (8 . 21) (9 . 22) (10 . 23) (11 . 24) (12 . 25)) 2.349 {0/21:28} B:0 1.14294 [ 1.28578] ((2 . 13) (4 . 14) (5 . 15) (9 . 22) (10 . 23) (11 . 24) (12 . 25)) 2.420 {0/16:21} B:0 1.80987 [ 1.95720] ((2 . 13) (4 . 14) (5 . 15) (8 . 23) (9 . 24)) 5.201 {1/7:10} B:0 5.03186 [ 5.05065] ((2 . 15) (4 . 14) (8 . 23) (9 . 24)) 8.643 {2/4:6} B:1 SIMILARITY (1/min{score1}): 0.9999 [and 1/min{score2}: 0.8888] [4688, 1878]: Comparing 1okg_A and 1gmx_A, based on their crossing files. There are 32 (14 H + 18 S) secondary structure elements in 1okg_A, of which 8 satisfy the size requirements. There are 13 (6 H + 7 S) secondary structure elements in 1gmx_A, of which 9 satisfy the size requirements. 1.01891 [ 1.13842] ((2 . 2) (4 . 3) (5 . 4) (8 . 7) (9 . 8) (10 . 9) (11 . 10) (12 . 11)) 2.913 {1/19:28} B:0 1.14291 [ 1.28575] ((2 . 2) (4 . 3) (5 . 4) (9 . 8) (10 . 9) (11 . 10) (12 . 11)) 2.118 {0/16:21} B:0 1.60222 [ 1.80156] ((8 . 4) (9 . 8) (10 . 9) (11 . 10) (12 . 11)) 6.988 {0/6:10} B:0 2.37856 [ 2.54021] ((2 . 2) (4 . 3) (5 . 4) (8 . 9)) 4.750 {1/5:6} B:0 2.72416 [ 2.83614] ((2 . 2) (4 . 3) (8 . 9) (9 . 10)) 4.995 {1/4:6} B:0 SIMILARITY (1/min{score1}): 0.9814 [and 1/min{score2}: 0.8784] [4688, 2348]: Comparing 1okg_A and 1hzm_A, based on their crossing files. There are 32 (14 H + 18 S) secondary structure elements in 1okg_A, of which 8 satisfy the size requirements. There are 9 (6 H + 3 S) secondary structure elements in 1hzm_A, of which 8 satisfy the size requirements. 1.60061 [ 1.60061] ((4 . 2) (5 . 3) (9 . 6) (10 . 7) (12 . 9)) 5.062 {0/6:10} B:0 2.00012 [ 2.00012] ((4 . 2) (5 . 4) (10 . 7) (12 . 9)) 3.957 {0/4:6} B:0 2.00012 [ 2.00012] ((4 . 2) (5 . 3) (8 . 5) (9 . 6)) 3.981 {0/2:6} B:0 2.00013 [ 2.00013] ((4 . 2) (5 . 3) (9 . 6) (10 . 7)) 4.096 {0/3:6} B:0 4.06148 [ 4.06148] ((2 . 3) (5 . 4) (8 . 7) (10 . 9)) 9.141 {2/5:6} B:0 SIMILARITY (1/min{score1}): 0.6249 [and 1/min{score2}: 0.6249] [4688, 4688]: Comparing 1okg_A and 1okg_A, based on their crossing files. There are 32 (14 H + 18 S) secondary structure elements in 1okg_A, of which 8 satisfy the size requirements. There are 32 (14 H + 18 S) secondary structure elements in 1okg_A, of which 8 satisfy the size requirements. 1.00000 [ 1.00000] ((2 . 2) (4 . 4) (5 . 5) (8 . 8) (9 . 9) (10 . 10) (11 . 11) (12 . 12)) 0.000 {0/22:28} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [4688, 4689]: Comparing 1okg_A and 1okg_A, based on their crossing files. There are 32 (14 H + 18 S) secondary structure elements in 1okg_A, of which 8 satisfy the size requirements. There are 32 (14 H + 18 S) secondary structure elements in 1okg_A, of which 7 satisfy the size requirements. 1.33336 [ 1.16670] ((4 . 15) (5 . 16) (8 . 21) (9 . 22) (10 . 23) (12 . 25)) 1.985 {0/10:15} B:0 2.00071 [ 1.75105] ((4 . 15) (8 . 21) (9 . 22) (12 . 26)) 6.205 {0/4:6} B:0 2.00066 [ 1.75098] ((4 . 15) (8 . 23) (9 . 22) (12 . 26)) 6.091 {0/4:6} B:1 1.47134 [ 1.35577] ((5 . 16) (8 . 21) (9 . 15) (10 . 23) (11 . 22) (12 . 25)) 3.342 {1/9:15} B:2 1.47240 [ 1.35713] ((5 . 16) (8 . 21) (9 . 15) (10 . 23) (11 . 22) (12 . 26)) 5.639 {1/9:15} B:2 SIMILARITY (1/min{score1}): 0.7500 [and 1/min{score2}: 0.8571] [4688, 5274]: Comparing 1okg_A and 1qb0_A, based on their crossing files. There are 32 (14 H + 18 S) secondary structure elements in 1okg_A, of which 8 satisfy the size requirements. There are 14 (7 H + 7 S) secondary structure elements in 1qb0_A, of which 9 satisfy the size requirements. 1.01614 [ 1.13644] ((2 . 2) (4 . 3) (5 . 4) (8 . 7) (9 . 8) (10 . 9) (11 . 10) (12 . 11)) 3.930 {1/20:28} B:0 1.14322 [ 1.28597] ((2 . 2) (4 . 3) (5 . 4) (9 . 8) (10 . 9) (11 . 10) (12 . 11)) 3.464 {0/17:21} B:0 1.33358 [ 1.50017] ((2 . 2) (4 . 3) (5 . 4) (9 . 8) (10 . 9) (11 . 10)) 3.510 {0/12:15} B:0 1.73238 [ 1.89703] ((2 . 2) (4 . 3) (5 . 4) (8 . 9) (11 . 10)) 5.274 {1/8:10} B:0 2.72419 [ 2.83617] ((2 . 2) (4 . 3) (8 . 9) (9 . 10)) 5.325 {1/4:6} B:0 SIMILARITY (1/min{score1}): 0.9841 [and 1/min{score2}: 0.8799] [4688, 5487]: Comparing 1okg_A and 1qxn_A, based on their crossing files. There are 32 (14 H + 18 S) secondary structure elements in 1okg_A, of which 8 satisfy the size requirements. There are 13 (6 H + 7 S) secondary structure elements in 1qxn_A, of which 11 satisfy the size requirements. 1.01546 [ 1.38105] ((2 . 3) (4 . 4) (5 . 5) (8 . 8) (9 . 9) (10 . 10) (11 . 11) (12 . 12)) 2.674 {1/20:28} B:0 1.47254 [ 1.89290] ((4 . 2) (5 . 5) (9 . 9) (10 . 10) (11 . 11) (12 . 12)) 5.790 {1/9:15} B:0 1.60495 [ 2.20191] ((2 . 1) (9 . 9) (10 . 10) (11 . 11) (12 . 12)) 8.548 {0/7:10} B:0 2.00007 [ 2.75003] ((2 . 3) (4 . 4) (5 . 5) (9 . 11)) 3.499 {0/5:6} B:0 2.00082 [ 2.75032] ((2 . 5) (4 . 7) (5 . 8) (8 . 10)) 6.448 {0/5:6} B:0 SIMILARITY (1/min{score1}): 0.9848 [and 1/min{score2}: 0.7241] [4688, 5635]: Comparing 1okg_A and 1rhs, based on their crossing files. There are 32 (14 H + 18 S) secondary structure elements in 1okg_A, of which 8 satisfy the size requirements. There are 25 (13 H + 12 S) secondary structure elements in 1rhs, of which 8 satisfy the size requirements. 1.00012 [ 1.00012] ((2 . 2) (4 . 3) (5 . 4) (8 . 6) (9 . 7) (10 . 8) (11 . 9) (12 . 10)) 2.387 {0/22:28} B:0 1.94774 [ 1.94774] ((2 . 2) (5 . 4) (8 . 6) (9 . 7) (12 . 8)) 9.464 {1/6:10} B:0 3.43734 [ 3.43734] ((2 . 4) (5 . 6) (8 . 8) (10 . 10)) 9.872 {1/3:6} B:0 SIMILARITY (1/min{score1}): 0.9999 [and 1/min{score2}: 0.9999] [4688, 5636]: Comparing 1okg_A and 1rhs, based on their crossing files. There are 32 (14 H + 18 S) secondary structure elements in 1okg_A, of which 8 satisfy the size requirements. There are 25 (13 H + 12 S) secondary structure elements in 1rhs, of which 8 satisfy the size requirements. 1.00007 [ 1.00007] ((2 . 13) (4 . 14) (5 . 15) (8 . 19) (9 . 20) (10 . 21) (11 . 22) (12 . 23)) 2.094 {0/22:28} B:0 5.03178 [ 5.03178] ((2 . 19) (4 . 20) (5 . 21) (8 . 23)) 7.317 {2/4:6} B:0 SIMILARITY (1/min{score1}): 0.9999 [and 1/min{score2}: 0.9999] [4688, 6087]: Comparing 1okg_A and 1urh_A, based on their crossing files. There are 32 (14 H + 18 S) secondary structure elements in 1okg_A, of which 8 satisfy the size requirements. There are 21 (12 H + 9 S) secondary structure elements in 1urh_A, of which 8 satisfy the size requirements. 1.00005 [ 1.00005] ((2 . 2) (4 . 3) (5 . 4) (8 . 7) (9 . 8) (10 . 9) (11 . 10) (12 . 11)) 1.929 {0/22:28} B:0 1.60008 [ 1.60008] ((2 . 2) (4 . 3) (5 . 4) (8 . 7) (9 . 10)) 3.080 {0/8:10} B:0 SIMILARITY (1/min{score1}): 0.9999 [and 1/min{score2}: 0.9999] [4688, 6088]: Comparing 1okg_A and 1urh_A, based on their crossing files. There are 32 (14 H + 18 S) secondary structure elements in 1okg_A, of which 8 satisfy the size requirements. There are 21 (12 H + 9 S) secondary structure elements in 1urh_A, of which 6 satisfy the size requirements. 1.33341 [ 1.00019] ((2 . 13) (4 . 14) (8 . 18) (9 . 19) (10 . 20) (11 . 21)) 2.647 {0/12:15} B:0 1.60001 [ 1.20002] ((4 . 14) (8 . 18) (9 . 19) (10 . 20) (11 . 21)) 1.803 {0/7:10} B:0 2.72418 [ 2.57750] ((2 . 13) (4 . 14) (8 . 20) (9 . 21)) 5.231 {1/4:6} B:0 4.30648 [ 4.29239] ((5 . 13) (8 . 18) (9 . 19) (10 . 20) (11 . 21)) 6.866 {3/7:10} B:0 1.80979 [ 1.58101] ((2 . 13) (4 . 14) (8 . 20) (9 . 19) (11 . 21)) 4.984 {1/7:10} B:1 SIMILARITY (1/min{score1}): 0.7500 [and 1/min{score2}: 0.9998] -------------------------------------------------------------------------------------------------------------------------