------------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------------- [1777, 1777]: Comparing 1g97_A and 1g97_A, based on their crossing files. There are 56 (14 H + 42 S) secondary structure elements in 1g97_A, of which 11 satisfy the size requirements. There are 56 (14 H + 42 S) secondary structure elements in 1g97_A, of which 11 satisfy the size requirements. 1.00000 [ 1.00000] ((31 . 31) (34 . 34) (37 . 37) (42 . 42) (43 . 43) (45 . 45) (46 . 46) (47 . 47) (49 . 49) (50 . 50) (52 . 52)) 0.000 {0/34:55} B:0 1.10000 [ 1.10000] ((31 . 31) (34 . 34) (37 . 37) (43 . 43) (45 . 45) (46 . 46) (47 . 47) (49 . 49) (50 . 50) (52 . 52)) 0.000 {0/25:45} B:0 1.89227 [ 1.89227] ((31 . 34) (34 . 37) (42 . 45) (43 . 46) (46 . 49) (47 . 50)) 1.418 {1/9:15} B:0 2.20000 [ 2.20000] ((34 . 31) (37 . 34) (45 . 42) (46 . 43) (49 . 46)) 1.536 {0/4:10} B:0 2.20001 [ 2.20001] ((42 . 34) (45 . 37) (47 . 42) (50 . 45) (52 . 47)) 2.133 {0/8:10} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [1777, 2715]: Comparing 1g97_A and 1j2z_A, based on their crossing files. There are 56 (14 H + 42 S) secondary structure elements in 1g97_A, of which 11 satisfy the size requirements. There are 31 (4 H + 27 S) secondary structure elements in 1j2z_A, of which 9 satisfy the size requirements. 2.20006 [ 1.80011] ((31 . 8) (34 . 11) (37 . 14) (50 . 26) (52 . 27)) 3.594 {0/4:10} B:0 2.75005 [ 2.25010] ((31 . 11) (34 . 14) (47 . 26) (49 . 27)) 4.157 {0/3:6} B:0 2.75041 [ 2.25075] ((31 . 8) (37 . 11) (42 . 14) (52 . 26)) 6.878 {0/1:6} B:0 SIMILARITY (1/min{score1}): 0.4545 [and 1/min{score2}: 0.5555] [1777, 3508]: Comparing 1g97_A and 1l0s_A, based on their crossing files. There are 56 (14 H + 42 S) secondary structure elements in 1g97_A, of which 11 satisfy the size requirements. There are 14 (0 H + 14 S) secondary structure elements in 1l0s_A, of which 12 satisfy the size requirements. 1.22307 [ 1.33399] ((34 . 1) (37 . 4) (42 . 5) (43 . 6) (45 . 7) (46 . 8) (47 . 9) (49 . 11) (52 . 14)) 4.492 {0/11:36} B:0 1.57534 [ 1.71731] ((37 . 1) (42 . 4) (43 . 5) (45 . 6) (46 . 7) (49 . 8) (52 . 11)) 7.952 {0/0:21} B:0 1.83338 [ 2.00004] ((43 . 3) (46 . 5) (47 . 6) (49 . 7) (50 . 8) (52 . 10)) 2.940 {0/5:15} B:0 1.83341 [ 2.00006] ((37 . 1) (42 . 5) (43 . 6) (45 . 7) (46 . 8) (52 . 14)) 3.380 {0/4:15} B:0 1.83363 [ 2.00023] ((45 . 3) (46 . 4) (47 . 5) (49 . 6) (50 . 7) (52 . 8)) 4.690 {0/5:15} B:0 SIMILARITY (1/min{score1}): 0.8176 [and 1/min{score2}: 0.7496] [1777, 4013]: Comparing 1g97_A and 1mr7_A, based on their crossing files. There are 56 (14 H + 42 S) secondary structure elements in 1g97_A, of which 11 satisfy the size requirements. There are 26 (11 H + 15 S) secondary structure elements in 1mr7_A, of which 12 satisfy the size requirements. 1.89234 [ 2.04608] ((34 . 3) (37 . 8) (42 . 10) (43 . 15) (50 . 21) (52 . 22)) 3.411 {1/9:15} B:0 1.89244 [ 2.04615] ((37 . 3) (43 . 8) (45 . 10) (46 . 15) (50 . 21) (52 . 22)) 4.177 {1/9:15} B:0 2.20007 [ 2.40005] ((34 . 3) (37 . 8) (43 . 15) (50 . 21) (52 . 22)) 3.704 {0/4:10} B:0 2.20007 [ 2.40005] ((37 . 1) (42 . 4) (47 . 8) (49 . 10) (50 . 15)) 3.740 {0/7:10} B:0 2.75012 [ 3.00009] ((34 . 8) (43 . 15) (50 . 21) (52 . 22)) 5.021 {0/3:6} B:0 SIMILARITY (1/min{score1}): 0.5284 [and 1/min{score2}: 0.4887] [1777, 4597]: Comparing 1g97_A and 1ocx_A, based on their crossing files. There are 56 (14 H + 42 S) secondary structure elements in 1g97_A, of which 11 satisfy the size requirements. There are 22 (4 H + 18 S) secondary structure elements in 1ocx_A, of which 14 satisfy the size requirements. 1.58821 [ 2.00822] ((37 . 6) (42 . 8) (43 . 9) (45 . 11) (46 . 15) (50 . 21) (52 . 22)) 4.096 {1/14:21} B:0 1.70946 [ 2.07229] ((42 . 4) (43 . 5) (45 . 7) (46 . 8) (47 . 9) (49 . 11) (50 . 15)) 2.040 {2/16:21} B:0 2.17127 [ 2.52379] ((42 . 4) (43 . 5) (45 . 7) (46 . 8) (47 . 9) (49 . 11)) 2.090 {2/11:15} B:0 2.20011 [ 2.80005] ((31 . 6) (34 . 9) (37 . 15) (43 . 21) (46 . 22)) 4.151 {0/0:10} B:0 2.20028 [ 2.80014] ((31 . 5) (34 . 8) (37 . 11) (42 . 21) (47 . 22)) 5.282 {0/7:10} B:0 SIMILARITY (1/min{score1}): 0.6296 [and 1/min{score2}: 0.4980] [1777, 4941]: Comparing 1g97_A and 1p9h_A, based on their crossing files. There are 56 (14 H + 42 S) secondary structure elements in 1g97_A, of which 11 satisfy the size requirements. There are 21 (1 H + 20 S) secondary structure elements in 1p9h_A, of which 10 satisfy the size requirements. 1.57143 [ 1.42858] ((31 . 5) (34 . 7) (37 . 9) (43 . 13) (46 . 15) (49 . 17) (52 . 19)) 1.413 {0/0:21} B:0 1.57143 [ 1.42858] ((31 . 1) (34 . 5) (37 . 7) (43 . 11) (46 . 13) (49 . 15) (52 . 17)) 1.473 {0/0:21} B:0 1.57145 [ 1.42860] ((31 . 1) (34 . 5) (37 . 7) (43 . 11) (46 . 13) (49 . 15) (52 . 19)) 2.097 {0/0:21} B:0 1.57146 [ 1.42861] ((31 . 1) (34 . 5) (37 . 7) (43 . 11) (46 . 13) (49 . 17) (52 . 19)) 2.312 {0/0:21} B:0 1.57147 [ 1.42862] ((31 . 1) (34 . 5) (37 . 7) (43 . 9) (46 . 11) (49 . 15) (52 . 17)) 2.508 {0/0:21} B:0 SIMILARITY (1/min{score1}): 0.6364 [and 1/min{score2}: 0.7000] [1777, 5433]: Comparing 1g97_A and 1qre_A, based on their crossing files. There are 56 (14 H + 42 S) secondary structure elements in 1g97_A, of which 11 satisfy the size requirements. There are 25 (3 H + 22 S) secondary structure elements in 1qre_A, of which 13 satisfy the size requirements. 1.83335 [ 2.16667] ((43 . 4) (46 . 7) (47 . 8) (49 . 10) (50 . 14) (52 . 16)) 2.167 {0/8:15} B:0 1.83342 [ 2.16672] ((31 . 4) (34 . 7) (37 . 10) (43 . 16) (46 . 18) (49 . 20)) 3.438 {0/2:15} B:0 1.83343 [ 2.16673] ((42 . 4) (43 . 5) (45 . 7) (46 . 8) (49 . 12) (52 . 14)) 3.570 {0/10:15} B:0 2.20000 [ 2.60000] ((42 . 4) (43 . 5) (45 . 7) (46 . 8) (49 . 14)) 1.682 {0/6:10} B:0 2.20001 [ 2.60001] ((42 . 4) (43 . 5) (45 . 7) (46 . 8) (52 . 14)) 2.483 {0/6:10} B:0 SIMILARITY (1/min{score1}): 0.6017 [and 1/min{score2}: 0.5224] [1777, 5898]: Comparing 1g97_A and 1tdt_A, based on their crossing files. There are 56 (14 H + 42 S) secondary structure elements in 1g97_A, of which 11 satisfy the size requirements. There are 30 (4 H + 26 S) secondary structure elements in 1tdt_A, of which 14 satisfy the size requirements. 2.75012 [ 3.50006] ((31 . 13) (34 . 16) (47 . 26) (49 . 27)) 5.072 {0/3:6} B:0 5.11069 [ 5.27639] ((31 . 13) (34 . 16) (47 . 26) (50 . 29)) 5.793 {2/4:6} B:0 2.20038 [ 2.80018] ((31 . 13) (34 . 16) (47 . 30) (50 . 26) (52 . 29)) 5.696 {0/6:10} B:1 2.75004 [ 3.50002] ((31 . 13) (34 . 16) (47 . 30) (50 . 26)) 3.924 {0/4:6} B:1 3.85657 [ 4.01264] ((31 . 13) (34 . 16) (42 . 30) (45 . 29) (50 . 26)) 6.744 {3/8:10} B:2 SIMILARITY (1/min{score1}): 0.4545 [and 1/min{score2}: 0.3571] [1777, 6167]: Comparing 1g97_A and 1v3w_A, based on their crossing files. There are 56 (14 H + 42 S) secondary structure elements in 1g97_A, of which 11 satisfy the size requirements. There are 22 (1 H + 21 S) secondary structure elements in 1v3w_A, of which 12 satisfy the size requirements. 1.57159 [ 1.71441] ((37 . 7) (42 . 9) (43 . 10) (45 . 12) (47 . 14) (50 . 17) (52 . 21)) 3.563 {0/16:21} B:0 1.57196 [ 1.71470] ((42 . 6) (43 . 7) (45 . 9) (46 . 10) (47 . 14) (50 . 17) (52 . 21)) 4.824 {0/16:21} B:0 1.61377 [ 1.74728] ((37 . 1) (43 . 4) (46 . 6) (47 . 7) (49 . 9) (50 . 10) (52 . 12)) 3.029 {1/11:21} B:0 1.79017 [ 1.89181] ((34 . 6) (37 . 7) (42 . 9) (43 . 10) (45 . 12) (47 . 14) (50 . 17)) 4.696 {2/14:21} B:0 1.83335 [ 2.00002] ((42 . 6) (43 . 7) (45 . 9) (46 . 10) (47 . 14) (50 . 17)) 2.428 {0/12:15} B:0 SIMILARITY (1/min{score1}): 0.6652 [and 1/min{score2}: 0.6240] [1777, 6339]: Comparing 1g97_A and 1xat, based on their crossing files. There are 56 (14 H + 42 S) secondary structure elements in 1g97_A, of which 11 satisfy the size requirements. There are 23 (8 H + 15 S) secondary structure elements in 1xat, of which 11 satisfy the size requirements. 1.89235 [ 1.89235] ((34 . 2) (37 . 6) (42 . 8) (43 . 11) (50 . 17) (52 . 18)) 3.451 {1/9:15} B:0 1.89244 [ 1.89244] ((37 . 2) (43 . 6) (45 . 8) (46 . 11) (50 . 17) (52 . 18)) 4.181 {1/9:15} B:0 2.20007 [ 2.20007] ((34 . 2) (37 . 6) (43 . 11) (47 . 17) (50 . 18)) 3.719 {0/3:10} B:0 2.66395 [ 2.66395] ((34 . 2) (37 . 6) (42 . 8) (43 . 11) (47 . 17) (50 . 18)) 3.595 {2/8:15} B:0 2.75009 [ 2.75009] ((31 . 2) (37 . 6) (50 . 17) (52 . 18)) 4.731 {0/3:6} B:0 SIMILARITY (1/min{score1}): 0.5284 [and 1/min{score2}: 0.5284] -------------------------------------------------------------------------------------------------------------------------