
#######################################################
#                                                     #
#                        LGA                          #
#                  ---------------                    #
#                                                     #
#               Local-Global Alignment                #
#        A Method for Finding 3-D Similarities        #
#               in Protein Structures                 #
#                                                     #
#                  --------------- 06/2006            #
#                                                     #
#      Adam Zemla (adamz@llnl.gov)                    #
#      Lawrence Livermore National Laboratory, CA     #
#                                                     #
#######################################################

# Molecule1: number of CA atoms   12 (  100),  selected   12 , name T0299TS490_1_1-D2
# Molecule2: number of CA atoms   89 (  757),  selected   12 , name T0299_D2.pdb
# PARAMETERS: T0299TS490_1_1-D2.T0299_D2.pdb  -3  -ie  -o1  -sda  -d:4  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12        79 - 90          1.76     1.76
  LCS_AVERAGE:     13.48

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12        79 - 90          1.76     1.76
  LCS_AVERAGE:     13.48

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10        79 - 88          0.98     2.06
  LCS_AVERAGE:     10.21

LCS_GDT    MOLECULE-1    MOLECULE-2    LENGTH_OF_THE
LCS_GDT     RESIDUE       RESIDUE         CONTINUOUS
LCS_GDT   NAME NUMBER   NAME NUMBER          SEGMENT     GLOBAL DISTANCE TEST - GDT_DATA_COLUMNS                             NUMBER OF THE RESIDUES:   89
LCS_GDT     L      79     L      79     10   12   12     6    8   10   11   11   11   11   12   12   12   12   12   12   12   12   12   12   12   12   12 
LCS_GDT     E      80     E      80     10   12   12     6    8   10   11   11   11   11   12   12   12   12   12   12   12   12   12   12   12   12   12 
LCS_GDT     D      81     D      81     10   12   12     6    8   10   11   11   11   11   12   12   12   12   12   12   12   12   12   12   12   12   12 
LCS_GDT     F      82     F      82     10   12   12     6    8   10   11   11   11   11   12   12   12   12   12   12   12   12   12   12   12   12   12 
LCS_GDT     E      83     E      83     10   12   12     6    8   10   11   11   11   11   12   12   12   12   12   12   12   12   12   12   12   12   12 
LCS_GDT     A      84     A      84     10   12   12     3    7    9   11   11   11   11   12   12   12   12   12   12   12   12   12   12   12   12   12 
LCS_GDT     E      85     E      85     10   12   12     5    7   10   11   11   11   11   12   12   12   12   12   12   12   12   12   12   12   12   12 
LCS_GDT     L      86     L      86     10   12   12     3    7   10   11   11   11   11   12   12   12   12   12   12   12   12   12   12   12   12   12 
LCS_GDT     E      87     E      87     10   12   12     6    8   10   11   11   11   11   12   12   12   12   12   12   12   12   12   12   12   12   12 
LCS_GDT     N      88     N      88     10   12   12     3    8   10   11   11   11   11   12   12   12   12   12   12   12   12   12   12   12   12   12 
LCS_GDT     L      89     L      89      6   12   12     3    8   10   11   11   11   11   12   12   12   12   12   12   12   12   12   12   12   12   12 
LCS_GDT     P      90     P      90      3   12   12     3    3    3    3    3    6    8   12   12   12   12   12   12   12   12   12   12   12   12   12 
LCS_AVERAGE  LCS_A:  12.39  (  10.21   13.48   13.48 )

GLOBAL_DISTANCE_TEST (the largest set of residues that can fit under specified DISTANCE_CUTOFF)
GDT DIST_CUTOFF  0.50   1.00   1.50   2.00   2.50   3.00   3.50   4.00   4.50   5.00   5.50   6.00   6.50   7.00   7.50   8.00   8.50   9.00   9.50  10.00
GDT NUMBER_CA      6      8     10     11     11     11     11     12     12     12     12     12     12     12     12     12     12     12     12     12 
GDT PERCENT_CA   6.74   8.99  11.24  12.36  12.36  12.36  12.36  13.48  13.48  13.48  13.48  13.48  13.48  13.48  13.48  13.48  13.48  13.48  13.48  13.48
GDT RMS_LOCAL    0.33   0.75   0.89   1.03   1.03   1.03   1.03   1.76   1.76   1.76   1.76   1.76   1.76   1.76   1.76   1.76   1.76   1.76   1.76   1.76
GDT RMS_ALL_CA   2.14   1.95   1.98   1.99   1.99   1.99   1.99   1.76   1.76   1.76   1.76   1.76   1.76   1.76   1.76   1.76   1.76   1.76   1.76   1.76

#      Molecule1      Molecule2       DISTANCE
LGA    L      79      L      79          2.300
LGA    E      80      E      80          2.167
LGA    D      81      D      81          1.668
LGA    F      82      F      82          1.239
LGA    E      83      E      83          0.741
LGA    A      84      A      84          2.089
LGA    E      85      E      85          0.762
LGA    L      86      L      86          1.897
LGA    E      87      E      87          1.456
LGA    N      88      N      88          1.278
LGA    L      89      L      89          1.682
LGA    P      90      P      90          3.855

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   12   89    4.0     12    1.76    12.079    12.675     0.647

LGA_LOCAL      RMSD =  1.756  Number of atoms =   12  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  1.933  Number of atoms =   12 
Std_ALL_ATOMS  RMSD =  1.756  (standard rmsd on all 12 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.216079 * X  +   0.292920 * Y  +   0.931401 * Z  + -21.147657
  Y_new =  -0.837342 * X  +  -0.546217 * Y  +  -0.022476 * Z  +  85.165726
  Z_new =   0.502163 * X  +  -0.784758 * Y  +   0.363300 * Z  + -24.150890 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.137229    2.004364  [ DEG:   -65.1584    114.8416 ]
  Theta =  -0.526099   -2.615494  [ DEG:   -30.1432   -149.8568 ]
  Phi   =  -1.823341    1.318252  [ DEG:  -104.4697     75.5303 ]
 
# END of job
REMARK  ---------------------------------------------------------- 
REMARK   Citing LGA: 
REMARK   Zemla A., LGA - a Method for Finding 3D Similarities in  
REMARK   Protein Structures, Nucleic Acids Research, 2003, V. 31, 
REMARK   No. 13, pp. 3370-3374. 
REMARK  ---------------------------------------------------------- 
REMARK   Superimposed MOLECULES (1=>2)   Output: 1 molecule      
REMARK     1: T0299TS490_1_1-D2                             
REMARK     2: T0299_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0299TS490_1_1-D2.T0299_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   12   89   4.0   12   1.76  12.675     1.76
REMARK  ---------------------------------------------------------- 
MOLECULE T0299TS490_1_1-D2
REMARK PARENT number 1
PFRMAT     TS
TARGET     T0299
PARENT     1zzmA          
ATOM   1384  N   LEU    79     -12.174  57.840  -3.521  1.00   .09       1SG1385
ATOM   1385  CA  LEU    79     -11.975  58.252  -4.879  1.00   .09       1SG1386
ATOM   1386  CB  LEU    79     -13.294  58.407  -5.654  1.00   .09       1SG1387
ATOM   1387  CG  LEU    79     -14.069  57.086  -5.814  1.00   .09       1SG1388
ATOM   1388  CD2 LEU    79     -13.180  55.987  -6.418  1.00   .09       1SG1389
ATOM   1389  CD1 LEU    79     -15.375  57.297  -6.597  1.00   .09       1SG1390
ATOM   1390  C   LEU    79     -11.295  59.582  -4.886  1.00   .09       1SG1391
ATOM   1391  O   LEU    79     -10.344  59.792  -5.638  1.00   .09       1SG1392
ATOM   1392  N   GLU    80     -11.755  60.520  -4.040  1.00   .18       1SG1393
ATOM   1393  CA  GLU    80     -11.158  61.822  -4.048  1.00   .18       1SG1394
ATOM   1394  CB  GLU    80     -11.924  62.853  -3.209  1.00   .18       1SG1395
ATOM   1395  CG  GLU    80     -13.301  63.205  -3.770  1.00   .18       1SG1396
ATOM   1396  CD  GLU    80     -13.931  64.226  -2.836  1.00   .18       1SG1397
ATOM   1397  OE1 GLU    80     -13.458  65.390  -2.828  1.00   .18       1SG1398
ATOM   1398  OE2 GLU    80     -14.888  63.847  -2.105  1.00   .18       1SG1399
ATOM   1399  C   GLU    80      -9.747  61.732  -3.548  1.00   .18       1SG1400
ATOM   1400  O   GLU    80      -8.864  62.434  -4.037  1.00   .18       1SG1401
ATOM   1401  N   ASP    81      -9.479  60.876  -2.543  1.00   .36       1SG1402
ATOM   1402  CA  ASP    81      -8.117  60.801  -2.092  1.00   .36       1SG1403
ATOM   1403  CB  ASP    81      -7.920  59.900  -0.865  1.00   .36       1SG1404
ATOM   1404  CG  ASP    81      -6.571  60.264  -0.261  1.00   .36       1SG1405
ATOM   1405  OD1 ASP    81      -5.672  60.701  -1.029  1.00   .36       1SG1406
ATOM   1406  OD2 ASP    81      -6.421  60.113   0.981  1.00   .36       1SG1407
ATOM   1407  C   ASP    81      -7.304  60.256  -3.226  1.00   .36       1SG1408
ATOM   1408  O   ASP    81      -6.205  60.739  -3.512  1.00   .36       1SG1409
ATOM   1409  N   PHE    82      -7.861  59.251  -3.933  1.00   .54       1SG1410
ATOM   1410  CA  PHE    82      -7.191  58.693  -5.069  1.00   .54       1SG1411
ATOM   1411  CB  PHE    82      -8.042  57.731  -5.929  1.00   .54       1SG1412
ATOM   1412  CG  PHE    82      -8.139  56.340  -5.399  1.00   .54       1SG1413
ATOM   1413  CD1 PHE    82      -7.125  55.439  -5.637  1.00   .54       1SG1414
ATOM   1414  CD2 PHE    82      -9.250  55.916  -4.709  1.00   .54       1SG1415
ATOM   1415  CE1 PHE    82      -7.207  54.147  -5.175  1.00   .54       1SG1416
ATOM   1416  CE2 PHE    82      -9.339  54.625  -4.243  1.00   .54       1SG1417
ATOM   1417  CZ  PHE    82      -8.316  53.737  -4.474  1.00   .54       1SG1418
ATOM   1418  C   PHE    82      -6.962  59.834  -5.989  1.00   .54       1SG1419
ATOM   1419  O   PHE    82      -5.921  59.882  -6.643  1.00   .54       1SG1420
ATOM   1420  N   GLU    83      -7.931  60.781  -6.019  1.00   .62       1SG1421
ATOM   1421  CA  GLU    83      -7.906  61.897  -6.917  1.00   .62       1SG1422
ATOM   1422  CB  GLU    83      -9.045  62.918  -6.722  1.00   .62       1SG1423
ATOM   1423  CG  GLU    83      -9.259  63.843  -7.926  1.00   .62       1SG1424
ATOM   1424  CD  GLU    83      -8.035  64.733  -8.096  1.00   .62       1SG1425
ATOM   1425  OE1 GLU    83      -7.720  65.494  -7.143  1.00   .62       1SG1426
ATOM   1426  OE2 GLU    83      -7.395  64.658  -9.179  1.00   .62       1SG1427
ATOM   1427  C   GLU    83      -6.615  62.571  -6.690  1.00   .62       1SG1428
ATOM   1428  O   GLU    83      -5.653  62.252  -7.389  1.00   .62       1SG1429
ATOM   1429  N   ALA    84      -6.442  63.605  -5.846  1.00   .64       1SG1430
ATOM   1430  CA  ALA    84      -5.064  63.484  -6.097  1.00   .64       1SG1431
ATOM   1431  CB  ALA    84      -4.354  64.838  -6.150  1.00   .64       1SG1432
ATOM   1432  C   ALA    84      -4.407  62.745  -4.998  1.00   .64       1SG1433
ATOM   1433  O   ALA    84      -4.777  62.807  -3.835  1.00   .64       1SG1434
ATOM   1434  N   GLU    85      -3.268  62.186  -5.367  1.00   .66       1SG1435
ATOM   1435  CA  GLU    85      -2.103  61.804  -4.675  1.00   .66       1SG1436
ATOM   1436  CB  GLU    85      -1.965  60.288  -4.426  1.00   .66       1SG1437
ATOM   1437  CG  GLU    85      -1.855  59.429  -5.685  1.00   .66       1SG1438
ATOM   1438  CD  GLU    85      -1.729  57.976  -5.250  1.00   .66       1SG1439
ATOM   1439  OE1 GLU    85      -1.673  57.730  -4.015  1.00   .66       1SG1440
ATOM   1440  OE2 GLU    85      -1.681  57.091  -6.147  1.00   .66       1SG1441
ATOM   1441  C   GLU    85      -1.242  62.191  -5.813  1.00   .66       1SG1442
ATOM   1442  O   GLU    85      -0.131  62.704  -5.709  1.00   .66       1SG1443
ATOM   1443  N   LEU    86      -1.879  61.934  -6.984  1.00   .61       1SG1444
ATOM   1444  CA  LEU    86      -1.377  62.133  -8.309  1.00   .61       1SG1445
ATOM   1445  CB  LEU    86      -2.296  61.570  -9.408  1.00   .61       1SG1446
ATOM   1446  CG  LEU    86      -2.574  60.060  -9.308  1.00   .61       1SG1447
ATOM   1447  CD2 LEU    86      -3.110  59.501 -10.636  1.00   .61       1SG1448
ATOM   1448  CD1 LEU    86      -3.489  59.743  -8.117  1.00   .61       1SG1449
ATOM   1449  C   LEU    86      -1.292  63.591  -8.578  1.00   .61       1SG1450
ATOM   1450  O   LEU    86      -0.250  64.084  -9.003  1.00   .61       1SG1451
ATOM   1451  N   GLU    87      -2.390  64.331  -8.329  1.00   .47       1SG1452
ATOM   1452  CA  GLU    87      -2.310  65.727  -8.637  1.00   .47       1SG1453
ATOM   1453  CB  GLU    87      -3.623  66.510  -8.446  1.00   .47       1SG1454
ATOM   1454  CG  GLU    87      -3.517  67.994  -8.808  1.00   .47       1SG1455
ATOM   1455  CD  GLU    87      -2.920  68.741  -7.623  1.00   .47       1SG1456
ATOM   1456  OE1 GLU    87      -2.870  68.153  -6.510  1.00   .47       1SG1457
ATOM   1457  OE2 GLU    87      -2.513  69.918  -7.816  1.00   .47       1SG1458
ATOM   1458  C   GLU    87      -1.276  66.279  -7.727  1.00   .47       1SG1459
ATOM   1459  O   GLU    87      -0.489  67.145  -8.111  1.00   .47       1SG1460
ATOM   1460  N   ASN    88      -1.240  65.763  -6.486  1.00   .33       1SG1461
ATOM   1461  CA  ASN    88      -0.240  66.239  -5.582  1.00   .33       1SG1462
ATOM   1462  CB  ASN    88      -0.286  65.522  -4.225  1.00   .33       1SG1463
ATOM   1463  CG  ASN    88      -1.608  65.876  -3.558  1.00   .33       1SG1464
ATOM   1464  OD1 ASN    88      -2.116  66.985  -3.718  1.00   .33       1SG1465
ATOM   1465  ND2 ASN    88      -2.182  64.911  -2.791  1.00   .33       1SG1466
ATOM   1466  C   ASN    88       1.082  65.938  -6.208  1.00   .33       1SG1467
ATOM   1467  O   ASN    88       1.958  66.801  -6.280  1.00   .33       1SG1468
ATOM   1468  N   LEU    89       1.254  64.697  -6.708  1.00   .33       1SG1469
ATOM   1469  CA  LEU    89       2.500  64.358  -7.339  1.00   .33       1SG1470
ATOM   1470  CB  LEU    89       2.669  62.837  -7.566  1.00   .33       1SG1471
ATOM   1471  CG  LEU    89       2.906  62.028  -6.279  1.00   .33       1SG1472
ATOM   1472  CD2 LEU    89       4.098  62.592  -5.486  1.00   .33       1SG1473
ATOM   1473  CD1 LEU    89       3.069  60.531  -6.583  1.00   .33       1SG1474
ATOM   1474  C   LEU    89       2.613  65.206  -8.585  1.00   .33       1SG1475
ATOM   1475  O   LEU    89       3.268  66.240  -8.483  1.00   .33       1SG1476
ATOM   1476  N   PRO    90       2.078  64.929  -9.758  1.00   .31       1SG1477
ATOM   1477  CA  PRO    90       2.230  65.960 -10.748  1.00   .31       1SG1478
ATOM   1478  CD  PRO    90       2.156  63.618 -10.398  1.00   .31       1SG1479
ATOM   1479  CB  PRO    90       2.319  65.283 -12.117  1.00   .31       1SG1480
ATOM   1480  CG  PRO    90       1.807  63.860 -11.872  1.00   .31       1SG1481
ATOM   1481  C   PRO    90       1.092  66.913 -10.629  1.00   .31       1SG1482
ATOM   1482  O   PRO    90      -0.003  66.599 -11.168  1.00   .31       1SG1483
ATOM   1483  OXT PRO    90       1.278  67.979  -9.983  1.00   .31       1SG1484
TER
END
