
#######################################################
#                                                     #
#                        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   18 (  141),  selected   18 , name T0356TS213_1_1-D1
# Molecule2: number of CA atoms  124 (  963),  selected   18 , name T0356_D1.pdb
# PARAMETERS: T0356TS213_1_1-D1.T0356_D1.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:    13       319 - 331         4.50    11.14
  LCS_AVERAGE:      9.32

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8       324 - 331         1.95    17.96
  LCS_AVERAGE:      5.42

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       327 - 331         0.42    17.06
  LCS_AVERAGE:      3.36

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:  124
LCS_GDT     D     314     D     314      3    4    7     0    3    3    3    4    4    4    4    4    5    5    6    6    7    7    7    7    8    9   10 
LCS_GDT     A     315     A     315      3    5    7     3    3    4    5    5    5    5    6    6    6    6    7    7    8    8    9    9    9    9   10 
LCS_GDT     I     316     I     316      4    5    7     3    3    4    5    5    5    5    6    6    6    6    7    7    8    8    9    9    9    9   10 
LCS_GDT     Y     317     Y     317      4    5    7     3    3    4    5    5    5    5    6    6    6    6    7    7    8    8    9    9   10   10   11 
LCS_GDT     H     318     H     318      4    5   11     3    3    4    5    5    5    5    6    6    6    6    7   10   10   13   14   14   14   14   14 
LCS_GDT     S     319     S     319      4    5   13     3    3    4    5    5    5    7    8    9   10   10   11   12   12   13   14   14   14   14   14 
LCS_GDT     T     320     T     320      4    7   13     0    3    4    5    6    8    9    9    9   10   10   11   12   12   13   14   14   14   14   14 
LCS_GDT     Y     321     Y     321      4    7   13     3    3    4    5    6    8    9    9    9   10   11   11   12   12   13   14   14   14   14   14 
LCS_GDT     T     322     T     322      4    7   13     3    3    4    5    6    8    9    9    9   10   11   11   12   12   13   14   14   14   14   14 
LCS_GDT     G     323     G     323      4    7   13     3    4    4    5    6    8    9    9    9   10   11   11   12   12   13   14   14   14   14   14 
LCS_GDT     R     324     R     324      4    8   13     3    4    5    6    7    8    9    9    9   10   11   11   12   12   13   14   14   14   14   14 
LCS_GDT     P     325     P     325      4    8   13     3    4    4    5    6    8    9    9    9   10   11   11   12   12   13   14   14   14   14   14 
LCS_GDT     P     326     P     326      4    8   13     2    4    5    6    7    8    9    9    9   10   11   11   12   12   13   14   14   14   14   14 
LCS_GDT     D     327     D     327      5    8   13     3    5    5    6    7    8    9    9    9   10   11   11   12   12   13   14   14   14   14   14 
LCS_GDT     E     328     E     328      5    8   13     3    5    5    6    7    7    8    8    9   10   11   11   12   12   13   14   14   14   14   14 
LCS_GDT     P     329     P     329      5    8   13     3    5    5    6    7    7    8    8    9    9   11   11   12   12   13   14   14   14   14   14 
LCS_GDT     A     330     A     330      5    8   13     3    5    5    6    7    7    8    8    9   10   11   11   12   12   13   14   14   14   14   14 
LCS_GDT     V     331     V     331      5    8   13     3    5    5    6    7    8    9    9    9   10   11   11   12   12   13   14   14   14   14   14 
LCS_AVERAGE  LCS_A:   6.03  (   3.36    5.42    9.32 )

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      3      5      5      6      7      8      9      9      9     10     11     11     12     12     13     14     14     14     14     14 
GDT PERCENT_CA   2.42   4.03   4.03   4.84   5.65   6.45   7.26   7.26   7.26   8.06   8.87   8.87   9.68   9.68  10.48  11.29  11.29  11.29  11.29  11.29
GDT RMS_LOCAL    0.05   0.42   0.42   1.27   1.48   2.24   2.40   2.40   2.40   3.02   3.79   3.54   4.05   4.05   4.50   5.16   5.16   5.16   5.16   5.16
GDT RMS_ALL_CA  16.72  17.06  17.06  17.76  17.89  11.55  11.61  11.61  11.61  11.19  13.49  11.40  12.14  12.14  11.14  10.45  10.45  10.45  10.45  10.45

#      Molecule1      Molecule2       DISTANCE
LGA    D     314      D     314         23.563
LGA    A     315      A     315         23.967
LGA    I     316      I     316         21.997
LGA    Y     317      Y     317         18.060
LGA    H     318      H     318         12.621
LGA    S     319      S     319          7.639
LGA    T     320      T     320          2.341
LGA    Y     321      Y     321          1.852
LGA    T     322      T     322          2.129
LGA    G     323      G     323          1.707
LGA    R     324      R     324          3.183
LGA    P     325      P     325          1.106
LGA    P     326      P     326          2.589
LGA    D     327      D     327          2.958
LGA    E     328      E     328          7.597
LGA    P     329      P     329         10.309
LGA    A     330      A     330          7.339
LGA    V     331      V     331          2.968

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   18  124    4.0      9    2.40     6.855     6.519     0.360

LGA_LOCAL      RMSD =  2.403  Number of atoms =    9  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 11.612  Number of atoms =   18 
Std_ALL_ATOMS  RMSD =  9.050  (standard rmsd on all 18 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.431972 * X  +   0.896429 * Y  +   0.099069 * Z  +  25.106897
  Y_new =   0.847225 * X  +   0.365675 * Y  +   0.385346 * Z  +  15.121372
  Z_new =   0.309208 * X  +   0.250392 * Y  +  -0.917439 * Z  +  74.648590 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.875156   -0.266436  [ DEG:   164.7343    -15.2657 ]
  Theta =  -0.314360   -2.827232  [ DEG:   -18.0115   -161.9885 ]
  Phi   =   2.042307   -1.099286  [ DEG:   117.0155    -62.9844 ]
 
# 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: T0356TS213_1_1-D1                             
REMARK     2: T0356_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0356TS213_1_1-D1.T0356_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   18  124   4.0    9   2.40   6.519     9.05
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS213_1_1-D1
REMARK PARENT number 1
PFRMAT TS
TARGET T0356
PARENT 1eje_A
ATOM   1375  N   ASP   314      63.603  67.385  79.206  1.00 59.03       1SG1376
ATOM   1376  CA  ASP   314      62.594  68.024  80.005  1.00 59.03       1SG1377
ATOM   1377  CB  ASP   314      62.975  69.443  80.466  1.00 59.03       1SG1378
ATOM   1378  CG  ASP   314      64.020  69.362  81.568  1.00 59.03       1SG1379
ATOM   1379  OD1 ASP   314      64.440  68.226  81.914  1.00 59.03       1SG1380
ATOM   1380  OD2 ASP   314      64.409  70.444  82.081  1.00 59.03       1SG1381
ATOM   1381  C   ASP   314      61.354  68.175  79.188  1.00 59.03       1SG1382
ATOM   1382  O   ASP   314      60.357  68.713  79.667  1.00 59.03       1SG1383
ATOM   1383  N   ALA   315      61.366  67.683  77.938  1.00 63.20       1SG1384
ATOM   1384  CA  ALA   315      60.204  67.850  77.115  1.00 63.20       1SG1385
ATOM   1385  CB  ALA   315      60.435  67.391  75.666  1.00 63.20       1SG1386
ATOM   1386  C   ALA   315      59.081  67.031  77.655  1.00 63.20       1SG1387
ATOM   1387  O   ALA   315      57.964  67.509  77.851  1.00 63.20       1SG1388
ATOM   1388  N   ILE   316      59.379  65.756  77.938  1.00 66.84       1SG1389
ATOM   1389  CA  ILE   316      58.370  64.860  78.400  1.00 66.84       1SG1390
ATOM   1390  CB  ILE   316      57.736  64.086  77.264  1.00 66.84       1SG1391
ATOM   1391  CG2 ILE   316      56.654  63.106  77.759  1.00 66.84       1SG1392
ATOM   1392  CG1 ILE   316      57.119  65.136  76.326  1.00 66.84       1SG1393
ATOM   1393  CD1 ILE   316      56.417  64.564  75.099  1.00 66.84       1SG1394
ATOM   1394  C   ILE   316      59.042  64.006  79.421  1.00 66.84       1SG1395
ATOM   1395  O   ILE   316      60.221  64.214  79.708  1.00 66.84       1SG1396
ATOM   1396  N   TYR   317      58.289  63.065  80.023  1.00245.16       1SG1397
ATOM   1397  CA  TYR   317      58.753  62.257  81.105  1.00245.16       1SG1398
ATOM   1398  CB  TYR   317      57.805  61.087  81.461  1.00245.16       1SG1399
ATOM   1399  CG  TYR   317      57.821  59.999  80.436  1.00245.16       1SG1400
ATOM   1400  CD1 TYR   317      58.733  58.973  80.527  1.00245.16       1SG1401
ATOM   1401  CD2 TYR   317      56.909  59.983  79.405  1.00245.16       1SG1402
ATOM   1402  CE1 TYR   317      58.751  57.958  79.600  1.00245.16       1SG1403
ATOM   1403  CE2 TYR   317      56.921  58.971  78.473  1.00245.16       1SG1404
ATOM   1404  CZ  TYR   317      57.842  57.957  78.571  1.00245.16       1SG1405
ATOM   1405  OH  TYR   317      57.856  56.913  77.619  1.00245.16       1SG1406
ATOM   1406  C   TYR   317      60.102  61.718  80.790  1.00245.16       1SG1407
ATOM   1407  O   TYR   317      60.320  61.072  79.770  1.00245.16       1SG1408
ATOM   1408  N   HIS   318      61.053  62.008  81.696  1.00185.94       1SG1409
ATOM   1409  CA  HIS   318      62.423  61.634  81.555  1.00185.94       1SG1410
ATOM   1410  ND1 HIS   318      65.817  62.234  81.499  1.00185.94       1SG1411
ATOM   1411  CG  HIS   318      64.687  62.564  80.785  1.00185.94       1SG1412
ATOM   1412  CB  HIS   318      63.341  62.861  81.381  1.00185.94       1SG1413
ATOM   1413  NE2 HIS   318      66.405  62.246  79.356  1.00185.94       1SG1414
ATOM   1414  CD2 HIS   318      65.064  62.570  79.477  1.00185.94       1SG1415
ATOM   1415  CE1 HIS   318      66.812  62.050  80.596  1.00185.94       1SG1416
ATOM   1416  C   HIS   318      62.777  60.967  82.843  1.00185.94       1SG1417
ATOM   1417  O   HIS   318      61.913  60.434  83.537  1.00185.94       1SG1418
ATOM   1418  N   SER   319      64.075  60.959  83.187  1.00 80.95       1SG1419
ATOM   1419  CA  SER   319      64.493  60.338  84.403  1.00 80.95       1SG1420
ATOM   1420  CB  SER   319      66.010  60.458  84.639  1.00 80.95       1SG1421
ATOM   1421  OG  SER   319      66.723  59.756  83.631  1.00 80.95       1SG1422
ATOM   1422  C   SER   319      63.807  61.034  85.534  1.00 80.95       1SG1423
ATOM   1423  O   SER   319      63.126  60.399  86.338  1.00 80.95       1SG1424
ATOM   1424  N   THR   320      63.938  62.375  85.604  1.00 92.73       1SG1425
ATOM   1425  CA  THR   320      63.347  63.084  86.700  1.00 92.73       1SG1426
ATOM   1426  CB  THR   320      63.614  64.563  86.678  1.00 92.73       1SG1427
ATOM   1427  OG1 THR   320      63.071  65.143  85.502  1.00 92.73       1SG1428
ATOM   1428  CG2 THR   320      65.133  64.805  86.744  1.00 92.73       1SG1429
ATOM   1429  C   THR   320      61.868  62.884  86.652  1.00 92.73       1SG1430
ATOM   1430  O   THR   320      61.258  62.522  87.657  1.00 92.73       1SG1431
ATOM   1431  N   TYR   321      61.237  63.077  85.477  1.00137.75       1SG1432
ATOM   1432  CA  TYR   321      59.824  62.867  85.492  1.00137.75       1SG1433
ATOM   1433  CB  TYR   321      59.056  63.970  84.750  1.00137.75       1SG1434
ATOM   1434  CG  TYR   321      59.328  65.196  85.551  1.00137.75       1SG1435
ATOM   1435  CD1 TYR   321      58.672  65.404  86.742  1.00137.75       1SG1436
ATOM   1436  CD2 TYR   321      60.237  66.135  85.118  1.00137.75       1SG1437
ATOM   1437  CE1 TYR   321      58.923  66.529  87.492  1.00137.75       1SG1438
ATOM   1438  CE2 TYR   321      60.492  67.263  85.864  1.00137.75       1SG1439
ATOM   1439  CZ  TYR   321      59.833  67.461  87.053  1.00137.75       1SG1440
ATOM   1440  OH  TYR   321      60.093  68.616  87.820  1.00137.75       1SG1441
ATOM   1441  C   TYR   321      59.595  61.543  84.854  1.00137.75       1SG1442
ATOM   1442  O   TYR   321      59.413  61.430  83.646  1.00137.75       1SG1443
ATOM   1443  N   THR   322      59.578  60.492  85.693  1.00116.63       1SG1444
ATOM   1444  CA  THR   322      59.476  59.154  85.202  1.00116.63       1SG1445
ATOM   1445  CB  THR   322      60.210  58.170  86.067  1.00116.63       1SG1446
ATOM   1446  OG1 THR   322      60.121  56.863  85.518  1.00116.63       1SG1447
ATOM   1447  CG2 THR   322      59.606  58.202  87.484  1.00116.63       1SG1448
ATOM   1448  C   THR   322      58.046  58.741  85.166  1.00116.63       1SG1449
ATOM   1449  O   THR   322      57.278  59.014  86.087  1.00116.63       1SG1450
ATOM   1450  N   GLY   323      57.651  58.089  84.057  1.00 63.54       1SG1451
ATOM   1451  CA  GLY   323      56.326  57.561  83.954  1.00 63.54       1SG1452
ATOM   1452  C   GLY   323      55.369  58.690  84.080  1.00 63.54       1SG1453
ATOM   1453  O   GLY   323      54.285  58.533  84.640  1.00 63.54       1SG1454
ATOM   1454  N   ARG   324      55.749  59.870  83.569  1.00273.36       1SG1455
ATOM   1455  CA  ARG   324      54.873  60.995  83.662  1.00273.36       1SG1456
ATOM   1456  CB  ARG   324      55.560  62.280  84.143  1.00273.36       1SG1457
ATOM   1457  CG  ARG   324      54.619  63.484  84.210  1.00273.36       1SG1458
ATOM   1458  CD  ARG   324      55.368  64.811  84.347  1.00273.36       1SG1459
ATOM   1459  NE  ARG   324      56.308  64.895  83.193  1.00273.36       1SG1460
ATOM   1460  CZ  ARG   324      57.101  65.992  83.033  1.00273.36       1SG1461
ATOM   1461  NH1 ARG   324      57.029  67.022  83.927  1.00273.36       1SG1462
ATOM   1462  NH2 ARG   324      57.962  66.064  81.975  1.00273.36       1SG1463
ATOM   1463  C   ARG   324      54.372  61.273  82.290  1.00273.36       1SG1464
ATOM   1464  O   ARG   324      54.958  60.870  81.288  1.00273.36       1SG1465
ATOM   1465  N   PRO   325      53.259  61.942  82.256  1.00185.93       1SG1466
ATOM   1466  CA  PRO   325      52.685  62.325  81.001  1.00185.93       1SG1467
ATOM   1467  CD  PRO   325      52.249  61.733  83.281  1.00185.93       1SG1468
ATOM   1468  CB  PRO   325      51.245  62.734  81.318  1.00185.93       1SG1469
ATOM   1469  CG  PRO   325      50.900  61.913  82.572  1.00185.93       1SG1470
ATOM   1470  C   PRO   325      53.553  63.410  80.461  1.00185.93       1SG1471
ATOM   1471  O   PRO   325      54.357  63.933  81.232  1.00185.93       1SG1472
ATOM   1472  N   PRO   326      53.441  63.737  79.200  1.00 89.35       1SG1473
ATOM   1473  CA  PRO   326      54.289  64.731  78.602  1.00 89.35       1SG1474
ATOM   1474  CD  PRO   326      52.183  63.597  78.482  1.00 89.35       1SG1475
ATOM   1475  CB  PRO   326      53.707  64.986  77.215  1.00 89.35       1SG1476
ATOM   1476  CG  PRO   326      52.208  64.700  77.410  1.00 89.35       1SG1477
ATOM   1477  C   PRO   326      54.269  65.977  79.423  1.00 89.35       1SG1478
ATOM   1478  O   PRO   326      53.199  66.377  79.882  1.00 89.35       1SG1479
ATOM   1479  N   ASP   327      55.447  66.592  79.634  1.00 57.39       1SG1480
ATOM   1480  CA  ASP   327      55.490  67.793  80.412  1.00 57.39       1SG1481
ATOM   1481  CB  ASP   327      56.921  68.340  80.565  1.00 57.39       1SG1482
ATOM   1482  CG  ASP   327      56.938  69.420  81.637  1.00 57.39       1SG1483
ATOM   1483  OD1 ASP   327      55.843  69.924  81.999  1.00 57.39       1SG1484
ATOM   1484  OD2 ASP   327      58.057  69.760  82.107  1.00 57.39       1SG1485
ATOM   1485  C   ASP   327      54.665  68.789  79.666  1.00 57.39       1SG1486
ATOM   1486  O   ASP   327      55.114  69.373  78.682  1.00 57.39       1SG1487
ATOM   1487  N   GLU   328      53.418  69.009  80.122  1.00118.76       1SG1488
ATOM   1488  CA  GLU   328      52.541  69.894  79.413  1.00118.76       1SG1489
ATOM   1489  CB  GLU   328      51.098  69.881  79.961  1.00118.76       1SG1490
ATOM   1490  CG  GLU   328      50.047  70.501  79.028  1.00118.76       1SG1491
ATOM   1491  CD  GLU   328      50.031  72.018  79.188  1.00118.76       1SG1492
ATOM   1492  OE1 GLU   328      49.368  72.500  80.145  1.00118.76       1SG1493
ATOM   1493  OE2 GLU   328      50.669  72.712  78.352  1.00118.76       1SG1494
ATOM   1494  C   GLU   328      53.051  71.298  79.487  1.00118.76       1SG1495
ATOM   1495  O   GLU   328      53.102  71.984  78.468  1.00118.76       1SG1496
ATOM   1496  N   PRO   329      53.452  71.771  80.635  1.00103.39       1SG1497
ATOM   1497  CA  PRO   329      53.880  73.137  80.688  1.00103.39       1SG1498
ATOM   1498  CD  PRO   329      52.908  71.326  81.907  1.00103.39       1SG1499
ATOM   1499  CB  PRO   329      54.032  73.474  82.168  1.00103.39       1SG1500
ATOM   1500  CG  PRO   329      53.006  72.544  82.844  1.00103.39       1SG1501
ATOM   1501  C   PRO   329      55.088  73.391  79.859  1.00103.39       1SG1502
ATOM   1502  O   PRO   329      55.162  74.447  79.234  1.00103.39       1SG1503
ATOM   1503  N   ALA   330      56.049  72.452  79.845  1.00 31.03       1SG1504
ATOM   1504  CA  ALA   330      57.229  72.652  79.062  1.00 31.03       1SG1505
ATOM   1505  CB  ALA   330      58.270  71.537  79.257  1.00 31.03       1SG1506
ATOM   1506  C   ALA   330      56.827  72.647  77.627  1.00 31.03       1SG1507
ATOM   1507  O   ALA   330      57.272  73.477  76.835  1.00 31.03       1SG1508
ATOM   1508  N   VAL   331      55.937  71.703  77.271  1.00 87.00       1SG1509
ATOM   1509  CA  VAL   331      55.536  71.539  75.907  1.00 87.00       1SG1510
ATOM   1510  CB  VAL   331      54.861  70.221  75.664  1.00 87.00       1SG1511
ATOM   1511  CG1 VAL   331      55.845  69.105  76.053  1.00 87.00       1SG1512
ATOM   1512  CG2 VAL   331      53.539  70.177  76.446  1.00 87.00       1SG1513
ATOM   1513  C   VAL   331      54.557  72.647  75.540  1.00 87.00       1SG1514
ATOM   1514  O   VAL   331      54.170  72.709  74.341  1.00 87.00       1SG1515
ATOM   1515  OXT VAL   331      54.188  73.445  76.443  1.00 87.00       1SG1516
TER
END
