
#######################################################
#                                                     #
#                        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   17 (  134),  selected   17 , name T0356TS418_1_1-D1
# Molecule2: number of CA atoms  124 (  963),  selected   17 , name T0356_D1.pdb
# PARAMETERS: T0356TS418_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       318 - 330         4.47    11.94
  LCS_AVERAGE:      9.54

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       324 - 330         1.97    16.85
  LCS_AVERAGE:      4.60

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       323 - 326         0.77    11.97
  LONGEST_CONTINUOUS_SEGMENT:     4       324 - 327         0.97    13.36
  LONGEST_CONTINUOUS_SEGMENT:     4       327 - 330         0.42    17.04
  LCS_AVERAGE:      2.80

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    3    8     0    3    3    3    3    3    4    4    4    6    6    7    7    7    8    8    8    8   10   10 
LCS_GDT     A     315     A     315      3    5    8     1    3    3    4    5    5    6    6    6    6    6    7    7    7    8    8    8    9   10   10 
LCS_GDT     I     316     I     316      3    5    8     3    3    4    4    5    5    6    6    6    6    6    7    7    7    8    8    8    9   10   10 
LCS_GDT     Y     317     Y     317      3    5    8     3    3    4    4    5    5    6    6    6    6    6    7    7    7    8    9   12   13   14   14 
LCS_GDT     H     318     H     318      3    5   13     3    3    4    4    5    5    6    6    6    6    6    9   10   13   13   13   13   13   14   14 
LCS_GDT     S     319     S     319      3    5   13     3    3    4    4    5    5    6    8    9   11   12   12   12   13   13   13   13   13   14   14 
LCS_GDT     T     320     T     320      3    4   13     0    3    4    4    6    8    8    9   11   11   12   12   12   13   13   13   13   13   14   14 
LCS_GDT     Y     321     Y     321      3    4   13     0    3    4    4    5    8    8   10   11   11   12   12   12   13   13   13   13   13   14   14 
LCS_GDT     T     322     T     322      3    6   13     3    3    4    4    6    8    8   10   11   11   12   12   12   13   13   13   13   13   14   14 
LCS_GDT     G     323     G     323      4    6   13     3    4    4    5    6    8    8   10   11   11   12   12   12   13   13   13   13   13   14   14 
LCS_GDT     R     324     R     324      4    7   13     3    4    4    5    6    8    8   10   11   11   12   12   12   13   13   13   13   13   14   14 
LCS_GDT     P     325     P     325      4    7   13     3    4    4    5    6    8    8   10   11   11   12   12   12   13   13   13   13   13   14   14 
LCS_GDT     P     326     P     326      4    7   13     3    4    4    5    6    8    8   10   11   11   12   12   12   13   13   13   13   13   14   14 
LCS_GDT     D     327     D     327      4    7   13     3    4    4    5    6    8    8   10   11   11   12   12   12   13   13   13   13   13   14   14 
LCS_GDT     E     328     E     328      4    7   13     3    4    4    5    6    7    8   10   11   11   12   12   12   13   13   13   13   13   14   14 
LCS_GDT     P     329     P     329      4    7   13     3    4    4    5    6    7    8   10   11   11   12   12   12   13   13   13   13   13   14   14 
LCS_GDT     A     330     A     330      4    7   13     3    4    4    4    6    7    8   10   11   11   12   12   12   13   13   13   13   13   14   14 
LCS_AVERAGE  LCS_A:   5.65  (   2.80    4.60    9.54 )

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      4      4      5      6      8      8     10     11     11     12     12     12     13     13     13     13     13     14     14 
GDT PERCENT_CA   2.42   3.23   3.23   4.03   4.84   6.45   6.45   8.06   8.87   8.87   9.68   9.68   9.68  10.48  10.48  10.48  10.48  10.48  11.29  11.29
GDT RMS_LOCAL    0.04   0.42   0.42   1.28   1.68   2.21   2.21   2.97   3.05   3.05   3.56   3.56   3.56   4.47   4.47   4.47   4.47   4.47   5.85   5.85
GDT RMS_ALL_CA  16.68  17.04  17.04  14.73  16.31  13.03  13.03  14.18  13.69  13.69  12.84  12.84  12.84  11.94  11.94  11.94  11.94  11.94  10.94  10.94

#      Molecule1      Molecule2       DISTANCE
LGA    D     314      D     314         32.347
LGA    A     315      A     315         29.423
LGA    I     316      I     316         25.345
LGA    Y     317      Y     317         20.875
LGA    H     318      H     318         14.727
LGA    S     319      S     319         10.042
LGA    T     320      T     320          4.477
LGA    Y     321      Y     321          3.535
LGA    T     322      T     322          3.690
LGA    G     323      G     323          2.144
LGA    R     324      R     324          2.912
LGA    P     325      P     325          1.980
LGA    P     326      P     326          1.826
LGA    D     327      D     327          1.724
LGA    E     328      E     328          3.581
LGA    P     329      P     329          3.622
LGA    A     330      A     330          3.609

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   17  124    4.0     10    2.97     6.452     6.240     0.325

LGA_LOCAL      RMSD =  2.973  Number of atoms =   10  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 14.176  Number of atoms =   17 
Std_ALL_ATOMS  RMSD =  9.229  (standard rmsd on all 17 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.313790 * X  +   0.887121 * Y  +  -0.338455 * Z  +  10.590580
  Y_new =   0.912702 * X  +  -0.183552 * Y  +   0.365081 * Z  +  36.323696
  Z_new =   0.261747 * X  +  -0.423467 * Y  +  -0.867274 * Z  + 111.859291 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.687370    0.454223  [ DEG:  -153.9749     26.0251 ]
  Theta =  -0.264832   -2.876761  [ DEG:   -15.1737   -164.8263 ]
  Phi   =   1.239653   -1.901940  [ DEG:    71.0269   -108.9731 ]
 
# 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: T0356TS418_1_1-D1                             
REMARK     2: T0356_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0356TS418_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:   17  124   4.0   10   2.97   6.240     9.23
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS418_1_1-D1
REMARK PARENT number 1
PFRMAT TS
TARGET T0356
PARENT 1eje_A
ATOM   1375  N   ASP   314      59.303  57.523  74.606  1.00 58.14       1SG1376
ATOM   1376  CA  ASP   314      59.833  58.241  75.721  1.00 58.14       1SG1377
ATOM   1377  CB  ASP   314      61.338  58.517  75.568  1.00 58.14       1SG1378
ATOM   1378  CG  ASP   314      62.064  57.178  75.590  1.00 58.14       1SG1379
ATOM   1379  OD1 ASP   314      62.035  56.502  76.654  1.00 58.14       1SG1380
ATOM   1380  OD2 ASP   314      62.660  56.812  74.541  1.00 58.14       1SG1381
ATOM   1381  C   ASP   314      59.125  59.553  75.807  1.00 58.14       1SG1382
ATOM   1382  O   ASP   314      59.625  60.487  76.431  1.00 58.14       1SG1383
ATOM   1383  N   ALA   315      57.934  59.665  75.193  1.00 50.57       1SG1384
ATOM   1384  CA  ALA   315      57.255  60.920  75.285  1.00 50.57       1SG1385
ATOM   1385  CB  ALA   315      55.937  60.953  74.490  1.00 50.57       1SG1386
ATOM   1386  C   ALA   315      56.911  61.106  76.718  1.00 50.57       1SG1387
ATOM   1387  O   ALA   315      57.210  62.137  77.320  1.00 50.57       1SG1388
ATOM   1388  N   ILE   316      56.283  60.075  77.310  1.00 68.13       1SG1389
ATOM   1389  CA  ILE   316      55.967  60.155  78.697  1.00 68.13       1SG1390
ATOM   1390  CB  ILE   316      54.514  59.843  78.943  1.00 68.13       1SG1391
ATOM   1391  CG2 ILE   316      54.204  59.969  80.443  1.00 68.13       1SG1392
ATOM   1392  CG1 ILE   316      53.630  60.756  78.078  1.00 68.13       1SG1393
ATOM   1393  CD1 ILE   316      52.178  60.287  77.997  1.00 68.13       1SG1394
ATOM   1394  C   ILE   316      56.803  59.087  79.316  1.00 68.13       1SG1395
ATOM   1395  O   ILE   316      56.363  58.325  80.175  1.00 68.13       1SG1396
ATOM   1396  N   TYR   317      58.067  58.986  78.877  1.00123.08       1SG1397
ATOM   1397  CA  TYR   317      58.872  58.000  79.517  1.00123.08       1SG1398
ATOM   1398  CB  TYR   317      59.048  56.675  78.749  1.00123.08       1SG1399
ATOM   1399  CG  TYR   317      57.799  55.871  78.914  1.00123.08       1SG1400
ATOM   1400  CD1 TYR   317      57.554  55.224  80.106  1.00123.08       1SG1401
ATOM   1401  CD2 TYR   317      56.887  55.739  77.893  1.00123.08       1SG1402
ATOM   1402  CE1 TYR   317      56.415  54.475  80.283  1.00123.08       1SG1403
ATOM   1403  CE2 TYR   317      55.745  54.988  78.063  1.00123.08       1SG1404
ATOM   1404  CZ  TYR   317      55.508  54.357  79.262  1.00123.08       1SG1405
ATOM   1405  OH  TYR   317      54.339  53.586  79.444  1.00123.08       1SG1406
ATOM   1406  C   TYR   317      60.225  58.548  79.785  1.00123.08       1SG1407
ATOM   1407  O   TYR   317      60.899  59.043  78.884  1.00123.08       1SG1408
ATOM   1408  N   HIS   318      60.624  58.473  81.067  1.00255.55       1SG1409
ATOM   1409  CA  HIS   318      61.921  58.822  81.557  1.00255.55       1SG1410
ATOM   1410  ND1 HIS   318      61.544  61.560  79.458  1.00255.55       1SG1411
ATOM   1411  CG  HIS   318      62.495  60.895  80.202  1.00255.55       1SG1412
ATOM   1412  CB  HIS   318      62.255  60.325  81.569  1.00255.55       1SG1413
ATOM   1413  NE2 HIS   318      63.385  61.476  78.212  1.00255.55       1SG1414
ATOM   1414  CD2 HIS   318      63.612  60.855  79.429  1.00255.55       1SG1415
ATOM   1415  CE1 HIS   318      62.131  61.882  78.277  1.00255.55       1SG1416
ATOM   1416  C   HIS   318      61.908  58.371  82.975  1.00255.55       1SG1417
ATOM   1417  O   HIS   318      60.844  58.150  83.550  1.00255.55       1SG1418
ATOM   1418  N   SER   319      63.089  58.195  83.585  1.00 45.18       1SG1419
ATOM   1419  CA  SER   319      63.056  57.788  84.951  1.00 45.18       1SG1420
ATOM   1420  CB  SER   319      64.456  57.580  85.550  1.00 45.18       1SG1421
ATOM   1421  OG  SER   319      65.162  58.814  85.584  1.00 45.18       1SG1422
ATOM   1422  C   SER   319      62.390  58.898  85.695  1.00 45.18       1SG1423
ATOM   1423  O   SER   319      61.579  58.672  86.591  1.00 45.18       1SG1424
ATOM   1424  N   THR   320      62.713  60.144  85.309  1.00 27.30       1SG1425
ATOM   1425  CA  THR   320      62.166  61.291  85.968  1.00 27.30       1SG1426
ATOM   1426  CB  THR   320      62.720  62.572  85.417  1.00 27.30       1SG1427
ATOM   1427  OG1 THR   320      64.136  62.573  85.528  1.00 27.30       1SG1428
ATOM   1428  CG2 THR   320      62.122  63.753  86.203  1.00 27.30       1SG1429
ATOM   1429  C   THR   320      60.680  61.319  85.763  1.00 27.30       1SG1430
ATOM   1430  O   THR   320      59.923  61.498  86.714  1.00 27.30       1SG1431
ATOM   1431  N   TYR   321      60.222  61.118  84.513  1.00174.16       1SG1432
ATOM   1432  CA  TYR   321      58.819  61.203  84.227  1.00174.16       1SG1433
ATOM   1433  CB  TYR   321      58.534  61.261  82.720  1.00174.16       1SG1434
ATOM   1434  CG  TYR   321      59.172  62.569  82.405  1.00174.16       1SG1435
ATOM   1435  CD1 TYR   321      58.497  63.749  82.623  1.00174.16       1SG1436
ATOM   1436  CD2 TYR   321      60.458  62.621  81.926  1.00174.16       1SG1437
ATOM   1437  CE1 TYR   321      59.099  64.955  82.360  1.00174.16       1SG1438
ATOM   1438  CE2 TYR   321      61.070  63.821  81.661  1.00174.16       1SG1439
ATOM   1439  CZ  TYR   321      60.386  64.990  81.880  1.00174.16       1SG1440
ATOM   1440  OH  TYR   321      61.011  66.224  81.608  1.00174.16       1SG1441
ATOM   1441  C   TYR   321      58.095  60.097  84.924  1.00174.16       1SG1442
ATOM   1442  O   TYR   321      56.979  60.288  85.402  1.00174.16       1SG1443
ATOM   1443  N   THR   322      58.715  58.902  84.969  1.00165.00       1SG1444
ATOM   1444  CA  THR   322      58.216  57.762  85.685  1.00165.00       1SG1445
ATOM   1445  CB  THR   322      58.342  57.860  87.186  1.00165.00       1SG1446
ATOM   1446  OG1 THR   322      58.048  56.602  87.777  1.00165.00       1SG1447
ATOM   1447  CG2 THR   322      57.384  58.928  87.739  1.00165.00       1SG1448
ATOM   1448  C   THR   322      56.798  57.465  85.323  1.00165.00       1SG1449
ATOM   1449  O   THR   322      55.986  57.131  86.185  1.00165.00       1SG1450
ATOM   1450  N   GLY   323      56.462  57.580  84.027  1.00 30.25       1SG1451
ATOM   1451  CA  GLY   323      55.159  57.187  83.581  1.00 30.25       1SG1452
ATOM   1452  C   GLY   323      54.197  58.304  83.795  1.00 30.25       1SG1453
ATOM   1453  O   GLY   323      53.039  58.212  83.392  1.00 30.25       1SG1454
ATOM   1454  N   ARG   324      54.639  59.396  84.435  1.00104.05       1SG1455
ATOM   1455  CA  ARG   324      53.690  60.448  84.610  1.00104.05       1SG1456
ATOM   1456  CB  ARG   324      54.083  61.458  85.701  1.00104.05       1SG1457
ATOM   1457  CG  ARG   324      54.006  60.827  87.095  1.00104.05       1SG1458
ATOM   1458  CD  ARG   324      54.360  61.755  88.259  1.00104.05       1SG1459
ATOM   1459  NE  ARG   324      54.094  60.989  89.512  1.00104.05       1SG1460
ATOM   1460  CZ  ARG   324      54.822  61.221  90.641  1.00104.05       1SG1461
ATOM   1461  NH1 ARG   324      55.812  62.164  90.634  1.00104.05       1SG1462
ATOM   1462  NH2 ARG   324      54.562  60.511  91.779  1.00104.05       1SG1463
ATOM   1463  C   ARG   324      53.578  61.114  83.286  1.00104.05       1SG1464
ATOM   1464  O   ARG   324      54.571  61.511  82.677  1.00104.05       1SG1465
ATOM   1465  N   PRO   325      52.360  61.262  82.855  1.00148.37       1SG1466
ATOM   1466  CA  PRO   325      52.047  61.721  81.535  1.00148.37       1SG1467
ATOM   1467  CD  PRO   325      51.196  61.177  83.723  1.00148.37       1SG1468
ATOM   1468  CB  PRO   325      50.515  61.799  81.481  1.00148.37       1SG1469
ATOM   1469  CG  PRO   325      50.081  61.907  82.956  1.00148.37       1SG1470
ATOM   1470  C   PRO   325      52.759  62.978  81.151  1.00148.37       1SG1471
ATOM   1471  O   PRO   325      53.044  63.113  79.963  1.00148.37       1SG1472
ATOM   1472  N   PRO   326      53.048  63.896  82.020  1.00159.41       1SG1473
ATOM   1473  CA  PRO   326      53.744  65.048  81.522  1.00159.41       1SG1474
ATOM   1474  CD  PRO   326      52.101  64.258  83.061  1.00159.41       1SG1475
ATOM   1475  CB  PRO   326      53.469  66.178  82.507  1.00159.41       1SG1476
ATOM   1476  CG  PRO   326      52.122  65.790  83.137  1.00159.41       1SG1477
ATOM   1477  C   PRO   326      55.205  64.817  81.305  1.00159.41       1SG1478
ATOM   1478  O   PRO   326      55.827  64.097  82.085  1.00159.41       1SG1479
ATOM   1479  N   ASP   327      55.760  65.421  80.242  1.00113.80       1SG1480
ATOM   1480  CA  ASP   327      57.170  65.431  79.989  1.00113.80       1SG1481
ATOM   1481  CB  ASP   327      57.630  64.338  79.010  1.00113.80       1SG1482
ATOM   1482  CG  ASP   327      59.150  64.369  78.900  1.00113.80       1SG1483
ATOM   1483  OD1 ASP   327      59.771  65.405  79.257  1.00113.80       1SG1484
ATOM   1484  OD2 ASP   327      59.714  63.340  78.443  1.00113.80       1SG1485
ATOM   1485  C   ASP   327      57.387  66.748  79.320  1.00113.80       1SG1486
ATOM   1486  O   ASP   327      57.565  66.820  78.106  1.00113.80       1SG1487
ATOM   1487  N   GLU   328      57.384  67.838  80.105  1.00120.38       1SG1488
ATOM   1488  CA  GLU   328      57.458  69.127  79.488  1.00120.38       1SG1489
ATOM   1489  CB  GLU   328      57.069  70.306  80.416  1.00120.38       1SG1490
ATOM   1490  CG  GLU   328      57.814  70.431  81.747  1.00120.38       1SG1491
ATOM   1491  CD  GLU   328      57.143  71.532  82.547  1.00120.38       1SG1492
ATOM   1492  OE1 GLU   328      55.937  71.360  82.869  1.00120.38       1SG1493
ATOM   1493  OE2 GLU   328      57.816  72.556  82.843  1.00120.38       1SG1494
ATOM   1494  C   GLU   328      58.772  69.366  78.804  1.00120.38       1SG1495
ATOM   1495  O   GLU   328      58.772  69.989  77.744  1.00120.38       1SG1496
ATOM   1496  N   PRO   329      59.899  68.932  79.303  1.00 93.51       1SG1497
ATOM   1497  CA  PRO   329      61.117  69.219  78.598  1.00 93.51       1SG1498
ATOM   1498  CD  PRO   329      60.129  68.801  80.731  1.00 93.51       1SG1499
ATOM   1499  CB  PRO   329      62.254  68.876  79.558  1.00 93.51       1SG1500
ATOM   1500  CG  PRO   329      61.624  69.087  80.946  1.00 93.51       1SG1501
ATOM   1501  C   PRO   329      61.202  68.516  77.284  1.00 93.51       1SG1502
ATOM   1502  O   PRO   329      61.891  69.011  76.393  1.00 93.51       1SG1503
ATOM   1503  N   ALA   330      60.519  67.366  77.136  1.00 18.81       1SG1504
ATOM   1504  CA  ALA   330      60.630  66.630  75.914  1.00 18.81       1SG1505
ATOM   1505  CB  ALA   330      59.875  65.290  75.941  1.00 18.81       1SG1506
ATOM   1506  C   ALA   330      60.046  67.465  74.783  1.00 18.81       1SG1507
ATOM   1507  O   ALA   330      58.807  67.384  74.573  1.00 18.81       1SG1508
ATOM   1508  OXT ALA   330      60.828  68.187  74.110  1.00 18.81       1SG1509
TER
END
