
#######################################################
#                                                     #
#                        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   10 (   84),  selected   10 , name T0386TS074_3_2-D1
# Molecule2: number of CA atoms  206 ( 1668),  selected   10 , name T0386_D1.pdb
# PARAMETERS: T0386TS074_3_2-D1.T0386_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:    10       209 - 218         0.83     0.83
  LCS_AVERAGE:      4.85

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10       209 - 218         0.83     0.83
  LCS_AVERAGE:      4.85

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10       209 - 218         0.83     0.83
  LCS_AVERAGE:      4.85

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:  206
LCS_GDT     P     209     P     209     10   10   10     3    6   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     M     210     M     210     10   10   10     6    9   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     Q     211     Q     211     10   10   10     5    9   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     H     212     H     212     10   10   10     5    9   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     L     213     L     213     10   10   10     5    9   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     F     214     F     214     10   10   10     6    9   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     E     215     E     215     10   10   10     6    9   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     D     216     D     216     10   10   10     6    9   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     I     217     I     217     10   10   10     6    9   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     S     218     S     218     10   10   10     6    9   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10 
LCS_AVERAGE  LCS_A:   4.85  (   4.85    4.85    4.85 )

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      9     10     10     10     10     10     10     10     10     10     10     10     10     10     10     10     10     10     10 
GDT PERCENT_CA   2.91   4.37   4.85   4.85   4.85   4.85   4.85   4.85   4.85   4.85   4.85   4.85   4.85   4.85   4.85   4.85   4.85   4.85   4.85   4.85
GDT RMS_LOCAL    0.22   0.61   0.83   0.83   0.83   0.83   0.83   0.83   0.83   0.83   0.83   0.83   0.83   0.83   0.83   0.83   0.83   0.83   0.83   0.83
GDT RMS_ALL_CA   1.38   0.95   0.83   0.83   0.83   0.83   0.83   0.83   0.83   0.83   0.83   0.83   0.83   0.83   0.83   0.83   0.83   0.83   0.83   0.83

#      Molecule1      Molecule2       DISTANCE
LGA    P     209      P     209          1.523
LGA    M     210      M     210          1.070
LGA    Q     211      Q     211          0.640
LGA    H     212      H     212          0.687
LGA    L     213      L     213          0.341
LGA    F     214      F     214          0.376
LGA    E     215      E     215          0.749
LGA    D     216      D     216          0.851
LGA    I     217      I     217          0.750
LGA    S     218      S     218          0.698

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   10  206    4.0     10    0.83     4.733     4.816     1.072

LGA_LOCAL      RMSD =  0.833  Number of atoms =   10  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  0.833  Number of atoms =   10 
Std_ALL_ATOMS  RMSD =  0.833  (standard rmsd on all 10 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.254532 * X  +  -0.950187 * Y  +  -0.179882 * Z  +  66.300636
  Y_new =  -0.902797 * X  +  -0.166793 * Y  +  -0.396406 * Z  +  58.372997
  Z_new =   0.346656 * X  +   0.263295 * Y  +  -0.900281 * Z  +  52.263191 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.857069   -0.284524  [ DEG:   163.6980    -16.3020 ]
  Theta =  -0.354004   -2.787588  [ DEG:   -20.2829   -159.7171 ]
  Phi   =  -1.295992    1.845601  [ DEG:   -74.2549    105.7451 ]
 
# 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: T0386TS074_3_2-D1                             
REMARK     2: T0386_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0386TS074_3_2-D1.T0386_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   10  206   4.0   10   0.83   4.816     0.83
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS074_3_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0386
PARENT 2g03_A
ATOM   1386  N   PRO   209      15.910  49.589  68.704  1.00  0.57
ATOM   1387  CA  PRO   209      15.694  50.783  67.901  1.00  0.57
ATOM   1388  C   PRO   209      14.234  50.753  67.551  1.00  0.57
ATOM   1389  O   PRO   209      13.499  51.624  68.002  1.00  0.57
ATOM   1390  CB  PRO   209      16.457  50.791  66.564  1.00  0.57
ATOM   1391  CG  PRO   209      17.311  49.550  66.298  1.00  0.67
ATOM   1392  CD  PRO   209      16.370  48.511  67.380  1.00  0.67
ATOM   1393  N   MET   210      13.847  49.699  66.814  1.00  0.50
ATOM   1394  CA  MET   210      12.515  49.557  66.289  1.00  0.50
ATOM   1395  C   MET   210      11.406  49.636  67.303  1.00  0.50
ATOM   1396  O   MET   210      10.535  50.477  67.142  1.00  0.50
ATOM   1397  CB  MET   210      12.428  48.243  65.514  1.00  0.50
ATOM   1398  CG  MET   210      13.304  48.170  64.259  1.00  0.60
ATOM   1399  SD  MET   210      12.785  49.376  62.974  1.00  0.60
ATOM   1400  CE  MET   210      11.253  48.678  62.455  1.00  0.80
ATOM   1401  N   GLN   211      11.571  48.940  68.405  1.00  0.50
ATOM   1402  CA  GLN   211      10.393  48.896  69.273  1.00  0.50
ATOM   1403  C   GLN   211      10.354  50.033  70.316  1.00  0.50
ATOM   1404  O   GLN   211       9.301  50.620  70.548  1.00  0.50
ATOM   1405  CB  GLN   211      10.251  47.519  69.941  1.00  0.50
ATOM   1406  CG  GLN   211       9.027  47.353  70.800  1.00  0.60
ATOM   1407  CD  GLN   211       7.746  47.407  70.105  1.00  0.60
ATOM   1408  OE1 GLN   211       7.504  46.575  69.212  1.00  0.80
ATOM   1409  NE2 GLN   211       6.856  48.323  70.478  1.00  0.80
ATOM   1410  N   HIS   212      11.493  50.361  70.916  1.00  0.50
ATOM   1411  CA  HIS   212      11.537  51.380  71.951  1.00  0.50
ATOM   1412  C   HIS   212      11.281  52.787  71.391  1.00  0.50
ATOM   1413  O   HIS   212      10.531  53.583  71.981  1.00  0.50
ATOM   1414  CB  HIS   212      12.868  51.329  72.687  1.00  0.50
ATOM   1415  CG  HIS   212      12.993  52.319  73.852  1.00  0.60
ATOM   1416  ND1 HIS   212      13.298  53.671  73.618  1.00  0.60
ATOM   1417  CD2 HIS   212      12.750  52.118  75.134  1.00  0.80
ATOM   1418  CE1 HIS   212      13.266  54.324  74.825  1.00  0.80
ATOM   1419  NE2 HIS   212      12.930  53.366  75.777  1.00  1.10
ATOM   1420  N   LEU   213      11.892  53.090  70.246  1.00  0.50
ATOM   1421  CA  LEU   213      11.668  54.354  69.556  1.00  0.50
ATOM   1422  C   LEU   213      10.214  54.461  69.119  1.00  0.50
ATOM   1423  O   LEU   213       9.590  55.506  69.309  1.00  0.50
ATOM   1424  CB  LEU   213      12.648  54.532  68.359  1.00  0.50
ATOM   1425  CG  LEU   213      12.503  55.948  67.801  1.00  0.60
ATOM   1426  CD1 LEU   213      13.788  56.463  67.332  1.00  0.60
ATOM   1427  CD2 LEU   213      11.658  55.753  66.393  1.00  0.80
ATOM   1428  N   PHE   214       9.662  53.396  68.541  1.00  0.50
ATOM   1429  CA  PHE   214       8.258  53.429  68.122  1.00  0.50
ATOM   1430  C   PHE   214       7.323  53.649  69.345  1.00  0.50
ATOM   1431  O   PHE   214       6.570  54.617  69.398  1.00  0.50
ATOM   1432  CB  PHE   214       7.850  52.154  67.338  1.00  0.50
ATOM   1433  CG  PHE   214       8.622  52.072  66.010  1.00  0.60
ATOM   1434  CD1 PHE   214       8.995  53.280  65.406  1.00  0.60
ATOM   1435  CD2 PHE   214       8.518  50.948  65.224  1.00  0.80
ATOM   1436  CE1 PHE   214       9.463  53.260  64.107  1.00  0.80
ATOM   1437  CE2 PHE   214       8.996  50.892  63.941  1.00  1.10
ATOM   1438  CZ  PHE   214       9.503  52.091  63.372  1.00  1.10
ATOM   1439  N   GLU   215       7.410  52.789  70.343  1.00  0.50
ATOM   1440  CA  GLU   215       6.457  52.845  71.445  1.00  0.50
ATOM   1441  C   GLU   215       6.616  54.010  72.439  1.00  0.50
ATOM   1442  O   GLU   215       5.615  54.569  72.858  1.00  0.50
ATOM   1443  CB  GLU   215       6.313  51.468  72.112  1.00  0.50
ATOM   1444  CG  GLU   215       5.283  51.474  73.209  1.00  0.60
ATOM   1445  CD  GLU   215       3.840  51.745  72.668  1.00  0.60
ATOM   1446  OE1 GLU   215       3.595  51.745  71.452  1.00  0.80
ATOM   1447  OE2 GLU   215       2.955  52.006  73.526  1.00  0.80
ATOM   1448  N   ASP   216       7.849  54.371  72.800  1.00  0.50
ATOM   1449  CA  ASP   216       8.080  55.563  73.617  1.00  0.50
ATOM   1450  C   ASP   216       7.707  56.820  72.842  1.00  0.50
ATOM   1451  O   ASP   216       7.291  57.817  73.437  1.00  0.50
ATOM   1452  CB  ASP   216       9.523  55.652  74.113  1.00  0.50
ATOM   1453  CG  ASP   216       9.880  54.617  75.154  1.00  0.60
ATOM   1454  OD1 ASP   216       8.993  53.962  75.756  1.00  0.60
ATOM   1455  OD2 ASP   216      11.048  54.445  75.512  1.00  0.80
ATOM   1456  N   ILE   217       7.848  56.764  71.514  1.00  0.50
ATOM   1457  CA  ILE   217       7.452  57.841  70.629  1.00  0.50
ATOM   1458  C   ILE   217       5.952  58.055  70.573  1.00  0.50
ATOM   1459  O   ILE   217       5.487  59.186  70.631  1.00  0.50
ATOM   1460  CB  ILE   217       7.301  58.711  71.878  1.00  0.50
ATOM   1461  CG1 ILE   217       8.587  58.924  72.678  1.00  0.60
ATOM   1462  CG2 ILE   217       6.156  58.121  72.712  1.00  0.60
ATOM   1463  CD1 ILE   217       9.266  60.233  72.435  1.00  0.80
ATOM   1464  N   SER   218       5.194  56.973  70.413  1.00  0.50
ATOM   1465  CA  SER   218       3.734  57.003  70.487  1.00  0.50
ATOM   1466  C   SER   218       3.273  57.569  71.836  1.00  0.50
ATOM   1467  O   SER   218       2.380  58.405  71.881  1.00  0.50
ATOM   1468  CB  SER   218       3.124  55.583  70.281  1.00  0.50
ATOM   1469  OG  SER   218       3.584  54.624  71.379  1.00  0.60
TER
END
