
#######################################################
#                                                     #
#                        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 (   78),  selected   10 , name T0318TS022_3_1-D2
# Molecule2: number of CA atoms  335 ( 2465),  selected   10 , name T0318_D2.pdb
# PARAMETERS: T0318TS022_3_1-D2.T0318_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:    10       156 - 165         3.75     3.75
  LCS_AVERAGE:      2.99

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       157 - 162         0.78     6.54
  LCS_AVERAGE:      1.46

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       157 - 162         0.78     6.54
  LCS_AVERAGE:      1.43

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:  335
LCS_GDT     T     156     T     156      3    3   10     0    3    3    4    4    5    6    7    8    8    9   10   10   10   10   10   10   10   10   10 
LCS_GDT     N     157     N     157      6    6   10     4    5    6    6    6    6    6    8    9    9    9   10   10   10   10   10   10   10   10   10 
LCS_GDT     E     158     E     158      6    6   10     4    5    6    6    6    6    6    8    9    9    9   10   10   10   10   10   10   10   10   10 
LCS_GDT     D     159     D     159      6    6   10     4    5    6    6    6    6    6    8    9    9    9   10   10   10   10   10   10   10   10   10 
LCS_GDT     A     160     A     160      6    6   10     4    5    6    6    6    6    6    8    9    9    9   10   10   10   10   10   10   10   10   10 
LCS_GDT     V     161     V     161      6    6   10     4    5    6    6    6    6    6    8    9    9    9   10   10   10   10   10   10   10   10   10 
LCS_GDT     F     162     F     162      6    6   10     3    4    6    6    6    6    6    7    9    9    9   10   10   10   10   10   10   10   10   10 
LCS_GDT     L     163     L     163      3    4   10     3    4    4    4    6    6    6    8    9    9    9   10   10   10   10   10   10   10   10   10 
LCS_GDT     T     164     T     164      3    3   10     3    4    4    5    6    6    6    8    9    9    9   10   10   10   10   10   10   10   10   10 
LCS_GDT     D     165     D     165      3    3   10     3    3    3    5    6    6    6    8    9    9    9   10   10   10   10   10   10   10   10   10 
LCS_AVERAGE  LCS_A:   1.96  (   1.43    1.46    2.99 )

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      4      5      6      6      6      6      6      8      9      9      9     10     10     10     10     10     10     10     10     10 
GDT PERCENT_CA   1.19   1.49   1.79   1.79   1.79   1.79   1.79   2.39   2.69   2.69   2.69   2.99   2.99   2.99   2.99   2.99   2.99   2.99   2.99   2.99
GDT RMS_LOCAL    0.17   0.40   0.78   0.78   0.78   0.78   0.78   2.90   3.33   3.33   3.33   3.75   3.75   3.75   3.75   3.75   3.75   3.75   3.75   3.75
GDT RMS_ALL_CA   6.83   6.78   6.54   6.54   6.54   6.54   6.54   4.15   4.01   4.01   4.01   3.75   3.75   3.75   3.75   3.75   3.75   3.75   3.75   3.75

#      Molecule1      Molecule2       DISTANCE
LGA    T     156      T     156          8.653
LGA    N     157      N     157          3.703
LGA    E     158      E     158          2.869
LGA    D     159      D     159          0.835
LGA    A     160      A     160          3.488
LGA    V     161      V     161          3.707
LGA    F     162      F     162          5.313
LGA    L     163      L     163          3.087
LGA    T     164      T     164          3.348
LGA    D     165      D     165          2.971

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   10  335    4.0      8    2.90     2.164     2.023     0.266

LGA_LOCAL      RMSD =  2.902  Number of atoms =    8  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  4.257  Number of atoms =   10 
Std_ALL_ATOMS  RMSD =  3.752  (standard rmsd on all 10 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.792355 * X  +  -0.610058 * Y  +  -0.001785 * Z  +  43.047298
  Y_new =  -0.517562 * X  +   0.670664 * Y  +   0.531356 * Z  +  17.502018
  Z_new =  -0.322961 * X  +   0.421946 * Y  +  -0.847147 * Z  +   9.269666 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.679483   -0.462109  [ DEG:   153.5231    -26.4769 ]
  Theta =   0.328856    2.812737  [ DEG:    18.8421    161.1579 ]
  Phi   =  -2.562974    0.578618  [ DEG:  -146.8476     33.1524 ]
 
# 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: T0318TS022_3_1-D2                             
REMARK     2: T0318_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0318TS022_3_1-D2.T0318_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   10  335   4.0    8   2.90   2.023     3.75
REMARK  ---------------------------------------------------------- 
MOLECULE T0318TS022_3_1-D2
REMARK PARENT number 1
PFRMAT TS
TARGET T0318
PARENT 1olm_A
ATOM   1170  N   THR   156      28.692  30.816   5.301  1.00  0.00
ATOM   1171  CA  THR   156      28.710  30.861   6.732  1.00  0.00
ATOM   1172  C   THR   156      27.325  30.499   7.125  1.00  0.00
ATOM   1173  O   THR   156      26.393  30.671   6.341  1.00  0.00
ATOM   1174  CB  THR   156      29.086  32.262   7.247  1.00  0.00
ATOM   1175  OG1 THR   156      28.087  33.207   6.844  1.00  0.00
ATOM   1176  CG2 THR   156      30.431  32.695   6.683  1.00  0.00
ATOM   1177  N   ASN   157      27.137  29.967   8.341  1.00  0.00
ATOM   1178  CA  ASN   157      25.804  29.599   8.699  1.00  0.00
ATOM   1179  C   ASN   157      25.123  30.800   9.264  1.00  0.00
ATOM   1180  O   ASN   157      25.761  31.686   9.831  1.00  0.00
ATOM   1181  CB  ASN   157      25.818  28.480   9.743  1.00  0.00
ATOM   1182  CG  ASN   157      26.319  27.165   9.180  1.00  0.00
ATOM   1183  OD1 ASN   157      26.235  26.921   7.976  1.00  0.00
ATOM   1184  ND2 ASN   157      26.843  26.312  10.052  1.00  0.00
ATOM   1185  N   GLU   158      23.790  30.871   9.094  1.00  0.00
ATOM   1186  CA  GLU   158      23.081  32.009   9.592  1.00  0.00
ATOM   1187  C   GLU   158      23.239  32.024  11.074  1.00  0.00
ATOM   1188  O   GLU   158      23.524  33.061  11.671  1.00  0.00
ATOM   1189  CB  GLU   158      21.598  31.919   9.226  1.00  0.00
ATOM   1190  CG  GLU   158      21.311  32.120   7.747  1.00  0.00
ATOM   1191  CD  GLU   158      19.853  31.888   7.400  1.00  0.00
ATOM   1192  OE1 GLU   158      19.084  31.491   8.301  1.00  0.00
ATOM   1193  OE2 GLU   158      19.480  32.104   6.228  1.00  0.00
ATOM   1194  N   ASP   159      23.053  30.854  11.707  1.00  0.00
ATOM   1195  CA  ASP   159      23.182  30.769  13.129  1.00  0.00
ATOM   1196  C   ASP   159      24.613  30.992  13.493  1.00  0.00
ATOM   1197  O   ASP   159      24.921  31.726  14.430  1.00  0.00
ATOM   1198  CB  ASP   159      22.740  29.391  13.625  1.00  0.00
ATOM   1199  CG  ASP   159      21.238  29.205  13.567  1.00  0.00
ATOM   1200  OD1 ASP   159      20.521  30.211  13.379  1.00  0.00
ATOM   1201  OD2 ASP   159      20.775  28.053  13.708  1.00  0.00
ATOM   1202  N   ALA   160      25.530  30.377  12.723  1.00  0.00
ATOM   1203  CA  ALA   160      26.919  30.392  13.080  1.00  0.00
ATOM   1204  C   ALA   160      27.439  31.780  13.113  1.00  0.00
ATOM   1205  O   ALA   160      28.077  32.184  14.081  1.00  0.00
ATOM   1206  CB  ALA   160      27.735  29.599  12.071  1.00  0.00
ATOM   1207  N   VAL   161      27.152  32.569  12.070  1.00  0.00
ATOM   1208  CA  VAL   161      27.653  33.907  12.063  1.00  0.00
ATOM   1209  C   VAL   161      26.646  34.707  12.795  1.00  0.00
ATOM   1210  O   VAL   161      25.543  34.227  13.048  1.00  0.00
ATOM   1211  CB  VAL   161      27.826  34.437  10.628  1.00  0.00
ATOM   1212  CG1 VAL   161      28.822  33.579   9.860  1.00  0.00
ATOM   1213  CG2 VAL   161      26.499  34.411   9.886  1.00  0.00
ATOM   1214  N   PHE   162      27.020  35.930  13.210  1.00  0.00
ATOM   1215  CA  PHE   162      26.044  36.749  13.837  1.00  0.00
ATOM   1216  C   PHE   162      25.328  37.278  12.652  1.00  0.00
ATOM   1217  O   PHE   162      25.474  38.439  12.273  1.00  0.00
ATOM   1218  CB  PHE   162      26.716  37.839  14.674  1.00  0.00
ATOM   1219  CG  PHE   162      25.786  38.530  15.631  1.00  0.00
ATOM   1220  CD1 PHE   162      25.346  37.888  16.775  1.00  0.00
ATOM   1221  CD2 PHE   162      25.352  39.821  15.385  1.00  0.00
ATOM   1222  CE1 PHE   162      24.490  38.524  17.655  1.00  0.00
ATOM   1223  CE2 PHE   162      24.496  40.456  16.265  1.00  0.00
ATOM   1224  CZ  PHE   162      24.065  39.813  17.396  1.00  0.00
ATOM   1225  N   LEU   163      24.519  36.401  12.039  1.00  0.00
ATOM   1226  CA  LEU   163      23.875  36.732  10.816  1.00  0.00
ATOM   1227  C   LEU   163      22.890  37.792  11.141  1.00  0.00
ATOM   1228  O   LEU   163      22.183  37.714  12.144  1.00  0.00
ATOM   1229  CB  LEU   163      23.174  35.504  10.232  1.00  0.00
ATOM   1230  CG  LEU   163      22.546  35.678   8.846  1.00  0.00
ATOM   1231  CD1 LEU   163      23.619  35.924   7.797  1.00  0.00
ATOM   1232  CD2 LEU   163      21.769  34.432   8.449  1.00  0.00
ATOM   1233  N   THR   164      22.833  38.832  10.295  1.00  0.00
ATOM   1234  CA  THR   164      21.901  39.884  10.551  1.00  0.00
ATOM   1235  C   THR   164      21.259  40.226   9.251  1.00  0.00
ATOM   1236  O   THR   164      21.519  39.591   8.229  1.00  0.00
ATOM   1237  CB  THR   164      22.601  41.130  11.128  1.00  0.00
ATOM   1238  OG1 THR   164      23.477  41.689  10.142  1.00  0.00
ATOM   1239  CG2 THR   164      23.415  40.761  12.359  1.00  0.00
ATOM   1240  N   ASP   165      20.373  41.236   9.281  1.00  0.00
ATOM   1241  CA  ASP   165      19.700  41.682   8.099  1.00  0.00
ATOM   1242  C   ASP   165      20.777  41.948   7.052  1.00  0.00
ATOM   1243  O   ASP   165      21.758  42.664   7.387  1.00  0.00
ATOM   1244  CB  ASP   165      18.907  42.960   8.382  1.00  0.00
ATOM   1245  CG  ASP   165      18.019  43.364   7.223  1.00  0.00
ATOM   1246  OD1 ASP   165      18.006  42.642   6.204  1.00  0.00
ATOM   1247  OD2 ASP   165      17.336  44.405   7.333  1.00  0.00
TER
END
