
#######################################################
#                                                     #
#                        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_1_1-D2
# Molecule2: number of CA atoms  335 ( 2465),  selected   10 , name T0318_D2.pdb
# PARAMETERS: T0318TS022_1_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         0.71     0.71
  LCS_AVERAGE:      2.99

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10       156 - 165         0.71     0.71
  LCS_AVERAGE:      2.99

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10       156 - 165         0.71     0.71
  LCS_AVERAGE:      2.99

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     10   10   10     4    9   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     N     157     N     157     10   10   10     4    9   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     E     158     E     158     10   10   10     4    9   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     D     159     D     159     10   10   10     7    9   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     A     160     A     160     10   10   10     7    9   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     V     161     V     161     10   10   10     7    9   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     F     162     F     162     10   10   10     7    9   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     L     163     L     163     10   10   10     7    9   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     T     164     T     164     10   10   10     7    9   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     D     165     D     165     10   10   10     7    9   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10 
LCS_AVERAGE  LCS_A:   2.99  (   2.99    2.99    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      7      9     10     10     10     10     10     10     10     10     10     10     10     10     10     10     10     10     10     10 
GDT PERCENT_CA   2.09   2.69   2.99   2.99   2.99   2.99   2.99   2.99   2.99   2.99   2.99   2.99   2.99   2.99   2.99   2.99   2.99   2.99   2.99   2.99
GDT RMS_LOCAL    0.25   0.58   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71
GDT RMS_ALL_CA   0.89   0.76   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71

#      Molecule1      Molecule2       DISTANCE
LGA    T     156      T     156          1.221
LGA    N     157      N     157          1.026
LGA    E     158      E     158          0.748
LGA    D     159      D     159          0.439
LGA    A     160      A     160          0.430
LGA    V     161      V     161          0.405
LGA    F     162      F     162          0.461
LGA    L     163      L     163          0.594
LGA    T     164      T     164          0.682
LGA    D     165      D     165          0.579

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   10  335    4.0     10    0.71     2.910     2.962     1.238

LGA_LOCAL      RMSD =  0.708  Number of atoms =   10  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  0.708  Number of atoms =   10 
Std_ALL_ATOMS  RMSD =  0.708  (standard rmsd on all 10 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.135334 * X  +  -0.118499 * Y  +  -0.983688 * Z  +   3.210226
  Y_new =  -0.799053 * X  +   0.600082 * Y  +   0.037644 * Z  +  39.699520
  Z_new =   0.585832 * X  +   0.791113 * Y  +  -0.175899 * Z  + -31.317171 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.789581   -1.352012  [ DEG:   102.5354    -77.4646 ]
  Theta =  -0.625907   -2.515686  [ DEG:   -35.8618   -144.1382 ]
  Phi   =  -1.738573    1.403020  [ DEG:   -99.6129     80.3871 ]
 
# 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_1_1-D2                             
REMARK     2: T0318_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0318TS022_1_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   10   0.71   2.962     0.71
REMARK  ---------------------------------------------------------- 
MOLECULE T0318TS022_1_1-D2
REMARK PARENT number 1
PFRMAT TS
TARGET T0318
PARENT 1gyt_A
ATOM   1209  N   THR   156      26.770  26.279  15.755  1.00  0.00
ATOM   1210  CA  THR   156      26.446  26.328  14.366  1.00  0.00
ATOM   1211  C   THR   156      27.041  27.596  13.830  1.00  0.00
ATOM   1212  O   THR   156      26.805  28.683  14.357  1.00  0.00
ATOM   1213  CB  THR   156      24.923  26.328  14.141  1.00  0.00
ATOM   1214  OG1 THR   156      24.356  25.131  14.689  1.00  0.00
ATOM   1215  CG2 THR   156      24.603  26.388  12.655  1.00  0.00
ATOM   1216  N   ASN   157      27.854  27.467  12.765  1.00  0.00
ATOM   1217  CA  ASN   157      28.518  28.567  12.125  1.00  0.00
ATOM   1218  C   ASN   157      27.476  29.411  11.469  1.00  0.00
ATOM   1219  O   ASN   157      27.594  30.632  11.392  1.00  0.00
ATOM   1220  CB  ASN   157      29.508  28.058  11.075  1.00  0.00
ATOM   1221  CG  ASN   157      30.741  27.429  11.694  1.00  0.00
ATOM   1222  OD1 ASN   157      31.067  27.689  12.852  1.00  0.00
ATOM   1223  ND2 ASN   157      31.431  26.597  10.921  1.00  0.00
ATOM   1224  N   GLU   158      26.404  28.754  10.996  1.00  0.00
ATOM   1225  CA  GLU   158      25.372  29.379  10.225  1.00  0.00
ATOM   1226  C   GLU   158      24.740  30.465  11.027  1.00  0.00
ATOM   1227  O   GLU   158      24.231  31.437  10.475  1.00  0.00
ATOM   1228  CB  GLU   158      24.299  28.359   9.837  1.00  0.00
ATOM   1229  CG  GLU   158      24.753  27.346   8.799  1.00  0.00
ATOM   1230  CD  GLU   158      23.699  26.295   8.510  1.00  0.00
ATOM   1231  OE1 GLU   158      22.641  26.319   9.171  1.00  0.00
ATOM   1232  OE2 GLU   158      23.932  25.449   7.621  1.00  0.00
ATOM   1233  N   ASP   159      24.752  30.339  12.360  1.00  0.00
ATOM   1234  CA  ASP   159      24.097  31.304  13.190  1.00  0.00
ATOM   1235  C   ASP   159      24.704  32.656  12.959  1.00  0.00
ATOM   1236  O   ASP   159      24.026  33.675  13.068  1.00  0.00
ATOM   1237  CB  ASP   159      24.253  30.934  14.667  1.00  0.00
ATOM   1238  CG  ASP   159      23.400  29.745  15.063  1.00  0.00
ATOM   1239  OD1 ASP   159      22.520  29.354  14.267  1.00  0.00
ATOM   1240  OD2 ASP   159      23.611  29.204  16.169  1.00  0.00
ATOM   1241  N   ALA   160      26.003  32.704  12.617  1.00  0.00
ATOM   1242  CA  ALA   160      26.706  33.949  12.496  1.00  0.00
ATOM   1243  C   ALA   160      26.044  34.831  11.481  1.00  0.00
ATOM   1244  O   ALA   160      25.976  36.045  11.665  1.00  0.00
ATOM   1245  CB  ALA   160      28.143  33.707  12.058  1.00  0.00
ATOM   1246  N   VAL   161      25.546  34.256  10.374  1.00  0.00
ATOM   1247  CA  VAL   161      24.952  35.065   9.349  1.00  0.00
ATOM   1248  C   VAL   161      23.756  35.791   9.888  1.00  0.00
ATOM   1249  O   VAL   161      23.550  36.963   9.577  1.00  0.00
ATOM   1250  CB  VAL   161      24.492  34.213   8.152  1.00  0.00
ATOM   1251  CG1 VAL   161      23.692  35.057   7.172  1.00  0.00
ATOM   1252  CG2 VAL   161      25.693  33.633   7.419  1.00  0.00
ATOM   1253  N   PHE   162      22.942  35.124  10.730  1.00  0.00
ATOM   1254  CA  PHE   162      21.721  35.711  11.207  1.00  0.00
ATOM   1255  C   PHE   162      22.028  36.948  11.991  1.00  0.00
ATOM   1256  O   PHE   162      21.334  37.958  11.862  1.00  0.00
ATOM   1257  CB  PHE   162      20.971  34.729  12.110  1.00  0.00
ATOM   1258  CG  PHE   162      20.227  33.663  11.358  1.00  0.00
ATOM   1259  CD1 PHE   162      20.748  32.385  11.242  1.00  0.00
ATOM   1260  CD2 PHE   162      19.006  33.937  10.767  1.00  0.00
ATOM   1261  CE1 PHE   162      20.062  31.405  10.551  1.00  0.00
ATOM   1262  CE2 PHE   162      18.321  32.955  10.075  1.00  0.00
ATOM   1263  CZ  PHE   162      18.844  31.694   9.966  1.00  0.00
ATOM   1264  N   LEU   163      23.067  36.902  12.842  1.00  0.00
ATOM   1265  CA  LEU   163      23.360  38.032  13.673  1.00  0.00
ATOM   1266  C   LEU   163      23.736  39.211  12.835  1.00  0.00
ATOM   1267  O   LEU   163      23.344  40.333  13.150  1.00  0.00
ATOM   1268  CB  LEU   163      24.524  37.717  14.616  1.00  0.00
ATOM   1269  CG  LEU   163      24.241  36.702  15.725  1.00  0.00
ATOM   1270  CD1 LEU   163      25.519  36.347  16.469  1.00  0.00
ATOM   1271  CD2 LEU   163      23.248  37.267  16.731  1.00  0.00
ATOM   1272  N   THR   164      24.499  39.005  11.745  1.00  0.00
ATOM   1273  CA  THR   164      24.861  40.142  10.949  1.00  0.00
ATOM   1274  C   THR   164      23.593  40.752  10.453  1.00  0.00
ATOM   1275  O   THR   164      23.427  41.971  10.478  1.00  0.00
ATOM   1276  CB  THR   164      25.743  39.736   9.753  1.00  0.00
ATOM   1277  OG1 THR   164      26.961  39.152  10.232  1.00  0.00
ATOM   1278  CG2 THR   164      26.080  40.951   8.903  1.00  0.00
ATOM   1279  N   ASP   165      22.648  39.910   9.997  1.00  0.00
ATOM   1280  CA  ASP   165      21.406  40.431   9.515  1.00  0.00
ATOM   1281  C   ASP   165      20.507  40.602  10.726  1.00  0.00
ATOM   1282  O   ASP   165      20.823  41.480  11.574  1.00  0.00
ATOM   1283  CB  ASP   165      20.772  39.464   8.514  1.00  0.00
ATOM   1284  CG  ASP   165      19.608  40.082   7.765  1.00  0.00
ATOM   1285  OD1 ASP   165      19.413  41.311   7.878  1.00  0.00
ATOM   1286  OD2 ASP   165      18.889  39.337   7.065  1.00  0.00
TER
END
