
#######################################################
#                                                     #
#                        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    9 (   75),  selected    9 , name T0372TS021_1_2-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected    9 , name T0372_D1.pdb
# PARAMETERS: T0372TS021_1_2-D1.T0372_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:     9       290 - 298         2.23     2.23
  LCS_AVERAGE:      7.14

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8       290 - 297         1.52     2.65
  LCS_AVERAGE:      6.08

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       291 - 297         0.99     2.80
  LCS_AVERAGE:      4.94

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:  126
LCS_GDT     K     290     K     290      4    8    9     3    3    4    5    6    8    8    9    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     Y     291     Y     291      7    8    9     3    4    7    7    7    8    8    9    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     M     292     M     292      7    8    9     3    5    7    7    7    8    8    9    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     A     293     A     293      7    8    9     3    4    7    7    7    8    8    9    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     C     294     C     294      7    8    9     4    5    7    7    7    8    8    9    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     L     295     L     295      7    8    9     4    5    7    7    7    8    8    9    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     K     296     K     296      7    8    9     4    5    7    7    7    8    8    9    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     D     297     D     297      7    8    9     4    5    7    7    7    8    8    9    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     H     298     H     298      3    5    9     3    3    3    4    4    7    8    9    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_AVERAGE  LCS_A:   6.06  (   4.94    6.08    7.14 )

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      7      7      7      8      8      9      9      9      9      9      9      9      9      9      9      9      9      9 
GDT PERCENT_CA   3.17   3.97   5.56   5.56   5.56   6.35   6.35   7.14   7.14   7.14   7.14   7.14   7.14   7.14   7.14   7.14   7.14   7.14   7.14   7.14
GDT RMS_LOCAL    0.20   0.59   0.99   0.99   0.99   1.52   1.52   2.23   2.23   2.23   2.23   2.23   2.23   2.23   2.23   2.23   2.23   2.23   2.23   2.23
GDT RMS_ALL_CA   3.04   2.88   2.80   2.80   2.80   2.65   2.65   2.23   2.23   2.23   2.23   2.23   2.23   2.23   2.23   2.23   2.23   2.23   2.23   2.23

#      Molecule1      Molecule2       DISTANCE
LGA    K     290      K     290          2.783
LGA    Y     291      Y     291          1.225
LGA    M     292      M     292          1.390
LGA    A     293      A     293          1.036
LGA    C     294      C     294          1.383
LGA    L     295      L     295          2.794
LGA    K     296      K     296          2.672
LGA    D     297      D     297          1.354
LGA    H     298      H     298          3.699

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    9  126    4.0      9    2.23     5.952     6.200     0.387

LGA_LOCAL      RMSD =  2.227  Number of atoms =    9  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  2.227  Number of atoms =    9 
Std_ALL_ATOMS  RMSD =  2.227  (standard rmsd on all 9 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.411834 * X  +  -0.001360 * Y  +   0.911258 * Z  +  33.850014
  Y_new =   0.560461 * X  +  -0.788873 * Y  +   0.252117 * Z  +  22.137388
  Z_new =   0.718524 * X  +   0.614555 * Y  +   0.325647 * Z  + -68.854156 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.083524   -2.058069  [ DEG:    62.0813   -117.9187 ]
  Theta =  -0.801678   -2.339915  [ DEG:   -45.9327   -134.0673 ]
  Phi   =   2.204507   -0.937086  [ DEG:   126.3089    -53.6911 ]
 
# 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: T0372TS021_1_2-D1                             
REMARK     2: T0372_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0372TS021_1_2-D1.T0372_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    9  126   4.0    9   2.23   6.200     2.23
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS021_1_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0372
PARENT N/A
ATOM   1225  N   LYS   290      27.255  49.356   4.150  1.00108.36       1SG1226
ATOM   1226  CA  LYS   290      26.761  48.390   5.091  1.00108.36       1SG1227
ATOM   1227  CB  LYS   290      25.778  48.987   6.109  1.00108.36       1SG1228
ATOM   1228  CG  LYS   290      26.397  50.083   6.977  1.00108.36       1SG1229
ATOM   1229  CD  LYS   290      27.628  49.629   7.763  1.00108.36       1SG1230
ATOM   1230  CE  LYS   290      28.253  50.740   8.609  1.00108.36       1SG1231
ATOM   1231  NZ  LYS   290      29.528  50.275   9.196  1.00108.36       1SG1232
ATOM   1232  C   LYS   290      26.024  47.346   4.323  1.00108.36       1SG1233
ATOM   1233  O   LYS   290      26.202  46.149   4.550  1.00108.36       1SG1234
ATOM   1234  N   TYR   291      25.199  47.782   3.360  1.00148.84       1SG1235
ATOM   1235  CA  TYR   291      24.500  46.854   2.528  1.00148.84       1SG1236
ATOM   1236  CB  TYR   291      23.152  47.379   2.012  1.00148.84       1SG1237
ATOM   1237  CG  TYR   291      22.359  47.288   3.266  1.00148.84       1SG1238
ATOM   1238  CD1 TYR   291      22.461  48.260   4.232  1.00148.84       1SG1239
ATOM   1239  CD2 TYR   291      21.541  46.204   3.488  1.00148.84       1SG1240
ATOM   1240  CE1 TYR   291      21.748  48.157   5.402  1.00148.84       1SG1241
ATOM   1241  CE2 TYR   291      20.824  46.093   4.655  1.00148.84       1SG1242
ATOM   1242  CZ  TYR   291      20.930  47.073   5.613  1.00148.84       1SG1243
ATOM   1243  OH  TYR   291      20.204  46.965   6.817  1.00148.84       1SG1244
ATOM   1244  C   TYR   291      25.466  46.523   1.451  1.00148.84       1SG1245
ATOM   1245  O   TYR   291      26.497  47.176   1.360  1.00148.84       1SG1246
ATOM   1246  N   MET   292      25.244  45.451   0.672  1.00196.46       1SG1247
ATOM   1247  CA  MET   292      26.289  45.077  -0.238  1.00196.46       1SG1248
ATOM   1248  CB  MET   292      25.965  43.810  -1.049  1.00196.46       1SG1249
ATOM   1249  CG  MET   292      27.163  43.274  -1.837  1.00196.46       1SG1250
ATOM   1250  SD  MET   292      26.985  41.557  -2.410  1.00196.46       1SG1251
ATOM   1251  CE  MET   292      27.386  40.828  -0.795  1.00196.46       1SG1252
ATOM   1252  C   MET   292      26.588  46.204  -1.175  1.00196.46       1SG1253
ATOM   1253  O   MET   292      27.750  46.589  -1.298  1.00196.46       1SG1254
ATOM   1254  N   ALA   293      25.542  46.800  -1.787  1.00130.69       1SG1255
ATOM   1255  CA  ALA   293      25.702  47.924  -2.670  1.00130.69       1SG1256
ATOM   1256  CB  ALA   293      26.002  49.239  -1.930  1.00130.69       1SG1257
ATOM   1257  C   ALA   293      26.822  47.650  -3.619  1.00130.69       1SG1258
ATOM   1258  O   ALA   293      27.764  48.432  -3.716  1.00130.69       1SG1259
ATOM   1259  N   CYS   294      26.736  46.526  -4.352  1.00 78.24       1SG1260
ATOM   1260  CA  CYS   294      27.803  46.148  -5.228  1.00 78.24       1SG1261
ATOM   1261  CB  CYS   294      27.532  44.866  -6.036  1.00 78.24       1SG1262
ATOM   1262  SG  CYS   294      27.423  43.375  -5.003  1.00 78.24       1SG1263
ATOM   1263  C   CYS   294      27.992  47.245  -6.212  1.00 78.24       1SG1264
ATOM   1264  O   CYS   294      27.162  48.147  -6.319  1.00 78.24       1SG1265
ATOM   1265  N   LEU   295      29.127  47.204  -6.938  1.00 46.69       1SG1266
ATOM   1266  CA  LEU   295      29.379  48.229  -7.899  1.00 46.69       1SG1267
ATOM   1267  CB  LEU   295      30.660  48.008  -8.726  1.00 46.69       1SG1268
ATOM   1268  CG  LEU   295      31.958  48.010  -7.894  1.00 46.69       1SG1269
ATOM   1269  CD1 LEU   295      33.191  47.816  -8.791  1.00 46.69       1SG1270
ATOM   1270  CD2 LEU   295      32.056  49.263  -7.013  1.00 46.69       1SG1271
ATOM   1271  C   LEU   295      28.230  48.178  -8.841  1.00 46.69       1SG1272
ATOM   1272  O   LEU   295      27.892  47.121  -9.372  1.00 46.69       1SG1273
ATOM   1273  N   LYS   296      27.579  49.336  -9.050  1.00 90.70       1SG1274
ATOM   1274  CA  LYS   296      26.449  49.354  -9.920  1.00 90.70       1SG1275
ATOM   1275  CB  LYS   296      25.555  50.593  -9.726  1.00 90.70       1SG1276
ATOM   1276  CG  LYS   296      24.746  50.548  -8.425  1.00 90.70       1SG1277
ATOM   1277  CD  LYS   296      24.217  51.910  -7.963  1.00 90.70       1SG1278
ATOM   1278  CE  LYS   296      23.501  52.712  -9.052  1.00 90.70       1SG1279
ATOM   1279  NZ  LYS   296      22.977  53.977  -8.488  1.00 90.70       1SG1280
ATOM   1280  C   LYS   296      26.962  49.346 -11.313  1.00 90.70       1SG1281
ATOM   1281  O   LYS   296      27.794  50.169 -11.694  1.00 90.70       1SG1282
ATOM   1282  N   ASP   297      26.478  48.378 -12.108  1.00126.46       1SG1283
ATOM   1283  CA  ASP   297      26.892  48.284 -13.471  1.00126.46       1SG1284
ATOM   1284  CB  ASP   297      26.319  47.049 -14.193  1.00126.46       1SG1285
ATOM   1285  CG  ASP   297      24.801  47.172 -14.250  1.00126.46       1SG1286
ATOM   1286  OD1 ASP   297      24.188  47.464 -13.189  1.00126.46       1SG1287
ATOM   1287  OD2 ASP   297      24.234  46.973 -15.359  1.00126.46       1SG1288
ATOM   1288  C   ASP   297      26.386  49.505 -14.162  1.00126.46       1SG1289
ATOM   1289  O   ASP   297      27.078  50.092 -14.994  1.00126.46       1SG1290
ATOM   1290  N   HIS   298      25.166  49.934 -13.806  1.00156.53       1SG1291
ATOM   1291  CA  HIS   298      24.574  51.063 -14.465  1.00156.53       1SG1292
ATOM   1292  ND1 HIS   298      21.955  51.981 -16.238  1.00156.53       1SG1293
ATOM   1293  CG  HIS   298      22.432  52.295 -14.984  1.00156.53       1SG1294
ATOM   1294  CB  HIS   298      23.109  51.309 -14.076  1.00156.53       1SG1295
ATOM   1295  NE2 HIS   298      21.540  54.142 -15.927  1.00156.53       1SG1296
ATOM   1296  CD2 HIS   298      22.172  53.621 -14.811  1.00156.53       1SG1297
ATOM   1297  CE1 HIS   298      21.436  53.120 -16.757  1.00156.53       1SG1298
ATOM   1298  C   HIS   298      25.381  52.279 -14.113  1.00156.53       1SG1299
ATOM   1299  O   HIS   298      25.990  52.360 -13.048  1.00156.53       1SG1300
TER
END
