
#######################################################
#                                                     #
#                        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 (   79),  selected   10 , name T0318TS021_2_1-D2
# Molecule2: number of CA atoms  335 ( 2465),  selected   10 , name T0318_D2.pdb
# PARAMETERS: T0318TS021_2_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:     9       156 - 164         4.68     5.20
  LONGEST_CONTINUOUS_SEGMENT:     9       157 - 165         4.60     5.27
  LCS_AVERAGE:      2.69

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       162 - 165         1.79    10.00
  LCS_AVERAGE:      1.01

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
# WARNING! The change of the parameter DIST cutoff may give you better result.

  LONGEST_CONTINUOUS_SEGMENT:     3       156 - 158         0.67     8.90
  LONGEST_CONTINUOUS_SEGMENT:     3       158 - 160         0.23     8.98
  LONGEST_CONTINUOUS_SEGMENT:     3       159 - 161         0.53     7.37
  LONGEST_CONTINUOUS_SEGMENT:     3       160 - 162         0.93     7.98
  LONGEST_CONTINUOUS_SEGMENT:     3       161 - 163         0.72    10.19
  LONGEST_CONTINUOUS_SEGMENT:     3       162 - 164         0.55    11.70
  LONGEST_CONTINUOUS_SEGMENT:     3       163 - 165         0.32    15.37
  LCS_AVERAGE:      0.90

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    9     0    3    3    3    3    3    5    6    6    6    7    7    8   10   10   10   10   10   10   10 
LCS_GDT     N     157     N     157      3    3    9     0    3    3    3    3    4    5    6    6    6    7    8    9   10   10   10   10   10   10   10 
LCS_GDT     E     158     E     158      3    3    9     3    3    3    3    3    4    5    6    6    6    8    8    9   10   10   10   10   10   10   10 
LCS_GDT     D     159     D     159      3    3    9     3    3    3    3    3    4    5    6    6    7    8    8    9   10   10   10   10   10   10   10 
LCS_GDT     A     160     A     160      3    3    9     3    3    3    3    3    4    5    6    6    7    8    8    9   10   10   10   10   10   10   10 
LCS_GDT     V     161     V     161      3    3    9     0    3    3    3    3    4    5    6    6    7    8    8    9   10   10   10   10   10   10   10 
LCS_GDT     F     162     F     162      3    4    9     0    3    3    4    4    4    4    5    6    7    8    8    9   10   10   10   10   10   10   10 
LCS_GDT     L     163     L     163      3    4    9     3    3    3    4    4    4    4    5    6    7    8    8    9   10   10   10   10   10   10   10 
LCS_GDT     T     164     T     164      3    4    9     3    3    3    4    4    4    4    5    6    7    8    8    9   10   10   10   10   10   10   10 
LCS_GDT     D     165     D     165      3    4    9     3    3    3    4    4    4    4    5    5    7    8    8    9   10   10   10   10   10   10   10 
LCS_AVERAGE  LCS_A:   1.53  (   0.90    1.01    2.69 )

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      3      3      4      4      4      5      6      6      7      8      8      9     10     10     10     10     10     10     10 
GDT PERCENT_CA   0.90   0.90   0.90   1.19   1.19   1.19   1.49   1.79   1.79   2.09   2.39   2.39   2.69   2.99   2.99   2.99   2.99   2.99   2.99   2.99
GDT RMS_LOCAL    0.23   0.23   0.23   1.79   1.79   1.79   2.81   3.11   3.11   3.85   4.14   4.14   4.60   5.04   5.04   5.04   5.04   5.04   5.04   5.04
GDT RMS_ALL_CA   8.98   8.98   8.98  10.00  10.00  10.00   5.82   6.32   6.32   5.67   5.70   5.70   5.27   5.04   5.04   5.04   5.04   5.04   5.04   5.04

#      Molecule1      Molecule2       DISTANCE
LGA    T     156      T     156          3.630
LGA    N     157      N     157          2.879
LGA    E     158      E     158          3.031
LGA    D     159      D     159          3.001
LGA    A     160      A     160          2.358
LGA    V     161      V     161          3.580
LGA    F     162      F     162          7.647
LGA    L     163      L     163          8.978
LGA    T     164      T     164          9.326
LGA    D     165      D     165         10.718

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   10  335    4.0      6    3.11     1.716     1.520     0.187

LGA_LOCAL      RMSD =  3.110  Number of atoms =    6  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  6.316  Number of atoms =   10 
Std_ALL_ATOMS  RMSD =  5.042  (standard rmsd on all 10 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.043400 * X  +   0.842541 * Y  +  -0.536881 * Z  +   1.885751
  Y_new =  -0.208711 * X  +   0.517884 * Y  +   0.829600 * Z  +  19.012074
  Z_new =   0.977014 * X  +   0.148057 * Y  +   0.153372 * Z  + -32.569931 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.767770   -2.373823  [ DEG:    43.9900   -136.0100 ]
  Theta =  -1.355972   -1.785620  [ DEG:   -77.6915   -102.3085 ]
  Phi   =  -1.775816    1.365777  [ DEG:  -101.7468     78.2532 ]
 
# 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: T0318TS021_2_1-D2                             
REMARK     2: T0318_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0318TS021_2_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    6   3.11   1.520     5.04
REMARK  ---------------------------------------------------------- 
MOLECULE T0318TS021_2_1-D2
REMARK PARENT number 1
PFRMAT TS
TARGET T0318
PARENT N/A
ATOM   1201  N   THR   156      29.310  24.760  16.406  1.00200.09       1SG1202
ATOM   1202  CA  THR   156      28.750  24.473  15.113  1.00200.09       1SG1203
ATOM   1203  CB  THR   156      27.494  23.648  15.198  1.00200.09       1SG1204
ATOM   1204  OG1 THR   156      27.148  23.114  13.928  1.00200.09       1SG1205
ATOM   1205  CG2 THR   156      26.354  24.537  15.722  1.00200.09       1SG1206
ATOM   1206  C   THR   156      28.426  25.743  14.390  1.00200.09       1SG1207
ATOM   1207  O   THR   156      28.786  26.834  14.826  1.00200.09       1SG1208
ATOM   1208  N   ASN   157      27.752  25.603  13.228  1.00146.88       1SG1209
ATOM   1209  CA  ASN   157      27.428  26.697  12.361  1.00146.88       1SG1210
ATOM   1210  CB  ASN   157      26.979  26.274  10.950  1.00146.88       1SG1211
ATOM   1211  CG  ASN   157      28.173  25.737  10.170  1.00146.88       1SG1212
ATOM   1212  OD1 ASN   157      28.396  24.531  10.096  1.00146.88       1SG1213
ATOM   1213  ND2 ASN   157      28.957  26.662   9.554  1.00146.88       1SG1214
ATOM   1214  C   ASN   157      26.320  27.511  12.924  1.00146.88       1SG1215
ATOM   1215  O   ASN   157      25.412  27.007  13.580  1.00146.88       1SG1216
ATOM   1216  N   GLU   158      26.409  28.829  12.669  1.00293.46       1SG1217
ATOM   1217  CA  GLU   158      25.396  29.761  13.044  1.00293.46       1SG1218
ATOM   1218  CB  GLU   158      25.794  30.649  14.237  1.00293.46       1SG1219
ATOM   1219  CG  GLU   158      24.718  31.649  14.663  1.00293.46       1SG1220
ATOM   1220  CD  GLU   158      25.230  32.372  15.902  1.00293.46       1SG1221
ATOM   1221  OE1 GLU   158      25.440  31.692  16.940  1.00293.46       1SG1222
ATOM   1222  OE2 GLU   158      25.424  33.616  15.824  1.00293.46       1SG1223
ATOM   1223  C   GLU   158      25.214  30.633  11.844  1.00293.46       1SG1224
ATOM   1224  O   GLU   158      26.151  30.839  11.077  1.00293.46       1SG1225
ATOM   1225  N   ASP   159      23.980  31.132  11.625  1.00178.34       1SG1226
ATOM   1226  CA  ASP   159      23.747  31.984  10.497  1.00178.34       1SG1227
ATOM   1227  CB  ASP   159      22.332  31.862   9.903  1.00178.34       1SG1228
ATOM   1228  CG  ASP   159      22.246  30.533   9.170  1.00178.34       1SG1229
ATOM   1229  OD1 ASP   159      23.233  30.179   8.472  1.00178.34       1SG1230
ATOM   1230  OD2 ASP   159      21.191  29.855   9.290  1.00178.34       1SG1231
ATOM   1231  C   ASP   159      23.901  33.388  10.969  1.00178.34       1SG1232
ATOM   1232  O   ASP   159      22.939  34.031  11.384  1.00178.34       1SG1233
ATOM   1233  N   ALA   160      25.144  33.891  10.935  1.00 81.91       1SG1234
ATOM   1234  CA  ALA   160      25.400  35.234  11.349  1.00 81.91       1SG1235
ATOM   1235  CB  ALA   160      26.859  35.475  11.771  1.00 81.91       1SG1236
ATOM   1236  C   ALA   160      25.116  36.119  10.185  1.00 81.91       1SG1237
ATOM   1237  O   ALA   160      25.170  35.691   9.034  1.00 81.91       1SG1238
ATOM   1238  N   VAL   161      24.762  37.384  10.463  1.00171.94       1SG1239
ATOM   1239  CA  VAL   161      24.552  38.277   9.372  1.00171.94       1SG1240
ATOM   1240  CB  VAL   161      23.153  38.275   8.841  1.00171.94       1SG1241
ATOM   1241  CG1 VAL   161      22.239  39.009   9.838  1.00171.94       1SG1242
ATOM   1242  CG2 VAL   161      23.180  38.874   7.430  1.00171.94       1SG1243
ATOM   1243  C   VAL   161      24.826  39.647   9.880  1.00171.94       1SG1244
ATOM   1244  O   VAL   161      24.774  39.901  11.081  1.00171.94       1SG1245
ATOM   1245  N   PHE   162      25.154  40.569   8.967  1.00118.56       1SG1246
ATOM   1246  CA  PHE   162      25.392  41.902   9.411  1.00118.56       1SG1247
ATOM   1247  CB  PHE   162      26.822  42.396   9.144  1.00118.56       1SG1248
ATOM   1248  CG  PHE   162      27.720  41.642  10.060  1.00118.56       1SG1249
ATOM   1249  CD1 PHE   162      28.066  40.337   9.795  1.00118.56       1SG1250
ATOM   1250  CD2 PHE   162      28.224  42.245  11.189  1.00118.56       1SG1251
ATOM   1251  CE1 PHE   162      28.898  39.646  10.645  1.00118.56       1SG1252
ATOM   1252  CE2 PHE   162      29.055  41.561  12.042  1.00118.56       1SG1253
ATOM   1253  CZ  PHE   162      29.394  40.256  11.774  1.00118.56       1SG1254
ATOM   1254  C   PHE   162      24.458  42.777   8.662  1.00118.56       1SG1255
ATOM   1255  O   PHE   162      24.030  42.462   7.554  1.00118.56       1SG1256
ATOM   1256  N   LEU   163      24.082  43.897   9.292  1.00233.65       1SG1257
ATOM   1257  CA  LEU   163      23.209  44.842   8.681  1.00233.65       1SG1258
ATOM   1258  CB  LEU   163      22.326  45.587   9.694  1.00233.65       1SG1259
ATOM   1259  CG  LEU   163      21.414  44.648  10.520  1.00233.65       1SG1260
ATOM   1260  CD1 LEU   163      20.406  43.905   9.627  1.00233.65       1SG1261
ATOM   1261  CD2 LEU   163      22.229  43.691  11.407  1.00233.65       1SG1262
ATOM   1262  C   LEU   163      24.102  45.826   8.007  1.00233.65       1SG1263
ATOM   1263  O   LEU   163      25.268  45.953   8.377  1.00233.65       1SG1264
ATOM   1264  N   THR   164      23.581  46.547   6.994  1.00366.25       1SG1265
ATOM   1265  CA  THR   164      24.418  47.478   6.296  1.00366.25       1SG1266
ATOM   1266  CB  THR   164      23.709  48.278   5.244  1.00366.25       1SG1267
ATOM   1267  OG1 THR   164      23.151  47.418   4.261  1.00366.25       1SG1268
ATOM   1268  CG2 THR   164      24.711  49.256   4.602  1.00366.25       1SG1269
ATOM   1269  C   THR   164      24.932  48.449   7.293  1.00366.25       1SG1270
ATOM   1270  O   THR   164      24.171  49.038   8.058  1.00366.25       1SG1271
ATOM   1271  N   ASP   165      26.262  48.634   7.310  1.00458.31       1SG1272
ATOM   1272  CA  ASP   165      26.816  49.539   8.265  1.00458.31       1SG1273
ATOM   1273  CB  ASP   165      28.341  49.417   8.405  1.00458.31       1SG1274
ATOM   1274  CG  ASP   165      28.636  48.074   9.057  1.00458.31       1SG1275
ATOM   1275  OD1 ASP   165      27.721  47.531   9.734  1.00458.31       1SG1276
ATOM   1276  OD2 ASP   165      29.779  47.574   8.890  1.00458.31       1SG1277
ATOM   1277  C   ASP   165      26.482  50.945   7.799  1.00458.31       1SG1278
ATOM   1278  O   ASP   165      25.944  51.076   6.668  1.00458.31       1SG1279
ATOM   1279  OXT ASP   165      26.752  51.907   8.568  1.00458.31       1SG1280
TER
END
