
#######################################################
#                                                     #
#                        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   13 (  115),  selected   13 , name T0386TS389_2-D2
# Molecule2: number of CA atoms   81 (  636),  selected   13 , name T0386_D2.pdb
# PARAMETERS: T0386TS389_2-D2.T0386_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:    13       219 - 231         0.80     0.80
  LCS_AVERAGE:     16.05

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13       219 - 231         0.80     0.80
  LCS_AVERAGE:     16.05

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13       219 - 231         0.80     0.80
  LCS_AVERAGE:     16.05

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:   81
LCS_GDT     N     219     N     219     13   13   13     5   11   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     P     220     P     220     13   13   13     5   11   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     E     221     E     221     13   13   13     5   10   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     K     222     K     222     13   13   13    10   11   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     I     223     I     223     13   13   13    10   11   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     R     224     R     224     13   13   13    10   11   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     L     225     L     225     13   13   13    10   11   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     L     226     L     226     13   13   13    10   11   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     K     227     K     227     13   13   13    10   11   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     E     228     E     228     13   13   13    10   11   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     F     229     F     229     13   13   13    10   11   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     M     230     M     230     13   13   13    10   11   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     H     231     H     231     13   13   13    10   11   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_AVERAGE  LCS_A:  16.05  (  16.05   16.05   16.05 )

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     10     11     13     13     13     13     13     13     13     13     13     13     13     13     13     13     13     13     13     13 
GDT PERCENT_CA  12.35  13.58  16.05  16.05  16.05  16.05  16.05  16.05  16.05  16.05  16.05  16.05  16.05  16.05  16.05  16.05  16.05  16.05  16.05  16.05
GDT RMS_LOCAL    0.35   0.62   0.80   0.80   0.80   0.80   0.80   0.80   0.80   0.80   0.80   0.80   0.80   0.80   0.80   0.80   0.80   0.80   0.80   0.80
GDT RMS_ALL_CA   1.19   0.91   0.80   0.80   0.80   0.80   0.80   0.80   0.80   0.80   0.80   0.80   0.80   0.80   0.80   0.80   0.80   0.80   0.80   0.80

#      Molecule1      Molecule2       DISTANCE
LGA    N     219      N     219          0.796
LGA    P     220      P     220          0.979
LGA    E     221      E     221          1.313
LGA    K     222      K     222          0.613
LGA    I     223      I     223          0.700
LGA    R     224      R     224          1.127
LGA    L     225      L     225          0.809
LGA    L     226      L     226          0.453
LGA    K     227      K     227          0.427
LGA    E     228      E     228          0.470
LGA    F     229      F     229          0.655
LGA    M     230      M     230          0.673
LGA    H     231      H     231          0.852

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   13   81    4.0     13    0.80    15.432    15.854     1.444

LGA_LOCAL      RMSD =  0.800  Number of atoms =   13  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  0.800  Number of atoms =   13 
Std_ALL_ATOMS  RMSD =  0.800  (standard rmsd on all 13 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.527460 * X  +  -0.174023 * Y  +   0.831566 * Z  +  16.291502
  Y_new =  -0.470179 * X  +   0.755445 * Y  +   0.456327 * Z  +  67.931343
  Z_new =  -0.707614 * X  +  -0.631679 * Y  +   0.316645 * Z  +  73.026367 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.106129    2.035463  [ DEG:   -63.3765    116.6235 ]
  Theta =   0.786115    2.355477  [ DEG:    45.0411    134.9589 ]
  Phi   =  -0.728045    2.413548  [ DEG:   -41.7139    138.2861 ]
 
# 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: T0386TS389_2-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0386TS389_2-D2.T0386_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   13   81   4.0   13   0.80  15.854     0.80
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS389_2-D2
PFRMAT TS
TARGET T0386
MODEL  2
PARENT N/A
ATOM   1164  N   ASN   219       2.350  55.071  76.351  1.00  0.00
ATOM   1165  CA  ASN   219       2.606  56.025  75.270  1.00  0.00
ATOM   1166  CB  ASN   219       1.570  55.863  74.157  1.00  0.00
ATOM   1167  CG  ASN   219       1.782  54.603  73.341  1.00  0.00
ATOM   1168  ND2 ASN   219       0.739  54.167  72.644  1.00  0.00
ATOM   1169  OD1 ASN   219       2.872  54.030  73.338  1.00  0.00
ATOM   1170  O   ASN   219       3.387  58.299  75.317  1.00  0.00
ATOM   1171  C   ASN   219       2.550  57.500  75.724  1.00  0.00
ATOM   1172  N   PRO   220       1.592  57.847  76.577  1.00  0.00
ATOM   1173  CA  PRO   220       1.432  59.225  77.010  1.00  0.00
ATOM   1174  CB  PRO   220       0.104  59.221  77.770  1.00  0.00
ATOM   1175  CG  PRO   220      -0.108  57.793  78.146  1.00  0.00
ATOM   1176  CD  PRO   220       0.522  56.977  77.052  1.00  0.00
ATOM   1177  O   PRO   220       3.106  60.804  77.768  1.00  0.00
ATOM   1178  C   PRO   220       2.582  59.685  77.917  1.00  0.00
ATOM   1179  N   GLU   221       2.985  58.822  78.849  1.00  0.00
ATOM   1180  CA  GLU   221       4.124  59.091  79.718  1.00  0.00
ATOM   1181  CB  GLU   221       4.301  57.962  80.735  1.00  0.00
ATOM   1182  CG  GLU   221       3.223  57.917  81.806  1.00  0.00
ATOM   1183  CD  GLU   221       3.353  56.708  82.711  1.00  0.00
ATOM   1184  OE1 GLU   221       4.235  55.863  82.452  1.00  0.00
ATOM   1185  OE2 GLU   221       2.572  56.606  83.681  1.00  0.00
ATOM   1186  O   GLU   221       6.186  60.128  79.103  1.00  0.00
ATOM   1187  C   GLU   221       5.397  59.206  78.892  1.00  0.00
ATOM   1188  N   LYS   222       5.609  58.287  77.951  1.00  0.00
ATOM   1189  CA  LYS   222       6.803  58.359  77.106  1.00  0.00
ATOM   1190  CB  LYS   222       6.845  57.178  76.135  1.00  0.00
ATOM   1191  CG  LYS   222       7.069  55.832  76.803  1.00  0.00
ATOM   1192  CD  LYS   222       7.127  54.710  75.779  1.00  0.00
ATOM   1193  CE  LYS   222       7.273  53.356  76.452  1.00  0.00
ATOM   1194  NZ  LYS   222       7.377  52.250  75.460  1.00  0.00
ATOM   1195  O   LYS   222       7.730  60.480  76.381  1.00  0.00
ATOM   1196  C   LYS   222       6.812  59.673  76.275  1.00  0.00
ATOM   1197  N   ILE   223       5.773  59.914  75.499  1.00  0.00
ATOM   1198  CA  ILE   223       5.789  61.045  74.580  1.00  0.00
ATOM   1199  CB  ILE   223       4.643  60.956  73.554  1.00  0.00
ATOM   1200  CG1 ILE   223       4.865  59.774  72.607  1.00  0.00
ATOM   1201  CG2 ILE   223       4.568  62.229  72.726  1.00  0.00
ATOM   1202  CD1 ILE   223       3.667  59.452  71.743  1.00  0.00
ATOM   1203  O   ILE   223       6.322  63.359  74.765  1.00  0.00
ATOM   1204  C   ILE   223       5.641  62.445  75.203  1.00  0.00
ATOM   1205  N   ARG   224       4.778  62.604  76.206  1.00  0.00
ATOM   1206  CA  ARG   224       4.700  63.866  76.944  1.00  0.00
ATOM   1207  CB  ARG   224       3.529  63.838  77.930  1.00  0.00
ATOM   1208  CG  ARG   224       2.161  63.893  77.269  1.00  0.00
ATOM   1209  CD  ARG   224       1.047  63.778  78.299  1.00  0.00
ATOM   1210  NE  ARG   224      -0.275  63.819  77.680  1.00  0.00
ATOM   1211  CZ  ARG   224      -1.412  63.609  78.333  1.00  0.00
ATOM   1212  NH1 ARG   224      -2.569  63.666  77.689  1.00  0.00
ATOM   1213  NH2 ARG   224      -1.392  63.343  79.632  1.00  0.00
ATOM   1214  O   ARG   224       6.375  65.255  77.942  1.00  0.00
ATOM   1215  C   ARG   224       5.984  64.105  77.727  1.00  0.00
ATOM   1216  N   LEU   225       6.639  63.018  78.141  1.00  0.00
ATOM   1217  CA  LEU   225       7.920  63.073  78.816  1.00  0.00
ATOM   1218  CB  LEU   225       8.318  61.687  79.328  1.00  0.00
ATOM   1219  CG  LEU   225       7.489  61.130  80.488  1.00  0.00
ATOM   1220  CD1 LEU   225       7.863  59.683  80.770  1.00  0.00
ATOM   1221  CD2 LEU   225       7.728  61.937  81.754  1.00  0.00
ATOM   1222  O   LEU   225       9.852  64.384  78.342  1.00  0.00
ATOM   1223  C   LEU   225       9.050  63.555  77.929  1.00  0.00
ATOM   1224  N   LEU   226       9.147  63.001  76.721  1.00  0.00
ATOM   1225  CA  LEU   226      10.091  63.465  75.703  1.00  0.00
ATOM   1226  CB  LEU   226       9.906  62.676  74.406  1.00  0.00
ATOM   1227  CG  LEU   226      10.347  61.212  74.433  1.00  0.00
ATOM   1228  CD1 LEU   226       9.936  60.503  73.153  1.00  0.00
ATOM   1229  CD2 LEU   226      11.858  61.107  74.570  1.00  0.00
ATOM   1230  O   LEU   226      10.826  65.713  75.324  1.00  0.00
ATOM   1231  C   LEU   226       9.871  64.952  75.401  1.00  0.00
ATOM   1232  N   LYS   227       8.624  65.363  75.214  1.00  0.00
ATOM   1233  CA  LYS   227       8.339  66.783  75.034  1.00  0.00
ATOM   1234  CB  LYS   227       6.835  67.015  74.893  1.00  0.00
ATOM   1235  CG  LYS   227       6.248  66.504  73.586  1.00  0.00
ATOM   1236  CD  LYS   227       4.753  66.770  73.514  1.00  0.00
ATOM   1237  CE  LYS   227       4.161  66.236  72.216  1.00  0.00
ATOM   1238  NZ  LYS   227       2.690  66.460  72.145  1.00  0.00
ATOM   1239  O   LYS   227       9.318  68.750  75.968  1.00  0.00
ATOM   1240  C   LYS   227       8.813  67.661  76.199  1.00  0.00
ATOM   1241  N   GLU   228       8.636  67.196  77.431  1.00  0.00
ATOM   1242  CA  GLU   228       9.041  67.978  78.592  1.00  0.00
ATOM   1243  CB  GLU   228       8.495  67.352  79.876  1.00  0.00
ATOM   1244  CG  GLU   228       8.865  68.109  81.142  1.00  0.00
ATOM   1245  CD  GLU   228       8.214  69.477  81.213  1.00  0.00
ATOM   1246  OE1 GLU   228       7.320  69.753  80.385  1.00  0.00
ATOM   1247  OE2 GLU   228       8.598  70.271  82.096  1.00  0.00
ATOM   1248  O   GLU   228      11.137  69.078  78.892  1.00  0.00
ATOM   1249  C   GLU   228      10.565  68.025  78.678  1.00  0.00
ATOM   1250  N   PHE   229      11.216  66.880  78.491  1.00  0.00
ATOM   1251  CA  PHE   229      12.665  66.782  78.453  1.00  0.00
ATOM   1252  CB  PHE   229      13.095  65.380  78.016  1.00  0.00
ATOM   1253  CG  PHE   229      12.850  64.320  79.052  1.00  0.00
ATOM   1254  CD1 PHE   229      12.553  64.663  80.359  1.00  0.00
ATOM   1255  CD2 PHE   229      12.918  62.978  78.718  1.00  0.00
ATOM   1256  CE1 PHE   229      12.329  63.687  81.311  1.00  0.00
ATOM   1257  CE2 PHE   229      12.692  62.002  79.671  1.00  0.00
ATOM   1258  CZ  PHE   229      12.399  62.353  80.963  1.00  0.00
ATOM   1259  O   PHE   229      14.320  68.419  77.813  1.00  0.00
ATOM   1260  C   PHE   229      13.314  67.773  77.481  1.00  0.00
ATOM   1261  N   MET   230      12.750  67.872  76.279  1.00  0.00
ATOM   1262  CA  MET   230      13.248  68.779  75.235  1.00  0.00
ATOM   1263  CB  MET   230      12.574  68.474  73.896  1.00  0.00
ATOM   1264  CG  MET   230      13.144  69.256  72.723  1.00  0.00
ATOM   1265  SD  MET   230      14.885  68.896  72.425  1.00  0.00
ATOM   1266  CE  MET   230      14.777  67.246  71.738  1.00  0.00
ATOM   1267  O   MET   230      13.686  71.152  75.082  1.00  0.00
ATOM   1268  C   MET   230      12.974  70.251  75.560  1.00  0.00
ATOM   1269  N   HIS   231      11.944  70.483  76.369  1.00  0.00
ATOM   1270  CA  HIS   231      11.618  71.824  76.863  1.00  0.00
ATOM   1271  CB  HIS   231      10.240  71.832  77.528  1.00  0.00
ATOM   1272  CG  HIS   231       9.113  71.554  76.584  1.00  0.00
ATOM   1273  CD2 HIS   231       8.962  71.495  75.136  1.00  0.00
ATOM   1274  ND1 HIS   231       7.836  71.263  77.012  1.00  0.00
ATOM   1275  CE1 HIS   231       7.048  71.063  75.939  1.00  0.00
ATOM   1276  NE2 HIS   231       7.717  71.201  74.811  1.00  0.00
ATOM   1277  O   HIS   231      12.930  73.537  77.977  1.00  0.00
ATOM   1278  C   HIS   231      12.641  72.341  77.918  1.00  0.00
TER
END
