
#######################################################
#                                                     #
#                        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 T0372TS671_3-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected    9 , name T0372_D1.pdb
# PARAMETERS: T0372TS671_3-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         2.84     2.84
  LCS_AVERAGE:      7.14

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8       290 - 297         2.00     3.53
  LCS_AVERAGE:      6.17

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       291 - 295         0.82     3.91
  LCS_AVERAGE:      3.62

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    6    6    6    8    8    8    8    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     Y     291     Y     291      5    8    9     3    5    6    6    6    8    8    8    8    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     M     292     M     292      5    8    9     3    5    6    6    6    8    8    8    8    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     A     293     A     293      5    8    9     3    5    6    6    6    8    8    8    8    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     C     294     C     294      5    8    9     3    5    6    6    6    8    8    8    8    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     L     295     L     295      5    8    9     3    5    6    6    6    8    8    8    8    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     K     296     K     296      4    8    9     3    4    5    6    6    8    8    8    8    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     D     297     D     297      4    8    9     3    4    6    6    6    8    8    8    8    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     H     298     H     298      4    6    9     3    4    4    4    5    6    7    8    8    9    9    9    9    9    9    9    9    9    9    9 
LCS_AVERAGE  LCS_A:   5.64  (   3.62    6.17    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      3      5      6      6      6      8      8      8      8      9      9      9      9      9      9      9      9      9      9      9 
GDT PERCENT_CA   2.38   3.97   4.76   4.76   4.76   6.35   6.35   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
GDT RMS_LOCAL    0.03   0.82   1.14   1.14   1.14   2.00   2.00   2.00   2.00   2.84   2.84   2.84   2.84   2.84   2.84   2.84   2.84   2.84   2.84   2.84
GDT RMS_ALL_CA  10.26   3.91   3.48   3.48   3.48   3.53   3.53   3.53   3.53   2.84   2.84   2.84   2.84   2.84   2.84   2.84   2.84   2.84   2.84   2.84

#      Molecule1      Molecule2       DISTANCE
LGA    K     290      K     290          2.732
LGA    Y     291      Y     291          1.380
LGA    M     292      M     292          1.612
LGA    A     293      A     293          1.384
LGA    C     294      C     294          1.868
LGA    L     295      L     295          1.278
LGA    K     296      K     296          2.754
LGA    D     297      D     297          2.310
LGA    H     298      H     298          8.954

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    9  126    4.0      8    2.00     5.556     5.974     0.381

LGA_LOCAL      RMSD =  1.998  Number of atoms =    8  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.529  Number of atoms =    9 
Std_ALL_ATOMS  RMSD =  2.843  (standard rmsd on all 9 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.692101 * X  +   0.114776 * Y  +  -0.712617 * Z  +  46.760674
  Y_new =  -0.688678 * X  +  -0.400646 * Y  +   0.604322 * Z  +  41.526985
  Z_new =  -0.216146 * X  +   0.909015 * Y  +   0.356331 * Z  +  -5.229712 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.197208   -1.944384  [ DEG:    68.5950   -111.4050 ]
  Theta =   0.217865    2.923728  [ DEG:    12.4828    167.5172 ]
  Phi   =  -2.358674    0.782919  [ DEG:  -135.1420     44.8580 ]
 
# 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: T0372TS671_3-D1                               
REMARK     2: T0372_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0372TS671_3-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    8   2.00   5.974     2.84
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS671_3-D1
PFRMAT TS
TARGET T0372
MODEL  3  REFINED
PARENT 1NE9_A
ATOM   1245  N   LYS   290      25.648  44.116   6.798  1.00  0.00
ATOM   1246  CA  LYS   290      26.597  44.252   5.733  1.00  0.00
ATOM   1247  C   LYS   290      26.054  45.250   4.710  1.00  0.00
ATOM   1248  O   LYS   290      25.172  44.928   3.900  1.00  0.00
ATOM   1249  CB  LYS   290      26.736  42.858   5.021  1.00  0.00
ATOM   1250  CG  LYS   290      27.875  42.037   5.479  1.00  0.00
ATOM   1251  CD  LYS   290      28.475  41.426   4.173  1.00  0.00
ATOM   1252  CE  LYS   290      29.691  40.560   4.485  1.00  0.00
ATOM   1253  NZ  LYS   290      29.195  39.303   5.163  1.00  0.00
ATOM   1254  N   TYR   291      26.718  46.400   4.628  1.00  0.00
ATOM   1255  CA  TYR   291      26.369  47.544   3.816  1.00  0.00
ATOM   1256  C   TYR   291      26.980  47.391   2.419  1.00  0.00
ATOM   1257  O   TYR   291      28.199  47.244   2.274  1.00  0.00
ATOM   1258  CB  TYR   291      27.018  48.772   4.474  1.00  0.00
ATOM   1259  CG  TYR   291      26.337  49.291   5.739  1.00  0.00
ATOM   1260  CD1 TYR   291      25.118  49.939   5.686  1.00  0.00
ATOM   1261  CD2 TYR   291      26.931  49.097   6.989  1.00  0.00
ATOM   1262  CE1 TYR   291      24.506  50.392   6.834  1.00  0.00
ATOM   1263  CE2 TYR   291      26.319  49.534   8.152  1.00  0.00
ATOM   1264  CZ  TYR   291      25.108  50.182   8.066  1.00  0.00
ATOM   1265  OH  TYR   291      24.484  50.668   9.226  1.00  0.00
ATOM   1266  N   MET   292      26.095  47.566   1.408  1.00  0.00
ATOM   1267  CA  MET   292      26.517  47.352   0.065  1.00  0.00
ATOM   1268  C   MET   292      25.809  48.229  -0.982  1.00  0.00
ATOM   1269  O   MET   292      24.569  48.174  -1.097  1.00  0.00
ATOM   1270  CB  MET   292      26.494  45.802  -0.209  1.00  0.00
ATOM   1271  CG  MET   292      27.195  45.523  -1.561  1.00  0.00
ATOM   1272  SD  MET   292      25.818  45.312  -2.755  1.00  0.00
ATOM   1273  CE  MET   292      25.808  43.513  -2.957  1.00  0.00
ATOM   1274  N   ALA   293      26.588  48.967  -1.696  1.00  0.00
ATOM   1275  CA  ALA   293      26.068  49.733  -2.790  1.00  0.00
ATOM   1276  C   ALA   293      26.336  48.929  -4.098  1.00  0.00
ATOM   1277  O   ALA   293      27.544  48.774  -4.443  1.00  0.00
ATOM   1278  CB  ALA   293      26.684  51.167  -2.822  1.00  0.00
ATOM   1279  N   CYS   294      25.356  48.081  -4.430  1.00  0.00
ATOM   1280  CA  CYS   294      25.514  47.166  -5.548  1.00  0.00
ATOM   1281  C   CYS   294      26.284  47.841  -6.640  1.00  0.00
ATOM   1282  O   CYS   294      27.084  47.164  -7.306  1.00  0.00
ATOM   1283  CB  CYS   294      24.235  46.498  -5.992  1.00  0.00
ATOM   1284  SG  CYS   294      24.413  45.568  -7.464  1.00  0.00
ATOM   1285  N   LEU   295      25.721  48.897  -7.094  1.00  0.00
ATOM   1286  CA  LEU   295      26.247  49.923  -8.015  1.00  0.00
ATOM   1287  C   LEU   295      26.234  49.715  -9.524  1.00  0.00
ATOM   1288  O   LEU   295      25.351  50.324 -10.144  1.00  0.00
ATOM   1289  CB  LEU   295      27.438  50.588  -7.379  1.00  0.00
ATOM   1290  CG  LEU   295      27.816  52.022  -7.514  1.00  0.00
ATOM   1291  CD1 LEU   295      29.196  52.234  -6.923  1.00  0.00
ATOM   1292  CD2 LEU   295      27.825  52.536  -8.948  1.00  0.00
ATOM   1293  N   LYS   296      27.015  48.812 -10.172  1.00  0.00
ATOM   1294  CA  LYS   296      26.970  48.917 -11.633  1.00  0.00
ATOM   1295  C   LYS   296      26.105  47.897 -12.297  1.00  0.00
ATOM   1296  O   LYS   296      24.973  48.241 -12.568  1.00  0.00
ATOM   1297  CB  LYS   296      28.404  48.913 -12.203  1.00  0.00
ATOM   1298  CG  LYS   296      29.309  49.793 -11.426  1.00  0.00
ATOM   1299  CD  LYS   296      30.739  49.550 -11.558  1.00  0.00
ATOM   1300  CE  LYS   296      31.657  50.619 -10.816  1.00  0.00
ATOM   1301  NZ  LYS   296      30.883  51.130  -9.510  1.00  0.00
ATOM   1302  N   ASP   297      26.594  46.745 -12.612  1.00  0.00
ATOM   1303  CA  ASP   297      25.814  45.685 -13.211  1.00  0.00
ATOM   1304  C   ASP   297      25.789  44.400 -12.331  1.00  0.00
ATOM   1305  O   ASP   297      25.549  43.322 -12.923  1.00  0.00
ATOM   1306  CB  ASP   297      26.401  45.460 -14.606  1.00  0.00
ATOM   1307  CG  ASP   297      26.112  46.662 -15.540  1.00  0.00
ATOM   1308  OD1 ASP   297      25.072  47.316 -15.314  1.00  0.00
ATOM   1309  OD2 ASP   297      26.839  46.888 -16.525  1.00  0.00
ATOM   1310  N   HIS   298      26.136  44.448 -11.032  1.00  0.00
ATOM   1311  CA  HIS   298      26.082  43.262 -10.288  1.00  0.00
ATOM   1312  C   HIS   298      24.653  42.812 -10.301  1.00  0.00
ATOM   1313  O   HIS   298      23.733  43.714 -10.361  1.00  0.00
ATOM   1314  CB  HIS   298      26.695  43.413  -8.888  1.00  0.00
ATOM   1315  CG  HIS   298      26.423  42.369  -7.845  1.00  0.00
ATOM   1316  ND1 HIS   298      26.701  41.025  -7.984  1.00  0.00
ATOM   1317  CD2 HIS   298      25.870  42.502  -6.611  1.00  0.00
ATOM   1318  CE1 HIS   298      26.321  40.371  -6.894  1.00  0.00
ATOM   1319  NE2 HIS   298      25.804  41.242  -6.047  1.00  0.00
TER
END
