
#######################################################
#                                                     #
#                        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    8 (   68),  selected    8 , name T0316TS186_3-D2
# Molecule2: number of CA atoms   60 (  457),  selected    8 , name T0316_D2.pdb
# PARAMETERS: T0316TS186_3-D2.T0316_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:     8       276 - 283         4.74     4.74
  LCS_AVERAGE:     13.33

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       278 - 282         1.76     6.89
  LCS_AVERAGE:      7.50

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       276 - 279         0.82     8.35
  LCS_AVERAGE:      5.62

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:   60
LCS_GDT     Q     276     Q     276      4    4    8     3    3    4    4    4    4    4    4    6    6    6    7    7    7    7    7    8    8    8    8 
LCS_GDT     G     277     G     277      4    4    8     3    3    4    4    4    4    5    5    6    6    6    7    7    7    7    7    8    8    8    8 
LCS_GDT     F     278     F     278      4    5    8     3    3    4    4    4    5    5    5    6    6    6    7    7    7    7    7    8    8    8    8 
LCS_GDT     Y     279     Y     279      4    5    8     3    3    4    4    4    5    5    5    6    6    6    7    7    7    7    7    8    8    8    8 
LCS_GDT     H     280     H     280      4    5    8     3    3    4    4    4    5    5    5    6    6    6    7    7    7    7    7    8    8    8    8 
LCS_GDT     D     281     D     281      4    5    8     3    3    4    4    4    5    5    5    6    6    6    7    7    7    7    7    8    8    8    8 
LCS_GDT     S     282     S     282      3    5    8     0    3    3    4    4    5    5    5    6    6    6    7    7    7    7    7    8    8    8    8 
LCS_GDT     L     283     L     283      0    3    8     0    0    3    3    3    4    4    4    4    5    5    5    6    7    7    7    8    8    8    8 
LCS_AVERAGE  LCS_A:   8.82  (   5.62    7.50   13.33 )

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      4      4      4      5      5      5      6      6      6      7      7      7      7      7      8      8      8      8 
GDT PERCENT_CA   5.00   5.00   6.67   6.67   6.67   8.33   8.33   8.33  10.00  10.00  10.00  11.67  11.67  11.67  11.67  11.67  13.33  13.33  13.33  13.33
GDT RMS_LOCAL    0.23   0.23   0.82   0.82   0.82   1.76   1.76   1.76   2.88   2.88   2.88   3.64   3.64   3.64   3.64   3.64   4.74   4.74   4.74   4.74
GDT RMS_ALL_CA   7.60   7.60   8.35   8.35   8.35   6.89   6.89   6.89   5.20   5.20   5.20   5.09   5.09   5.09   5.09   5.09   4.74   4.74   4.74   4.74

#      Molecule1      Molecule2       DISTANCE
LGA    Q     276      Q     276         14.986
LGA    G     277      G     277          8.281
LGA    F     278      F     278          2.142
LGA    Y     279      Y     279          1.087
LGA    H     280      H     280          0.995
LGA    D     281      D     281          1.328
LGA    S     282      S     282          2.634
LGA    L     283      L     283          8.465

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    8   60    4.0      5    1.76     7.917     8.300     0.269

LGA_LOCAL      RMSD =  1.758  Number of atoms =    5  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  6.894  Number of atoms =    8 
Std_ALL_ATOMS  RMSD =  4.736  (standard rmsd on all 8 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.306798 * X  +   0.689299 * Y  +  -0.656309 * Z  +  29.309488
  Y_new =   0.597439 * X  +  -0.676261 * Y  +  -0.430974 * Z  +  84.412712
  Z_new =  -0.740906 * X  +  -0.259883 * Y  +  -0.619289 * Z  +  32.481007 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.744265    0.397327  [ DEG:  -157.2348     22.7652 ]
  Theta =   0.834418    2.307174  [ DEG:    47.8087    132.1913 ]
  Phi   =   1.096389   -2.045204  [ DEG:    62.8185   -117.1815 ]
 
# 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: T0316TS186_3-D2                               
REMARK     2: T0316_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0316TS186_3-D2.T0316_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    8   60   4.0    5   1.76   8.300     4.74
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS186_3-D2
PFRMAT TS
TARGET T0316
MODEL  3
PARENT 1j1z_A
ATOM   1295  N   GLN   276      12.607  22.067 -17.950  1.00  0.00
ATOM   1296  CA  GLN   276      12.912  23.274 -17.150  1.00  0.00
ATOM   1297  C   GLN   276      14.404  23.375 -16.835  1.00  0.00
ATOM   1298  O   GLN   276      14.815  24.174 -15.996  1.00  0.00
ATOM   1299  CB  GLN   276      12.152  23.245 -15.823  1.00  0.00
ATOM   1300  CG  GLN   276      10.659  23.504 -15.956  1.00  0.00
ATOM   1301  CD  GLN   276       9.913  23.295 -14.654  1.00  0.00
ATOM   1302  OE1 GLN   276      10.524  23.116 -13.600  1.00  0.00
ATOM   1303  NE2 GLN   276       8.588  23.319 -14.722  1.00  0.00
ATOM   1304  N   GLY   277      15.204  22.560 -17.516  1.00  0.00
ATOM   1305  CA  GLY   277      16.651  22.552 -17.328  1.00  0.00
ATOM   1306  C   GLY   277      17.311  21.709 -18.409  1.00  0.00
ATOM   1307  O   GLY   277      16.647  20.927 -19.091  1.00  0.00
ATOM   1308  N   PHE   278      18.622  21.878 -18.545  1.00  0.00
ATOM   1309  CA  PHE   278      19.437  21.168 -19.527  1.00  0.00
ATOM   1310  C   PHE   278      20.153  19.961 -18.898  1.00  0.00
ATOM   1311  O   PHE   278      20.422  19.947 -17.701  1.00  0.00
ATOM   1312  CB  PHE   278      20.505  22.097 -20.109  1.00  0.00
ATOM   1313  CG  PHE   278      19.944  23.233 -20.915  1.00  0.00
ATOM   1314  CD1 PHE   278      18.631  23.210 -21.353  1.00  0.00
ATOM   1315  CD2 PHE   278      20.731  24.326 -21.237  1.00  0.00
ATOM   1316  CE1 PHE   278      18.116  24.255 -22.095  1.00  0.00
ATOM   1317  CE2 PHE   278      20.215  25.372 -21.978  1.00  0.00
ATOM   1318  CZ  PHE   278      18.914  25.340 -22.407  1.00  0.00
ATOM   1319  N   TYR   279      20.474  18.963 -19.717  1.00  0.00
ATOM   1320  CA  TYR   279      21.151  17.762 -19.240  1.00  0.00
ATOM   1321  C   TYR   279      22.244  17.256 -20.170  1.00  0.00
ATOM   1322  O   TYR   279      22.189  17.462 -21.379  1.00  0.00
ATOM   1323  CB  TYR   279      20.153  16.615 -19.074  1.00  0.00
ATOM   1324  CG  TYR   279      19.500  16.180 -20.367  1.00  0.00
ATOM   1325  CD1 TYR   279      20.050  15.160 -21.134  1.00  0.00
ATOM   1326  CD2 TYR   279      18.336  16.789 -20.815  1.00  0.00
ATOM   1327  CE1 TYR   279      19.461  14.757 -22.316  1.00  0.00
ATOM   1328  CE2 TYR   279      17.732  16.398 -21.995  1.00  0.00
ATOM   1329  CZ  TYR   279      18.306  15.372 -22.746  1.00  0.00
ATOM   1330  OH  TYR   279      17.716  14.972 -23.924  1.00  0.00
ATOM   1331  N   HIS   280      23.243  16.599 -19.582  1.00  0.00
ATOM   1332  CA  HIS   280      24.321  15.962 -20.336  1.00  0.00
ATOM   1333  C   HIS   280      24.669  14.705 -19.558  1.00  0.00
ATOM   1334  O   HIS   280      25.136  14.779 -18.412  1.00  0.00
ATOM   1335  CB  HIS   280      25.528  16.896 -20.440  1.00  0.00
ATOM   1336  CG  HIS   280      25.221  18.212 -21.083  1.00  0.00
ATOM   1337  ND1 HIS   280      25.183  18.382 -22.450  1.00  0.00
ATOM   1338  CD2 HIS   280      24.905  19.552 -20.608  1.00  0.00
ATOM   1339  CE1 HIS   280      24.883  19.664 -22.724  1.00  0.00
ATOM   1340  NE2 HIS   280      24.715  20.371 -21.624  1.00  0.00
ATOM   1341  N   ASP   281      24.451  13.553 -20.185  1.00  0.00
ATOM   1342  CA  ASP   281      24.693  12.290 -19.522  1.00  0.00
ATOM   1343  C   ASP   281      25.660  11.356 -20.219  1.00  0.00
ATOM   1344  O   ASP   281      25.700  11.273 -21.437  1.00  0.00
ATOM   1345  CB  ASP   281      23.389  11.502 -19.378  1.00  0.00
ATOM   1346  CG  ASP   281      23.541  10.279 -18.496  1.00  0.00
ATOM   1347  OD1 ASP   281      24.631  10.099 -17.913  1.00  0.00
ATOM   1348  OD2 ASP   281      22.571   9.500 -18.387  1.00  0.00
ATOM   1349  N   SER   282      26.439  10.656 -19.409  1.00  0.00
ATOM   1350  CA  SER   282      27.398   9.682 -19.896  1.00  0.00
ATOM   1351  C   SER   282      27.696   8.688 -18.766  1.00  0.00
ATOM   1352  O   SER   282      27.170   8.814 -17.660  1.00  0.00
ATOM   1353  CB  SER   282      28.695  10.373 -20.323  1.00  0.00
ATOM   1354  OG  SER   282      29.380  10.908 -19.203  1.00  0.00
ATOM   1355  N   LEU   283      28.548   7.711 -19.053  1.00  0.00
ATOM   1356  CA  LEU   283      28.897   6.677 -18.092  1.00  0.00
ATOM   1357  C   LEU   283      29.441   7.183 -16.749  1.00  0.00
ATOM   1358  O   LEU   283      29.367   6.472 -15.749  1.00  0.00
ATOM   1359  CB  LEU   283      29.898   5.712 -18.731  1.00  0.00
ATOM   1360  CG  LEU   283      29.856   4.259 -18.265  1.00  0.00
ATOM   1361  CD1 LEU   283      28.413   3.755 -18.274  1.00  0.00
ATOM   1362  CD2 LEU   283      30.724   3.408 -19.189  1.00  0.00
TER
END
