
#######################################################
#                                                     #
#                        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 (   50),  selected    8 , name T0284TS239_3_2
# Molecule2: number of CA atoms  282 ( 2139),  selected    8 , name T0284.pdb
# PARAMETERS: T0284TS239_3_2.T0284.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       278 - 285         2.39     2.39
  LCS_AVERAGE:      2.84

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       279 - 284         1.73     3.13
  LONGEST_CONTINUOUS_SEGMENT:     6       280 - 285         1.92     2.63
  LCS_AVERAGE:      1.99

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       279 - 282         0.19     4.87
  LONGEST_CONTINUOUS_SEGMENT:     4       280 - 283         0.80     3.65
  LONGEST_CONTINUOUS_SEGMENT:     4       281 - 284         0.50     3.11
  LCS_AVERAGE:      1.20

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:  282
LCS_GDT     W     278     W     278      3    3    8     3    3    3    3    6    7    8    8    8    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     A     279     A     279      4    6    8     4    4    4    5    5    6    8    8    8    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     R     280     R     280      4    6    8     4    4    4    5    6    7    8    8    8    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     D     281     D     281      4    6    8     4    4    4    5    6    7    8    8    8    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     Y     282     Y     282      4    6    8     4    4    4    5    6    7    8    8    8    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     M     283     M     283      4    6    8     3    4    4    5    6    7    8    8    8    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     E     284     E     284      4    6    8     3    4    4    5    6    7    8    8    8    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     V     285     V     285      0    6    8     0    1    3    3    5    7    8    8    8    8    8    8    8    8    8    8    8    8    8    8 
LCS_AVERAGE  LCS_A:   2.01  (   1.20    1.99    2.84 )

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      4      4      5      6      7      8      8      8      8      8      8      8      8      8      8      8      8      8      8 
GDT PERCENT_CA   1.42   1.42   1.42   1.77   2.13   2.48   2.84   2.84   2.84   2.84   2.84   2.84   2.84   2.84   2.84   2.84   2.84   2.84   2.84   2.84
GDT RMS_LOCAL    0.19   0.19   0.19   1.21   1.58   1.98   2.39   2.39   2.39   2.39   2.39   2.39   2.39   2.39   2.39   2.39   2.39   2.39   2.39   2.39
GDT RMS_ALL_CA   4.87   4.87   4.87   4.15   2.71   2.53   2.39   2.39   2.39   2.39   2.39   2.39   2.39   2.39   2.39   2.39   2.39   2.39   2.39   2.39

#      Molecule1      Molecule2       DISTANCE
LGA    W     278      W     278          2.340
LGA    A     279      A     279          3.722
LGA    R     280      R     280          1.660
LGA    D     281      D     281          2.318
LGA    Y     282      Y     282          1.805
LGA    M     283      M     283          1.920
LGA    E     284      E     284          1.783
LGA    V     285      V     285          2.850

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   10  282    4.0      8    2.39     2.216     2.265     0.321

LGA_LOCAL      RMSD =  2.390  Number of atoms =    8  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  2.390  Number of atoms =    8 
Std_ALL_ATOMS  RMSD =  2.390  (standard rmsd on all 8 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.520401 * X  +   0.199405 * Y  +  -0.830314 * Z  +  89.924652
  Y_new =   0.719420 * X  +  -0.421440 * Y  +  -0.552109 * Z  + -37.826981
  Z_new =  -0.460021 * X  +  -0.884662 * Y  +   0.075862 * Z  + 106.703636 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.485253    1.656339  [ DEG:   -85.0988     94.9012 ]
  Theta =   0.478018    2.663574  [ DEG:    27.3884    152.6116 ]
  Phi   =   2.197030   -0.944563  [ DEG:   125.8805    -54.1195 ]
 
# 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: T0284TS239_3_2                                
REMARK     2: T0284.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0284TS239_3_2.T0284.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   10  282   4.0    8   2.39   2.265     2.39
REMARK  ---------------------------------------------------------- 
MOLECULE T0284TS239_3_2
REMARK PARENT number 2
PFRMAT TS
TARGET T0284
PARENT 1mum_A
ATOM   1328  N   TRP   278      91.712  73.471  44.417  1.00  9.99
ATOM   1329  CA  TRP   278      93.097  73.911  44.325  1.00  9.99
ATOM   1330  C   TRP   278      93.383  75.123  45.211  1.00  9.99
ATOM   1331  O   TRP   278      94.306  75.895  44.946  1.00  9.99
ATOM   1332  CB  TRP   278      93.482  74.226  42.863  1.00  9.99
ATOM   1333  N   ALA   279      92.585  75.272  46.267  1.00  9.99
ATOM   1334  CA  ALA   279      92.748  76.364  47.226  1.00  9.99
ATOM   1335  C   ALA   279      93.026  77.674  46.510  1.00  9.99
ATOM   1336  O   ALA   279      93.911  78.437  46.897  1.00  9.99
ATOM   1337  CB  ALA   279      93.895  76.040  48.186  1.00  9.99
ATOM   1338  N   ARG   280      92.253  77.921  45.459  1.00  9.99
ATOM   1339  CA  ARG   280      92.380  79.117  44.639  1.00  9.99
ATOM   1340  C   ARG   280      92.378  80.406  45.455  1.00  9.99
ATOM   1341  O   ARG   280      93.120  81.345  45.156  1.00  9.99
ATOM   1342  CB  ARG   280      91.225  79.165  43.642  1.00  9.99
ATOM   1343  N   ASP   281      91.544  80.443  46.487  1.00  9.99
ATOM   1344  CA  ASP   281      91.413  81.629  47.321  1.00  9.99
ATOM   1345  C   ASP   281      92.557  81.848  48.308  1.00  9.99
ATOM   1346  O   ASP   281      92.790  82.970  48.747  1.00  9.99
ATOM   1347  CB  ASP   281      90.063  81.575  48.038  1.00  9.99
ATOM   1348  N   TYR   282      93.268  80.781  48.657  1.00  9.99
ATOM   1349  CA  TYR   282      94.398  80.893  49.573  1.00  9.99
ATOM   1350  C   TYR   282      95.516  81.712  48.930  1.00  9.99
ATOM   1351  O   TYR   282      96.485  82.085  49.595  1.00  9.99
ATOM   1352  CB  TYR   282      94.944  79.509  49.926  1.00  9.99
ATOM   1353  N   MET   283      95.381  81.986  47.636  1.00  9.99
ATOM   1354  CA  MET   283      96.397  82.752  46.927  1.00  9.99
ATOM   1355  C   MET   283      96.273  84.257  47.100  1.00  9.99
ATOM   1356  O   MET   283      97.249  84.922  47.455  1.00  9.99
ATOM   1357  CB  MET   283      96.409  82.373  45.443  1.00  9.99
ATOM   1358  N   GLU   284      95.089  84.807  46.859  1.00  9.99
ATOM   1359  CA  GLU   284      94.933  86.243  47.031  1.00  9.99
ATOM   1360  C   GLU   284      95.010  86.559  48.521  1.00  9.99
ATOM   1361  O   GLU   284      95.339  87.680  48.913  1.00  9.99
ATOM   1362  CB  GLU   284      93.603  86.732  46.452  1.00  9.99
ATOM   1363  N   VAL   285      94.715  85.561  49.349  1.00  9.99
ATOM   1364  CA  VAL   285      94.766  85.741  50.794  1.00  9.99
ATOM   1365  C   VAL   285      96.213  85.935  51.222  1.00  9.99
ATOM   1366  O   VAL   285      96.503  86.771  52.077  1.00  9.99
ATOM   1367  CB  VAL   285      94.152  84.535  51.515  1.00  9.99
ATOM   1368  N   LYS   286      97.121  85.173  50.616  1.00  9.99
ATOM   1369  CA  LYS   286      98.536  85.299  50.945  1.00  9.99
ATOM   1370  C   LYS   286      99.053  86.669  50.517  1.00  9.99
ATOM   1371  O   LYS   286      99.870  87.278  51.214  1.00  9.99
ATOM   1372  CB  LYS   286      99.358  84.198  50.268  1.00  9.99
ATOM   1373  N   GLU   287      98.574  87.148  49.371  1.00  9.99
ATOM   1374  CA  GLU   287      98.982  88.453  48.864  1.00  9.99
ATOM   1375  C   GLU   287      98.577  89.540  49.851  1.00  9.99
ATOM   1376  O   GLU   287      99.354  90.451  50.138  1.00  9.99
ATOM   1377  CB  GLU   287      98.336  88.730  47.504  1.00  9.99
TER
END
