
#######################################################
#                                                     #
#                        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   15 (  120),  selected   15 , name T0316TS349_2-D3
# Molecule2: number of CA atoms   90 (  711),  selected   15 , name T0316_D3.pdb
# PARAMETERS: T0316TS349_2-D3.T0316_D3.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:    15       284 - 298         4.66     4.66
  LCS_AVERAGE:     16.67

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8       290 - 297         1.84    10.91
  LONGEST_CONTINUOUS_SEGMENT:     8       291 - 298         1.92    11.96
  LCS_AVERAGE:      7.26

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       291 - 295         0.60    12.46
  LCS_AVERAGE:      4.52

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:   90
LCS_GDT     M     284     M     284      3    3   15     0    3    3    3    3    3    4    5   11   11   12   12   14   15   15   15   15   15   15   15 
LCS_GDT     S     285     S     285      3    4   15     3    3    3    4    4    4    4    5    8    9   12   12   14   15   15   15   15   15   15   15 
LCS_GDT     T     286     T     286      3    4   15     3    3    3    4    4    4    6    6   11   11   12   12   14   15   15   15   15   15   15   15 
LCS_GDT     S     287     S     287      4    5   15     3    4    4    5    6    7    8    9   11   11   12   12   14   15   15   15   15   15   15   15 
LCS_GDT     L     288     L     288      4    5   15     3    4    4    5    6    7    8    9   11   11   12   12   14   15   15   15   15   15   15   15 
LCS_GDT     E     289     E     289      4    5   15     3    4    4    5    6    7    8    9   11   11   12   12   14   15   15   15   15   15   15   15 
LCS_GDT     A     290     A     290      4    8   15     3    4    4    5    6    8    8    9   11   11   12   12   14   15   15   15   15   15   15   15 
LCS_GDT     S     291     S     291      5    8   15     3    5    5    7    7    8    8    9    9   10   10   12   14   15   15   15   15   15   15   15 
LCS_GDT     Q     292     Q     292      5    8   15     3    5    5    7    7    8    8    9    9   10   10   12   14   15   15   15   15   15   15   15 
LCS_GDT     V     293     V     293      5    8   15     3    5    5    7    7    8    8    9   11   11   12   12   14   15   15   15   15   15   15   15 
LCS_GDT     H     294     H     294      5    8   15     3    5    5    7    7    8    8    9   11   11   12   12   14   15   15   15   15   15   15   15 
LCS_GDT     F     295     F     295      5    8   15     3    5    5    7    7    8    8    9   11   11   12   12   14   15   15   15   15   15   15   15 
LCS_GDT     T     296     T     296      4    8   15     3    4    5    7    7    8    8    9   11   11   12   12   14   15   15   15   15   15   15   15 
LCS_GDT     R     297     R     297      4    8   15     3    4    5    7    7    8    8    9   11   11   12   12   14   15   15   15   15   15   15   15 
LCS_GDT     E     298     E     298      3    8   15     3    3    3    3    4    4    8    9    9   10   10   12   14   15   15   15   15   15   15   15 
LCS_AVERAGE  LCS_A:   9.48  (   4.52    7.26   16.67 )

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      5      7      7      8      8      9     11     11     12     12     14     15     15     15     15     15     15     15 
GDT PERCENT_CA   3.33   5.56   5.56   7.78   7.78   8.89   8.89  10.00  12.22  12.22  13.33  13.33  15.56  16.67  16.67  16.67  16.67  16.67  16.67  16.67
GDT RMS_LOCAL    0.11   0.60   0.60   1.46   1.46   1.84   1.84   2.20   3.44   3.44   3.64   3.64   4.28   4.66   4.66   4.66   4.66   4.66   4.66   4.66
GDT RMS_ALL_CA  13.99  12.46  12.46  12.06  12.06  10.91  10.91  10.85   4.92   4.92   4.95   4.95   4.86   4.66   4.66   4.66   4.66   4.66   4.66   4.66

#      Molecule1      Molecule2       DISTANCE
LGA    M     284      M     284         21.734
LGA    S     285      S     285         17.581
LGA    T     286      T     286         20.787
LGA    S     287      S     287         18.084
LGA    L     288      L     288         11.045
LGA    E     289      E     289          7.828
LGA    A     290      A     290          3.221
LGA    S     291      S     291          1.065
LGA    Q     292      Q     292          2.314
LGA    V     293      V     293          0.952
LGA    H     294      H     294          2.076
LGA    F     295      F     295          1.204
LGA    T     296      T     296          1.744
LGA    R     297      R     297          2.150
LGA    E     298      E     298          3.515

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   15   90    4.0      9    2.20    10.000     9.437     0.391

LGA_LOCAL      RMSD =  2.200  Number of atoms =    9  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 10.855  Number of atoms =   15 
Std_ALL_ATOMS  RMSD =  4.664  (standard rmsd on all 15 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.502711 * X  +   0.741334 * Y  +  -0.444640 * Z  +  54.559872
  Y_new =  -0.374519 * X  +  -0.650357 * Y  +  -0.660887 * Z  +  34.771500
  Z_new =  -0.779113 * X  +  -0.165709 * Y  +   0.604586 * Z  +  29.657888 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.267517    2.874076  [ DEG:   -15.3276    164.6724 ]
  Theta =   0.893249    2.248343  [ DEG:    51.1794    128.8206 ]
  Phi   =  -2.501300    0.640293  [ DEG:  -143.3139     36.6861 ]
 
# 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: T0316TS349_2-D3                               
REMARK     2: T0316_D3.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0316TS349_2-D3.T0316_D3.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   15   90   4.0    9   2.20   9.437     4.66
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS349_2-D3
PFRMAT TS
TARGET T0316
MODEL  2  REFINED
PARENT 1VL2_A
ATOM   2184  N   MET   284      42.810   4.693  -3.948  1.00  0.00
ATOM   2185  CA  MET   284      41.857   5.083  -5.006  1.00  0.00
ATOM   2186  C   MET   284      40.617   5.797  -4.339  1.00  0.00
ATOM   2187  O   MET   284      40.197   6.803  -4.913  1.00  0.00
ATOM   2188  CB  MET   284      41.487   3.867  -5.833  1.00  0.00
ATOM   2189  CG  MET   284      42.543   3.231  -6.699  1.00  0.00
ATOM   2190  SD  MET   284      43.252   4.330  -7.957  1.00  0.00
ATOM   2191  CE  MET   284      41.847   4.382  -8.992  1.00  0.00
ATOM   2192  N   SER   285      39.988   5.264  -3.253  1.00  0.00
ATOM   2193  CA  SER   285      38.893   5.922  -2.512  1.00  0.00
ATOM   2194  C   SER   285      39.346   7.336  -1.950  1.00  0.00
ATOM   2195  O   SER   285      38.434   8.117  -1.674  1.00  0.00
ATOM   2196  CB  SER   285      38.438   4.983  -1.387  1.00  0.00
ATOM   2197  OG  SER   285      37.589   3.889  -1.754  1.00  0.00
ATOM   2198  N   THR   286      40.579   7.521  -1.402  1.00  0.00
ATOM   2199  CA  THR   286      41.157   8.810  -0.914  1.00  0.00
ATOM   2200  C   THR   286      41.339   9.799  -2.097  1.00  0.00
ATOM   2201  O   THR   286      40.988  10.975  -1.913  1.00  0.00
ATOM   2202  CB  THR   286      42.473   8.614  -0.084  1.00  0.00
ATOM   2203  OG1 THR   286      43.640   8.413  -0.959  1.00  0.00
ATOM   2204  CG2 THR   286      42.376   7.375   0.869  1.00  0.00
ATOM   2205  N   SER   287      42.108   9.482  -3.153  1.00  0.00
ATOM   2206  CA  SER   287      42.265  10.312  -4.380  1.00  0.00
ATOM   2207  C   SER   287      40.904  10.922  -4.818  1.00  0.00
ATOM   2208  O   SER   287      40.887  12.130  -5.105  1.00  0.00
ATOM   2209  CB  SER   287      42.931   9.472  -5.490  1.00  0.00
ATOM   2210  OG  SER   287      44.331   9.256  -5.396  1.00  0.00
ATOM   2211  N   LEU   288      39.895  10.087  -5.090  1.00  0.00
ATOM   2212  CA  LEU   288      38.551  10.446  -5.453  1.00  0.00
ATOM   2213  C   LEU   288      37.809  10.401  -4.141  1.00  0.00
ATOM   2214  O   LEU   288      37.403   9.295  -3.757  1.00  0.00
ATOM   2215  CB  LEU   288      38.033   9.256  -6.321  1.00  0.00
ATOM   2216  CG  LEU   288      38.438   9.280  -7.795  1.00  0.00
ATOM   2217  CD1 LEU   288      37.634   8.187  -8.472  1.00  0.00
ATOM   2218  CD2 LEU   288      38.157  10.591  -8.497  1.00  0.00
ATOM   2219  N   GLU   289      37.271  11.536  -3.603  1.00  0.00
ATOM   2220  CA  GLU   289      36.663  11.398  -2.242  1.00  0.00
ATOM   2221  C   GLU   289      35.352  10.651  -2.302  1.00  0.00
ATOM   2222  O   GLU   289      34.370  11.148  -2.886  1.00  0.00
ATOM   2223  CB  GLU   289      36.368  12.725  -1.561  1.00  0.00
ATOM   2224  CG  GLU   289      35.773  12.721  -0.157  1.00  0.00
ATOM   2225  CD  GLU   289      34.284  12.979  -0.220  1.00  0.00
ATOM   2226  OE1 GLU   289      33.744  13.959  -0.772  1.00  0.00
ATOM   2227  OE2 GLU   289      33.698  12.067   0.401  1.00  0.00
ATOM   2228  N   ALA   290      35.379   9.426  -1.763  1.00  0.00
ATOM   2229  CA  ALA   290      34.193   8.593  -1.670  1.00  0.00
ATOM   2230  C   ALA   290      33.661   8.290  -0.204  1.00  0.00
ATOM   2231  O   ALA   290      32.446   8.073  -0.108  1.00  0.00
ATOM   2232  CB  ALA   290      34.595   7.266  -2.330  1.00  0.00
ATOM   2233  N   SER   291      34.423   8.537   0.894  1.00  0.00
ATOM   2234  CA  SER   291      33.970   8.170   2.234  1.00  0.00
ATOM   2235  C   SER   291      34.094   9.349   3.235  1.00  0.00
ATOM   2236  O   SER   291      35.151   9.565   3.853  1.00  0.00
ATOM   2237  CB  SER   291      34.773   6.939   2.687  1.00  0.00
ATOM   2238  OG  SER   291      36.186   7.109   2.744  1.00  0.00
ATOM   2239  N   GLN   292      32.950   9.965   3.506  1.00  0.00
ATOM   2240  CA  GLN   292      32.744  11.058   4.464  1.00  0.00
ATOM   2241  C   GLN   292      31.586  10.704   5.435  1.00  0.00
ATOM   2242  O   GLN   292      30.436  10.549   4.978  1.00  0.00
ATOM   2243  CB  GLN   292      32.296  12.275   3.656  1.00  0.00
ATOM   2244  CG  GLN   292      33.262  13.105   2.859  1.00  0.00
ATOM   2245  CD  GLN   292      34.392  13.722   3.662  1.00  0.00
ATOM   2246  OE1 GLN   292      35.203  13.023   4.279  1.00  0.00
ATOM   2247  NE2 GLN   292      34.456  15.051   3.723  1.00  0.00
ATOM   2248  N   VAL   293      31.873  10.330   6.694  1.00  0.00
ATOM   2249  CA  VAL   293      30.827  10.038   7.679  1.00  0.00
ATOM   2250  C   VAL   293      30.786  11.180   8.704  1.00  0.00
ATOM   2251  O   VAL   293      31.609  11.200   9.632  1.00  0.00
ATOM   2252  CB  VAL   293      31.073   8.693   8.353  1.00  0.00
ATOM   2253  CG1 VAL   293      30.034   8.390   9.459  1.00  0.00
ATOM   2254  CG2 VAL   293      31.063   7.517   7.312  1.00  0.00
ATOM   2255  N   HIS   294      29.832  12.047   8.608  1.00  0.00
ATOM   2256  CA  HIS   294      29.678  13.152   9.567  1.00  0.00
ATOM   2257  C   HIS   294      28.269  12.996  10.142  1.00  0.00
ATOM   2258  O   HIS   294      27.274  13.435   9.529  1.00  0.00
ATOM   2259  CB  HIS   294      29.942  14.508   8.896  1.00  0.00
ATOM   2260  CG  HIS   294      29.797  15.669   9.829  1.00  0.00
ATOM   2261  ND1 HIS   294      28.697  16.504   9.857  1.00  0.00
ATOM   2262  CD2 HIS   294      30.645  16.139  10.778  1.00  0.00
ATOM   2263  CE1 HIS   294      28.866  17.431  10.781  1.00  0.00
ATOM   2264  NE2 HIS   294      30.040  17.232  11.353  1.00  0.00
ATOM   2265  N   PHE   295      28.173  12.431  11.345  1.00  0.00
ATOM   2266  CA  PHE   295      26.865  12.235  12.021  1.00  0.00
ATOM   2267  C   PHE   295      27.094  11.951  13.531  1.00  0.00
ATOM   2268  O   PHE   295      28.030  11.210  13.887  1.00  0.00
ATOM   2269  CB  PHE   295      26.002  11.190  11.349  1.00  0.00
ATOM   2270  CG  PHE   295      26.230   9.747  11.510  1.00  0.00
ATOM   2271  CD1 PHE   295      26.900   9.074  10.464  1.00  0.00
ATOM   2272  CD2 PHE   295      25.828   9.027  12.604  1.00  0.00
ATOM   2273  CE1 PHE   295      27.139   7.709  10.510  1.00  0.00
ATOM   2274  CE2 PHE   295      26.109   7.647  12.703  1.00  0.00
ATOM   2275  CZ  PHE   295      26.768   6.992  11.641  1.00  0.00
ATOM   2276  N   THR   296      26.038  12.199  14.307  1.00  0.00
ATOM   2277  CA  THR   296      26.210  12.056  15.744  1.00  0.00
ATOM   2278  C   THR   296      25.555  10.732  16.306  1.00  0.00
ATOM   2279  O   THR   296      24.340  10.520  16.221  1.00  0.00
ATOM   2280  CB  THR   296      25.728  13.386  16.407  1.00  0.00
ATOM   2281  OG1 THR   296      26.557  14.523  15.976  1.00  0.00
ATOM   2282  CG2 THR   296      25.840  13.302  17.982  1.00  0.00
ATOM   2283  N   ARG   297      26.482   9.782  16.551  1.00  0.00
ATOM   2284  CA  ARG   297      26.253   8.450  17.155  1.00  0.00
ATOM   2285  C   ARG   297      25.664   8.548  18.602  1.00  0.00
ATOM   2286  O   ARG   297      26.145   9.367  19.406  1.00  0.00
ATOM   2287  CB  ARG   297      27.609   7.776  17.280  1.00  0.00
ATOM   2288  CG  ARG   297      27.833   6.554  16.480  1.00  0.00
ATOM   2289  CD  ARG   297      27.758   5.262  17.181  1.00  0.00
ATOM   2290  NE  ARG   297      28.881   5.311  18.052  1.00  0.00
ATOM   2291  CZ  ARG   297      29.161   4.397  18.984  1.00  0.00
ATOM   2292  NH1 ARG   297      28.664   3.157  19.032  1.00  0.00
ATOM   2293  NH2 ARG   297      30.087   4.770  19.856  1.00  0.00
ATOM   2294  N   GLU   298      24.874   7.529  18.964  1.00  0.00
ATOM   2295  CA  GLU   298      24.270   7.381  20.280  1.00  0.00
ATOM   2296  C   GLU   298      25.398   7.155  21.314  1.00  0.00
ATOM   2297  O   GLU   298      25.607   7.969  22.205  1.00  0.00
ATOM   2298  CB  GLU   298      23.313   6.190  20.261  1.00  0.00
ATOM   2299  CG  GLU   298      22.037   6.456  19.494  1.00  0.00
ATOM   2300  CD  GLU   298      20.938   5.445  19.432  1.00  0.00
ATOM   2301  OE1 GLU   298      19.837   5.796  18.991  1.00  0.00
ATOM   2302  OE2 GLU   298      21.202   4.300  19.835  1.00  0.00
ATOM   2303  OXT GLU   298      26.008   6.093  21.230  1.00  0.00
TER
END
