
#######################################################
#                                                     #
#                        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   16 (  127),  selected   16 , name T0316TS609_1-D3
# Molecule2: number of CA atoms   90 (  711),  selected   16 , name T0316_D3.pdb
# PARAMETERS: T0316TS609_1-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:    11       284 - 294         4.59    14.31
  LONGEST_CONTINUOUS_SEGMENT:    11       289 - 299         4.48    13.75
  LCS_AVERAGE:     12.22

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       291 - 297         1.88    18.27
  LCS_AVERAGE:      6.81

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       287 - 291         0.92    14.10
  LONGEST_CONTINUOUS_SEGMENT:     5       292 - 296         0.73    18.26
  LCS_AVERAGE:      4.72

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    5   11     3    3    3    4    5    6    8    8    9    9   10   10   10   10   11   12   12   12   12   12 
LCS_GDT     S     285     S     285      3    6   11     3    3    4    5    6    6    8    8    9    9   10   10   10   10   11   12   12   12   13   13 
LCS_GDT     T     286     T     286      3    6   11     3    3    3    4    6    6    8    8    9    9   10   10   10   10   11   12   13   14   14   14 
LCS_GDT     S     287     S     287      5    6   11     3    4    5    5    6    6    8    8    9    9   10   10   10   10   11   12   13   14   14   14 
LCS_GDT     L     288     L     288      5    6   11     4    4    5    5    6    6    8    8    9    9   10   10   10   10   11   12   13   14   14   14 
LCS_GDT     E     289     E     289      5    6   11     4    4    5    5    6    6    8    8    9    9   10   10   10   11   11   12   13   14   14   14 
LCS_GDT     A     290     A     290      5    6   11     4    4    5    5    6    6    8    8    9    9   10   10   10   11   11   12   13   14   14   14 
LCS_GDT     S     291     S     291      5    7   11     4    4    5    5    6    7    8    8    9    9   10   10   10   11   11   12   13   14   14   14 
LCS_GDT     Q     292     Q     292      5    7   11     3    4    5    5    6    7    7    8    9    9   10   10   10   11   11   12   13   14   14   14 
LCS_GDT     V     293     V     293      5    7   11     4    4    5    5    6    7    7    8    9    9   10   10   10   11   11   12   13   14   14   14 
LCS_GDT     H     294     H     294      5    7   11     4    4    5    5    6    7    7    8    9    9    9    9   10   11   11   12   13   14   14   14 
LCS_GDT     F     295     F     295      5    7   11     4    4    5    5    6    7    7    8    9    9    9    9   10   11   11   12   13   14   14   14 
LCS_GDT     T     296     T     296      5    7   11     4    4    5    5    6    7    7    8    9    9    9    9   10   11   11   11   13   14   14   14 
LCS_GDT     R     297     R     297      3    7   11     3    3    5    5    6    7    7    8    9    9    9    9   10   11   11   11   13   14   14   14 
LCS_GDT     E     298     E     298      3    4   11     3    3    4    4    4    5    7    8    9    9    9    9   10   11   11   11   12   14   14   14 
LCS_GDT     M     299     M     299      3    4   11     3    3    4    4    4    4    4    4    5    5    6    6   10   11   11   11   13   14   14   14 
LCS_AVERAGE  LCS_A:   7.92  (   4.72    6.81   12.22 )

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      5      5      6      7      8      8      9      9     10     10     10     11     11     12     13     14     14     14 
GDT PERCENT_CA   4.44   4.44   5.56   5.56   6.67   7.78   8.89   8.89  10.00  10.00  11.11  11.11  11.11  12.22  12.22  13.33  14.44  15.56  15.56  15.56
GDT RMS_LOCAL    0.27   0.27   0.73   0.73   1.47   1.88   2.56   2.56   2.84   2.84   3.38   3.38   3.38   4.48   4.48   5.45   6.62   6.71   6.71   6.71
GDT RMS_ALL_CA  18.46  18.46  18.26  18.26  16.24  18.27  17.91  17.91  17.96  17.96  16.47  16.47  16.47  13.75  13.75  11.39   8.76   9.03   9.03   9.03

#      Molecule1      Molecule2       DISTANCE
LGA    M     284      M     284          3.430
LGA    S     285      S     285          2.307
LGA    T     286      T     286          3.054
LGA    S     287      S     287          2.957
LGA    L     288      L     288          2.629
LGA    E     289      E     289          1.317
LGA    A     290      A     290          1.343
LGA    S     291      S     291          2.631
LGA    Q     292      Q     292          5.073
LGA    V     293      V     293          7.802
LGA    H     294      H     294         14.213
LGA    F     295      F     295         20.066
LGA    T     296      T     296         26.331
LGA    R     297      R     297         32.101
LGA    E     298      E     298         35.858
LGA    M     299      M     299         37.102

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   16   90    4.0      8    2.56     8.056     8.056     0.300

LGA_LOCAL      RMSD =  2.562  Number of atoms =    8  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 17.906  Number of atoms =   16 
Std_ALL_ATOMS  RMSD =  8.183  (standard rmsd on all 16 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.652112 * X  +   0.276288 * Y  +  -0.705985 * Z  +  37.306080
  Y_new =   0.040629 * X  +  -0.917153 * Y  +  -0.396458 * Z  +  43.281631
  Z_new =  -0.757033 * X  +  -0.287218 * Y  +   0.586862 * Z  + -86.831436 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.455143    2.686450  [ DEG:   -26.0778    153.9222 ]
  Theta =   0.858760    2.282832  [ DEG:    49.2033    130.7966 ]
  Phi   =   3.079370   -0.062223  [ DEG:   176.4349     -3.5651 ]
 
# 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: T0316TS609_1-D3                               
REMARK     2: T0316_D3.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0316TS609_1-D3.T0316_D3.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   16   90   4.0    8   2.56   8.056     8.18
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS609_1-D3
PFRMAT TS
TARGET T0316
MODEL 1
PARENT 1wy5_A                                           
ATOM   2220  N   MET   284      22.305   7.507 -15.269  1.00303.87       1SG    
ATOM   2221  CA  MET   284      23.349   8.175 -14.569  1.00303.87       1SG    
ATOM   2222  CB  MET   284      24.238   9.033 -15.481  1.00303.87       1SG    
ATOM   2223  CG  MET   284      25.033   8.200 -16.488  1.00303.87       1SG    
ATOM   2224  SD  MET   284      26.356   7.193 -15.760  1.00303.87       1SG    
ATOM   2225  CE  MET   284      27.499   8.590 -15.577  1.00303.87       1SG    
ATOM   2226  C   MET   284      22.610   9.070 -13.637  1.00303.87       1SG    
ATOM   2227  O   MET   284      21.480   9.452 -13.913  1.00303.87       1SG    
ATOM   2228  N   SER   285      23.197   9.385 -12.479  1.00235.45       1SG    
ATOM   2229  CA  SER   285      22.547  10.185 -11.482  1.00235.45       1SG    
ATOM   2230  CB  SER   285      21.035   9.911 -11.276  1.00235.45       1SG    
ATOM   2231  OG  SER   285      20.759   8.518 -11.221  1.00235.45       1SG    
ATOM   2232  C   SER   285      23.257   9.829 -10.232  1.00235.45       1SG    
ATOM   2233  O   SER   285      24.354  10.314  -9.968  1.00235.45       1SG    
ATOM   2234  N   THR   286      22.631   8.974  -9.408  1.00224.05       1SG    
ATOM   2235  CA  THR   286      23.332   8.530  -8.249  1.00224.05       1SG    
ATOM   2236  CB  THR   286      22.570   7.535  -7.424  1.00224.05       1SG    
ATOM   2237  OG1 THR   286      21.341   8.099  -6.990  1.00224.05       1SG    
ATOM   2238  CG2 THR   286      23.430   7.140  -6.211  1.00224.05       1SG    
ATOM   2239  C   THR   286      24.557   7.854  -8.775  1.00224.05       1SG    
ATOM   2240  O   THR   286      24.500   7.154  -9.784  1.00224.05       1SG    
ATOM   2241  N   SER   287      25.707   8.066  -8.111  1.00168.82       1SG    
ATOM   2242  CA  SER   287      26.940   7.526  -8.608  1.00168.82       1SG    
ATOM   2243  CB  SER   287      27.791   8.549  -9.380  1.00168.82       1SG    
ATOM   2244  OG  SER   287      27.107   8.961 -10.555  1.00168.82       1SG    
ATOM   2245  C   SER   287      27.767   7.054  -7.454  1.00168.82       1SG    
ATOM   2246  O   SER   287      27.243   6.729  -6.390  1.00168.82       1SG    
ATOM   2247  N   LEU   288      29.101   6.994  -7.664  1.00169.84       1SG    
ATOM   2248  CA  LEU   288      30.016   6.462  -6.695  1.00169.84       1SG    
ATOM   2249  CB  LEU   288      31.465   6.383  -7.231  1.00169.84       1SG    
ATOM   2250  CG  LEU   288      32.501   5.620  -6.369  1.00169.84       1SG    
ATOM   2251  CD1 LEU   288      33.878   5.643  -7.054  1.00169.84       1SG    
ATOM   2252  CD2 LEU   288      32.591   6.122  -4.918  1.00169.84       1SG    
ATOM   2253  C   LEU   288      29.981   7.335  -5.491  1.00169.84       1SG    
ATOM   2254  O   LEU   288      30.044   8.562  -5.579  1.00169.84       1SG    
ATOM   2255  N   GLU   289      29.890   6.696  -4.311  1.00 87.25       1SG    
ATOM   2256  CA  GLU   289      29.811   7.437  -3.093  1.00 87.25       1SG    
ATOM   2257  CB  GLU   289      28.527   7.164  -2.290  1.00 87.25       1SG    
ATOM   2258  CG  GLU   289      28.380   5.706  -1.847  1.00 87.25       1SG    
ATOM   2259  CD  GLU   289      27.078   5.583  -1.070  1.00 87.25       1SG    
ATOM   2260  OE1 GLU   289      26.370   6.615  -0.932  1.00 87.25       1SG    
ATOM   2261  OE2 GLU   289      26.774   4.452  -0.602  1.00 87.25       1SG    
ATOM   2262  C   GLU   289      30.962   7.052  -2.231  1.00 87.25       1SG    
ATOM   2263  O   GLU   289      31.552   5.982  -2.369  1.00 87.25       1SG    
ATOM   2264  N   ALA   290      31.307   7.970  -1.317  1.00 52.78       1SG    
ATOM   2265  CA  ALA   290      32.353   7.808  -0.357  1.00 52.78       1SG    
ATOM   2266  CB  ALA   290      33.500   8.817  -0.507  1.00 52.78       1SG    
ATOM   2267  C   ALA   290      31.670   8.083   0.934  1.00 52.78       1SG    
ATOM   2268  O   ALA   290      30.443   8.157   0.960  1.00 52.78       1SG    
ATOM   2269  N   SER   291      32.432   8.203   2.039  1.00 85.85       1SG    
ATOM   2270  CA  SER   291      31.816   8.409   3.317  1.00 85.85       1SG    
ATOM   2271  CB  SER   291      32.838   8.690   4.434  1.00 85.85       1SG    
ATOM   2272  OG  SER   291      32.167   8.887   5.670  1.00 85.85       1SG    
ATOM   2273  C   SER   291      30.904   9.592   3.231  1.00 85.85       1SG    
ATOM   2274  O   SER   291      29.687   9.438   3.299  1.00 85.85       1SG    
ATOM   2275  N   GLN   292      31.450  10.811   3.047  1.00178.06       1SG    
ATOM   2276  CA  GLN   292      30.553  11.924   2.939  1.00178.06       1SG    
ATOM   2277  CB  GLN   292      30.649  12.887   4.132  1.00178.06       1SG    
ATOM   2278  CG  GLN   292      32.007  13.580   4.251  1.00178.06       1SG    
ATOM   2279  CD  GLN   292      31.961  14.499   5.464  1.00178.06       1SG    
ATOM   2280  OE1 GLN   292      31.168  13.747   4.900  1.00178.06       1SG    
ATOM   2281  NE2 GLN   292      33.251  14.903   5.312  1.00178.06       1SG    
ATOM   2282  C   GLN   292      30.952  12.694   1.725  1.00178.06       1SG    
ATOM   2283  O   GLN   292      30.607  13.867   1.586  1.00178.06       1SG    
ATOM   2284  N   VAL   293      31.659  12.032   0.789  1.00100.97       1SG    
ATOM   2285  CA  VAL   293      32.095  12.734  -0.380  1.00100.97       1SG    
ATOM   2286  CB  VAL   293      33.576  12.992  -0.416  1.00100.97       1SG    
ATOM   2287  CG1 VAL   293      34.315  11.649  -0.531  1.00100.97       1SG    
ATOM   2288  CG2 VAL   293      33.882  13.973  -1.559  1.00100.97       1SG    
ATOM   2289  C   VAL   293      31.731  11.902  -1.565  1.00100.97       1SG    
ATOM   2290  O   VAL   293      31.357  10.740  -1.429  1.00100.97       1SG    
ATOM   2291  N   HIS   294      31.784  12.512  -2.763  1.00128.28       1SG    
ATOM   2292  CA  HIS   294      31.451  11.836  -3.983  1.00128.28       1SG    
ATOM   2293  ND1 HIS   294      28.466  10.700  -5.663  1.00128.28       1SG    
ATOM   2294  CG  HIS   294      29.533  11.569  -5.693  1.00128.28       1SG    
ATOM   2295  CB  HIS   294      30.063  12.278  -4.484  1.00128.28       1SG    
ATOM   2296  NE2 HIS   294      29.123  10.824  -7.783  1.00128.28       1SG    
ATOM   2297  CD2 HIS   294      29.925  11.632  -6.995  1.00128.28       1SG    
ATOM   2298  CE1 HIS   294      28.263  10.285  -6.939  1.00128.28       1SG    
ATOM   2299  C   HIS   294      32.444  12.315  -4.990  1.00128.28       1SG    
ATOM   2300  O   HIS   294      32.513  13.509  -5.270  1.00128.28       1SG    
ATOM   2301  N   PHE   295      33.250  11.411  -5.576  1.00 93.06       1SG    
ATOM   2302  CA  PHE   295      34.210  11.894  -6.524  1.00 93.06       1SG    
ATOM   2303  CB  PHE   295      35.653  11.461  -6.214  1.00 93.06       1SG    
ATOM   2304  CG  PHE   295      36.531  12.041  -7.269  1.00 93.06       1SG    
ATOM   2305  CD1 PHE   295      36.988  13.333  -7.171  1.00 93.06       1SG    
ATOM   2306  CD2 PHE   295      36.896  11.286  -8.362  1.00 93.06       1SG    
ATOM   2307  CE1 PHE   295      37.797  13.867  -8.145  1.00 93.06       1SG    
ATOM   2308  CE2 PHE   295      37.706  11.815  -9.340  1.00 93.06       1SG    
ATOM   2309  CZ  PHE   295      38.158  13.109  -9.232  1.00 93.06       1SG    
ATOM   2310  C   PHE   295      33.863  11.349  -7.863  1.00 93.06       1SG    
ATOM   2311  O   PHE   295      33.707  10.141  -8.025  1.00 93.06       1SG    
ATOM   2312  N   THR   296      33.696  12.234  -8.864  1.00151.73       1SG    
ATOM   2313  CA  THR   296      33.432  11.728 -10.176  1.00151.73       1SG    
ATOM   2314  CB  THR   296      31.973  11.535 -10.469  1.00151.73       1SG    
ATOM   2315  OG1 THR   296      31.289  12.777 -10.396  1.00151.73       1SG    
ATOM   2316  CG2 THR   296      31.391  10.545  -9.446  1.00151.73       1SG    
ATOM   2317  C   THR   296      33.947  12.707 -11.173  1.00151.73       1SG    
ATOM   2318  O   THR   296      33.709  13.909 -11.063  1.00151.73       1SG    
ATOM   2319  N   ARG   297      34.665  12.198 -12.191  1.00295.88       1SG    
ATOM   2320  CA  ARG   297      35.170  13.046 -13.227  1.00295.88       1SG    
ATOM   2321  CB  ARG   297      36.695  13.233 -13.184  1.00295.88       1SG    
ATOM   2322  CG  ARG   297      37.472  11.922 -13.331  1.00295.88       1SG    
ATOM   2323  CD  ARG   297      38.991  12.104 -13.290  1.00295.88       1SG    
ATOM   2324  NE  ARG   297      39.373  12.923 -14.473  1.00295.88       1SG    
ATOM   2325  CZ  ARG   297      39.636  12.318 -15.668  1.00295.88       1SG    
ATOM   2326  NH1 ARG   297      39.541  10.961 -15.779  1.00295.88       1SG    
ATOM   2327  NH2 ARG   297      39.991  13.069 -16.751  1.00295.88       1SG    
ATOM   2328  C   ARG   297      34.846  12.371 -14.516  1.00295.88       1SG    
ATOM   2329  O   ARG   297      34.841  11.144 -14.599  1.00295.88       1SG    
ATOM   2330  N   GLU   298      34.541  13.162 -15.561  1.00229.44       1SG    
ATOM   2331  CA  GLU   298      34.236  12.559 -16.823  1.00229.44       1SG    
ATOM   2332  CB  GLU   298      32.824  12.889 -17.336  1.00229.44       1SG    
ATOM   2333  CG  GLU   298      31.707  12.271 -16.492  1.00229.44       1SG    
ATOM   2334  CD  GLU   298      30.375  12.675 -17.106  1.00229.44       1SG    
ATOM   2335  OE1 GLU   298      30.391  13.450 -18.100  1.00229.44       1SG    
ATOM   2336  OE2 GLU   298      29.321  12.213 -16.591  1.00229.44       1SG    
ATOM   2337  C   GLU   298      35.203  13.101 -17.819  1.00229.44       1SG    
ATOM   2338  O   GLU   298      35.519  14.289 -17.811  1.00229.44       1SG    
ATOM   2339  N   MET   299      35.721  12.220 -18.695  1.00285.52       1SG    
ATOM   2340  CA  MET   299      36.628  12.672 -19.705  1.00285.52       1SG    
ATOM   2341  CB  MET   299      37.477  11.547 -20.321  1.00285.52       1SG    
ATOM   2342  CG  MET   299      38.481  12.040 -21.366  1.00285.52       1SG    
ATOM   2343  SD  MET   299      39.864  13.000 -20.682  1.00285.52       1SG    
ATOM   2344  CE  MET   299      40.624  11.593 -19.822  1.00285.52       1SG    
ATOM   2345  C   MET   299      35.788  13.255 -20.788  1.00285.52       1SG    
ATOM   2346  O   MET   299      34.661  12.818 -21.020  1.00285.52       1SG    
TER
END
