
#######################################################
#                                                     #
#                        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   11 (   81),  selected   11 , name T0316TS705_1-D3
# Molecule2: number of CA atoms   90 (  711),  selected   11 , name T0316_D3.pdb
# PARAMETERS: T0316TS705_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         4.77     4.77
  LCS_AVERAGE:     12.22

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       290 - 294         1.72     8.68
  LCS_AVERAGE:      4.75

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       290 - 293         0.88     9.05
  LCS_AVERAGE:      3.74

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   11     0    0    3    3    3    4    5    5    6    7    9    9   10   11   11   11   11   11   11   11 
LCS_GDT     S     285     S     285      3    4   11     3    3    3    4    4    4    5    5    7    9    9   10   10   11   11   11   11   11   11   11 
LCS_GDT     T     286     T     286      3    4   11     3    3    3    4    4    4    5    5    6    9    9   10   10   11   11   11   11   11   11   11 
LCS_GDT     S     287     S     287      3    4   11     3    3    3    4    4    4    5    5    7    9    9   10   10   11   11   11   11   11   11   11 
LCS_GDT     L     288     L     288      3    4   11     0    3    3    4    4    4    6    6    7    9    9   10   10   11   11   11   11   11   11   11 
LCS_GDT     E     289     E     289      3    3   11     0    3    3    3    3    5    6    6    7    9    9   10   10   11   11   11   11   11   11   11 
LCS_GDT     A     290     A     290      4    5   11     0    3    4    4    5    5    6    6    7    9    9   10   10   11   11   11   11   11   11   11 
LCS_GDT     S     291     S     291      4    5   11     3    3    4    4    5    5    6    6    7    9    9   10   10   11   11   11   11   11   11   11 
LCS_GDT     Q     292     Q     292      4    5   11     3    3    4    4    5    5    5    6    6    8    9   10   10   11   11   11   11   11   11   11 
LCS_GDT     V     293     V     293      4    5   11     3    3    4    4    5    5    6    6    7    9    9   10   10   11   11   11   11   11   11   11 
LCS_GDT     H     294     H     294      3    5   11     3    3    3    4    5    5    6    6    6    9    9   10   10   11   11   11   11   11   11   11 
LCS_AVERAGE  LCS_A:   6.90  (   3.74    4.75   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      3      3      4      4      5      5      6      6      7      9      9     10     10     11     11     11     11     11     11     11 
GDT PERCENT_CA   3.33   3.33   4.44   4.44   5.56   5.56   6.67   6.67   7.78  10.00  10.00  11.11  11.11  12.22  12.22  12.22  12.22  12.22  12.22  12.22
GDT RMS_LOCAL    0.02   0.02   0.88   0.88   1.72   1.72   2.80   2.65   3.83   4.15   4.15   4.38   4.38   4.77   4.77   4.77   4.77   4.77   4.77   4.77
GDT RMS_ALL_CA  14.09  14.09   9.05   9.05   8.68   8.68   6.93   7.80   5.01   4.94   4.94   4.94   4.94   4.77   4.77   4.77   4.77   4.77   4.77   4.77

#      Molecule1      Molecule2       DISTANCE
LGA    M     284      M     284         15.480
LGA    S     285      S     285         10.324
LGA    T     286      T     286         10.378
LGA    S     287      S     287         10.569
LGA    L     288      L     288          7.878
LGA    E     289      E     289          3.894
LGA    A     290      A     290          2.873
LGA    S     291      S     291          1.573
LGA    Q     292      Q     292          2.905
LGA    V     293      V     293          1.884
LGA    H     294      H     294          2.039

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   11   90    4.0      6    2.65     6.667     6.596     0.218

LGA_LOCAL      RMSD =  2.647  Number of atoms =    6  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  7.803  Number of atoms =   11 
Std_ALL_ATOMS  RMSD =  4.769  (standard rmsd on all 11 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.863057 * X  +  -0.392417 * Y  +   0.318027 * Z  +  34.069263
  Y_new =  -0.467926 * X  +   0.384061 * Y  +  -0.795954 * Z  +  41.700703
  Z_new =   0.190204 * X  +  -0.835767 * Y  +  -0.515089 * Z  +  95.427711 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.123120    1.018473  [ DEG:  -121.6458     58.3542 ]
  Theta =  -0.191370   -2.950222  [ DEG:   -10.9647   -169.0353 ]
  Phi   =  -2.644779    0.496813  [ DEG:  -151.5347     28.4653 ]
 
# 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: T0316TS705_1-D3                               
REMARK     2: T0316_D3.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0316TS705_1-D3.T0316_D3.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   11   90   4.0    6   2.65   6.596     4.77
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS705_1-D3
PFRMAT TS
TARGET T0316
MODEL  1  REFINED
PARENT 1jgt_A
ATOM   2220  N   MET   284      36.650   5.754  -7.498  1.00  0.00              
ATOM   2221  CA  MET   284      35.387   5.211  -7.096  1.00  0.00              
ATOM   2222  C   MET   284      35.516   3.980  -6.183  1.00  0.00              
ATOM   2223  O   MET   284      36.200   2.789  -6.859  1.00  0.00              
ATOM   2224  CB  MET   284      35.266   2.059  -8.237  1.00  0.00              
ATOM   2225  CG  MET   284      34.015   1.275  -7.179  1.00  0.00              
ATOM   2226  SD  MET   284      34.705   6.280  -6.307  1.00  0.00              
ATOM   2227  CE  MET   284      35.071   6.565  -5.167  1.00  0.00              
ATOM   2228  N   SER   285      33.683   6.903  -6.919  1.00  0.00              
ATOM   2229  CA  SER   285      32.969   7.975  -6.297  1.00  0.00              
ATOM   2230  C   SER   285      32.012   8.687  -7.269  1.00  0.00              
ATOM   2231  O   SER   285      31.086   7.759  -7.811  1.00  0.00              
ATOM   2232  CB  SER   285      32.187   7.434  -5.146  1.00  0.00              
ATOM   2233  OG  SER   285      31.855   8.168  -4.217  1.00  0.00              
ATOM   2234  N   THR   286      31.860   6.131  -5.183  1.00  0.00              
ATOM   2235  CA  THR   286      31.094   5.545  -4.123  1.00  0.00              
ATOM   2236  C   THR   286      30.768   4.104  -4.379  1.00  0.00              
ATOM   2237  O   THR   286      30.039   3.970  -5.590  1.00  0.00              
ATOM   2238  CB  THR   286      29.935   3.574  -3.199  1.00  0.00              
ATOM   2239  OG1 THR   286      31.887   5.595  -2.854  1.00  0.00              
ATOM   2240  CG2 THR   286      31.375   5.995  -1.809  1.00  0.00              
ATOM   2241  N   SER   287      33.171   5.199  -2.920  1.00  0.00              
ATOM   2242  CA  SER   287      33.999   5.130  -1.750  1.00  0.00              
ATOM   2243  C   SER   287      35.379   4.510  -2.030  1.00  0.00              
ATOM   2244  O   SER   287      35.235   3.158  -2.436  1.00  0.00              
ATOM   2245  CB  SER   287      34.239   6.501  -1.208  1.00  0.00              
ATOM   2246  OG  SER   287      34.235   6.706   0.006  1.00  0.00              
ATOM   2247  N   LEU   288      34.427   7.492  -2.098  1.00  0.00              
ATOM   2248  CA  LEU   288      34.758   8.804  -1.630  1.00  0.00              
ATOM   2249  C   LEU   288      34.958   9.825  -2.761  1.00  0.00              
ATOM   2250  O   LEU   288      35.312  11.214  -2.209  1.00  0.00              
ATOM   2251  CB  LEU   288      36.569  11.129  -1.333  1.00  0.00              
ATOM   2252  CG  LEU   288      35.429  12.262  -3.328  1.00  0.00              
ATOM   2253  CD1 LEU   288      33.644   9.295  -0.767  1.00  0.00              
ATOM   2254  CD2 LEU   288      33.876   9.914   0.270  1.00  0.00              
ATOM   2255  N   GLU   289      32.398   9.027  -1.183  1.00  0.00              
ATOM   2256  CA  GLU   289      31.267   9.470  -0.426  1.00  0.00              
ATOM   2257  C   GLU   289      29.932   9.140  -1.113  1.00  0.00              
ATOM   2258  O   GLU   289      28.720   9.767  -0.423  1.00  0.00              
ATOM   2259  CB  GLU   289      28.682  11.239  -0.807  1.00  0.00              
ATOM   2260  CG  GLU   289      29.504  11.646  -1.671  1.00  0.00              
ATOM   2261  CD  GLU   289      27.829  11.977  -0.245  1.00  0.00              
ATOM   2262  OE1 GLU   289      31.270   8.776   0.899  1.00  0.00              
ATOM   2263  OE2 GLU   289      30.993   9.388   1.929  1.00  0.00              
ATOM   2264  N   ALA   290      31.596   7.469   0.910  1.00  0.00              
ATOM   2265  CA  ALA   290      31.515   6.717   2.130  1.00  0.00              
ATOM   2266  C   ALA   290      31.874   5.233   1.936  1.00  0.00              
ATOM   2267  O   ALA   290      32.455   7.271   3.154  1.00  0.00              
ATOM   2268  CB  ALA   290      32.065   7.499   4.298  1.00  0.00              
ATOM   2269  N   SER   291      33.715   7.534   2.764  1.00  0.00              
ATOM   2270  CA  SER   291      34.666   8.024   3.720  1.00  0.00              
ATOM   2271  C   SER   291      36.080   8.175   3.133  1.00  0.00              
ATOM   2272  O   SER   291      36.596   6.905   2.766  1.00  0.00              
ATOM   2273  CB  SER   291      34.215   9.374   4.161  1.00  0.00              
ATOM   2274  OG  SER   291      34.294   9.723   5.339  1.00  0.00              
ATOM   2275  N   GLN   292      33.698  10.158   3.202  1.00  0.00              
ATOM   2276  CA  GLN   292      33.258  11.498   3.441  1.00  0.00              
ATOM   2277  C   GLN   292      32.726  12.148   2.149  1.00  0.00              
ATOM   2278  O   GLN   292      32.056  13.509   2.339  1.00  0.00              
ATOM   2279  CB  GLN   292      30.596  13.280   2.708  1.00  0.00              
ATOM   2280  CG  GLN   292      30.213  13.386   3.872  1.00  0.00              
ATOM   2281  CD  GLN   292      29.757  12.945   1.690  1.00  0.00              
ATOM   2282  OE1 GLN   292      32.148  11.470   4.433  1.00  0.00              
ATOM   2283  NE2 GLN   292      32.112  12.280   5.357  1.00  0.00              
ATOM   2284  N   VAL   293      31.212  10.519   4.285  1.00  0.00              
ATOM   2285  CA  VAL   293      30.119  10.519   5.204  1.00  0.00              
ATOM   2286  C   VAL   293      28.891   9.823   4.687  1.00  0.00              
ATOM   2287  O   VAL   293      28.363  10.617   3.480  1.00  0.00              
ATOM   2288  CB  VAL   293      29.238   8.362   4.354  1.00  0.00              
ATOM   2289  CG1 VAL   293      30.582   9.829   6.440  1.00  0.00              
ATOM   2290  CG2 VAL   293      31.024   8.684   6.408  1.00  0.00              
ATOM   2291  N   HIS   294      30.513  10.538   7.577  1.00  0.00              
ATOM   2292  CA  HIS   294      30.956   9.961   8.808  1.00  0.00              
ATOM   2293  C   HIS   294      29.440  12.868   9.462  1.00  0.00              
ATOM   2294  O   HIS   294      29.814  11.754  10.180  1.00  0.00              
ATOM   2295  CB  HIS   294      31.084  10.993   9.941  1.00  0.00              
ATOM   2296  CG  HIS   294      27.823  12.494  10.941  1.00  0.00              
ATOM   2297  ND1 HIS   294      28.815  11.540  11.079  1.00  0.00              
ATOM   2298  CD2 HIS   294      28.242  13.270   9.958  1.00  0.00              
ATOM   2299  CE1 HIS   294      29.926   8.925   9.234  1.00  0.00              
ATOM   2300  NE2 HIS   294      29.503   8.116   8.364  1.00  0.00              
TER
END
