
#######################################################
#                                                     #
#                        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 (   65),  selected    8 , name T0372TS022_1_2-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected    8 , name T0372_D1.pdb
# PARAMETERS: T0372TS022_1_2-D1.T0372_D1.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       290 - 297         4.96     4.96
  LCS_AVERAGE:      6.35

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       293 - 297         1.82     7.52
  LCS_AVERAGE:      3.67

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       290 - 293         0.78     9.31
  LONGEST_CONTINUOUS_SEGMENT:     4       294 - 297         0.36     8.65
  LCS_AVERAGE:      3.17

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:  126
LCS_GDT     K     290     K     290      4    4    8     3    3    4    4    4    4    4    4    4    5    5    6    7    7    7    8    8    8    8    8 
LCS_GDT     Y     291     Y     291      4    4    8     3    3    4    4    4    4    5    5    6    6    6    7    7    7    7    8    8    8    8    8 
LCS_GDT     M     292     M     292      4    4    8     3    3    4    4    4    4    5    5    6    6    6    7    7    7    7    8    8    8    8    8 
LCS_GDT     A     293     A     293      4    5    8     3    3    4    4    4    5    5    5    6    6    6    7    7    7    7    8    8    8    8    8 
LCS_GDT     C     294     C     294      4    5    8     4    4    4    4    4    5    5    5    6    6    6    7    7    7    7    8    8    8    8    8 
LCS_GDT     L     295     L     295      4    5    8     4    4    4    4    4    5    5    5    6    6    6    7    7    7    7    8    8    8    8    8 
LCS_GDT     K     296     K     296      4    5    8     4    4    4    4    4    5    5    5    6    6    6    7    7    7    7    8    8    8    8    8 
LCS_GDT     D     297     D     297      4    5    8     4    4    4    4    4    5    5    5    5    5    6    7    7    7    7    8    8    8    8    8 
LCS_AVERAGE  LCS_A:   4.40  (   3.17    3.67    6.35 )

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      4      4      5      5      5      6      6      6      7      7      7      7      8      8      8      8      8 
GDT PERCENT_CA   3.17   3.17   3.17   3.17   3.17   3.97   3.97   3.97   4.76   4.76   4.76   5.56   5.56   5.56   5.56   6.35   6.35   6.35   6.35   6.35
GDT RMS_LOCAL    0.36   0.36   0.36   0.36   0.36   1.82   1.82   1.82   3.34   3.34   3.34   3.99   3.99   3.99   3.99   4.96   4.96   4.96   4.96   4.96
GDT RMS_ALL_CA   8.65   8.65   8.65   8.65   8.65   7.52   7.52   7.52   5.51   5.51   5.51   5.42   5.42   5.42   5.42   4.96   4.96   4.96   4.96   4.96

#      Molecule1      Molecule2       DISTANCE
LGA    K     290      K     290         16.011
LGA    Y     291      Y     291         10.670
LGA    M     292      M     292          8.078
LGA    A     293      A     293          2.894
LGA    C     294      C     294          2.058
LGA    L     295      L     295          0.663
LGA    K     296      K     296          0.971
LGA    D     297      D     297          1.594

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    8  126    4.0      5    1.82     4.167     4.054     0.261

LGA_LOCAL      RMSD =  1.819  Number of atoms =    5  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  7.516  Number of atoms =    8 
Std_ALL_ATOMS  RMSD =  4.963  (standard rmsd on all 8 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.082239 * X  +   0.830681 * Y  +   0.550641 * Z  +  17.643433
  Y_new =  -0.309755 * X  +   0.503844 * Y  +  -0.806346 * Z  +  56.722122
  Z_new =  -0.947253 * X  +  -0.236877 * Y  +   0.215872 * Z  +  -6.122986 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.831760    2.309833  [ DEG:   -47.6563    132.3437 ]
  Theta =   1.244554    1.897039  [ DEG:    71.3077    108.6923 ]
  Phi   =  -1.830307    1.311286  [ DEG:  -104.8689     75.1311 ]
 
# 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: T0372TS022_1_2-D1                             
REMARK     2: T0372_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0372TS022_1_2-D1.T0372_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    8  126   4.0    5   1.82   4.054     4.96
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS022_1_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0372
PARENT 1ne9_A
ATOM   2233  N   LYS   290      32.382  44.618  -8.946  1.00  0.00
ATOM   2234  CA  LYS   290      32.154  44.314  -7.569  1.00  0.00
ATOM   2235  C   LYS   290      30.700  44.038  -7.424  1.00  0.00
ATOM   2236  O   LYS   290      29.949  44.121  -8.396  1.00  0.00
ATOM   2237  CB  LYS   290      32.560  45.494  -6.684  1.00  0.00
ATOM   2238  CG  LYS   290      34.036  45.849  -6.763  1.00  0.00
ATOM   2239  CD  LYS   290      34.396  46.938  -5.766  1.00  0.00
ATOM   2240  CE  LYS   290      35.875  47.283  -5.836  1.00  0.00
ATOM   2241  NZ  LYS   290      36.245  48.340  -4.853  1.00  0.00
ATOM   2242  N   TYR   291      30.279  43.680  -6.196  1.00  0.00
ATOM   2243  CA  TYR   291      28.911  43.346  -5.948  1.00  0.00
ATOM   2244  C   TYR   291      28.030  44.423  -6.474  1.00  0.00
ATOM   2245  O   TYR   291      28.427  45.580  -6.596  1.00  0.00
ATOM   2246  CB  TYR   291      28.661  43.192  -4.447  1.00  0.00
ATOM   2247  CG  TYR   291      29.251  41.931  -3.854  1.00  0.00
ATOM   2248  CD1 TYR   291      30.397  41.982  -3.071  1.00  0.00
ATOM   2249  CD2 TYR   291      28.659  40.695  -4.080  1.00  0.00
ATOM   2250  CE1 TYR   291      30.942  40.835  -2.526  1.00  0.00
ATOM   2251  CE2 TYR   291      29.190  39.538  -3.543  1.00  0.00
ATOM   2252  CZ  TYR   291      30.341  39.617  -2.761  1.00  0.00
ATOM   2253  OH  TYR   291      30.882  38.474  -2.218  1.00  0.00
ATOM   2254  N   MET   292      26.799  44.020  -6.830  1.00  0.00
ATOM   2255  CA  MET   292      25.827  44.835  -7.491  1.00  0.00
ATOM   2256  C   MET   292      25.557  46.020  -6.629  1.00  0.00
ATOM   2257  O   MET   292      25.279  47.111  -7.125  1.00  0.00
ATOM   2258  CB  MET   292      24.532  44.052  -7.713  1.00  0.00
ATOM   2259  CG  MET   292      24.654  42.923  -8.723  1.00  0.00
ATOM   2260  SD  MET   292      25.129  43.505 -10.362  1.00  0.00
ATOM   2261  CE  MET   292      23.658  44.403 -10.843  1.00  0.00
ATOM   2262  N   ALA   293      25.618  45.840  -5.303  1.00  0.00
ATOM   2263  CA  ALA   293      25.302  46.949  -4.459  1.00  0.00
ATOM   2264  C   ALA   293      26.245  48.082  -4.742  1.00  0.00
ATOM   2265  O   ALA   293      25.811  49.227  -4.846  1.00  0.00
ATOM   2266  CB  ALA   293      25.430  46.555  -2.995  1.00  0.00
ATOM   2267  N   CYS   294      27.557  47.811  -4.906  1.00  0.00
ATOM   2268  CA  CYS   294      28.449  48.921  -5.108  1.00  0.00
ATOM   2269  C   CYS   294      28.075  49.670  -6.341  1.00  0.00
ATOM   2270  O   CYS   294      27.815  50.871  -6.287  1.00  0.00
ATOM   2271  CB  CYS   294      29.891  48.429  -5.258  1.00  0.00
ATOM   2272  SG  CYS   294      31.106  49.744  -5.505  1.00  0.00
ATOM   2273  N   LEU   295      28.008  48.977  -7.491  1.00  0.00
ATOM   2274  CA  LEU   295      27.727  49.678  -8.710  1.00  0.00
ATOM   2275  C   LEU   295      26.592  48.990  -9.387  1.00  0.00
ATOM   2276  O   LEU   295      26.434  47.776  -9.281  1.00  0.00
ATOM   2277  CB  LEU   295      28.953  49.674  -9.626  1.00  0.00
ATOM   2278  CG  LEU   295      30.207  50.363  -9.082  1.00  0.00
ATOM   2279  CD1 LEU   295      31.391  50.132 -10.009  1.00  0.00
ATOM   2280  CD2 LEU   295      29.985  51.862  -8.958  1.00  0.00
ATOM   2281  N   LYS   296      25.753  49.763 -10.095  1.00  0.00
ATOM   2282  CA  LYS   296      24.655  49.138 -10.765  1.00  0.00
ATOM   2283  C   LYS   296      25.211  48.615 -12.048  1.00  0.00
ATOM   2284  O   LYS   296      25.928  49.331 -12.743  1.00  0.00
ATOM   2285  CB  LYS   296      23.540  50.152 -11.028  1.00  0.00
ATOM   2286  CG  LYS   296      22.304  49.559 -11.684  1.00  0.00
ATOM   2287  CD  LYS   296      21.215  50.606 -11.859  1.00  0.00
ATOM   2288  CE  LYS   296      19.978  50.012 -12.512  1.00  0.00
ATOM   2289  NZ  LYS   296      18.904  51.027 -12.693  1.00  0.00
ATOM   2290  N   ASP   297      24.860  47.354 -12.382  1.00  0.00
ATOM   2291  CA  ASP   297      25.303  46.610 -13.533  1.00  0.00
ATOM   2292  C   ASP   297      26.685  47.042 -14.013  1.00  0.00
ATOM   2293  O   ASP   297      27.611  47.095 -13.161  1.00  0.00
ATOM   2294  CB  ASP   297      24.334  46.803 -14.701  1.00  0.00
ATOM   2295  CG  ASP   297      24.604  45.848 -15.847  1.00  0.00
ATOM   2296  OD1 ASP   297      25.358  44.874 -15.643  1.00  0.00
ATOM   2297  OD2 ASP   297      24.062  46.075 -16.950  1.00  0.00
TER
END
