
#######################################################
#                                                     #
#                        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 (   78),  selected   11 , name T0385TS009_2_2
# Molecule2: number of CA atoms  142 ( 1050),  selected   11 , name T0385.pdb
# PARAMETERS: T0385TS009_2_2.T0385.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        96 - 106         2.53     2.53
  LCS_AVERAGE:      7.75

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10        97 - 106         1.95     2.80
  LCS_AVERAGE:      6.98

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8        97 - 104         0.80     2.97
  LCS_AVERAGE:      4.80

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:  142
LCS_GDT     A      96     A      96      3    9   11     0    3    5    5    8    9    9    9   11   11   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     A      97     A      97      8   10   11     4    7    8    9    9    9   10   10   11   11   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     D      98     D      98      8   10   11     4    7    8    9    9    9   10   10   11   11   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     A      99     A      99      8   10   11     4    7    8    9    9    9   10   10   11   11   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     A     100     A     100      8   10   11     4    7    8    9    9    9   10   10   11   11   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     R     101     R     101      8   10   11     4    7    8    9    9    9   10   10   11   11   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     L     102     L     102      8   10   11     4    7    8    9    9    9   10   10   11   11   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     A     103     A     103      8   10   11     4    7    8    9    9    9   10   10   11   11   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     V     104     V     104      8   10   11     3    6    8    9    9    9   10   10   11   11   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     R     105     R     105      4   10   11     3    4    5    9    9    9   10   10   11   11   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     M     106     M     106      4   10   11     3    4    5    5    7    9   10   10   11   11   11   11   11   11   11   11   11   11   11   11 
LCS_AVERAGE  LCS_A:   6.51  (   4.80    6.98    7.75 )

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      7      8      9      9      9     10     10     11     11     11     11     11     11     11     11     11     11     11     11 
GDT PERCENT_CA   2.82   4.93   5.63   6.34   6.34   6.34   7.04   7.04   7.75   7.75   7.75   7.75   7.75   7.75   7.75   7.75   7.75   7.75   7.75   7.75
GDT RMS_LOCAL    0.18   0.65   0.80   1.27   1.27   1.27   1.95   1.95   2.53   2.53   2.53   2.53   2.53   2.53   2.53   2.53   2.53   2.53   2.53   2.53
GDT RMS_ALL_CA   2.90   2.87   2.97   2.86   2.86   2.86   2.80   2.80   2.53   2.53   2.53   2.53   2.53   2.53   2.53   2.53   2.53   2.53   2.53   2.53

#      Molecule1      Molecule2       DISTANCE
LGA    A      96      A      96          6.943
LGA    A      97      A      97          1.899
LGA    D      98      D      98          1.291
LGA    A      99      A      99          1.844
LGA    A     100      A     100          1.074
LGA    R     101      R     101          1.214
LGA    L     102      L     102          1.431
LGA    A     103      A     103          0.896
LGA    V     104      V     104          2.261
LGA    R     105      R     105          1.698
LGA    M     106      M     106          3.971

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   11  142    4.0     10    1.95     6.514     6.819     0.488

LGA_LOCAL      RMSD =  1.947  Number of atoms =   10  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  2.798  Number of atoms =   11 
Std_ALL_ATOMS  RMSD =  2.529  (standard rmsd on all 11 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.103444 * X  +  -0.876802 * Y  +  -0.469594 * Z  + -45.346668
  Y_new =   0.968636 * X  +  -0.196047 * Y  +   0.152674 * Z  +  12.303169
  Z_new =  -0.225927 * X  +  -0.439072 * Y  +   0.869582 * Z  +  47.506142 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.467579    2.674014  [ DEG:   -26.7903    153.2097 ]
  Theta =   0.227895    2.913698  [ DEG:    13.0574    166.9426 ]
  Phi   =   1.677187   -1.464406  [ DEG:    96.0957    -83.9043 ]
 
# 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: T0385TS009_2_2                                
REMARK     2: T0385.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0385TS009_2_2.T0385.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   11  142   4.0   10   1.95   6.819     2.53
REMARK  ---------------------------------------------------------- 
MOLECULE T0385TS009_2_2
REMARK PARENT number 2
PFRMAT TS                                                                       
TARGET T0385                                                                    
PARENT N/A                                                                      
ATOM    690  N   ALA    96      17.178  16.967   4.542  1.00  0.00              
ATOM    691  CA  ALA    96      16.178  16.259   3.750  1.00  0.00              
ATOM    692  C   ALA    96      15.734  14.976   4.444  1.00  0.00              
ATOM    693  O   ALA    96      14.558  14.809   4.767  1.00  0.00              
ATOM    694  CB  ALA    96      14.979  17.157   3.489  1.00  0.00              
ATOM    695  N   ALA    97      16.681  14.072   4.668  1.00  0.00              
ATOM    696  CA  ALA    97      16.389  12.802   5.322  1.00  0.00              
ATOM    697  C   ALA    97      16.586  12.901   6.831  1.00  0.00              
ATOM    698  O   ALA    97      15.969  13.735   7.494  1.00  0.00              
ATOM    699  CB  ALA    97      14.970  12.357   5.006  1.00  0.00              
ATOM    700  N   ASP    98      17.449  12.045   7.368  1.00  0.00              
ATOM    701  CA  ASP    98      17.728  12.034   8.800  1.00  0.00              
ATOM    702  C   ASP    98      18.938  12.901   9.132  1.00  0.00              
ATOM    703  O   ASP    98      19.016  13.486  10.212  1.00  0.00              
ATOM    704  CB  ASP    98      16.507  12.511   9.587  1.00  0.00              
ATOM    705  CG  ASP    98      15.712  11.366  10.183  1.00  0.00              
ATOM    706  OD1 ASP    98      15.266  11.490  11.342  1.00  0.00              
ATOM    707  OD2 ASP    98      15.536  10.341   9.489  1.00  0.00              
ATOM    708  N   ALA    99      19.878  12.977   8.197  1.00  0.00              
ATOM    709  CA  ALA    99      21.086  13.773   8.389  1.00  0.00              
ATOM    710  C   ALA    99      20.925  14.748   9.550  1.00  0.00              
ATOM    711  O   ALA    99      21.401  14.494  10.656  1.00  0.00              
ATOM    712  CB  ALA    99      22.285  12.868   8.626  1.00  0.00              
ATOM    713  N   ALA   100      20.253  15.865   9.289  1.00  0.00              
ATOM    714  CA  ALA   100      20.029  16.879  10.311  1.00  0.00              
ATOM    715  C   ALA   100      19.326  16.289  11.529  1.00  0.00              
ATOM    716  O   ALA   100      19.543  16.730  12.658  1.00  0.00              
ATOM    717  CB  ALA   100      21.346  17.517  10.723  1.00  0.00              
ATOM    718  N   ARG   101      18.482  15.290  11.294  1.00  0.00              
ATOM    719  CA  ARG   101      17.746  14.638  12.370  1.00  0.00              
ATOM    720  C   ARG   101      18.690  14.134  13.457  1.00  0.00              
ATOM    721  O   ARG   101      19.019  14.863  14.394  1.00  0.00              
ATOM    722  CB  ARG   101      16.715  15.596  12.971  1.00  0.00              
ATOM    723  CG  ARG   101      15.272  15.194  12.717  1.00  0.00              
ATOM    724  CD  ARG   101      14.344  16.396  12.777  1.00  0.00              
ATOM    725  NE  ARG   101      12.939  16.002  12.795  1.00  0.00              
ATOM    726  CZ  ARG   101      12.374  15.289  13.764  1.00  0.00              
ATOM    727  NH1 ARG   101      13.097  14.890  14.801  1.00  0.00              
ATOM    728  NH2 ARG   101      11.087  14.979  13.695  1.00  0.00              
ATOM    729  N   LEU   102      19.122  12.884  13.326  1.00  0.00              
ATOM    730  CA  LEU   102      20.028  12.281  14.296  1.00  0.00              
ATOM    731  C   LEU   102      21.149  13.243  14.675  1.00  0.00              
ATOM    732  O   LEU   102      21.829  13.052  15.684  1.00  0.00              
ATOM    733  CB  LEU   102      19.261  11.846  15.546  1.00  0.00              
ATOM    734  CG  LEU   102      19.456  10.394  15.990  1.00  0.00              
ATOM    735  CD1 LEU   102      18.780  10.146  17.329  1.00  0.00              
ATOM    736  CD2 LEU   102      20.935  10.047  16.057  1.00  0.00              
ATOM    737  N   ALA   103      21.337  14.276  13.860  1.00  0.00              
ATOM    738  CA  ALA   103      22.375  15.268  14.109  1.00  0.00              
ATOM    739  C   ALA   103      22.277  15.826  15.525  1.00  0.00              
ATOM    740  O   ALA   103      22.642  15.160  16.492  1.00  0.00              
ATOM    741  CB  ALA   103      23.752  14.665  13.878  1.00  0.00              
ATOM    742  N   VAL   104      21.782  17.055  15.637  1.00  0.00              
ATOM    743  CA  VAL   104      21.630  17.720  16.964  1.00  0.00              
ATOM    744  C   VAL   104      20.267  17.421  17.578  1.00  0.00              
ATOM    745  O   VAL   104      20.172  17.036  18.744  1.00  0.00              
ATOM    746  CB  VAL   104      22.733  17.280  17.945  1.00  0.00              
ATOM    747  CG1 VAL   104      23.512  18.486  18.446  1.00  0.00              
ATOM    748  CG2 VAL   104      23.663  16.272  17.284  1.00  0.00              
ATOM    749  N   ARG   105      19.214  17.601  16.788  1.00  0.00              
ATOM    750  CA  ARG   105      17.855  17.350  17.252  1.00  0.00              
ATOM    751  C   ARG   105      17.793  16.104  18.128  1.00  0.00              
ATOM    752  O   ARG   105      18.173  16.136  19.298  1.00  0.00              
ATOM    753  CB  ARG   105      17.321  18.561  18.021  1.00  0.00              
ATOM    754  CG  ARG   105      16.056  19.161  17.431  1.00  0.00              
ATOM    755  CD  ARG   105      15.903  20.623  17.822  1.00  0.00              
ATOM    756  NE  ARG   105      14.530  21.092  17.660  1.00  0.00              
ATOM    757  CZ  ARG   105      13.621  21.094  18.629  1.00  0.00              
ATOM    758  NH1 ARG   105      13.940  20.650  19.837  1.00  0.00              
ATOM    759  NH2 ARG   105      12.396  21.540  18.389  1.00  0.00              
ATOM    760  N   MET   106      17.311  15.006  17.554  1.00  0.00              
ATOM    761  CA  MET   106      17.197  13.747  18.280  1.00  0.00              
ATOM    762  C   MET   106      18.508  12.969  18.242  1.00  0.00              
ATOM    763  O   MET   106      19.158  12.777  19.269  1.00  0.00              
ATOM    764  CB  MET   106      16.779  14.002  19.730  1.00  0.00              
ATOM    765  CG  MET   106      15.406  13.454  20.084  1.00  0.00              
ATOM    766  SD  MET   106      14.999  13.670  21.827  1.00  0.00              
ATOM    767  CE  MET   106      13.462  12.758  21.931  1.00  0.00              
TER
END
