
#######################################################
#                                                     #
#                        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   17 (   68),  selected   17 , name T0338AL509_1-D2
# Molecule2: number of CA atoms  113 (  914),  selected   17 , name T0338_D2.pdb
# PARAMETERS: T0338AL509_1-D2.T0338_D2.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:    17       184 - 200         0.37     0.37
  LCS_AVERAGE:     15.04

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17       184 - 200         0.37     0.37
  LCS_AVERAGE:     15.04

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17       184 - 200         0.37     0.37
  LCS_AVERAGE:     15.04

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:  113
LCS_GDT     Y     184     Y     184     17   17   17    14   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17 
LCS_GDT     K     185     K     185     17   17   17    14   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17 
LCS_GDT     P     186     P     186     17   17   17    14   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17 
LCS_GDT     T     187     T     187     17   17   17    14   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17 
LCS_GDT     V     188     V     188     17   17   17    14   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17 
LCS_GDT     I     189     I     189     17   17   17    14   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17 
LCS_GDT     A     190     A     190     17   17   17    14   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17 
LCS_GDT     C     191     C     191     17   17   17    14   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17 
LCS_GDT     V     192     V     192     17   17   17    14   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17 
LCS_GDT     C     193     C     193     17   17   17    14   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17 
LCS_GDT     I     194     I     194     17   17   17    14   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17 
LCS_GDT     H     195     H     195     17   17   17    14   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17 
LCS_GDT     L     196     L     196     17   17   17    14   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17 
LCS_GDT     A     197     A     197     17   17   17    14   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17 
LCS_GDT     C     198     C     198     17   17   17    12   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17 
LCS_GDT     K     199     K     199     17   17   17    14   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17 
LCS_GDT     W     200     W     200     17   17   17    12   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17   17 
LCS_AVERAGE  LCS_A:  15.04  (  15.04   15.04   15.04 )

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     14     17     17     17     17     17     17     17     17     17     17     17     17     17     17     17     17     17     17     17 
GDT PERCENT_CA  12.39  15.04  15.04  15.04  15.04  15.04  15.04  15.04  15.04  15.04  15.04  15.04  15.04  15.04  15.04  15.04  15.04  15.04  15.04  15.04
GDT RMS_LOCAL    0.28   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37
GDT RMS_ALL_CA   0.43   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37

#      Molecule1      Molecule2       DISTANCE
LGA    Y     184      Y     184          0.565
LGA    K     185      K     185          0.287
LGA    P     186      P     186          0.277
LGA    T     187      T     187          0.334
LGA    V     188      V     188          0.206
LGA    I     189      I     189          0.167
LGA    A     190      A     190          0.189
LGA    C     191      C     191          0.247
LGA    V     192      V     192          0.438
LGA    C     193      C     193          0.333
LGA    I     194      I     194          0.276
LGA    H     195      H     195          0.381
LGA    L     196      L     196          0.312
LGA    A     197      A     197          0.442
LGA    C     198      C     198          0.564
LGA    K     199      K     199          0.386
LGA    W     200      W     200          0.579

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   17  113    4.0     17    0.37    15.044    15.044     3.587

LGA_LOCAL      RMSD =  0.374  Number of atoms =   17  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  0.374  Number of atoms =   17 
Std_ALL_ATOMS  RMSD =  0.374  (standard rmsd on all 17 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.094909 * X  +   0.995311 * Y  +  -0.018636 * Z  + -47.532631
  Y_new =   0.522966 * X  +   0.033922 * Y  +  -0.851678 * Z  +  24.113949
  Z_new =  -0.847053 * X  +  -0.090578 * Y  +  -0.523733 * Z  + 118.137909 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.970340    0.171253  [ DEG:  -170.1879      9.8121 ]
  Theta =   1.010416    2.131176  [ DEG:    57.8926    122.1074 ]
  Phi   =   1.750325   -1.391268  [ DEG:   100.2862    -79.7138 ]
 
# 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: T0338AL509_1-D2                               
REMARK     2: T0338_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0338AL509_1-D2.T0338_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   17  113   4.0   17   0.37  15.044     0.37
REMARK  ---------------------------------------------------------- 
MOLECULE T0338AL509_1-D2
REMARK Aligment from pdb entry: 1vin
ATOM    177  N   TYR   184     -17.903  11.102  60.516  1.00  0.00              
ATOM    178  CA  TYR   184     -19.105  10.637  61.196  1.00  0.00              
ATOM    179  C   TYR   184     -20.422  11.281  60.730  1.00  0.00              
ATOM    180  O   TYR   184     -20.449  12.440  60.338  1.00  0.00              
ATOM    181  N   LYS   185     -21.504  10.506  60.844  1.00  0.00              
ATOM    182  CA  LYS   185     -22.840  10.983  60.502  1.00  0.00              
ATOM    183  C   LYS   185     -23.322  11.771  61.698  1.00  0.00              
ATOM    184  O   LYS   185     -22.845  11.552  62.806  1.00  0.00              
ATOM    185  N   PRO   186     -24.221  12.748  61.474  1.00  0.00              
ATOM    186  CA  PRO   186     -24.762  13.564  62.560  1.00  0.00              
ATOM    187  C   PRO   186     -25.367  12.755  63.715  1.00  0.00              
ATOM    188  O   PRO   186     -25.248  13.169  64.859  1.00  0.00              
ATOM    189  N   THR   187     -26.048  11.640  63.433  1.00  0.00              
ATOM    190  CA  THR   187     -26.688  10.805  64.476  1.00  0.00              
ATOM    191  C   THR   187     -25.653  10.189  65.446  1.00  0.00              
ATOM    192  O   THR   187     -25.917  10.016  66.629  1.00  0.00              
ATOM    193  N   VAL   188     -24.529   9.788  64.865  1.00  0.00              
ATOM    194  CA  VAL   188     -23.426   9.214  65.605  1.00  0.00              
ATOM    195  C   VAL   188     -22.781  10.247  66.526  1.00  0.00              
ATOM    196  O   VAL   188     -22.554   9.980  67.704  1.00  0.00              
ATOM    197  N   ILE   189     -22.541  11.445  66.000  1.00  0.00              
ATOM    198  CA  ILE   189     -21.932  12.507  66.779  1.00  0.00              
ATOM    199  C   ILE   189     -22.880  12.928  67.864  1.00  0.00              
ATOM    200  O   ILE   189     -22.448  13.217  68.992  1.00  0.00              
ATOM    201  N   ALA   190     -24.169  12.967  67.554  1.00  0.00              
ATOM    202  CA  ALA   190     -25.181  13.326  68.527  1.00  0.00              
ATOM    203  C   ALA   190     -25.230  12.268  69.654  1.00  0.00              
ATOM    204  O   ALA   190     -25.430  12.606  70.836  1.00  0.00              
ATOM    205  N   CYS   191     -25.077  10.993  69.295  1.00  0.00              
ATOM    206  CA  CYS   191     -25.114   9.911  70.279  1.00  0.00              
ATOM    207  C   CYS   191     -23.912   9.999  71.219  1.00  0.00              
ATOM    208  O   CYS   191     -24.088   9.966  72.431  1.00  0.00              
ATOM    209  N   VAL   192     -22.724  10.197  70.639  1.00  0.00              
ATOM    210  CA  VAL   192     -21.495  10.298  71.413  1.00  0.00              
ATOM    211  C   VAL   192     -21.573  11.509  72.320  1.00  0.00              
ATOM    212  O   VAL   192     -21.276  11.425  73.517  1.00  0.00              
ATOM    213  N   CYS   193     -22.100  12.599  71.768  1.00  0.00              
ATOM    214  CA  CYS   193     -22.240  13.862  72.485  1.00  0.00              
ATOM    215  C   CYS   193     -23.198  13.739  73.664  1.00  0.00              
ATOM    216  O   CYS   193     -22.928  14.286  74.751  1.00  0.00              
ATOM    217  N   ILE   194     -24.296  13.008  73.462  1.00  0.00              
ATOM    218  CA  ILE   194     -25.299  12.770  74.518  1.00  0.00              
ATOM    219  C   ILE   194     -24.724  11.860  75.627  1.00  0.00              
ATOM    220  O   ILE   194     -24.814  12.174  76.821  1.00  0.00              
ATOM    221  N   HIS   195     -24.134  10.739  75.233  1.00  0.00              
ATOM    222  CA  HIS   195     -23.537   9.845  76.219  1.00  0.00              
ATOM    223  C   HIS   195     -22.538  10.603  77.084  1.00  0.00              
ATOM    224  O   HIS   195     -22.637  10.616  78.305  1.00  0.00              
ATOM    225  N   LEU   196     -21.614  11.287  76.421  1.00  0.00              
ATOM    226  CA  LEU   196     -20.556  12.013  77.083  1.00  0.00              
ATOM    227  C   LEU   196     -21.080  13.068  78.034  1.00  0.00              
ATOM    228  O   LEU   196     -20.598  13.195  79.165  1.00  0.00              
ATOM    229  N   ALA   197     -22.107  13.781  77.594  1.00  0.00              
ATOM    230  CA  ALA   197     -22.690  14.830  78.413  1.00  0.00              
ATOM    231  C   ALA   197     -23.359  14.181  79.630  1.00  0.00              
ATOM    232  O   ALA   197     -23.225  14.688  80.749  1.00  0.00              
ATOM    233  N   CYS   198     -24.093  13.089  79.390  1.00  0.00              
ATOM    234  CA  CYS   198     -24.765  12.343  80.463  1.00  0.00              
ATOM    235  C   CYS   198     -23.752  11.850  81.498  1.00  0.00              
ATOM    236  O   CYS   198     -23.901  12.108  82.691  1.00  0.00              
ATOM    237  N   LYS   199     -22.703  11.191  81.014  1.00  0.00              
ATOM    238  CA  LYS   199     -21.651  10.650  81.846  1.00  0.00              
ATOM    239  C   LYS   199     -20.951  11.735  82.648  1.00  0.00              
ATOM    240  O   LYS   199     -20.801  11.582  83.857  1.00  0.00              
ATOM    241  N   TRP   200     -20.553  12.832  82.004  1.00  0.00              
ATOM    242  CA  TRP   200     -19.871  13.907  82.713  1.00  0.00              
ATOM    243  C   TRP   200     -20.711  14.546  83.823  1.00  0.00              
ATOM    244  O   TRP   200     -20.201  14.870  84.892  1.00  0.00              
END
