
#######################################################
#                                                     #
#                        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   23 (   92),  selected   23 , name T0347AL242_4-D2
# Molecule2: number of CA atoms   71 (  561),  selected   23 , name T0347_D2.pdb
# PARAMETERS: T0347AL242_4-D2.T0347_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:    18       135 - 152         4.70    10.75
  LCS_AVERAGE:     25.05

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14       135 - 148         1.85    13.25
  LCS_AVERAGE:     14.57

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12       136 - 147         0.87    13.52
  LCS_AVERAGE:     11.15

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:   71
LCS_GDT     P     135     P     135      5   14   18     3    5    9   11   13   13   13   14   14   14   14   15   16   17   17   18   19   19   19   21 
LCS_GDT     F     136     F     136     12   14   18     3    5    9   12   13   13   13   14   14   14   14   15   16   17   17   18   19   19   20   21 
LCS_GDT     R     137     R     137     12   14   18     4   11   11   12   13   13   13   14   14   14   14   15   16   17   17   18   19   19   20   21 
LCS_GDT     S     138     S     138     12   14   18    10   11   11   12   13   13   13   14   14   14   14   15   16   17   17   18   19   19   20   21 
LCS_GDT     L     139     L     139     12   14   18    10   11   11   12   13   13   13   14   14   14   14   15   16   17   17   18   19   19   20   21 
LCS_GDT     A     140     A     140     12   14   18    10   11   11   12   13   13   13   14   14   14   14   15   16   17   17   18   19   19   20   21 
LCS_GDT     G     141     G     141     12   14   18    10   11   11   12   13   13   13   14   14   14   14   15   16   17   17   18   19   19   20   21 
LCS_GDT     A     142     A     142     12   14   18    10   11   11   12   13   13   13   14   14   14   14   15   16   17   17   18   19   19   20   21 
LCS_GDT     L     143     L     143     12   14   18    10   11   11   12   13   13   13   14   14   14   14   15   16   17   17   18   19   19   20   21 
LCS_GDT     R     144     R     144     12   14   18    10   11   11   12   13   13   13   14   14   14   14   15   16   17   17   18   19   19   20   21 
LCS_GDT     M     145     M     145     12   14   18    10   11   11   12   13   13   13   14   14   14   14   15   16   17   17   18   19   19   20   21 
LCS_GDT     A     146     A     146     12   14   18    10   11   11   12   13   13   13   14   14   14   14   15   16   17   17   18   19   19   20   21 
LCS_GDT     G     147     G     147     12   14   18    10   11   11   12   13   13   13   14   14   14   14   15   16   16   17   18   19   19   20   21 
LCS_GDT     G     148     G     148      4   14   18     3    3    4    5    6    7   11   14   14   14   14   15   16   16   17   18   19   19   20   21 
LCS_GDT     Y     149     Y     149      4    4   18     3    3    4    5    6    7    8    9   13   13   14   15   16   17   17   18   19   19   20   21 
LCS_GDT     A     150     A     150      4    5   18     3    4    4    5    7    8    9   11   13   13   14   15   16   17   17   18   19   19   20   21 
LCS_GDT     K     151     K     151      3    5   18     3    3    4    4    7    8    9   11   13   13   14   15   16   17   17   18   19   19   20   21 
LCS_GDT     V     152     V     152      3    5   18     3    4    4    5    6    7    9   11   12   13   14   15   16   17   17   18   19   19   20   21 
LCS_GDT     I     153     I     153      3    5   17     3    4    4    5    5    7    9   11   12   13   14   15   16   17   17   18   19   19   20   21 
LCS_GDT     I     154     I     154      3    5   17     3    3    4    4    6    7    8   10   12   13   14   14   15   16   17   18   19   19   20   21 
LCS_GDT     P     155     P     155      3    5   17     3    3    4    4    6    7    8   10   12   13   14   14   15   16   17   18   19   19   20   21 
LCS_GDT     F     156     F     156      3    5   17     3    3    3    4    6    7    8    9   12   13   14   14   15   16   16   16   19   19   20   20 
LCS_GDT     S     157     S     157      3    3   17     0    3    3    3    3    5    5    5    6    8    9   12   13   16   16   16   17   17   20   20 
LCS_AVERAGE  LCS_A:  16.92  (  11.15   14.57   25.05 )

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     10     11     11     12     13     13     13     14     14     14     14     15     16     17     17     18     19     19     20     21 
GDT PERCENT_CA  14.08  15.49  15.49  16.90  18.31  18.31  18.31  19.72  19.72  19.72  19.72  21.13  22.54  23.94  23.94  25.35  26.76  26.76  28.17  29.58
GDT RMS_LOCAL    0.34   0.44   0.44   0.87   1.16   1.16   1.16   1.85   1.85   1.85   1.85   2.74   4.07   4.49   4.15   4.86   5.20   5.45   6.00   6.20
GDT RMS_ALL_CA  14.03  13.92  13.92  13.52  13.37  13.37  13.37  13.25  13.25  13.25  13.25  12.36  10.03   9.06  10.96   9.10   9.31   8.14   7.64   7.38

#      Molecule1      Molecule2       DISTANCE
LGA    P     135      P     135          0.943
LGA    F     136      F     136          1.157
LGA    R     137      R     137          1.839
LGA    S     138      S     138          1.089
LGA    L     139      L     139          1.312
LGA    A     140      A     140          1.462
LGA    G     141      G     141          1.299
LGA    A     142      A     142          0.846
LGA    L     143      L     143          1.237
LGA    R     144      R     144          3.345
LGA    M     145      M     145          3.305
LGA    A     146      A     146          2.260
LGA    G     147      G     147          3.902
LGA    G     148      G     148          3.709
LGA    Y     149      Y     149          6.645
LGA    A     150      A     150         10.322
LGA    K     151      K     151         13.078
LGA    V     152      V     152         17.618
LGA    I     153      I     153         19.454
LGA    I     154      I     154         23.249
LGA    P     155      P     155         24.975
LGA    F     156      F     156         26.277
LGA    S     157      S     157         22.975

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   23   71    4.0     14    1.85    19.366    17.957     0.717

LGA_LOCAL      RMSD =  1.851  Number of atoms =   14  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 12.272  Number of atoms =   23 
Std_ALL_ATOMS  RMSD =  7.011  (standard rmsd on all 23 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.520550 * X  +   0.833415 * Y  +  -0.185600 * Z  +  53.584949
  Y_new =  -0.160575 * X  +  -0.309051 * Y  +  -0.937392 * Z  +  78.410667
  Z_new =  -0.838596 * X  +  -0.458156 * Y  +   0.294702 * Z  +  -4.731885 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.999191    2.142401  [ DEG:   -57.2495    122.7505 ]
  Theta =   0.994701    2.146891  [ DEG:    56.9922    123.0078 ]
  Phi   =  -2.842381    0.299211  [ DEG:  -162.8564     17.1436 ]
 
# 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: T0347AL242_4-D2                               
REMARK     2: T0347_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0347AL242_4-D2.T0347_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   23   71   4.0   14   1.85  17.957     7.01
REMARK  ---------------------------------------------------------- 
MOLECULE T0347AL242_4-D2
REMARK Aligment from pdb entry: 3crd
ATOM    309  N   PRO   135       8.277  59.723  -1.265  1.00  0.00              
ATOM    310  CA  PRO   135       8.223  58.636  -2.248  1.00  0.00              
ATOM    311  C   PRO   135       9.275  57.560  -1.996  1.00  0.00              
ATOM    312  O   PRO   135       9.551  56.740  -2.871  1.00  0.00              
ATOM    313  N   PHE   136       9.867  57.589  -0.810  1.00  0.00              
ATOM    314  CA  PHE   136      10.920  56.635  -0.416  1.00  0.00              
ATOM    315  C   PHE   136      11.010  55.403  -1.323  1.00  0.00              
ATOM    316  O   PHE   136      12.061  55.143  -1.910  1.00  0.00              
ATOM    317  N   ARG   137       9.924  54.612  -1.435  1.00  0.00              
ATOM    318  CA  ARG   137       9.901  53.402  -2.251  1.00  0.00              
ATOM    319  C   ARG   137      10.802  53.482  -3.481  1.00  0.00              
ATOM    320  O   ARG   137      11.323  52.467  -3.941  1.00  0.00              
ATOM    321  N   SER   138      10.982  54.685  -4.010  1.00  0.00              
ATOM    322  CA  SER   138      11.826  54.876  -5.183  1.00  0.00              
ATOM    323  C   SER   138      12.882  55.950  -4.943  1.00  0.00              
ATOM    324  O   SER   138      13.956  55.917  -5.543  1.00  0.00              
ATOM    325  N   LEU   139      12.583  56.901  -4.064  1.00  0.00              
ATOM    326  CA  LEU   139      13.524  57.972  -3.769  1.00  0.00              
ATOM    327  C   LEU   139      14.518  57.541  -2.698  1.00  0.00              
ATOM    328  O   LEU   139      15.697  57.877  -2.769  1.00  0.00              
ATOM    329  N   ALA   140      14.030  56.797  -1.709  1.00  0.00              
ATOM    330  CA  ALA   140      14.873  56.320  -0.619  1.00  0.00              
ATOM    331  C   ALA   140      15.847  55.262  -1.120  1.00  0.00              
ATOM    332  O   ALA   140      17.033  55.296  -0.795  1.00  0.00              
ATOM    333  N   GLY   141      15.347  54.333  -1.923  1.00  0.00              
ATOM    334  CA  GLY   141      16.187  53.288  -2.471  1.00  0.00              
ATOM    335  C   GLY   141      17.295  53.907  -3.298  1.00  0.00              
ATOM    336  O   GLY   141      18.474  53.688  -3.034  1.00  0.00              
ATOM    337  N   ALA   142      16.905  54.693  -4.292  1.00  0.00              
ATOM    338  CA  ALA   142      17.869  55.356  -5.152  1.00  0.00              
ATOM    339  C   ALA   142      18.784  56.265  -4.338  1.00  0.00              
ATOM    340  O   ALA   142      19.882  56.612  -4.775  1.00  0.00              
ATOM    341  N   LEU   143      18.333  56.649  -3.146  1.00  0.00              
ATOM    342  CA  LEU   143      19.123  57.515  -2.287  1.00  0.00              
ATOM    343  C   LEU   143      20.183  56.728  -1.547  1.00  0.00              
ATOM    344  O   LEU   143      21.380  56.916  -1.764  1.00  0.00              
ATOM    345  N   ARG   144      19.738  55.835  -0.681  1.00  0.00              
ATOM    346  CA  ARG   144      20.656  55.013   0.074  1.00  0.00              
ATOM    347  C   ARG   144      21.555  54.279  -0.891  1.00  0.00              
ATOM    348  O   ARG   144      22.655  53.858  -0.533  1.00  0.00              
ATOM    349  N   MET   145      21.109  54.175  -2.140  1.00  0.00              
ATOM    350  CA  MET   145      21.924  53.549  -3.148  1.00  0.00              
ATOM    351  C   MET   145      23.110  54.462  -3.405  1.00  0.00              
ATOM    352  O   MET   145      24.251  54.019  -3.533  1.00  0.00              
ATOM    353  N   ALA   146      22.808  55.760  -3.458  1.00  0.00              
ATOM    354  CA  ALA   146      23.819  56.776  -3.676  1.00  0.00              
ATOM    355  C   ALA   146      24.652  56.977  -2.416  1.00  0.00              
ATOM    356  O   ALA   146      25.699  57.613  -2.455  1.00  0.00              
ATOM    357  N   GLY   147      24.203  56.408  -1.302  1.00  0.00              
ATOM    358  CA  GLY   147      24.942  56.517  -0.062  1.00  0.00              
ATOM    359  C   GLY   147      26.057  55.506  -0.119  1.00  0.00              
ATOM    360  O   GLY   147      27.170  55.727   0.359  1.00  0.00              
ATOM    361  N   GLY   148      25.726  54.400  -0.746  1.00  0.00              
ATOM    362  CA  GLY   148      26.650  53.311  -0.942  1.00  0.00              
ATOM    363  C   GLY   148      27.561  53.611  -2.131  1.00  0.00              
ATOM    364  O   GLY   148      28.726  53.212  -2.155  1.00  0.00              
ATOM    365  N   TYR   149      27.006  54.311  -3.121  1.00  0.00              
ATOM    366  CA  TYR   149      27.744  54.668  -4.329  1.00  0.00              
ATOM    367  C   TYR   149      28.431  56.032  -4.213  1.00  0.00              
ATOM    368  O   TYR   149      29.638  56.143  -4.430  1.00  0.00              
ATOM    369  N   ALA   150      27.657  57.073  -3.898  1.00  0.00              
ATOM    370  CA  ALA   150      28.206  58.426  -3.789  1.00  0.00              
ATOM    371  C   ALA   150      29.298  58.509  -2.728  1.00  0.00              
ATOM    372  O   ALA   150      30.270  59.250  -2.884  1.00  0.00              
ATOM    373  N   LYS   151      29.139  57.749  -1.651  1.00  0.00              
ATOM    374  CA  LYS   151      30.119  57.749  -0.570  1.00  0.00              
ATOM    375  C   LYS   151      31.482  57.275  -1.068  1.00  0.00              
ATOM    376  O   LYS   151      31.663  56.100  -1.386  1.00  0.00              
ATOM    377  N   VAL   152      32.438  58.198  -1.129  1.00  0.00              
ATOM    378  CA  VAL   152      33.787  57.873  -1.583  1.00  0.00              
ATOM    379  C   VAL   152      34.333  56.665  -0.831  1.00  0.00              
ATOM    380  O   VAL   152      34.510  56.708   0.387  1.00  0.00              
ATOM    381  N   ILE   153      34.592  55.586  -1.560  1.00  0.00              
ATOM    382  CA  ILE   153      35.112  54.364  -0.960  1.00  0.00              
ATOM    383  C   ILE   153      36.619  54.246  -1.170  1.00  0.00              
ATOM    384  O   ILE   153      37.160  54.744  -2.158  1.00  0.00              
ATOM    385  N   ILE   154      37.289  53.580  -0.235  1.00  0.00              
ATOM    386  CA  ILE   154      38.732  53.390  -0.317  1.00  0.00              
ATOM    387  C   ILE   154      39.069  52.189  -1.193  1.00  0.00              
ATOM    388  O   ILE   154      39.924  52.268  -2.074  1.00  0.00              
ATOM    389  N   PRO   155      38.391  51.056  -0.956  1.00  0.00              
ATOM    390  CA  PRO   155      38.607  49.823  -1.719  1.00  0.00              
ATOM    391  C   PRO   155      38.447  50.037  -3.221  1.00  0.00              
ATOM    392  O   PRO   155      38.199  51.154  -3.676  1.00  0.00              
ATOM    393  N   PHE   156      38.590  48.960  -3.984  1.00  0.00              
ATOM    394  CA  PHE   156      38.459  49.029  -5.433  1.00  0.00              
ATOM    395  C   PHE   156      38.626  47.651  -6.064  1.00  0.00              
ATOM    396  O   PHE   156      39.703  47.306  -6.551  1.00  0.00              
ATOM    397  N   SER   157      37.553  46.866  -6.051  1.00  0.00              
ATOM    398  CA  SER   157      37.602  45.534  -6.624  1.00  0.00              
ATOM    399  C   SER   157      37.483  44.446  -5.576  1.00  0.00              
ATOM    400  O   SER   157      36.786  44.671  -4.564  1.00  0.00              
END
