
#######################################################
#                                                     #
#                        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 (   44),  selected   11 , name T0316AL380_4-D2
# Molecule2: number of CA atoms   60 (  457),  selected   11 , name T0316_D2.pdb
# PARAMETERS: T0316AL380_4-D2.T0316_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:     9       220 - 228         3.96     7.73
  LCS_AVERAGE:     14.39

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       221 - 226         1.93     9.58
  LCS_AVERAGE:      8.94

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       222 - 225         0.49    11.53
  LONGEST_CONTINUOUS_SEGMENT:     4       227 - 230         0.66    14.81
  LCS_AVERAGE:      6.21

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:   60
LCS_GDT     G     220     G     220      3    3    9     0    3    3    3    3    4    4    5    6    8    9    9    9    9    9    9    9   10   10   10 
LCS_GDT     R     221     R     221      3    6    9     3    3    3    4    5    6    6    7    7    8    9    9    9    9    9    9    9   10   10   10 
LCS_GDT     M     222     M     222      4    6    9     3    4    4    5    5    6    6    7    7    8    9    9    9    9    9    9    9   10   10   10 
LCS_GDT     M     223     M     223      4    6    9     3    4    4    5    5    6    6    7    7    8    9    9    9    9    9    9    9   10   10   10 
LCS_GDT     T     224     T     224      4    6    9     3    4    4    5    5    6    6    7    7    8    9    9    9    9    9    9    9   10   10   10 
LCS_GDT     V     225     V     225      4    6    9     1    4    4    5    5    6    6    7    7    8    9    9    9    9    9    9    9   10   10   10 
LCS_GDT     D     226     D     226      3    6    9     0    3    4    5    5    6    6    7    7    8    9    9    9    9    9    9    9   10   10   10 
LCS_GDT     G     227     G     227      4    5    9     3    4    4    4    5    5    6    7    7    8    9    9    9    9    9    9    9   10   10   10 
LCS_GDT     R     228     R     228      4    5    9     3    4    4    4    5    5    5    6    6    8    9    9    9    9    9    9    9   10   10   10 
LCS_GDT     D     229     D     229      4    5    7     3    4    4    4    5    5    5    6    6    6    6    6    6    7    7    7    7   10   10   10 
LCS_GDT     M     230     M     230      4    5    7     3    4    4    4    5    5    5    6    6    6    6    6    6    6    7    7    7    7    8    8 
LCS_AVERAGE  LCS_A:   9.85  (   6.21    8.94   14.39 )

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      4      4      5      5      6      6      7      7      8      9      9      9      9      9      9      9     10     10     10 
GDT PERCENT_CA   5.00   6.67   6.67   8.33   8.33  10.00  10.00  11.67  11.67  13.33  15.00  15.00  15.00  15.00  15.00  15.00  15.00  16.67  16.67  16.67
GDT RMS_LOCAL    0.18   0.49   0.49   1.42   1.42   1.93   1.93   2.54   2.54   3.28   3.96   3.96   3.96   3.96   3.96   3.96   3.96   5.32   5.32   5.32
GDT RMS_ALL_CA  14.21  11.53  11.53   9.89   9.89   9.58   9.58   9.02   9.02   8.65   7.73   7.73   7.73   7.73   7.73   7.73   7.73   7.05   7.05   7.05

#      Molecule1      Molecule2       DISTANCE
LGA    G     220      G     220          5.709
LGA    R     221      R     221          2.862
LGA    M     222      M     222          1.659
LGA    M     223      M     223          1.818
LGA    T     224      T     224          2.910
LGA    V     225      V     225          2.208
LGA    D     226      D     226          3.678
LGA    G     227      G     227          3.494
LGA    R     228      R     228          8.770
LGA    D     229      D     229         14.797
LGA    M     230      M     230         21.007

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   11   60    4.0      7    2.54    10.417    10.320     0.266

LGA_LOCAL      RMSD =  2.535  Number of atoms =    7  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  8.650  Number of atoms =   11 
Std_ALL_ATOMS  RMSD =  6.687  (standard rmsd on all 11 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.590698 * X  +   0.403470 * Y  +   0.698776 * Z  +  52.463959
  Y_new =   0.335846 * X  +  -0.664492 * Y  +   0.667576 * Z  +   4.555908
  Z_new =   0.733678 * X  +   0.629017 * Y  +   0.257010 * Z  + -169.411896 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.182907   -1.958686  [ DEG:    67.7756   -112.2244 ]
  Theta =  -0.823720   -2.317873  [ DEG:   -47.1957   -132.8044 ]
  Phi   =   2.624613   -0.516980  [ DEG:   150.3792    -29.6208 ]
 
# 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: T0316AL380_4-D2                               
REMARK     2: T0316_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0316AL380_4-D2.T0316_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   11   60   4.0    7   2.54  10.320     6.69
REMARK  ---------------------------------------------------------- 
MOLECULE T0316AL380_4-D2
REMARK Aligment from pdb entry: 1gpmB
ATOM    693  N   GLY   220      42.893  18.960 -24.962  1.00  0.00              
ATOM    694  CA  GLY   220      42.107  17.918 -24.296  1.00  0.00              
ATOM    695  C   GLY   220      41.042  18.459 -23.329  1.00  0.00              
ATOM    696  O   GLY   220      39.920  17.941 -23.269  1.00  0.00              
ATOM    697  N   ARG   221      41.414  19.481 -22.564  1.00  0.00              
ATOM    698  CA  ARG   221      40.516  20.099 -21.594  1.00  0.00              
ATOM    699  C   ARG   221      39.534  21.047 -22.273  1.00  0.00              
ATOM    700  O   ARG   221      38.632  21.579 -21.627  1.00  0.00              
ATOM    701  N   MET   222      39.733  21.281 -23.568  1.00  0.00              
ATOM    702  CA  MET   222      38.882  22.191 -24.332  1.00  0.00              
ATOM    703  C   MET   222      37.593  21.539 -24.842  1.00  0.00              
ATOM    704  O   MET   222      36.591  22.228 -25.053  1.00  0.00              
ATOM    705  N   MET   223      37.626  20.222 -25.044  1.00  0.00              
ATOM    706  CA  MET   223      36.464  19.479 -25.538  1.00  0.00              
ATOM    707  C   MET   223      35.733  18.687 -24.452  1.00  0.00              
ATOM    708  O   MET   223      36.364  18.148 -23.537  1.00  0.00              
ATOM    709  N   THR   224      34.409  18.596 -24.575  1.00  0.00              
ATOM    710  CA  THR   224      33.586  17.850 -23.621  1.00  0.00              
ATOM    711  C   THR   224      33.820  16.351 -23.788  1.00  0.00              
ATOM    712  O   THR   224      33.903  15.599 -22.807  1.00  0.00              
ATOM    713  N   VAL   225      33.950  15.923 -25.039  1.00  0.00              
ATOM    714  CA  VAL   225      34.179  14.524 -25.341  1.00  0.00              
ATOM    715  C   VAL   225      34.884  14.424 -26.684  1.00  0.00              
ATOM    716  O   VAL   225      34.685  15.269 -27.552  1.00  0.00              
ATOM    717  N   ASP   226      35.727  13.412 -26.845  1.00  0.00              
ATOM    718  CA  ASP   226      36.471  13.242 -28.083  1.00  0.00              
ATOM    719  C   ASP   226      36.866  11.794 -28.323  1.00  0.00              
ATOM    720  O   ASP   226      37.610  11.201 -27.534  1.00  0.00              
ATOM    721  N   GLY   227      36.388  11.233 -29.426  1.00  0.00              
ATOM    722  CA  GLY   227      36.708   9.858 -29.760  1.00  0.00              
ATOM    723  C   GLY   227      36.904   9.609 -31.244  1.00  0.00              
ATOM    724  O   GLY   227      36.780  10.515 -32.065  1.00  0.00              
ATOM    725  N   ARG   228      37.240   8.375 -31.575  1.00  0.00              
ATOM    726  CA  ARG   228      37.444   7.972 -32.947  1.00  0.00              
ATOM    727  C   ARG   228      36.459   6.845 -33.228  1.00  0.00              
ATOM    728  O   ARG   228      36.240   5.977 -32.381  1.00  0.00              
ATOM    729  N   ASP   229      35.802   6.921 -34.381  1.00  0.00              
ATOM    730  CA  ASP   229      34.829   5.917 -34.804  1.00  0.00              
ATOM    731  C   ASP   229      35.465   5.190 -35.986  1.00  0.00              
ATOM    732  O   ASP   229      36.164   5.802 -36.799  1.00  0.00              
ATOM    733  N   MET   230      35.285   3.883 -36.056  1.00  0.00              
ATOM    734  CA  MET   230      35.857   3.120 -37.148  1.00  0.00              
ATOM    735  C   MET   230      34.785   2.887 -38.211  1.00  0.00              
ATOM    736  O   MET   230      33.688   2.431 -37.903  1.00  0.00              
END
