
#######################################################
#                                                     #
#                        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   27 (  108),  selected   27 , name T0316AL044_5-D3
# Molecule2: number of CA atoms   90 (  711),  selected   27 , name T0316_D3.pdb
# PARAMETERS: T0316AL044_5-D3.T0316_D3.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       284 - 291         4.39    21.25
  LONGEST_CONTINUOUS_SEGMENT:     8       288 - 297         4.56    15.08
  LONGEST_CONTINUOUS_SEGMENT:     8       289 - 298         4.87    15.34
  LCS_AVERAGE:      7.57

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       284 - 287         1.95    19.34
  LONGEST_CONTINUOUS_SEGMENT:     4       289 - 292         0.55    21.33
  LONGEST_CONTINUOUS_SEGMENT:     4       301 - 305         1.75    16.76
  LONGEST_CONTINUOUS_SEGMENT:     4       305 - 309         1.88    17.08
  LONGEST_CONTINUOUS_SEGMENT:     4       327 - 331         2.00    20.11
  LCS_AVERAGE:      3.87

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       289 - 292         0.55    21.33
  LCS_AVERAGE:      2.26

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:   90
LCS_GDT     M     284     M     284      3    4    8     3    3    3    4    4    6    6    6    7    7    7    8    8   11   13   13   14   14   15   16 
LCS_GDT     S     285     S     285      3    4    8     3    3    4    4    4    6    6    6    7    7    8    9   10   11   13   13   14   14   15   16 
LCS_GDT     T     286     T     286      3    4    8     3    3    3    4    4    6    6    6    7    7    8    9   10   11   13   13   14   15   15   16 
LCS_GDT     S     287     S     287      0    4    8     0    1    2    3    4    6    6    6    7    7    8    9   10   11   13   14   14   15   16   17 
LCS_GDT     L     288     L     288      0    3    8     0    0    2    2    3    4    5    5    7    7    8    9   10   12   13   14   14   15   16   17 
LCS_GDT     E     289     E     289      4    4    8     3    4    5    5    5    6    8   10   10   13   13   13   14   15   15   15   15   15   16   17 
LCS_GDT     A     290     A     290      4    4    8     3    4    5    5    5    6    9   10   10   13   13   13   14   15   15   15   15   15   16   17 
LCS_GDT     S     291     S     291      4    4    8     3    4    4    4    5    6    9   10   10   13   13   13   14   15   15   15   15   15   16   17 
LCS_GDT     Q     292     Q     292      4    4    8     3    4    4    4    4    6    9   10   10   13   13   13   14   15   15   15   15   15   16   17 
LCS_GDT     V     293     V     293      0    3    8     0    3    3    3    4    4    5    8   10   13   13   13   14   15   15   15   15   15   16   17 
LCS_GDT     T     296     T     296      0    0    8     1    3    5    5    5    6    9   10   10   13   13   13   14   15   15   15   15   15   16   17 
LCS_GDT     R     297     R     297      0    0    8     0    4    5    5    5    6    9   10   10   13   13   13   14   15   15   15   15   15   16   17 
LCS_GDT     E     298     E     298      0    3    8     0    0    2    3    3    3    3    3    3    4    5    6    6    6   11   12   13   14   16   17 
LCS_GDT     M     299     M     299      0    3    3     0    0    0    3    3    3    3    3    3    3    3    3    3    4    5    8   12   14   16   17 
LCS_GDT     P     300     P     300      0    3    3     0    0    2    3    3    3    3    3    3    3    3    3    3    3    5    8    9   11   15   17 
LCS_GDT     E     301     E     301      3    4    7     0    4    4    4    4    6    9   10   10   12   13   13   14   15   15   15   15   15   16   17 
LCS_GDT     E     302     E     302      3    4    7     0    3    3    3    5    6    7    8   10   13   13   13   14   15   15   15   15   15   16   17 
LCS_GDT     F     303     F     303      3    4    7     0    3    3    3    3    5    5    6    6   13   13   13   14   15   15   15   15   15   16   16 
LCS_GDT     L     305     L     305      0    4    7     0    1    1    2    3    4    5    6    6    7    9   10   10   10   11   13   13   14   15   16 
LCS_GDT     C     307     C     307      3    4    7     1    3    3    3    3    4    5    6    7    7    9   10   10   11   13   13   14   14   15   15 
LCS_GDT     T     308     T     308      3    4    7     1    3    3    4    4    6    6    6    7    7    9   10   10   11   13   13   14   14   15   15 
LCS_GDT     A     309     A     309      3    4    7     0    3    3    3    3    6    6    6    7    7    9   10   10   11   13   13   14   14   15   15 
LCS_GDT     E     327     E     327      0    4    5     0    3    5    5    5    6    9   10   10   11   13   13   14   15   15   15   15   15   16   17 
LCS_GDT     T     329     T     329      3    4    5     0    3    4    4    4    6    9   10   10   13   13   13   14   15   15   15   15   15   16   17 
LCS_GDT     E     330     E     330      3    4    5     3    3    4    4    5    6    9   10   10   13   13   13   14   15   15   15   15   15   16   17 
LCS_GDT     V     331     V     331      3    4    5     3    3    4    4    5    6    7    8   10   13   13   13   14   15   15   15   15   15   16   17 
LCS_GDT     I     332     I     332      3    3    5     3    3    3    3    4    6    7    8   10   13   13   13   14   15   15   15   15   15   16   16 
LCS_AVERAGE  LCS_A:   4.57  (   2.26    3.87    7.57 )

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      5      5      5      6      9     10     10     13     13     13     14     15     15     15     15     15     16     17 
GDT PERCENT_CA   3.33   4.44   5.56   5.56   5.56   6.67  10.00  11.11  11.11  14.44  14.44  14.44  15.56  16.67  16.67  16.67  16.67  16.67  17.78  18.89
GDT RMS_LOCAL    0.00   0.55   1.00   1.00   1.00   1.74   2.89   2.98   2.98   3.82   3.82   3.82   4.26   4.49   4.49   4.49   4.49   4.49   5.30   6.90
GDT RMS_ALL_CA  15.49  21.33  15.04  15.04  15.04  14.45  13.55  13.66  13.66  12.82  12.82  12.82  12.83  12.86  12.86  12.86  12.86  12.86  12.76  13.00

#      Molecule1      Molecule2       DISTANCE
LGA    M     284      M     284         31.531
LGA    S     285      S     285         26.317
LGA    T     286      T     286         20.508
LGA    S     287      S     287         14.269
LGA    L     288      L     288         11.813
LGA    E     289      E     289          3.172
LGA    A     290      A     290          2.053
LGA    S     291      S     291          3.775
LGA    Q     292      Q     292          3.364
LGA    V     293      V     293          5.939
LGA    T     296      T     296          3.089
LGA    R     297      R     297          1.278
LGA    E     298      E     298         14.452
LGA    M     299      M     299         14.904
LGA    P     300      P     300         16.689
LGA    E     301      E     301          2.258
LGA    E     302      E     302          7.902
LGA    F     303      F     303         10.426
LGA    L     305      L     305         14.375
LGA    C     307      C     307         17.527
LGA    T     308      T     308         20.485
LGA    A     309      A     309         20.587
LGA    E     327      E     327          2.903
LGA    T     329      T     329          3.339
LGA    E     330      E     330          3.650
LGA    V     331      V     331          7.742
LGA    I     332      I     332         12.951

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   27   90    4.0     10    2.98     9.444     8.316     0.324

LGA_LOCAL      RMSD =  2.984  Number of atoms =   10  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 13.663  Number of atoms =   27 
Std_ALL_ATOMS  RMSD = 12.143  (standard rmsd on all 27 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.934440 * X  +   0.139882 * Y  +   0.327498 * Z  + 111.372932
  Y_new =  -0.154701 * X  +   0.668877 * Y  +  -0.727097 * Z  +  30.960524
  Z_new =  -0.320764 * X  +  -0.730093 * Y  +  -0.603386 * Z  + 131.323242 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.261459    0.880134  [ DEG:  -129.5721     50.4279 ]
  Theta =   0.326536    2.815057  [ DEG:    18.7091    161.2909 ]
  Phi   =  -2.977526    0.164067  [ DEG:  -170.5997      9.4003 ]
 
# 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: T0316AL044_5-D3                               
REMARK     2: T0316_D3.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0316AL044_5-D3.T0316_D3.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   27   90   4.0   10   2.98   8.316    12.14
REMARK  ---------------------------------------------------------- 
MOLECULE T0316AL044_5-D3
REMARK Aligment from pdb entry: 1gpm_A
ATOM    821  N   MET   284      23.387  -3.602  13.394  1.00  0.00              
ATOM    822  CA  MET   284      24.233  -2.420  13.367  1.00  0.00              
ATOM    823  C   MET   284      23.466  -1.277  12.757  1.00  0.00              
ATOM    824  O   MET   284      22.735  -1.458  11.781  1.00  0.00              
ATOM    825  N   SER   285      23.539  -0.131  13.417  1.00  0.00              
ATOM    826  CA  SER   285      22.903   1.076  12.923  1.00  0.00              
ATOM    827  C   SER   285      23.914   1.680  11.954  1.00  0.00              
ATOM    828  O   SER   285      25.130   1.564  12.153  1.00  0.00              
ATOM    829  N   THR   286      23.423   2.320  10.903  1.00  0.00              
ATOM    830  CA  THR   286      24.310   2.913   9.907  1.00  0.00              
ATOM    831  C   THR   286      23.714   4.234   9.462  1.00  0.00              
ATOM    832  O   THR   286      22.530   4.309   9.144  1.00  0.00              
ATOM    833  N   SER   287      25.102   7.994   7.416  1.00  0.00              
ATOM    834  CA  SER   287      26.180   8.747   6.783  1.00  0.00              
ATOM    835  C   SER   287      25.740  10.060   6.162  1.00  0.00              
ATOM    836  O   SER   287      24.567  10.248   5.816  1.00  0.00              
ATOM    837  N   LEU   288      26.718  10.941   5.987  1.00  0.00              
ATOM    838  CA  LEU   288      26.539  12.230   5.339  1.00  0.00              
ATOM    839  C   LEU   288      27.373  12.096   4.074  1.00  0.00              
ATOM    840  O   LEU   288      28.605  12.067   4.120  1.00  0.00              
ATOM    841  N   GLU   289      31.781   9.234  -3.786  1.00  0.00              
ATOM    842  CA  GLU   289      32.973   8.479  -3.437  1.00  0.00              
ATOM    843  C   GLU   289      33.395   8.785  -1.997  1.00  0.00              
ATOM    844  O   GLU   289      34.265   8.114  -1.440  1.00  0.00              
ATOM    845  N   ALA   290      32.712   9.737  -1.371  1.00  0.00              
ATOM    846  CA  ALA   290      33.025  10.120  -0.003  1.00  0.00              
ATOM    847  C   ALA   290      31.772  10.376   0.829  1.00  0.00              
ATOM    848  O   ALA   290      30.876  11.114   0.414  1.00  0.00              
ATOM    849  N   SER   291      31.706   9.739   1.995  1.00  0.00              
ATOM    850  CA  SER   291      30.580   9.885   2.921  1.00  0.00              
ATOM    851  C   SER   291      31.113   9.691   4.333  1.00  0.00              
ATOM    852  O   SER   291      31.919   8.802   4.572  1.00  0.00              
ATOM    853  N   GLN   292      30.691  10.530   5.264  1.00  0.00              
ATOM    854  CA  GLN   292      31.173  10.420   6.635  1.00  0.00              
ATOM    855  C   GLN   292      30.140   9.779   7.550  1.00  0.00              
ATOM    856  O   GLN   292      28.943   9.978   7.358  1.00  0.00              
ATOM    857  N   VAL   293      27.792   9.629  10.446  1.00  0.00              
ATOM    858  CA  VAL   293      27.119  10.651  11.245  1.00  0.00              
ATOM    859  C   VAL   293      27.438  10.606  12.741  1.00  0.00              
ATOM    860  O   VAL   293      27.344   9.559  13.388  1.00  0.00              
ATOM    861  N   THR   296      27.766  11.760  13.303  1.00  0.00              
ATOM    862  CA  THR   296      28.080  11.841  14.721  1.00  0.00              
ATOM    863  C   THR   296      26.784  11.999  15.501  1.00  0.00              
ATOM    864  O   THR   296      26.544  13.050  16.098  1.00  0.00              
ATOM    865  N   ARG   297      25.946  10.968  15.496  1.00  0.00              
ATOM    866  CA  ARG   297      24.670  11.051  16.201  1.00  0.00              
ATOM    867  C   ARG   297      24.848  11.181  17.716  1.00  0.00              
ATOM    868  O   ARG   297      25.684  10.498  18.317  1.00  0.00              
ATOM    869  N   GLU   298      15.387  -0.917  20.863  1.00  0.00              
ATOM    870  CA  GLU   298      15.569  -2.104  20.031  1.00  0.00              
ATOM    871  C   GLU   298      15.771  -3.372  20.856  1.00  0.00              
ATOM    872  O   GLU   298      15.102  -4.375  20.611  1.00  0.00              
ATOM    873  N   MET   299      16.671  -3.334  21.833  1.00  0.00              
ATOM    874  CA  MET   299      16.910  -4.530  22.634  1.00  0.00              
ATOM    875  C   MET   299      15.697  -4.918  23.480  1.00  0.00              
ATOM    876  O   MET   299      15.389  -6.100  23.614  1.00  0.00              
ATOM    877  N   PRO   300      12.343  -5.539  20.459  1.00  0.00              
ATOM    878  CA  PRO   300      12.426  -6.574  19.436  1.00  0.00              
ATOM    879  C   PRO   300      12.943  -7.872  20.030  1.00  0.00              
ATOM    880  O   PRO   300      14.138  -8.021  20.267  1.00  0.00              
ATOM    881  N   GLU   301      27.918   1.744  13.266  1.00  0.00              
ATOM    882  CA  GLU   301      28.985   1.759  12.270  1.00  0.00              
ATOM    883  C   GLU   301      29.753   3.076  12.317  1.00  0.00              
ATOM    884  O   GLU   301      29.181   4.153  12.109  1.00  0.00              
ATOM    885  N   GLU   302      31.046   2.987  12.606  1.00  0.00              
ATOM    886  CA  GLU   302      31.878   4.172  12.695  1.00  0.00              
ATOM    887  C   GLU   302      32.950   4.145  11.624  1.00  0.00              
ATOM    888  O   GLU   302      34.042   4.682  11.803  1.00  0.00              
ATOM    889  N   PHE   303      32.626   3.509  10.506  1.00  0.00              
ATOM    890  CA  PHE   303      33.541   3.412   9.379  1.00  0.00              
ATOM    891  C   PHE   303      33.043   4.374   8.309  1.00  0.00              
ATOM    892  O   PHE   303      31.868   4.345   7.938  1.00  0.00              
ATOM    893  N   LEU   305      33.922   5.245   7.836  1.00  0.00              
ATOM    894  CA  LEU   305      33.540   6.204   6.820  1.00  0.00              
ATOM    895  C   LEU   305      33.812   5.713   5.415  1.00  0.00              
ATOM    896  O   LEU   305      34.251   4.579   5.203  1.00  0.00              
ATOM    897  N   CYS   307      33.515   6.563   4.445  1.00  0.00              
ATOM    898  CA  CYS   307      33.755   6.248   3.049  1.00  0.00              
ATOM    899  C   CYS   307      34.630   7.346   2.457  1.00  0.00              
ATOM    900  O   CYS   307      34.224   8.513   2.401  1.00  0.00              
ATOM    901  N   THR   308      35.890   7.018   2.151  1.00  0.00              
ATOM    902  CA  THR   308      36.482   5.692   2.350  1.00  0.00              
ATOM    903  C   THR   308      36.967   5.583   3.806  1.00  0.00              
ATOM    904  O   THR   308      36.773   6.510   4.600  1.00  0.00              
ATOM    905  N   ALA   309      37.602   4.459   4.179  1.00  0.00              
ATOM    906  CA  ALA   309      37.921   3.273   3.386  1.00  0.00              
ATOM    907  C   ALA   309      36.811   2.232   3.282  1.00  0.00              
ATOM    908  O   ALA   309      36.988   1.199   2.630  1.00  0.00              
ATOM    909  N   GLU   327      35.677   2.479   3.927  1.00  0.00              
ATOM    910  CA  GLU   327      34.573   1.529   3.853  1.00  0.00              
ATOM    911  C   GLU   327      33.500   2.086   2.923  1.00  0.00              
ATOM    912  O   GLU   327      33.572   3.241   2.511  1.00  0.00              
ATOM    913  N   THR   329      32.547   1.241   2.544  1.00  0.00              
ATOM    914  CA  THR   329      31.441   1.654   1.692  1.00  0.00              
ATOM    915  C   THR   329      30.257   1.955   2.603  1.00  0.00              
ATOM    916  O   THR   329      30.293   1.644   3.811  1.00  0.00              
ATOM    917  N   GLU   330      29.222   2.583   2.043  1.00  0.00              
ATOM    918  CA  GLU   330      28.019   2.918   2.810  1.00  0.00              
ATOM    919  C   GLU   330      27.272   1.646   3.184  1.00  0.00              
ATOM    920  O   GLU   330      26.956   1.433   4.359  1.00  0.00              
ATOM    921  N   VAL   331      27.018   0.796   2.194  1.00  0.00              
ATOM    922  CA  VAL   331      26.337  -0.465   2.423  1.00  0.00              
ATOM    923  C   VAL   331      27.416  -1.482   2.781  1.00  0.00              
ATOM    924  O   VAL   331      28.592  -1.253   2.521  1.00  0.00              
ATOM    925  N   ILE   332      27.025  -2.554   3.462  1.00  0.00              
ATOM    926  CA  ILE   332      27.952  -3.596   3.877  1.00  0.00              
ATOM    927  C   ILE   332      28.144  -4.693   2.841  1.00  0.00              
ATOM    928  O   ILE   332      29.107  -5.464   2.935  1.00  0.00              
END
