
#######################################################
#                                                     #
#                        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 (   72),  selected   17 , name T0386AL170_1-D2
# Molecule2: number of CA atoms   81 (  636),  selected   17 , name T0386_D2.pdb
# PARAMETERS: T0386AL170_1-D2.T0386_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       219 - 237         3.37     3.37
  LCS_AVERAGE:     20.99

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12       226 - 237         1.35     4.09
  LCS_AVERAGE:     12.93

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9       226 - 234         0.57     3.90
  LCS_AVERAGE:      8.35

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:   81
LCS_GDT     N     219     N     219      5    6   17     5    5    5    5    5    7   10   14   14   15   16   17   17   17   17   17   17   17   17   17 
LCS_GDT     P     220     P     220      5    6   17     5    5    5    5    5    7   12   14   14   15   16   17   17   17   17   17   17   17   17   17 
LCS_GDT     E     221     E     221      5    6   17     5    5    5    5    5    6    8   12   14   15   16   17   17   17   17   17   17   17   17   17 
LCS_GDT     K     222     K     222      5    6   17     5    5    5    5    5    7    9   14   14   15   16   17   17   17   17   17   17   17   17   17 
LCS_GDT     I     223     I     223      5   10   17     5    5    5    5    5    7   10   14   14   15   16   17   17   17   17   17   17   17   17   17 
LCS_GDT     L     226     L     226      9   12   17     6   10   10   10   12   12   12   14   14   15   16   17   17   17   17   17   17   17   17   17 
LCS_GDT     K     227     K     227      9   12   17     6   10   10   10   12   12   12   14   14   15   16   17   17   17   17   17   17   17   17   17 
LCS_GDT     E     228     E     228      9   12   17     6   10   10   10   12   12   12   14   14   15   16   17   17   17   17   17   17   17   17   17 
LCS_GDT     F     229     F     229      9   12   17     6   10   10   10   12   12   12   14   14   15   16   17   17   17   17   17   17   17   17   17 
LCS_GDT     M     230     M     230      9   12   17     6   10   10   10   12   12   12   14   14   15   16   17   17   17   17   17   17   17   17   17 
LCS_GDT     H     231     H     231      9   12   17     6   10   10   10   12   12   12   14   14   15   16   17   17   17   17   17   17   17   17   17 
LCS_GDT     T     232     T     232      9   12   17     6   10   10   10   12   12   12   14   14   15   16   17   17   17   17   17   17   17   17   17 
LCS_GDT     M     233     M     233      9   12   17     5   10   10   10   12   12   12   14   14   15   16   17   17   17   17   17   17   17   17   17 
LCS_GDT     K     234     K     234      9   12   17     5   10   10   10   12   12   12   14   14   15   16   17   17   17   17   17   17   17   17   17 
LCS_GDT     N     235     N     235      3   12   17     3    3    4    8   12   12   12   13   14   15   16   17   17   17   17   17   17   17   17   17 
LCS_GDT     T     236     T     236      3   12   17     6   10   10   10   12   12   12   14   14   15   16   17   17   17   17   17   17   17   17   17 
LCS_GDT     G     237     G     237      3   12   17     3    3    4    8   12   12   12   13   14   15   16   17   17   17   17   17   17   17   17   17 
LCS_AVERAGE  LCS_A:  14.09  (   8.35   12.93   20.99 )

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      6     10     10     10     12     12     12     14     14     15     16     17     17     17     17     17     17     17     17     17 
GDT PERCENT_CA   7.41  12.35  12.35  12.35  14.81  14.81  14.81  17.28  17.28  18.52  19.75  20.99  20.99  20.99  20.99  20.99  20.99  20.99  20.99  20.99
GDT RMS_LOCAL    0.24   0.64   0.64   0.64   1.35   1.35   1.35   2.83   2.31   2.76   3.08   3.37   3.37   3.37   3.37   3.37   3.37   3.37   3.37   3.37
GDT RMS_ALL_CA   3.74   3.95   3.95   3.95   4.09   4.09   4.09   3.48   3.68   3.53   3.42   3.37   3.37   3.37   3.37   3.37   3.37   3.37   3.37   3.37

#      Molecule1      Molecule2       DISTANCE
LGA    N     219      N     219          3.927
LGA    P     220      P     220          3.772
LGA    E     221      E     221          5.144
LGA    K     222      K     222          3.958
LGA    I     223      I     223          3.628
LGA    L     226      L     226          2.845
LGA    K     227      K     227          1.433
LGA    E     228      E     228          2.244
LGA    F     229      F     229          2.827
LGA    M     230      M     230          2.266
LGA    H     231      H     231          2.345
LGA    T     232      T     232          2.930
LGA    M     233      M     233          2.111
LGA    K     234      K     234          3.342
LGA    N     235      N     235          7.735
LGA    T     236      T     236          3.348
LGA    G     237      G     237          5.553

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   17   81    4.0     14    2.83    15.741    15.372     0.477

LGA_LOCAL      RMSD =  2.834  Number of atoms =   14  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.795  Number of atoms =   17 
Std_ALL_ATOMS  RMSD =  3.368  (standard rmsd on all 17 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.684503 * X  +   0.470917 * Y  +   0.556500 * Z  + -21.728956
  Y_new =  -0.370393 * X  +   0.432839 * Y  +  -0.821863 * Z  +  31.146935
  Z_new =  -0.627905 * X  +  -0.768692 * Y  +  -0.121855 * Z  + 118.680794 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.728011    1.413581  [ DEG:   -99.0078     80.9922 ]
  Theta =   0.678858    2.462735  [ DEG:    38.8957    141.1043 ]
  Phi   =  -2.645599    0.495994  [ DEG:  -151.5816     28.4184 ]
 
# 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: T0386AL170_1-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0386AL170_1-D2.T0386_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   17   81   4.0   14   2.83  15.372     3.37
REMARK  ---------------------------------------------------------- 
MOLECULE T0386AL170_1-D2
REMARK Aligment from pdb entry: 2G03_A
ATOM    633  N   ASN   219       5.474  56.270  78.563  1.00  0.00              
ATOM    634  CA  ASN   219       4.391  57.007  77.949  1.00  0.00              
ATOM    635  C   ASN   219       4.919  58.002  76.899  1.00  0.00              
ATOM    636  O   ASN   219       5.806  58.807  77.183  1.00  0.00              
ATOM    637  N   PRO   220       4.400  57.916  75.677  1.00  0.00              
ATOM    638  CA  PRO   220       4.856  58.775  74.584  1.00  0.00              
ATOM    639  C   PRO   220       4.777  60.282  74.912  1.00  0.00              
ATOM    640  O   PRO   220       5.694  61.030  74.587  1.00  0.00              
ATOM    641  N   GLU   221       3.709  60.715  75.572  1.00  0.00              
ATOM    642  CA  GLU   221       3.527  62.126  75.871  1.00  0.00              
ATOM    643  C   GLU   221       4.533  62.632  76.914  1.00  0.00              
ATOM    644  O   GLU   221       5.111  63.723  76.769  1.00  0.00              
ATOM    645  N   LYS   222       4.755  61.836  77.960  1.00  0.00              
ATOM    646  CA  LYS   222       5.751  62.149  78.978  1.00  0.00              
ATOM    647  C   LYS   222       7.142  62.171  78.361  1.00  0.00              
ATOM    648  O   LYS   222       7.918  63.091  78.627  1.00  0.00              
ATOM    649  N   ILE   223       7.468  61.177  77.537  1.00  0.00              
ATOM    650  CA  ILE   223       8.784  61.159  76.891  1.00  0.00              
ATOM    651  C   ILE   223       8.968  62.403  75.978  1.00  0.00              
ATOM    652  O   ILE   223       9.884  63.196  76.169  1.00  0.00              
ATOM    653  N   LEU   226       8.073  62.603  75.028  1.00  0.00              
ATOM    654  CA  LEU   226       8.272  63.658  74.043  1.00  0.00              
ATOM    655  C   LEU   226       8.074  65.106  74.529  1.00  0.00              
ATOM    656  O   LEU   226       8.846  65.969  74.140  1.00  0.00              
ATOM    657  N   LYS   227       7.069  65.362  75.365  1.00  0.00              
ATOM    658  CA  LYS   227       6.916  66.679  75.986  1.00  0.00              
ATOM    659  C   LYS   227       8.067  66.951  76.945  1.00  0.00              
ATOM    660  O   LYS   227       8.457  68.106  77.134  1.00  0.00              
ATOM    661  N   GLU   228       8.613  65.886  77.538  1.00  0.00              
ATOM    662  CA  GLU   228       9.772  65.968  78.405  1.00  0.00              
ATOM    663  C   GLU   228      11.043  66.354  77.676  1.00  0.00              
ATOM    664  O   GLU   228      11.796  67.196  78.150  1.00  0.00              
ATOM    665  N   PHE   229      11.312  65.706  76.545  1.00  0.00              
ATOM    666  CA  PHE   229      12.419  66.068  75.660  1.00  0.00              
ATOM    667  C   PHE   229      12.300  67.532  75.217  1.00  0.00              
ATOM    668  O   PHE   229      13.279  68.264  75.238  1.00  0.00              
ATOM    669  N   MET   230      11.112  67.953  74.803  1.00  0.00              
ATOM    670  CA  MET   230      10.907  69.360  74.474  1.00  0.00              
ATOM    671  C   MET   230      11.219  70.316  75.630  1.00  0.00              
ATOM    672  O   MET   230      11.790  71.373  75.405  1.00  0.00              
ATOM    673  N   HIS   231      10.834  69.953  76.850  1.00  0.00              
ATOM    674  CA  HIS   231      11.075  70.815  78.000  1.00  0.00              
ATOM    675  C   HIS   231      12.567  70.838  78.326  1.00  0.00              
ATOM    676  O   HIS   231      13.132  71.892  78.550  1.00  0.00              
ATOM    677  N   THR   232      13.203  69.667  78.330  1.00  0.00              
ATOM    678  CA  THR   232      14.634  69.536  78.534  1.00  0.00              
ATOM    679  C   THR   232      15.460  70.434  77.608  1.00  0.00              
ATOM    680  O   THR   232      16.424  71.083  78.048  1.00  0.00              
ATOM    681  N  AMET   233      15.098  70.451  76.327  1.00  0.00              
ATOM    682  N  BMET   233      15.093  70.434  76.339  1.00  0.00              
ATOM    683  CA AMET   233      15.784  71.263  75.312  1.00  0.00              
ATOM    684  CA BMET   233      15.763  71.224  75.332  1.00  0.00              
ATOM    685  C  AMET   233      15.513  72.760  75.478  1.00  0.00              
ATOM    686  C  BMET   233      15.556  72.723  75.579  1.00  0.00              
ATOM    687  O  AMET   233      16.320  73.607  75.055  1.00  0.00              
ATOM    688  O  BMET   233      16.444  73.535  75.286  1.00  0.00              
ATOM    689  N   LYS   234      14.375  73.077  76.092  1.00  0.00              
ATOM    690  CA  LYS   234      14.020  74.460  76.428  1.00  0.00              
ATOM    691  C   LYS   234      14.880  75.036  77.591  1.00  0.00              
ATOM    692  O   LYS   234      15.195  76.226  77.607  1.00  0.00              
ATOM    693  N   ASN   235      15.290  74.185  78.529  1.00  0.00              
ATOM    694  CA  ASN   235      16.033  74.616  79.705  1.00  0.00              
ATOM    695  C   ASN   235      17.304  75.327  79.308  1.00  0.00              
ATOM    696  O   ASN   235      17.748  76.248  79.996  1.00  0.00              
ATOM    697  N   THR   236      17.902  74.931  78.191  1.00  0.00              
ATOM    698  CA  THR   236      19.161  75.590  77.834  1.00  0.00              
ATOM    699  C   THR   236      19.106  76.306  76.503  1.00  0.00              
ATOM    700  O   THR   236      20.138  76.515  75.892  1.00  0.00              
ATOM    701  N   GLY   237      17.917  76.738  76.090  1.00  0.00              
ATOM    702  CA  GLY   237      17.745  77.423  74.797  1.00  0.00              
ATOM    703  C   GLY   237      16.375  78.058  74.641  1.00  0.00              
ATOM    704  O   GLY   237      15.886  78.274  73.517  1.00  0.00              
END
