
#######################################################
#                                                     #
#                        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   19 (   80),  selected   19 , name T0386AL242_1-D2
# Molecule2: number of CA atoms   81 (  636),  selected   19 , name T0386_D2.pdb
# PARAMETERS: T0386AL242_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:    19       219 - 237         3.39     3.39
  LCS_AVERAGE:     23.46

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17       221 - 237         1.48     3.88
  LCS_AVERAGE:     19.30

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14       221 - 234         0.89     3.84
  LCS_AVERAGE:     13.71

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      3    4   19     3    3    3    3    4    6    7    8    8   10   10   13   13   13   15   16   19   19   19   19 
LCS_GDT     P     220     P     220      3    4   19     3    3    3    3    4    6    7    8   12   15   18   18   18   18   18   18   19   19   19   19 
LCS_GDT     E     221     E     221     14   17   19     4   11   13   15   16   16   17   17   17   17   18   18   18   18   18   18   19   19   19   19 
LCS_GDT     K     222     K     222     14   17   19     8   12   14   15   16   16   17   17   17   17   18   18   18   18   18   18   19   19   19   19 
LCS_GDT     I     223     I     223     14   17   19     8   12   14   15   16   16   17   17   17   17   18   18   18   18   18   18   19   19   19   19 
LCS_GDT     R     224     R     224     14   17   19     8   12   14   15   16   16   17   17   17   17   18   18   18   18   18   18   19   19   19   19 
LCS_GDT     L     225     L     225     14   17   19     8   12   14   15   16   16   17   17   17   17   18   18   18   18   18   18   19   19   19   19 
LCS_GDT     L     226     L     226     14   17   19     8   12   14   15   16   16   17   17   17   17   18   18   18   18   18   18   19   19   19   19 
LCS_GDT     K     227     K     227     14   17   19     8   12   14   15   16   16   17   17   17   17   18   18   18   18   18   18   19   19   19   19 
LCS_GDT     E     228     E     228     14   17   19     8   12   14   15   16   16   17   17   17   17   18   18   18   18   18   18   19   19   19   19 
LCS_GDT     F     229     F     229     14   17   19     8   12   14   15   16   16   17   17   17   17   18   18   18   18   18   18   19   19   19   19 
LCS_GDT     M     230     M     230     14   17   19     8   12   14   15   16   16   17   17   17   17   18   18   18   18   18   18   19   19   19   19 
LCS_GDT     H     231     H     231     14   17   19     8   12   14   15   16   16   17   17   17   17   18   18   18   18   18   18   19   19   19   19 
LCS_GDT     T     232     T     232     14   17   19     5   12   14   15   16   16   17   17   17   17   18   18   18   18   18   18   19   19   19   19 
LCS_GDT     M     233     M     233     14   17   19     5   10   14   15   16   16   17   17   17   17   18   18   18   18   18   18   19   19   19   19 
LCS_GDT     K     234     K     234     14   17   19     5   12   14   15   16   16   17   17   17   17   18   18   18   18   18   18   19   19   19   19 
LCS_GDT     N     235     N     235      3   17   19     3    3    4    8   13   16   17   17   17   17   18   18   18   18   18   18   19   19   19   19 
LCS_GDT     T     236     T     236      3   17   19     3    9   14   15   16   16   17   17   17   17   18   18   18   18   18   18   19   19   19   19 
LCS_GDT     G     237     G     237      3   17   19     3    3    4    8   16   16   17   17   17   17   18   18   18   18   18   18   19   19   19   19 
LCS_AVERAGE  LCS_A:  18.82  (  13.71   19.30   23.46 )

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      8     12     14     15     16     16     17     17     17     17     18     18     18     18     18     18     19     19     19     19 
GDT PERCENT_CA   9.88  14.81  17.28  18.52  19.75  19.75  20.99  20.99  20.99  20.99  22.22  22.22  22.22  22.22  22.22  22.22  23.46  23.46  23.46  23.46
GDT RMS_LOCAL    0.32   0.72   0.91   1.02   1.21   1.21   1.48   1.48   1.48   1.48   2.37   2.37   2.37   2.37   2.37   2.37   3.39   3.39   3.39   3.39
GDT RMS_ALL_CA   3.85   3.91   3.98   3.86   3.84   3.84   3.88   3.88   3.88   3.88   3.55   3.55   3.55   3.55   3.55   3.55   3.39   3.39   3.39   3.39

#      Molecule1      Molecule2       DISTANCE
LGA    N     219      N     219         13.071
LGA    P     220      P     220          8.838
LGA    E     221      E     221          2.116
LGA    K     222      K     222          0.783
LGA    I     223      I     223          0.921
LGA    R     224      R     224          1.075
LGA    L     225      L     225          0.721
LGA    L     226      L     226          0.410
LGA    K     227      K     227          1.367
LGA    E     228      E     228          1.334
LGA    F     229      F     229          0.917
LGA    M     230      M     230          0.945
LGA    H     231      H     231          1.233
LGA    T     232      T     232          0.611
LGA    M     233      M     233          1.078
LGA    K     234      K     234          1.311
LGA    N     235      N     235          3.420
LGA    T     236      T     236          1.201
LGA    G     237      G     237          2.461

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   19   81    4.0     17    1.48    19.136    19.748     1.077

LGA_LOCAL      RMSD =  1.478  Number of atoms =   17  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.880  Number of atoms =   19 
Std_ALL_ATOMS  RMSD =  3.394  (standard rmsd on all 19 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.278482 * X  +   0.885266 * Y  +   0.372494 * Z  + -44.371368
  Y_new =  -0.845506 * X  +  -0.041993 * Y  +  -0.532313 * Z  +  59.754925
  Z_new =  -0.455596 * X  +  -0.463185 * Y  +   0.760192 * Z  + 106.270287 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.547230    2.594363  [ DEG:   -31.3540    148.6460 ]
  Theta =   0.473042    2.668550  [ DEG:    27.1033    152.8967 ]
  Phi   =  -1.888973    1.252620  [ DEG:  -108.2302     71.7698 ]
 
# 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: T0386AL242_1-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0386AL242_1-D2.T0386_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   19   81   4.0   17   1.48  19.748     3.39
REMARK  ---------------------------------------------------------- 
MOLECULE T0386AL242_1-D2
REMARK Aligment from pdb entry: 2g03_A
ATOM    649  N   ASN   219       2.885  62.323  85.354  1.00  0.00              
ATOM    650  CA  ASN   219       4.300  62.627  85.604  1.00  0.00              
ATOM    651  C   ASN   219       5.266  61.662  84.900  1.00  0.00              
ATOM    652  O   ASN   219       6.474  61.953  84.800  1.00  0.00              
ATOM    653  N   PRO   220       4.738  60.537  84.420  1.00  0.00              
ATOM    654  CA  PRO   220       5.556  59.481  83.832  1.00  0.00              
ATOM    655  C   PRO   220       5.200  59.215  82.376  1.00  0.00              
ATOM    656  O   PRO   220       5.616  58.221  81.802  1.00  0.00              
ATOM    657  N   GLU   221       4.427  60.109  81.790  1.00  0.00              
ATOM    658  CA  GLU   221       4.016  59.978  80.410  1.00  0.00              
ATOM    659  C   GLU   221       5.203  60.187  79.453  1.00  0.00              
ATOM    660  O   GLU   221       5.914  61.188  79.538  1.00  0.00              
ATOM    661  N   LYS   222       5.438  59.219  78.570  1.00  0.00              
ATOM    662  CA  LYS   222       6.567  59.283  77.640  1.00  0.00              
ATOM    663  C   LYS   222       6.594  60.571  76.790  1.00  0.00              
ATOM    664  O   LYS   222       7.654  61.156  76.595  1.00  0.00              
ATOM    665  N   ILE   223       5.437  61.023  76.317  1.00  0.00              
ATOM    666  CA  ILE   223       5.379  62.196  75.461  1.00  0.00              
ATOM    667  C   ILE   223       5.715  63.486  76.222  1.00  0.00              
ATOM    668  O   ILE   223       6.462  64.346  75.724  1.00  0.00              
ATOM    669  N   ARG   224       5.176  63.619  77.434  1.00  0.00              
ATOM    670  CA  ARG   224       5.483  64.748  78.302  1.00  0.00              
ATOM    671  C   ARG   224       6.960  64.742  78.667  1.00  0.00              
ATOM    672  O   ARG   224       7.612  65.787  78.611  1.00  0.00              
ATOM    673  N   LEU   225       7.501  63.583  79.036  1.00  0.00              
ATOM    674  CA  LEU   225       8.926  63.509  79.373  1.00  0.00              
ATOM    675  C   LEU   225       9.803  63.896  78.149  1.00  0.00              
ATOM    676  O   LEU   225      10.587  64.838  78.207  1.00  0.00              
ATOM    677  N   LEU   226       9.633  63.211  77.033  1.00  0.00              
ATOM    678  CA  LEU   226      10.528  63.417  75.902  1.00  0.00              
ATOM    679  C   LEU   226      10.360  64.730  75.117  1.00  0.00              
ATOM    680  O   LEU   226      11.359  65.321  74.736  1.00  0.00              
ATOM    681  N   LYS   227       9.126  65.179  74.889  1.00  0.00              
ATOM    682  CA  LYS   227       8.897  66.494  74.286  1.00  0.00              
ATOM    683  C   LYS   227       9.356  67.598  75.229  1.00  0.00              
ATOM    684  O   LYS   227       9.777  68.665  74.777  1.00  0.00              
ATOM    685  N   GLU   228       9.281  67.333  76.536  1.00  0.00              
ATOM    686  CA  GLU   228       9.763  68.242  77.558  1.00  0.00              
ATOM    687  C   GLU   228      11.270  68.401  77.561  1.00  0.00              
ATOM    688  O   GLU   228      11.774  69.514  77.658  1.00  0.00              
ATOM    689  N   PHE   229      11.996  67.287  77.504  1.00  0.00              
ATOM    690  CA  PHE   229      13.450  67.287  77.352  1.00  0.00              
ATOM    691  C   PHE   229      13.861  68.050  76.086  1.00  0.00              
ATOM    692  O   PHE   229      14.780  68.856  76.123  1.00  0.00              
ATOM    693  N   MET   230      13.197  67.786  74.968  1.00  0.00              
ATOM    694  CA  MET   230      13.465  68.557  73.758  1.00  0.00              
ATOM    695  C   MET   230      13.254  70.065  73.927  1.00  0.00              
ATOM    696  O   MET   230      14.034  70.848  73.404  1.00  0.00              
ATOM    697  N   HIS   231      12.203  70.464  74.636  1.00  0.00              
ATOM    698  CA  HIS   231      11.922  71.881  74.827  1.00  0.00              
ATOM    699  C   HIS   231      12.962  72.494  75.762  1.00  0.00              
ATOM    700  O   HIS   231      13.489  73.555  75.486  1.00  0.00              
ATOM    701  N   THR   232      13.266  71.806  76.861  1.00  0.00              
ATOM    702  CA  THR   232      14.297  72.214  77.799  1.00  0.00              
ATOM    703  C   THR   232      15.642  72.508  77.127  1.00  0.00              
ATOM    704  O   THR   232      16.301  73.513  77.441  1.00  0.00              
ATOM    705  N  AMET   233      16.056  71.620  76.226  1.00  0.00              
ATOM    706  N  BMET   233      16.042  71.615  76.241  1.00  0.00              
ATOM    707  CA AMET   233      17.321  71.758  75.489  1.00  0.00              
ATOM    708  CA BMET   233      17.285  71.737  75.516  1.00  0.00              
ATOM    709  C  AMET   233      17.277  72.888  74.457  1.00  0.00              
ATOM    710  C  BMET   233      17.250  72.935  74.559  1.00  0.00              
ATOM    711  O  AMET   233      18.321  73.455  74.086  1.00  0.00              
ATOM    712  O  BMET   233      18.282  73.579  74.324  1.00  0.00              
ATOM    713  N   LYS   234      16.069  73.206  73.999  1.00  0.00              
ATOM    714  CA  LYS   234      15.844  74.337  73.092  1.00  0.00              
ATOM    715  C   LYS   234      16.007  75.716  73.798  1.00  0.00              
ATOM    716  O   LYS   234      16.469  76.680  73.187  1.00  0.00              
ATOM    717  N   ASN   235      15.672  75.789  75.084  1.00  0.00              
ATOM    718  CA  ASN   235      15.706  77.039  75.831  1.00  0.00              
ATOM    719  C   ASN   235      17.089  77.644  75.803  1.00  0.00              
ATOM    720  O   ASN   235      17.238  78.867  75.805  1.00  0.00              
ATOM    721  N   THR   236      18.121  76.809  75.757  1.00  0.00              
ATOM    722  CA  THR   236      19.462  77.399  75.780  1.00  0.00              
ATOM    723  C   THR   236      20.279  77.073  74.550  1.00  0.00              
ATOM    724  O   THR   236      21.494  77.113  74.611  1.00  0.00              
ATOM    725  N   GLY   237      19.616  76.817  73.424  1.00  0.00              
ATOM    726  CA  GLY   237      20.311  76.462  72.176  1.00  0.00              
ATOM    727  C   GLY   237      19.396  76.469  70.965  1.00  0.00              
ATOM    728  O   GLY   237      19.656  75.793  69.953  1.00  0.00              
END
