
#######################################################
#                                                     #
#                        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   24 (  177),  selected   19 , name T0296TS351_2
# Molecule2: number of CA atoms  414 ( 2974),  selected   19 , name T0296.pdb
# PARAMETERS: T0296TS351_2.T0296.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       423 - 439         4.88     5.60
  LCS_AVERAGE:      4.07

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9       425 - 433         1.63    13.50
  LONGEST_CONTINUOUS_SEGMENT:     9       426 - 434         1.93    12.42
  LONGEST_CONTINUOUS_SEGMENT:     9       432 - 440         1.56    11.07
  LCS_AVERAGE:      2.05

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8       426 - 433         0.93    13.73
  LCS_AVERAGE:      1.61

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:  414
LCS_GDT     N     422     N     422      3    5   15     0    3    3    4    5    5    6    6    7   11   12   14   15   16   18   18   19   19   19   19 
LCS_GDT     G     423     G     423      3    5   17     3    3    5    5    5    5    6    8    8   11   12   15   16   17   18   18   19   19   19   19 
LCS_GDT     A     424     A     424      4    7   17     3    4    5    5    5    7    8    8   10   11   13   15   16   17   18   18   19   19   19   19 
LCS_GDT     S     425     S     425      4    9   17     3    4    5    6    8    8    9   10   11   12   13   15   16   17   18   18   19   19   19   19 
LCS_GDT     S     426     S     426      8    9   17     6    7    7    8    8    8    9   10   11   12   13   15   16   17   18   18   19   19   19   19 
LCS_GDT     V     427     V     427      8    9   17     6    7    7    8    8    8    9   10   11   12   13   14   14   16   17   18   19   19   19   19 
LCS_GDT     D     428     D     428      8    9   17     6    7    7    8    8    8    9   11   11   12   13   15   16   17   18   18   19   19   19   19 
LCS_GDT     F     429     F     429      8    9   17     6    7    7    8    8    8   10   11   11   12   13   15   16   17   18   18   19   19   19   19 
LCS_GDT     I     430     I     430      8    9   17     6    7    7    8    8    8    9   10   11   12   13   15   16   17   18   18   19   19   19   19 
LCS_GDT     S     431     S     431      8    9   17     6    7    7    8    8    8    9   11   11   12   13   15   16   17   18   18   19   19   19   19 
LCS_GDT     R     432     R     432      8    9   17     3    7    7    8    9    9   10   11   11   12   13   15   16   17   18   18   19   19   19   19 
LCS_GDT     G     433     G     433      8    9   17     3    4    7    8    9    9   10   11   11   12   13   15   16   17   18   18   19   19   19   19 
LCS_GDT     G     434     G     434      7    9   17     3    6    7    7    9    9   10   11   11   12   13   15   16   17   18   18   19   19   19   19 
LCS_GDT     Q     435     Q     435      7    9   17     3    6    7    8    9    9   10   11   11   12   13   15   16   17   18   18   19   19   19   19 
LCS_GDT     I     436     I     436      7    9   17     3    6    7    8    9    9   10   11   11   12   13   15   16   17   18   18   19   19   19   19 
LCS_GDT     P     437     P     437      7    9   17     3    6    7    8    9    9   10   11   11   12   13   14   16   17   18   18   19   19   19   19 
LCS_GDT     A     438     A     438      7    9   17     3    5    7    8    9    9   10   11   11   12   13   15   16   17   18   18   19   19   19   19 
LCS_GDT     P     439     P     439      7    9   17     3    6    7    8    9    9   10   11   11   12   13   15   16   17   18   18   19   19   19   19 
LCS_GDT     I     440     I     440      7    9   16     3    6    7    8    9    9   10   10   10   12   13   14   15   17   18   18   19   19   19   19 
LCS_AVERAGE  LCS_A:   2.58  (   1.61    2.05    4.07 )

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      7      7      8      9      9     10     11     11     12     13     15     16     17     18     18     19     19     19     19 
GDT PERCENT_CA   1.45   1.69   1.69   1.93   2.17   2.17   2.42   2.66   2.66   2.90   3.14   3.62   3.86   4.11   4.35   4.35   4.59   4.59   4.59   4.59
GDT RMS_LOCAL    0.32   0.44   0.44   0.93   1.56   1.56   2.24   2.98   2.98   3.05   3.39   4.53   4.67   4.90   5.09   5.09   5.34   5.34   5.34   5.34
GDT RMS_ALL_CA  13.56  13.68  13.68  13.73  11.07  11.07   7.67   7.78   7.78   8.21   7.88   5.59   5.51   5.38   5.37   5.37   5.34   5.34   5.34   5.34

#      Molecule1      Molecule2       DISTANCE
LGA    N     422      N     422         15.270
LGA    G     423      G     423         15.180
LGA    A     424      A     424         13.342
LGA    S     425      S     425         10.476
LGA    S     426      S     426          9.639
LGA    V     427      V     427          8.431
LGA    D     428      D     428          3.772
LGA    F     429      F     429          3.638
LGA    I     430      I     430          5.350
LGA    S     431      S     431          3.969
LGA    R     432      R     432          2.318
LGA    G     433      G     433          2.205
LGA    G     434      G     434          3.119
LGA    Q     435      Q     435          2.772
LGA    I     436      I     436          2.150
LGA    P     437      P     437          3.914
LGA    A     438      A     438          3.113
LGA    P     439      P     439          2.453
LGA    I     440      I     440          4.790

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   24  414    4.0     11    2.98     2.657     2.486     0.357

LGA_LOCAL      RMSD =  2.982  Number of atoms =   11  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  7.516  Number of atoms =   19 
Std_ALL_ATOMS  RMSD =  5.340  (standard rmsd on all 19 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.582878 * X  +  -0.201147 * Y  +   0.787269 * Z  +  47.713776
  Y_new =  -0.796798 * X  +  -0.331397 * Y  +   0.505262 * Z  +  -6.760428
  Z_new =   0.159266 * X  +  -0.921800 * Y  +  -0.353438 * Z  +  80.084785 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.936929    1.204663  [ DEG:  -110.9779     69.0221 ]
  Theta =  -0.159947   -2.981645  [ DEG:    -9.1643   -170.8357 ]
  Phi   =  -0.939224    2.202369  [ DEG:   -53.8136    126.1864 ]
 
# 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: T0296TS351_2                                  
REMARK     2: T0296.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0296TS351_2.T0296.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   24  414   4.0   11   2.98   2.486     5.34
REMARK  ---------------------------------------------------------- 
MOLECULE T0296TS351_2
PFRMAT TS
TARGET T0296
MODEL  2  REFINED
PARENT N/A
ATOM      1  N   ASN   422      29.388   9.167  61.535  1.00  0.00
ATOM      2  CA  ASN   422      30.584  10.021  61.777  1.00  0.00
ATOM      3  C   ASN   422      31.855   9.250  62.249  1.00  0.00
ATOM      4  O   ASN   422      32.645   9.735  63.080  1.00  0.00
ATOM      5  CB  ASN   422      30.146  11.020  62.869  1.00  0.00
ATOM      6  CG  ASN   422      29.830  10.464  64.259  1.00  0.00
ATOM      7  OD1 ASN   422      29.838   9.234  64.506  1.00  0.00
ATOM      8  ND2 ASN   422      29.486  11.351  65.190  1.00  0.00
ATOM      9  N   GLY   423      32.199   8.213  61.516  1.00  0.00
ATOM     10  CA  GLY   423      33.345   7.379  61.733  1.00  0.00
ATOM     11  C   GLY   423      34.589   8.103  61.177  1.00  0.00
ATOM     12  O   GLY   423      34.508   8.779  60.141  1.00  0.00
ATOM     13  N   ALA   424      35.711   7.581  61.600  1.00  0.00
ATOM     14  CA  ALA   424      36.995   8.104  61.226  1.00  0.00
ATOM     15  C   ALA   424      37.379   7.590  59.826  1.00  0.00
ATOM     16  O   ALA   424      37.323   6.387  59.495  1.00  0.00
ATOM     17  CB  ALA   424      38.008   7.697  62.299  1.00  0.00
ATOM     18  N   SER   425      37.647   8.595  58.976  1.00  0.00
ATOM     19  CA  SER   425      38.008   8.331  57.626  1.00  0.00
ATOM     20  C   SER   425      39.171   9.264  57.227  1.00  0.00
ATOM     21  O   SER   425      39.192  10.445  57.586  1.00  0.00
ATOM     22  CB  SER   425      36.763   8.510  56.767  1.00  0.00
ATOM     23  OG  SER   425      36.951   8.419  55.369  1.00  0.00
ATOM     24  N   SER   426      40.180   8.650  56.621  1.00  0.00
ATOM     25  CA  SER   426      41.346   9.389  56.105  1.00  0.00
ATOM     26  C   SER   426      40.889  10.577  55.213  1.00  0.00
ATOM     27  O   SER   426      41.639  11.537  55.166  1.00  0.00
ATOM     28  CB  SER   426      42.273   8.397  55.346  1.00  0.00
ATOM     29  OG  SER   426      43.314   7.818  56.177  1.00  0.00
ATOM     30  N   VAL   427      39.866  10.423  54.343  1.00  0.00
ATOM     31  CA  VAL   427      39.398  11.495  53.466  1.00  0.00
ATOM     32  C   VAL   427      39.002  12.745  54.297  1.00  0.00
ATOM     33  O   VAL   427      39.383  13.856  53.907  1.00  0.00
ATOM     34  CB  VAL   427      38.361  11.043  52.477  1.00  0.00
ATOM     35  CG1 VAL   427      37.157  10.374  53.209  1.00  0.00
ATOM     36  CG2 VAL   427      37.765  11.929  51.407  1.00  0.00
ATOM     37  N   ASP   428      38.014  12.566  55.215  1.00  0.00
ATOM     38  CA  ASP   428      37.563  13.579  56.128  1.00  0.00
ATOM     39  C   ASP   428      38.772  14.154  56.907  1.00  0.00
ATOM     40  O   ASP   428      38.912  15.367  56.959  1.00  0.00
ATOM     41  CB  ASP   428      36.485  12.956  57.025  1.00  0.00
ATOM     42  CG  ASP   428      35.495  13.909  57.654  1.00  0.00
ATOM     43  OD1 ASP   428      35.824  14.894  58.298  1.00  0.00
ATOM     44  OD2 ASP   428      34.268  13.624  57.628  1.00  0.00
ATOM     45  N   PHE   429      39.512  13.338  57.621  1.00  0.00
ATOM     46  CA  PHE   429      40.737  13.671  58.346  1.00  0.00
ATOM     47  C   PHE   429      41.716  14.657  57.591  1.00  0.00
ATOM     48  O   PHE   429      42.079  15.635  58.176  1.00  0.00
ATOM     49  CB  PHE   429      41.536  12.426  58.642  1.00  0.00
ATOM     50  CG  PHE   429      42.677  12.437  59.564  1.00  0.00
ATOM     51  CD1 PHE   429      42.490  12.830  60.885  1.00  0.00
ATOM     52  CD2 PHE   429      43.952  12.061  59.145  1.00  0.00
ATOM     53  CE1 PHE   429      43.566  12.885  61.769  1.00  0.00
ATOM     54  CE2 PHE   429      45.040  12.110  60.009  1.00  0.00
ATOM     55  CZ  PHE   429      44.836  12.525  61.321  1.00  0.00
ATOM     56  N   ILE   430      42.150  14.299  56.344  1.00  0.00
ATOM     57  CA  ILE   430      42.992  15.193  55.493  1.00  0.00
ATOM     58  C   ILE   430      42.336  16.591  55.367  1.00  0.00
ATOM     59  O   ILE   430      43.112  17.532  55.172  1.00  0.00
ATOM     60  CB  ILE   430      43.203  14.549  54.077  1.00  0.00
ATOM     61  CG1 ILE   430      43.963  13.190  54.297  1.00  0.00
ATOM     62  CG2 ILE   430      44.034  15.496  53.166  1.00  0.00
ATOM     63  CD1 ILE   430      44.076  12.366  52.990  1.00  0.00
ATOM     64  N   SER   431      41.099  16.639  54.858  1.00  0.00
ATOM     65  CA  SER   431      40.359  17.850  54.763  1.00  0.00
ATOM     66  C   SER   431      40.386  18.608  56.116  1.00  0.00
ATOM     67  O   SER   431      40.616  19.813  56.078  1.00  0.00
ATOM     68  CB  SER   431      38.922  17.559  54.265  1.00  0.00
ATOM     69  OG  SER   431      38.218  18.695  53.770  1.00  0.00
ATOM     70  N   ARG   432      40.002  18.017  57.260  1.00  0.00
ATOM     71  CA  ARG   432      40.064  18.660  58.548  1.00  0.00
ATOM     72  C   ARG   432      41.460  19.298  58.805  1.00  0.00
ATOM     73  O   ARG   432      41.494  20.519  59.055  1.00  0.00
ATOM     74  CB  ARG   432      39.704  17.745  59.704  1.00  0.00
ATOM     75  CG  ARG   432      38.478  16.914  59.748  1.00  0.00
ATOM     76  CD  ARG   432      37.361  17.142  60.650  1.00  0.00
ATOM     77  NE  ARG   432      36.755  15.891  61.183  1.00  0.00
ATOM     78  CZ  ARG   432      35.467  15.696  61.353  1.00  0.00
ATOM     79  NH1 ARG   432      34.607  16.705  61.007  1.00  0.00
ATOM     80  NH2 ARG   432      34.915  14.590  61.853  1.00  0.00
ATOM     81  N   GLY   433      42.557  18.536  58.809  1.00  0.00
ATOM     82  CA  GLY   433      43.881  19.030  59.099  1.00  0.00
ATOM     83  C   GLY   433      44.555  19.757  57.943  1.00  0.00
ATOM     84  O   GLY   433      45.535  20.450  58.216  1.00  0.00
ATOM     85  N   GLY   434      44.148  19.570  56.728  1.00  0.00
ATOM     86  CA  GLY   434      44.808  20.189  55.563  1.00  0.00
ATOM     87  C   GLY   434      46.188  19.517  55.270  1.00  0.00
ATOM     88  O   GLY   434      47.124  20.222  54.861  1.00  0.00
ATOM     89  N   GLN   435      46.262  18.211  55.531  1.00  0.00
ATOM     90  CA  GLN   435      47.432  17.407  55.390  1.00  0.00
ATOM     91  C   GLN   435      47.301  16.490  54.172  1.00  0.00
ATOM     92  O   GLN   435      46.421  16.712  53.338  1.00  0.00
ATOM     93  CB  GLN   435      47.544  16.609  56.702  1.00  0.00
ATOM     94  CG  GLN   435      48.135  17.452  57.812  1.00  0.00
ATOM     95  CD  GLN   435      49.516  17.955  57.562  1.00  0.00
ATOM     96  OE1 GLN   435      50.456  17.140  57.529  1.00  0.00
ATOM     97  NE2 GLN   435      49.686  19.271  57.340  1.00  0.00
ATOM     98  N   ILE   436      48.399  15.911  53.821  1.00  0.00
ATOM     99  CA  ILE   436      48.360  15.028  52.715  1.00  0.00
ATOM    100  C   ILE   436      48.956  13.656  53.033  1.00  0.00
ATOM    101  O   ILE   436      50.028  13.710  53.723  1.00  0.00
ATOM    102  CB  ILE   436      49.095  15.696  51.507  1.00  0.00
ATOM    103  CG1 ILE   436      50.550  15.983  51.792  1.00  0.00
ATOM    104  CG2 ILE   436      48.364  16.952  50.989  1.00  0.00
ATOM    105  CD1 ILE   436      51.370  16.346  50.507  1.00  0.00
ATOM    106  N   PRO   437      48.407  12.478  52.646  1.00  0.00
ATOM    107  CA  PRO   437      49.069  11.266  52.883  1.00  0.00
ATOM    108  C   PRO   437      50.407  11.124  52.097  1.00  0.00
ATOM    109  O   PRO   437      50.741  11.957  51.230  1.00  0.00
ATOM    110  CB  PRO   437      48.145  10.084  52.399  1.00  0.00
ATOM    111  CG  PRO   437      47.337  10.828  51.334  1.00  0.00
ATOM    112  CD  PRO   437      47.070  12.181  51.990  1.00  0.00
ATOM    113  N   ALA   438      51.223  10.114  52.477  1.00  0.00
ATOM    114  CA  ALA   438      52.529   9.756  51.877  1.00  0.00
ATOM    115  C   ALA   438      52.223   8.797  50.777  1.00  0.00
ATOM    116  O   ALA   438      51.759   7.676  51.079  1.00  0.00
ATOM    117  CB  ALA   438      53.506   9.175  52.898  1.00  0.00
ATOM    118  N   PRO   439      52.239   9.179  49.417  1.00  0.00
ATOM    119  CA  PRO   439      51.759   8.301  48.476  1.00  0.00
ATOM    120  C   PRO   439      52.328   6.861  48.666  1.00  0.00
ATOM    121  O   PRO   439      53.446   6.779  49.164  1.00  0.00
ATOM    122  CB  PRO   439      52.059   8.747  47.045  1.00  0.00
ATOM    123  CG  PRO   439      53.242   9.731  47.341  1.00  0.00
ATOM    124  CD  PRO   439      52.966  10.335  48.700  1.00  0.00
ATOM    125  N   ILE   440      51.561   5.972  48.082  1.00  0.00
ATOM    126  CA  ILE   440      51.763   4.573  48.051  1.00  0.00
ATOM    127  C   ILE   440      53.084   4.219  47.262  1.00  0.00
ATOM    128  O   ILE   440      53.694   3.189  47.611  1.00  0.00
ATOM    129  CB  ILE   440      50.489   3.944  47.461  1.00  0.00
ATOM    130  CG1 ILE   440      49.282   4.176  48.402  1.00  0.00
ATOM    131  CG2 ILE   440      50.662   2.449  47.228  1.00  0.00
ATOM    132  CD1 ILE   440      47.945   4.081  47.585  1.00  0.00
ATOM    133  N   HIS   441      53.555   5.020  46.284  1.00  0.00
ATOM    134  CA  HIS   441      54.811   4.844  45.550  1.00  0.00
ATOM    135  C   HIS   441      56.104   4.996  46.444  1.00  0.00
ATOM    136  O   HIS   441      57.068   4.312  46.115  1.00  0.00
ATOM    137  CB  HIS   441      54.827   5.949  44.479  1.00  0.00
ATOM    138  CG  HIS   441      53.684   5.996  43.505  1.00  0.00
ATOM    139  ND1 HIS   441      53.250   7.113  42.820  1.00  0.00
ATOM    140  CD2 HIS   441      52.742   5.118  43.270  1.00  0.00
ATOM    141  CE1 HIS   441      52.071   6.747  42.189  1.00  0.00
ATOM    142  NE2 HIS   441      51.780   5.490  42.450  1.00  0.00
ATOM    143  N   SER   442      56.061   5.673  47.600  1.00  0.00
ATOM    144  CA  SER   442      57.183   5.807  48.504  1.00  0.00
ATOM    145  C   SER   442      57.568   4.485  49.257  1.00  0.00
ATOM    146  O   SER   442      58.748   4.343  49.600  1.00  0.00
ATOM    147  CB  SER   442      56.828   6.921  49.463  1.00  0.00
ATOM    148  OG  SER   442      55.767   6.684  50.364  1.00  0.00
ATOM    149  N   PHE   443      56.636   3.608  49.632  1.00  0.00
ATOM    150  CA  PHE   443      56.891   2.395  50.411  1.00  0.00
ATOM    151  C   PHE   443      57.121   1.182  49.501  1.00  0.00
ATOM    152  O   PHE   443      56.582   1.084  48.382  1.00  0.00
ATOM    153  CB  PHE   443      55.700   2.186  51.329  1.00  0.00
ATOM    154  CG  PHE   443      55.531   3.169  52.406  1.00  0.00
ATOM    155  CD1 PHE   443      54.856   4.376  52.141  1.00  0.00
ATOM    156  CD2 PHE   443      56.068   2.981  53.680  1.00  0.00
ATOM    157  CE1 PHE   443      54.685   5.334  53.133  1.00  0.00
ATOM    158  CE2 PHE   443      55.876   3.943  54.694  1.00  0.00
ATOM    159  CZ  PHE   443      55.212   5.130  54.419  1.00  0.00
ATOM    160  N   LYS   444      57.775   0.208  50.072  1.00  0.00
ATOM    161  CA  LYS   444      58.027  -1.027  49.390  1.00  0.00
ATOM    162  C   LYS   444      56.713  -1.789  49.080  1.00  0.00
ATOM    163  O   LYS   444      55.731  -1.671  49.829  1.00  0.00
ATOM    164  CB  LYS   444      58.917  -1.891  50.268  1.00  0.00
ATOM    165  CG  LYS   444      60.280  -1.491  50.757  1.00  0.00
ATOM    166  CD  LYS   444      60.911  -2.503  51.724  1.00  0.00
ATOM    167  CE  LYS   444      62.209  -2.051  52.383  1.00  0.00
ATOM    168  NZ  LYS   444      63.227  -1.965  51.285  1.00  0.00
ATOM    169  N   ASN   445      56.648  -2.457  47.934  1.00  0.00
ATOM    170  CA  ASN   445      55.473  -3.253  47.558  1.00  0.00
ATOM    171  C   ASN   445      54.911  -4.007  48.798  1.00  0.00
ATOM    172  O   ASN   445      53.723  -3.898  49.130  1.00  0.00
ATOM    173  CB  ASN   445      55.869  -4.226  46.454  1.00  0.00
ATOM    174  CG  ASN   445      56.085  -3.525  45.137  1.00  0.00
ATOM    175  OD1 ASN   445      55.107  -2.993  44.581  1.00  0.00
ATOM    176  ND2 ASN   445      57.318  -3.512  44.632  1.00  0.00
ATOM    177  OXT ASN   445      55.690  -4.783  49.404  1.00  0.00
TER
END
