
#######################################################
#                                                     #
#                        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 (  163),  selected   19 , name T0329TS677_1_3-D2
# Molecule2: number of CA atoms   92 (  716),  selected   19 , name T0329_D2.pdb
# PARAMETERS: T0329TS677_1_3-D2.T0329_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        90 - 108         1.65     1.65
  LCS_AVERAGE:     20.65

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    19        90 - 108         1.65     1.65
  LCS_AVERAGE:     20.65

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15        90 - 104         0.97     1.92
  LCS_AVERAGE:     13.79

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:   92
LCS_GDT     N      90     N      90     15   19   19     5   14   15   16   16   19   19   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     R      91     R      91     15   19   19     5   14   15   16   16   19   19   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     V      92     V      92     15   19   19     9   14   15   16   16   19   19   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     L      93     L      93     15   19   19     9   14   15   16   16   19   19   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     E      94     E      94     15   19   19     9   14   15   16   16   19   19   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     V      95     V      95     15   19   19     9   14   15   16   16   19   19   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     F      96     F      96     15   19   19     9   14   15   16   16   19   19   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     K      97     K      97     15   19   19     5   14   15   16   16   19   19   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     P      98     P      98     15   19   19     5   10   15   16   16   19   19   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     Y      99     Y      99     15   19   19     5   14   15   16   16   19   19   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     Y     100     Y     100     15   19   19     9   14   15   16   16   19   19   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     A     101     A     101     15   19   19     9   14   15   16   16   19   19   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     D     102     D     102     15   19   19     9   14   15   16   16   19   19   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     H     103     H     103     15   19   19     9   14   15   16   16   19   19   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     C     104     C     104     15   19   19     4    4    5   16   16   19   19   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     Q     105     Q     105      5   19   19     4    4    5    8   12   19   19   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     I     106     I     106      5   19   19     4    4    5    8   14   19   19   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     K     107     K     107      3   19   19     3    3    5    8   16   19   19   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     T     108     T     108      3   19   19     5   14   15   16   16   19   19   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_AVERAGE  LCS_A:  18.36  (  13.79   20.65   20.65 )

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      9     14     15     16     16     19     19     19     19     19     19     19     19     19     19     19     19     19     19     19 
GDT PERCENT_CA   9.78  15.22  16.30  17.39  17.39  20.65  20.65  20.65  20.65  20.65  20.65  20.65  20.65  20.65  20.65  20.65  20.65  20.65  20.65  20.65
GDT RMS_LOCAL    0.41   0.69   0.75   0.96   0.96   1.65   1.65   1.65   1.65   1.65   1.65   1.65   1.65   1.65   1.65   1.65   1.65   1.65   1.65   1.65
GDT RMS_ALL_CA   1.93   1.77   1.78   1.84   1.84   1.65   1.65   1.65   1.65   1.65   1.65   1.65   1.65   1.65   1.65   1.65   1.65   1.65   1.65   1.65

#      Molecule1      Molecule2       DISTANCE
LGA    N      90      N      90          0.382
LGA    R      91      R      91          1.359
LGA    V      92      V      92          0.608
LGA    L      93      L      93          0.905
LGA    E      94      E      94          1.351
LGA    V      95      V      95          0.667
LGA    F      96      F      96          0.664
LGA    K      97      K      97          1.096
LGA    P      98      P      98          1.442
LGA    Y      99      Y      99          1.252
LGA    Y     100      Y     100          0.625
LGA    A     101      A     101          0.568
LGA    D     102      D     102          0.625
LGA    H     103      H     103          1.088
LGA    C     104      C     104          2.915
LGA    Q     105      Q     105          3.463
LGA    I     106      I     106          3.188
LGA    K     107      K     107          2.637
LGA    T     108      T     108          0.989

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   19   92    4.0     19    1.65    18.478    19.456     1.087

LGA_LOCAL      RMSD =  1.648  Number of atoms =   19  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  1.648  Number of atoms =   19 
Std_ALL_ATOMS  RMSD =  1.648  (standard rmsd on all 19 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.475462 * X  +  -0.873248 * Y  +   0.106649 * Z  +  41.397724
  Y_new =  -0.323827 * X  +   0.286442 * Y  +   0.901713 * Z  +  -9.637598
  Z_new =  -0.817968 * X  +   0.394194 * Y  +  -0.418973 * Z  +  47.111042 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.386657   -0.754935  [ DEG:   136.7454    -43.2546 ]
  Theta =   0.957870    2.183722  [ DEG:    54.8819    125.1181 ]
  Phi   =  -2.543678    0.597914  [ DEG:  -145.7420     34.2580 ]
 
# 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: T0329TS677_1_3-D2                             
REMARK     2: T0329_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0329TS677_1_3-D2.T0329_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   19   92   4.0   19   1.65  19.456     1.65
REMARK  ---------------------------------------------------------- 
MOLECULE T0329TS677_1_3-D2
REMARK PARENT number 3
PFRMAT     TS
TARGET     T0329
PARENT     2ah5A
ATOM    452  N   ASN    90     -13.608  26.991  32.006  1.00  0.35
ATOM    453  CA  ASN    90     -12.387  27.645  32.369  1.00  0.35
ATOM    454  C   ASN    90     -12.460  28.012  33.815  1.00  0.35
ATOM    455  O   ASN    90     -11.501  27.828  34.564  1.00  0.35
ATOM    456  CB  ASN    90     -12.154  28.940  31.573  1.00  0.35
ATOM    457  CG  ASN    90     -10.749  29.437  31.875  1.00  0.35
ATOM    458  OD1 ASN    90     -10.082  28.942  32.782  1.00  0.35
ATOM    459  ND2 ASN    90     -10.287  30.453  31.098  1.00  0.35
ATOM    460  N   ARG    91     -13.623  28.530  34.248  1.00  0.53
ATOM    461  CA  ARG    91     -13.782  28.971  35.602  1.00  0.53
ATOM    462  C   ARG    91     -13.651  27.806  36.531  1.00  0.53
ATOM    463  O   ARG    91     -12.996  27.907  37.568  1.00  0.53
ATOM    464  CB  ARG    91     -15.159  29.604  35.862  1.00  0.53
ATOM    465  CG  ARG    91     -15.417  30.863  35.034  1.00  0.53
ATOM    466  CD  ARG    91     -14.616  32.082  35.494  1.00  0.53
ATOM    467  NE  ARG    91     -14.972  33.213  34.590  1.00  0.53
ATOM    468  CZ  ARG    91     -14.144  34.292  34.485  1.00  0.53
ATOM    469  NH1 ARG    91     -12.981  34.333  35.198  1.00  0.53
ATOM    470  NH2 ARG    91     -14.478  35.330  33.663  1.00  0.53
ATOM    471  N   VAL    92     -14.256  26.655  36.179  1.00  0.69
ATOM    472  CA  VAL    92     -14.243  25.538  37.080  1.00  0.69
ATOM    473  C   VAL    92     -12.835  25.074  37.289  1.00  0.69
ATOM    474  O   VAL    92     -12.454  24.723  38.404  1.00  0.69
ATOM    475  CB  VAL    92     -15.047  24.358  36.613  1.00  0.69
ATOM    476  CG1 VAL    92     -16.503  24.808  36.405  1.00  0.69
ATOM    477  CG2 VAL    92     -14.373  23.744  35.381  1.00  0.69
ATOM    478  N   LEU    93     -12.017  25.057  36.222  1.00  0.68
ATOM    479  CA  LEU    93     -10.659  24.607  36.345  1.00  0.68
ATOM    480  C   LEU    93      -9.960  25.540  37.280  1.00  0.68
ATOM    481  O   LEU    93      -9.143  25.129  38.103  1.00  0.68
ATOM    482  CB  LEU    93      -9.896  24.654  35.011  1.00  0.68
ATOM    483  CG  LEU    93     -10.493  23.741  33.928  1.00  0.68
ATOM    484  CD1 LEU    93      -9.686  23.825  32.623  1.00  0.68
ATOM    485  CD2 LEU    93     -10.657  22.302  34.440  1.00  0.68
ATOM    486  N   GLU    94     -10.299  26.835  37.160  1.00  0.54
ATOM    487  CA  GLU    94      -9.738  27.940  37.881  1.00  0.54
ATOM    488  C   GLU    94     -10.065  27.845  39.335  1.00  0.54
ATOM    489  O   GLU    94      -9.365  28.419  40.159  1.00  0.54
ATOM    490  CB  GLU    94     -10.264  29.292  37.372  1.00  0.54
ATOM    491  CG  GLU    94      -9.813  29.604  35.944  1.00  0.54
ATOM    492  CD  GLU    94     -10.396  30.951  35.546  1.00  0.54
ATOM    493  OE1 GLU    94     -11.650  31.083  35.565  1.00  0.54
ATOM    494  OE2 GLU    94      -9.597  31.867  35.217  1.00  0.54
ATOM    495  N   VAL    95     -11.149  27.156  39.718  1.00  0.50
ATOM    496  CA  VAL    95     -11.469  27.125  41.117  1.00  0.50
ATOM    497  C   VAL    95     -10.931  25.849  41.684  1.00  0.50
ATOM    498  O   VAL    95     -10.431  25.810  42.808  1.00  0.50
ATOM    499  CB  VAL    95     -12.948  27.153  41.379  1.00  0.50
ATOM    500  CG1 VAL    95     -13.587  25.892  40.774  1.00  0.50
ATOM    501  CG2 VAL    95     -13.170  27.294  42.894  1.00  0.50
ATOM    502  N   PHE    96     -10.997  24.771  40.889  1.00  0.59
ATOM    503  CA  PHE    96     -10.565  23.469  41.298  1.00  0.59
ATOM    504  C   PHE    96      -9.129  23.534  41.720  1.00  0.59
ATOM    505  O   PHE    96      -8.758  22.989  42.760  1.00  0.59
ATOM    506  CB  PHE    96     -10.666  22.484  40.116  1.00  0.59
ATOM    507  CG  PHE    96     -10.092  21.159  40.484  1.00  0.59
ATOM    508  CD1 PHE    96      -8.737  20.933  40.416  1.00  0.59
ATOM    509  CD2 PHE    96     -10.911  20.130  40.875  1.00  0.59
ATOM    510  CE1 PHE    96      -8.200  19.715  40.750  1.00  0.59
ATOM    511  CE2 PHE    96     -10.381  18.907  41.208  1.00  0.59
ATOM    512  CZ  PHE    96      -9.026  18.696  41.149  1.00  0.59
ATOM    513  N   LYS    97      -8.279  24.207  40.925  1.00  0.71
ATOM    514  CA  LYS    97      -6.873  24.218  41.218  1.00  0.71
ATOM    515  C   LYS    97      -6.622  24.936  42.515  1.00  0.71
ATOM    516  O   LYS    97      -5.765  24.522  43.292  1.00  0.71
ATOM    517  CB  LYS    97      -6.018  24.884  40.116  1.00  0.71
ATOM    518  CG  LYS    97      -6.155  24.232  38.737  1.00  0.71
ATOM    519  CD  LYS    97      -5.754  22.757  38.694  1.00  0.71
ATOM    520  CE  LYS    97      -5.916  22.129  37.307  1.00  0.71
ATOM    521  NZ  LYS    97      -7.329  22.220  36.874  1.00  0.71
ATOM    522  N   PRO    98      -7.327  26.006  42.772  1.00  0.64
ATOM    523  CA  PRO    98      -7.098  26.733  43.991  1.00  0.64
ATOM    524  C   PRO    98      -7.514  26.018  45.224  1.00  0.64
ATOM    525  O   PRO    98      -7.160  26.465  46.313  1.00  0.64
ATOM    526  CB  PRO    98      -7.725  28.107  43.804  1.00  0.64
ATOM    527  CG  PRO    98      -7.542  28.339  42.302  1.00  0.64
ATOM    528  CD  PRO    98      -7.582  26.926  41.690  1.00  0.64
ATOM    529  N   TYR    99      -8.258  24.913  45.096  1.00  0.42
ATOM    530  CA  TYR    99      -8.616  24.217  46.289  1.00  0.42
ATOM    531  C   TYR    99      -7.603  23.120  46.395  1.00  0.42
ATOM    532  O   TYR    99      -7.086  22.825  47.472  1.00  0.42
ATOM    533  CB  TYR    99     -10.027  23.610  46.189  1.00  0.42
ATOM    534  CG  TYR    99     -10.427  23.090  47.526  1.00  0.42
ATOM    535  CD1 TYR    99     -10.789  23.950  48.537  1.00  0.42
ATOM    536  CD2 TYR    99     -10.467  21.739  47.764  1.00  0.42
ATOM    537  CE1 TYR    99     -11.166  23.464  49.768  1.00  0.42
ATOM    538  CE2 TYR    99     -10.841  21.245  48.989  1.00  0.42
ATOM    539  CZ  TYR    99     -11.190  22.110  49.996  1.00  0.42
ATOM    540  OH  TYR    99     -11.577  21.608  51.257  1.00  0.42
ATOM    541  N   TYR   100      -7.258  22.535  45.236  1.00  0.34
ATOM    542  CA  TYR   100      -6.349  21.428  45.116  1.00  0.34
ATOM    543  C   TYR   100      -4.988  21.815  45.627  1.00  0.34
ATOM    544  O   TYR   100      -4.379  21.090  46.413  1.00  0.34
ATOM    545  CB  TYR   100      -6.177  21.061  43.629  1.00  0.34
ATOM    546  CG  TYR   100      -5.488  19.752  43.451  1.00  0.34
ATOM    547  CD1 TYR   100      -4.126  19.623  43.614  1.00  0.34
ATOM    548  CD2 TYR   100      -6.226  18.639  43.121  1.00  0.34
ATOM    549  CE1 TYR   100      -3.512  18.404  43.438  1.00  0.34
ATOM    550  CE2 TYR   100      -5.618  17.418  42.943  1.00  0.34
ATOM    551  CZ  TYR   100      -4.258  17.300  43.099  1.00  0.34
ATOM    552  OH  TYR   100      -3.629  16.050  42.917  1.00  0.34
ATOM    553  N   ALA   101      -4.483  22.988  45.201  1.00  0.25
ATOM    554  CA  ALA   101      -3.139  23.399  45.506  1.00  0.25
ATOM    555  C   ALA   101      -2.935  23.602  46.974  1.00  0.25
ATOM    556  O   ALA   101      -1.922  23.172  47.522  1.00  0.25
ATOM    557  CB  ALA   101      -2.754  24.718  44.814  1.00  0.25
ATOM    558  N   ASP   102      -3.884  24.260  47.666  1.00  0.16
ATOM    559  CA  ASP   102      -3.589  24.549  49.040  1.00  0.16
ATOM    560  C   ASP   102      -4.362  23.677  49.972  1.00  0.16
ATOM    561  O   ASP   102      -4.309  23.886  51.183  1.00  0.16
ATOM    562  CB  ASP   102      -3.888  26.005  49.430  1.00  0.16
ATOM    563  CG  ASP   102      -2.813  26.874  48.797  1.00  0.16
ATOM    564  OD1 ASP   102      -1.865  26.300  48.198  1.00  0.16
ATOM    565  OD2 ASP   102      -2.921  28.125  48.910  1.00  0.16
ATOM    566  N   HIS   103      -5.088  22.662  49.470  1.00  0.17
ATOM    567  CA  HIS   103      -5.830  21.897  50.432  1.00  0.17
ATOM    568  C   HIS   103      -5.885  20.468  50.005  1.00  0.17
ATOM    569  O   HIS   103      -5.551  19.565  50.771  1.00  0.17
ATOM    570  CB  HIS   103      -7.287  22.369  50.566  1.00  0.17
ATOM    571  CG  HIS   103      -7.399  23.758  51.117  1.00  0.17
ATOM    572  ND1 HIS   103      -7.417  24.055  52.462  1.00  0.17
ATOM    573  CD2 HIS   103      -7.494  24.952  50.472  1.00  0.17
ATOM    574  CE1 HIS   103      -7.521  25.404  52.563  1.00  0.17
ATOM    575  NE2 HIS   103      -7.571  25.992  51.381  1.00  0.17
ATOM    576  N   CYS   104      -6.294  20.237  48.746  1.00  0.27
ATOM    577  CA  CYS   104      -6.534  18.920  48.231  1.00  0.27
ATOM    578  C   CYS   104      -5.306  18.077  48.291  1.00  0.27
ATOM    579  O   CYS   104      -5.373  16.920  48.703  1.00  0.27
ATOM    580  CB  CYS   104      -6.960  18.948  46.760  1.00  0.27
ATOM    581  SG  CYS   104      -8.616  19.635  46.543  1.00  0.27
ATOM    582  N   GLN   105      -4.150  18.645  47.909  1.00  0.43
ATOM    583  CA  GLN   105      -2.933  17.895  47.767  1.00  0.43
ATOM    584  C   GLN   105      -2.595  17.211  49.056  1.00  0.43
ATOM    585  O   GLN   105      -2.063  16.101  49.051  1.00  0.43
ATOM    586  CB  GLN   105      -1.739  18.786  47.377  1.00  0.43
ATOM    587  CG  GLN   105      -1.854  19.374  45.969  1.00  0.43
ATOM    588  CD  GLN   105      -0.621  20.230  45.714  1.00  0.43
ATOM    589  OE1 GLN   105      -0.108  20.869  46.631  1.00  0.43
ATOM    590  NE2 GLN   105      -0.129  20.241  44.445  1.00  0.43
ATOM    591  N   ILE   106      -2.872  17.877  50.190  1.00  0.62
ATOM    592  CA  ILE   106      -2.592  17.342  51.492  1.00  0.62
ATOM    593  C   ILE   106      -3.464  16.155  51.751  1.00  0.62
ATOM    594  O   ILE   106      -3.026  15.191  52.376  1.00  0.62
ATOM    595  CB  ILE   106      -2.852  18.333  52.596  1.00  0.62
ATOM    596  CG1 ILE   106      -1.941  19.566  52.452  1.00  0.62
ATOM    597  CG2 ILE   106      -2.683  17.603  53.940  1.00  0.62
ATOM    598  CD1 ILE   106      -2.264  20.431  51.235  1.00  0.62
ATOM    599  N   LYS   107      -4.729  16.191  51.285  1.00  0.83
ATOM    600  CA  LYS   107      -5.646  15.128  51.585  1.00  0.83
ATOM    601  C   LYS   107      -5.349  13.934  50.732  1.00  0.83
ATOM    602  O   LYS   107      -6.058  13.662  49.762  1.00  0.83
ATOM    603  CB  LYS   107      -7.117  15.516  51.364  1.00  0.83
ATOM    604  CG  LYS   107      -8.094  14.579  52.072  1.00  0.83
ATOM    605  CD  LYS   107      -8.044  14.689  53.595  1.00  0.83
ATOM    606  CE  LYS   107      -8.726  15.947  54.135  1.00  0.83
ATOM    607  NZ  LYS   107      -8.010  17.152  53.659  1.00  0.83
ATOM    608  N   THR   108      -4.284  13.185  51.098  1.00  0.67
ATOM    609  CA  THR   108      -3.885  11.996  50.398  1.00  0.67
ATOM    610  C   THR   108      -2.997  11.195  51.324  1.00  0.67
ATOM    611  O   THR   108      -2.295  11.754  52.164  1.00  0.67
ATOM    612  CB  THR   108      -3.060  12.273  49.171  1.00  0.67
ATOM    613  OG1 THR   108      -1.858  12.935  49.535  1.00  0.67
ATOM    614  CG2 THR   108      -3.867  13.144  48.191  1.00  0.67
TER
END
