
#######################################################
#                                                     #
#                        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   37 (  148),  selected    9 , name T0351AL381_2
# Molecule2: number of CA atoms   56 (  935),  selected    9 , name T0351.pdb
# PARAMETERS: T0351AL381_2.T0351.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:     9        48 - 56          0.38     0.38
  LCS_AVERAGE:     16.07

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9        48 - 56          0.38     0.38
  LCS_AVERAGE:     16.07

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9        48 - 56          0.38     0.38
  LCS_AVERAGE:     16.07

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:   56
LCS_GDT     T      48     T      48      9    9    9     8    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     W      49     W      49      9    9    9     8    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     W      50     W      50      9    9    9     8    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     E      51     E      51      9    9    9     8    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     E      52     E      52      9    9    9     8    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     L      53     L      53      9    9    9     8    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     Q      54     Q      54      9    9    9     7    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     K      55     K      55      9    9    9     8    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     N      56     N      56      9    9    9     8    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_AVERAGE  LCS_A:  16.07  (  16.07   16.07   16.07 )

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      8      9      9      9      9      9      9      9      9      9      9      9      9      9      9      9      9      9      9      9 
GDT PERCENT_CA  14.29  16.07  16.07  16.07  16.07  16.07  16.07  16.07  16.07  16.07  16.07  16.07  16.07  16.07  16.07  16.07  16.07  16.07  16.07  16.07
GDT RMS_LOCAL    0.35   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38
GDT RMS_ALL_CA   0.41   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38

#      Molecule1      Molecule2       DISTANCE
LGA    T      48      T      48          0.153
LGA    W      49      W      49          0.290
LGA    W      50      W      50          0.428
LGA    E      51      E      51          0.490
LGA    E      52      E      52          0.301
LGA    L      53      L      53          0.323
LGA    Q      54      Q      54          0.504
LGA    K      55      K      55          0.431
LGA    N      56      N      56          0.398

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   37   56    4.0      9    0.38    16.071    16.071     1.861

LGA_LOCAL      RMSD =  0.384  Number of atoms =    9  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  0.384  Number of atoms =    9 
Std_ALL_ATOMS  RMSD =  0.384  (standard rmsd on all 9 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.248959 * X  +   0.288151 * Y  +  -0.924656 * Z  +  35.486240
  Y_new =   0.798539 * X  +   0.601309 * Y  +  -0.027617 * Z  + -39.607868
  Z_new =   0.548046 * X  +  -0.745249 * Y  +  -0.379801 * Z  + -20.057528 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.042118    1.099474  [ DEG:  -117.0048     62.9952 ]
  Theta =  -0.580026   -2.561566  [ DEG:   -33.2331   -146.7670 ]
  Phi   =   1.873014   -1.268578  [ DEG:   107.3158    -72.6842 ]
 
# 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: T0351AL381_2                                  
REMARK     2: T0351.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0351AL381_2.T0351.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   37   56   4.0    9   0.38  16.071     0.38
REMARK  ---------------------------------------------------------- 
MOLECULE T0351AL381_2
REMARK Aligment from pdb entry: 1q2hA
ATOM      1  N   THR    48      -1.339  -8.377  -3.071  1.00  0.00              
ATOM      2  CA  THR    48      -0.074  -9.116  -3.021  1.00  0.00              
ATOM      3  C   THR    48       0.865  -8.522  -1.975  1.00  0.00              
ATOM      4  O   THR    48       1.598  -9.243  -1.291  1.00  0.00              
ATOM      5  N   TRP    49       0.831  -7.197  -1.864  1.00  0.00              
ATOM      6  CA  TRP    49       1.633  -6.452  -0.900  1.00  0.00              
ATOM      7  C   TRP    49       1.253  -6.891   0.524  1.00  0.00              
ATOM      8  O   TRP    49       2.114  -7.232   1.335  1.00  0.00              
ATOM      9  N   TRP    50      -0.043  -6.881   0.820  1.00  0.00              
ATOM     10  CA  TRP    50      -0.510  -7.286   2.144  1.00  0.00              
ATOM     11  C   TRP    50      -0.140  -8.734   2.432  1.00  0.00              
ATOM     12  O   TRP    50       0.255  -9.076   3.548  1.00  0.00              
ATOM     13  N   GLU    51      -0.250  -9.581   1.417  1.00  0.00              
ATOM     14  CA  GLU    51       0.064 -10.995   1.575  1.00  0.00              
ATOM     15  C   GLU    51       1.570 -11.168   1.791  1.00  0.00              
ATOM     16  O   GLU    51       2.004 -12.044   2.546  1.00  0.00              
ATOM     17  N   GLU    52       2.367 -10.324   1.141  1.00  0.00              
ATOM     18  CA  GLU    52       3.819 -10.396   1.292  1.00  0.00              
ATOM     19  C   GLU    52       4.230  -9.973   2.703  1.00  0.00              
ATOM     20  O   GLU    52       5.135 -10.562   3.292  1.00  0.00              
ATOM     21  N   LEU    53       3.572  -8.946   3.236  1.00  0.00              
ATOM     22  CA  LEU    53       3.894  -8.454   4.566  1.00  0.00              
ATOM     23  C   LEU    53       3.388  -9.387   5.661  1.00  0.00              
ATOM     24  O   LEU    53       3.851  -9.322   6.799  1.00  0.00              
ATOM     25  N   GLN    54       2.432 -10.242   5.315  1.00  0.00              
ATOM     26  CA  GLN    54       1.905 -11.207   6.268  1.00  0.00              
ATOM     27  C   GLN    54       2.903 -12.352   6.386  1.00  0.00              
ATOM     28  O   GLN    54       3.143 -12.869   7.479  1.00  0.00              
ATOM     29  N   LYS    55       3.479 -12.745   5.251  1.00  0.00              
ATOM     30  CA  LYS    55       4.452 -13.830   5.227  1.00  0.00              
ATOM     31  C   LYS    55       5.835 -13.366   5.672  1.00  0.00              
ATOM     32  O   LYS    55       6.685 -14.184   6.030  1.00  0.00              
ATOM     33  N   ASN    56       6.054 -12.058   5.661  1.00  0.00              
ATOM     34  CA  ASN    56       7.338 -11.486   6.044  1.00  0.00              
ATOM     35  C   ASN    56       7.092 -10.228   6.879  1.00  0.00              
ATOM     36  O   ASN    56       7.431  -9.128   6.469  1.00  0.00              
ATOM     37  N   PRO    57       6.501 -10.386   8.080  1.00  0.00              
ATOM     38  CA  PRO    57       6.205  -9.254   8.968  1.00  0.00              
ATOM     39  C   PRO    57       7.362  -8.309   9.283  1.00  0.00              
ATOM     40  O   PRO    57       7.148  -7.141   9.610  1.00  0.00              
ATOM     41  N   PRO    58       8.594  -8.796   9.188  1.00  0.00              
ATOM     42  CA  PRO    58       9.726  -7.924   9.463  1.00  0.00              
ATOM     43  C   PRO    58       9.715  -6.753   8.469  1.00  0.00              
ATOM     44  O   PRO    58      10.236  -5.678   8.755  1.00  0.00              
ATOM     45  N   TYR    59       9.116  -6.968   7.301  1.00  0.00              
ATOM     46  CA  TYR    59       9.038  -5.931   6.269  1.00  0.00              
ATOM     47  C   TYR    59       7.916  -4.917   6.501  1.00  0.00              
ATOM     48  O   TYR    59       7.934  -3.827   5.923  1.00  0.00              
ATOM     49  N   GLU    60       6.938  -5.272   7.331  1.00  0.00              
ATOM     50  CA  GLU    60       5.817  -4.368   7.597  1.00  0.00              
ATOM     51  C   GLU    60       6.192  -3.281   8.591  1.00  0.00              
ATOM     52  O   GLU    60       6.136  -3.487   9.811  1.00  0.00              
ATOM     53  N   PRO    61       6.551  -2.120   8.053  1.00  0.00              
ATOM     54  CA  PRO    61       6.970  -0.969   8.838  1.00  0.00              
ATOM     55  C   PRO    61       6.234   0.266   8.342  1.00  0.00              
ATOM     56  O   PRO    61       5.558   0.219   7.319  1.00  0.00              
ATOM     57  N   PRO    62       6.361   1.397   9.057  1.00  0.00              
ATOM     58  CA  PRO    62       5.668   2.604   8.603  1.00  0.00              
ATOM     59  C   PRO    62       6.133   3.077   7.226  1.00  0.00              
ATOM     60  O   PRO    62       5.475   3.908   6.608  1.00  0.00              
ATOM     61  N   ASP    63       7.261   2.547   6.750  1.00  0.00              
ATOM     62  CA  ASP    63       7.797   2.937   5.444  1.00  0.00              
ATOM     63  C   ASP    63       7.357   2.031   4.289  1.00  0.00              
ATOM     64  O   ASP    63       7.379   2.444   3.124  1.00  0.00              
ATOM     65  N   GLN    64       6.987   0.797   4.619  1.00  0.00              
ATOM     66  CA  GLN    64       6.587  -0.200   3.627  1.00  0.00              
ATOM     67  C   GLN    64       5.603   0.236   2.531  1.00  0.00              
ATOM     68  O   GLN    64       5.868   0.041   1.340  1.00  0.00              
ATOM     69  N   VAL    65       4.467   0.805   2.919  1.00  0.00              
ATOM     70  CA  VAL    65       3.478   1.208   1.931  1.00  0.00              
ATOM     71  C   VAL    65       4.033   2.080   0.821  1.00  0.00              
ATOM     72  O   VAL    65       3.834   1.805  -0.379  1.00  0.00              
ATOM     73  N   GLU    66       4.722   3.137   1.231  1.00  0.00              
ATOM     74  CA  GLU    66       5.321   4.084   0.303  1.00  0.00              
ATOM     75  C   GLU    66       6.437   3.450  -0.527  1.00  0.00              
ATOM     76  O   GLU    66       6.496   3.643  -1.743  1.00  0.00              
ATOM     77  N   LEU    67       7.316   2.703   0.134  1.00  0.00              
ATOM     78  CA  LEU    67       8.447   2.050  -0.528  1.00  0.00              
ATOM     79  C   LEU    67       8.014   1.065  -1.612  1.00  0.00              
ATOM     80  O   LEU    67       8.487   1.128  -2.751  1.00  0.00              
ATOM     81  N   LEU    68       7.124   0.150  -1.240  1.00  0.00              
ATOM     82  CA  LEU    68       6.626  -0.869  -2.155  1.00  0.00              
ATOM     83  C   LEU    68       5.827  -0.300  -3.322  1.00  0.00              
ATOM     84  O   LEU    68       6.111  -0.608  -4.478  1.00  0.00              
ATOM     85  N   ALA    69       4.821   0.520  -3.023  1.00  0.00              
ATOM     86  CA  ALA    69       3.973   1.075  -4.068  1.00  0.00              
ATOM     87  C   ALA    69       4.756   1.917  -5.054  1.00  0.00              
ATOM     88  O   ALA    69       4.529   1.843  -6.265  1.00  0.00              
ATOM     89  N   GLN    70       5.681   2.721  -4.545  1.00  0.00              
ATOM     90  CA  GLN    70       6.455   3.563  -5.439  1.00  0.00              
ATOM     91  C   GLN    70       7.421   2.764  -6.301  1.00  0.00              
ATOM     92  O   GLN    70       7.624   3.098  -7.470  1.00  0.00              
ATOM     93  N   GLU    71       7.999   1.704  -5.743  1.00  0.00              
ATOM     94  CA  GLU    71       8.936   0.885  -6.514  1.00  0.00              
ATOM     95  C   GLU    71       8.156   0.101  -7.580  1.00  0.00              
ATOM     96  O   GLU    71       8.613  -0.047  -8.718  1.00  0.00              
ATOM     97  N   LEU    72       6.982  -0.402  -7.216  1.00  0.00              
ATOM     98  CA  LEU    72       6.165  -1.124  -8.189  1.00  0.00              
ATOM     99  C   LEU    72       5.755  -0.160  -9.308  1.00  0.00              
ATOM    100  O   LEU    72       5.904  -0.466 -10.490  1.00  0.00              
ATOM    101  N   SER    73       5.254   1.013  -8.931  1.00  0.00              
ATOM    102  CA  SER    73       4.803   1.989  -9.916  1.00  0.00              
ATOM    103  C   SER    73       5.913   2.417 -10.880  1.00  0.00              
ATOM    104  O   SER    73       5.672   2.536 -12.085  1.00  0.00              
ATOM    105  N   GLN    74       7.121   2.648 -10.372  1.00  0.00              
ATOM    106  CA  GLN    74       8.223   3.059 -11.249  1.00  0.00              
ATOM    107  C   GLN    74       8.595   1.955 -12.237  1.00  0.00              
ATOM    108  O   GLN    74       8.795   2.215 -13.422  1.00  0.00              
ATOM    109  N   GLU    75       8.672   0.722 -11.751  1.00  0.00              
ATOM    110  CA  GLU    75       9.037  -0.400 -12.604  1.00  0.00              
ATOM    111  C   GLU    75       7.933  -0.712 -13.609  1.00  0.00              
ATOM    112  O   GLU    75       8.213  -1.076 -14.751  1.00  0.00              
ATOM    113  N   LYS    76       6.680  -0.583 -13.177  1.00  0.00              
ATOM    114  CA  LYS    76       5.540  -0.834 -14.059  1.00  0.00              
ATOM    115  C   LYS    76       5.633   0.102 -15.259  1.00  0.00              
ATOM    116  O   LYS    76       5.557  -0.327 -16.411  1.00  0.00              
ATOM    117  N   LEU    77       5.784   1.395 -14.985  1.00  0.00              
ATOM    118  CA  LEU    77       5.864   2.374 -16.058  1.00  0.00              
ATOM    119  C   LEU    77       7.032   2.102 -17.010  1.00  0.00              
ATOM    120  O   LEU    77       6.867   2.211 -18.227  1.00  0.00              
ATOM    121  N   ALA    78       8.200   1.750 -16.473  1.00  0.00              
ATOM    122  CA  ALA    78       9.358   1.452 -17.323  1.00  0.00              
ATOM    123  C   ALA    78       9.043   0.279 -18.241  1.00  0.00              
ATOM    124  O   ALA    78       9.210   0.365 -19.458  1.00  0.00              
ATOM    125  N   THR    88       8.598  -0.824 -17.650  1.00  0.00              
ATOM    126  CA  THR    88       8.247  -2.020 -18.419  1.00  0.00              
ATOM    127  C   THR    88       7.151  -1.730 -19.449  1.00  0.00              
ATOM    128  O   THR    88       7.189  -2.242 -20.576  1.00  0.00              
ATOM    129  N   LEU    89       6.176  -0.915 -19.058  1.00  0.00              
ATOM    130  CA  LEU    89       5.073  -0.545 -19.941  1.00  0.00              
ATOM    131  C   LEU    89       5.609   0.077 -21.235  1.00  0.00              
ATOM    132  O   LEU    89       5.264  -0.348 -22.339  1.00  0.00              
ATOM    133  N   GLY    90       6.462   1.082 -21.094  1.00  0.00              
ATOM    134  CA  GLY    90       7.023   1.719 -22.272  1.00  0.00              
ATOM    135  C   GLY    90       7.742   0.729 -23.166  1.00  0.00              
ATOM    136  O   GLY    90       7.538   0.706 -24.383  1.00  0.00              
ATOM    137  N   ASN    91       8.578  -0.106 -22.562  1.00  0.00              
ATOM    138  CA  ASN    91       9.343  -1.101 -23.309  1.00  0.00              
ATOM    139  C   ASN    91       8.499  -2.128 -24.068  1.00  0.00              
ATOM    140  O   ASN    91       8.805  -2.460 -25.215  1.00  0.00              
ATOM    141  N   GLU    92       7.448  -2.642 -23.439  1.00  0.00              
ATOM    142  CA  GLU    92       6.605  -3.635 -24.099  1.00  0.00              
ATOM    143  C   GLU    92       5.798  -2.993 -25.222  1.00  0.00              
ATOM    144  O   GLU    92       5.610  -3.595 -26.282  1.00  0.00              
ATOM    145  N   LEU    93       5.325  -1.771 -24.999  1.00  0.00              
ATOM    146  CA  LEU    93       4.563  -1.083 -26.037  1.00  0.00              
ATOM    147  C   LEU    93       5.432  -0.939 -27.290  1.00  0.00              
ATOM    148  O   LEU    93       4.992  -1.263 -28.393  1.00  0.00              
END
