
#######################################################
#                                                     #
#                        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   20 (  169),  selected   20 , name T0335TS389_5-D1
# Molecule2: number of CA atoms   36 (  584),  selected   20 , name T0335_D1.pdb
# PARAMETERS: T0335TS389_5-D1.T0335_D1.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:    20        21 - 40          1.57     1.57
  LCS_AVERAGE:     55.56

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    20        21 - 40          1.57     1.57
  LCS_AVERAGE:     55.56

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    16        25 - 40          0.86     1.96
  LCS_AVERAGE:     39.44

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:   36
LCS_GDT     V      21     V      21      7   20   20     3    3    9   13   16   19   20   20   20   20   20   20   20   20   20   20   20   20   20   20 
LCS_GDT     I      22     I      22      7   20   20     3    6    9   15   19   19   20   20   20   20   20   20   20   20   20   20   20   20   20   20 
LCS_GDT     T      23     T      23      7   20   20     4    6   12   17   19   19   20   20   20   20   20   20   20   20   20   20   20   20   20   20 
LCS_GDT     E      24     E      24      7   20   20     4    6   12   17   19   19   20   20   20   20   20   20   20   20   20   20   20   20   20   20 
LCS_GDT     E      25     E      25     16   20   20     4    6   12   17   19   19   20   20   20   20   20   20   20   20   20   20   20   20   20   20 
LCS_GDT     E      26     E      26     16   20   20     6   15   15   17   19   19   20   20   20   20   20   20   20   20   20   20   20   20   20   20 
LCS_GDT     K      27     K      27     16   20   20    10   15   15   17   19   19   20   20   20   20   20   20   20   20   20   20   20   20   20   20 
LCS_GDT     A      28     A      28     16   20   20    10   15   15   17   19   19   20   20   20   20   20   20   20   20   20   20   20   20   20   20 
LCS_GDT     E      29     E      29     16   20   20    10   15   15   17   19   19   20   20   20   20   20   20   20   20   20   20   20   20   20   20 
LCS_GDT     Q      30     Q      30     16   20   20    10   15   15   17   19   19   20   20   20   20   20   20   20   20   20   20   20   20   20   20 
LCS_GDT     Q      31     Q      31     16   20   20     6   15   15   17   19   19   20   20   20   20   20   20   20   20   20   20   20   20   20   20 
LCS_GDT     K      32     K      32     16   20   20     6   15   15   17   19   19   20   20   20   20   20   20   20   20   20   20   20   20   20   20 
LCS_GDT     L      33     L      33     16   20   20    10   15   15   17   19   19   20   20   20   20   20   20   20   20   20   20   20   20   20   20 
LCS_GDT     R      34     R      34     16   20   20    10   15   15   17   19   19   20   20   20   20   20   20   20   20   20   20   20   20   20   20 
LCS_GDT     Q      35     Q      35     16   20   20    10   15   15   17   19   19   20   20   20   20   20   20   20   20   20   20   20   20   20   20 
LCS_GDT     E      36     E      36     16   20   20    10   15   15   17   19   19   20   20   20   20   20   20   20   20   20   20   20   20   20   20 
LCS_GDT     Y      37     Y      37     16   20   20    10   15   15   17   19   19   20   20   20   20   20   20   20   20   20   20   20   20   20   20 
LCS_GDT     L      38     L      38     16   20   20    10   15   15   17   19   19   20   20   20   20   20   20   20   20   20   20   20   20   20   20 
LCS_GDT     K      39     K      39     16   20   20     9   15   15   17   19   19   20   20   20   20   20   20   20   20   20   20   20   20   20   20 
LCS_GDT     G      40     G      40     16   20   20     3   15   15   16   19   19   20   20   20   20   20   20   20   20   20   20   20   20   20   20 
LCS_AVERAGE  LCS_A:  50.19  (  39.44   55.56   55.56 )

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     10     15     15     17     19     19     20     20     20     20     20     20     20     20     20     20     20     20     20     20 
GDT PERCENT_CA  27.78  41.67  41.67  47.22  52.78  52.78  55.56  55.56  55.56  55.56  55.56  55.56  55.56  55.56  55.56  55.56  55.56  55.56  55.56  55.56
GDT RMS_LOCAL    0.35   0.54   0.54   1.21   1.39   1.39   1.57   1.57   1.57   1.57   1.57   1.57   1.57   1.57   1.57   1.57   1.57   1.57   1.57   1.57
GDT RMS_ALL_CA   2.32   2.20   2.20   1.69   1.61   1.61   1.57   1.57   1.57   1.57   1.57   1.57   1.57   1.57   1.57   1.57   1.57   1.57   1.57   1.57

#      Molecule1      Molecule2       DISTANCE
LGA    V      21      V      21          3.245
LGA    I      22      I      22          2.387
LGA    T      23      T      23          2.171
LGA    E      24      E      24          2.268
LGA    E      25      E      25          1.733
LGA    E      26      E      26          1.166
LGA    K      27      K      27          1.634
LGA    A      28      A      28          1.453
LGA    E      29      E      29          1.418
LGA    Q      30      Q      30          1.201
LGA    Q      31      Q      31          0.582
LGA    K      32      K      32          0.656
LGA    L      33      L      33          0.620
LGA    R      34      R      34          1.061
LGA    Q      35      Q      35          0.472
LGA    E      36      E      36          0.556
LGA    Y      37      Y      37          1.309
LGA    L      38      L      38          0.693
LGA    K      39      K      39          1.302
LGA    G      40      G      40          1.940

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   20   36    4.0     20    1.57    50.000    52.485     1.199

LGA_LOCAL      RMSD =  1.568  Number of atoms =   20  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  1.568  Number of atoms =   20 
Std_ALL_ATOMS  RMSD =  1.568  (standard rmsd on all 20 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.834610 * X  +   0.407722 * Y  +  -0.370389 * Z  +   1.530766
  Y_new =  -0.503064 * X  +  -0.290268 * Y  +   0.814046 * Z  +   0.745975
  Z_new =   0.224392 * X  +   0.865741 * Y  +   0.447371 * Z  +  -7.657369 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.093839   -2.047754  [ DEG:    62.6724   -117.3276 ]
  Theta =  -0.226319   -2.915274  [ DEG:   -12.9671   -167.0329 ]
  Phi   =  -2.599151    0.542441  [ DEG:  -148.9204     31.0796 ]
 
# 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: T0335TS389_5-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0335TS389_5-D1.T0335_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   20   36   4.0   20   1.57  52.485     1.57
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS389_5-D1
PFRMAT TS
TARGET T0335
MODEL  5
PARENT N/A
ATOM      2  N   VAL    21      -9.254   4.086   7.780  1.00  0.00
ATOM      3  CA  VAL    21      -8.024   4.860   7.665  1.00  0.00
ATOM      4  CB  VAL    21      -7.793   5.743   8.906  1.00  0.00
ATOM      5  CG1 VAL    21      -8.939   6.726   9.082  1.00  0.00
ATOM      6  CG2 VAL    21      -7.702   4.884  10.158  1.00  0.00
ATOM      7  O   VAL    21      -6.865   2.781   7.991  1.00  0.00
ATOM      8  C   VAL    21      -6.831   3.917   7.518  1.00  0.00
ATOM      9  N   ILE    22      -5.785   4.379   6.844  1.00  0.00
ATOM     10  CA  ILE    22      -4.576   3.579   6.725  1.00  0.00
ATOM     11  CB  ILE    22      -3.692   4.062   5.560  1.00  0.00
ATOM     12  CG1 ILE    22      -4.433   3.915   4.230  1.00  0.00
ATOM     13  CG2 ILE    22      -2.411   3.246   5.491  1.00  0.00
ATOM     14  CD1 ILE    22      -3.734   4.577   3.065  1.00  0.00
ATOM     15  O   ILE    22      -3.610   4.941   8.443  1.00  0.00
ATOM     16  C   ILE    22      -3.920   3.805   8.089  1.00  0.00
ATOM     17  N   THR    23      -3.725   2.734   8.883  1.00  0.00
ATOM     18  CA  THR    23      -3.110   2.866  10.209  1.00  0.00
ATOM     19  CB  THR    23      -2.775   1.491  10.815  1.00  0.00
ATOM     20  CG2 THR    23      -2.187   1.652  12.209  1.00  0.00
ATOM     21  OG1 THR    23      -3.968   0.701  10.904  1.00  0.00
ATOM     22  O   THR    23      -0.964   3.447   9.310  1.00  0.00
ATOM     23  C   THR    23      -1.807   3.661  10.180  1.00  0.00
ATOM     24  N   GLU    24      -1.635   4.592  11.131  1.00  0.00
ATOM     25  CA  GLU    24      -0.439   5.435  11.243  1.00  0.00
ATOM     26  CB  GLU    24      -0.416   6.155  12.593  1.00  0.00
ATOM     27  CG  GLU    24       0.780   7.075  12.784  1.00  0.00
ATOM     28  CD  GLU    24       0.748   7.802  14.114  1.00  0.00
ATOM     29  OE1 GLU    24      -0.228   7.614  14.871  1.00  0.00
ATOM     30  OE2 GLU    24       1.698   8.561  14.399  1.00  0.00
ATOM     31  O   GLU    24       1.771   5.022  10.397  1.00  0.00
ATOM     32  C   GLU    24       0.861   4.642  11.135  1.00  0.00
ATOM     33  N   GLU    25       0.937   3.532  11.860  1.00  0.00
ATOM     34  CA  GLU    25       2.134   2.695  11.859  1.00  0.00
ATOM     35  CB  GLU    25       1.996   1.562  12.877  1.00  0.00
ATOM     36  CG  GLU    25       1.996   2.025  14.325  1.00  0.00
ATOM     37  CD  GLU    25       1.749   0.889  15.299  1.00  0.00
ATOM     38  OE1 GLU    25       1.554  -0.254  14.842  1.00  0.00
ATOM     39  OE2 GLU    25       1.753   1.147  16.522  1.00  0.00
ATOM     40  O   GLU    25       3.534   1.520  10.318  1.00  0.00
ATOM     41  C   GLU    25       2.438   2.034  10.512  1.00  0.00
ATOM     42  N   GLU    26       1.481   2.046   9.587  1.00  0.00
ATOM     43  CA  GLU    26       1.664   1.398   8.285  1.00  0.00
ATOM     44  CB  GLU    26       0.390   0.661   7.867  1.00  0.00
ATOM     45  CG  GLU    26      -0.001  -0.476   8.798  1.00  0.00
ATOM     46  CD  GLU    26      -1.291  -1.154   8.377  1.00  0.00
ATOM     47  OE1 GLU    26      -1.889  -0.719   7.373  1.00  0.00
ATOM     48  OE2 GLU    26      -1.702  -2.120   9.055  1.00  0.00
ATOM     49  O   GLU    26       2.520   1.930   6.104  1.00  0.00
ATOM     50  C   GLU    26       1.999   2.349   7.141  1.00  0.00
ATOM     51  N   LYS    27       1.693   3.626   7.336  1.00  0.00
ATOM     52  CA  LYS    27       1.879   4.624   6.298  1.00  0.00
ATOM     53  CB  LYS    27       1.670   6.031   6.865  1.00  0.00
ATOM     54  CG  LYS    27       1.815   7.142   5.837  1.00  0.00
ATOM     55  CD  LYS    27       1.523   8.500   6.449  1.00  0.00
ATOM     56  CE  LYS    27       1.698   9.616   5.429  1.00  0.00
ATOM     57  NZ  LYS    27       1.408  10.954   6.013  1.00  0.00
ATOM     58  O   LYS    27       3.269   4.792   4.378  1.00  0.00
ATOM     59  C   LYS    27       3.226   4.696   5.606  1.00  0.00
ATOM     60  N   ALA    28       4.320   4.638   6.359  1.00  0.00
ATOM     61  CA  ALA    28       5.642   4.705   5.732  1.00  0.00
ATOM     62  CB  ALA    28       6.732   4.698   6.792  1.00  0.00
ATOM     63  O   ALA    28       6.322   3.670   3.676  1.00  0.00
ATOM     64  C   ALA    28       5.861   3.511   4.812  1.00  0.00
ATOM     65  N   GLU    29       5.525   2.318   5.294  1.00  0.00
ATOM     66  CA  GLU    29       5.684   1.119   4.480  1.00  0.00
ATOM     67  CB  GLU    29       5.344  -0.130   5.297  1.00  0.00
ATOM     68  CG  GLU    29       6.366  -0.465   6.371  1.00  0.00
ATOM     69  CD  GLU    29       5.938  -1.633   7.238  1.00  0.00
ATOM     70  OE1 GLU    29       4.810  -2.133   7.046  1.00  0.00
ATOM     71  OE2 GLU    29       6.730  -2.048   8.109  1.00  0.00
ATOM     72  O   GLU    29       5.146   0.773   2.158  1.00  0.00
ATOM     73  C   GLU    29       4.753   1.161   3.259  1.00  0.00
ATOM     74  N   GLN    30       3.528   1.633   3.449  1.00  0.00
ATOM     75  CA  GLN    30       2.580   1.700   2.337  1.00  0.00
ATOM     76  CB  GLN    30       1.219   2.199   2.823  1.00  0.00
ATOM     77  CG  GLN    30       0.137   2.190   1.753  1.00  0.00
ATOM     78  CD  GLN    30      -0.183   0.794   1.260  1.00  0.00
ATOM     79  OE1 GLN    30      -0.348  -0.133   2.054  1.00  0.00
ATOM     80  NE2 GLN    30      -0.272   0.640  -0.056  1.00  0.00
ATOM     81  O   GLN    30       3.005   2.383   0.066  1.00  0.00
ATOM     82  C   GLN    30       3.102   2.658   1.266  1.00  0.00
ATOM     83  N   GLN    31       3.663   3.782   1.700  1.00  0.00
ATOM     84  CA  GLN    31       4.200   4.753   0.762  1.00  0.00
ATOM     85  CB  GLN    31       4.692   5.998   1.504  1.00  0.00
ATOM     86  CG  GLN    31       3.579   6.852   2.090  1.00  0.00
ATOM     87  CD  GLN    31       4.106   8.012   2.912  1.00  0.00
ATOM     88  OE1 GLN    31       5.311   8.134   3.127  1.00  0.00
ATOM     89  NE2 GLN    31       3.200   8.867   3.375  1.00  0.00
ATOM     90  O   GLN    31       5.545   4.432  -1.207  1.00  0.00
ATOM     91  C   GLN    31       5.378   4.159  -0.016  1.00  0.00
ATOM     92  N   LYS    32       6.189   3.343   0.652  1.00  0.00
ATOM     93  CA  LYS    32       7.329   2.705  -0.003  1.00  0.00
ATOM     94  CB  LYS    32       8.124   1.870   1.002  1.00  0.00
ATOM     95  CG  LYS    32       9.356   1.200   0.414  1.00  0.00
ATOM     96  CD  LYS    32      10.136   0.448   1.479  1.00  0.00
ATOM     97  CE  LYS    32      11.340  -0.264   0.882  1.00  0.00
ATOM     98  NZ  LYS    32      12.102  -1.025   1.911  1.00  0.00
ATOM     99  O   LYS    32       7.351   1.814  -2.230  1.00  0.00
ATOM    100  C   LYS    32       6.829   1.791  -1.122  1.00  0.00
ATOM    101  N   LEU    33       5.820   0.980  -0.823  1.00  0.00
ATOM    102  CA  LEU    33       5.250   0.083  -1.821  1.00  0.00
ATOM    103  CB  LEU    33       4.155  -0.787  -1.198  1.00  0.00
ATOM    104  CG  LEU    33       4.622  -1.848  -0.198  1.00  0.00
ATOM    105  CD1 LEU    33       3.430  -2.510   0.475  1.00  0.00
ATOM    106  CD2 LEU    33       5.434  -2.926  -0.898  1.00  0.00
ATOM    107  O   LEU    33       4.721   0.457  -4.123  1.00  0.00
ATOM    108  C   LEU    33       4.632   0.872  -2.974  1.00  0.00
ATOM    109  N   ARG    34       4.010   2.005  -2.662  1.00  0.00
ATOM    110  CA  ARG    34       3.392   2.825  -3.697  1.00  0.00
ATOM    111  CB  ARG    34       2.692   4.034  -3.075  1.00  0.00
ATOM    112  CG  ARG    34       1.434   3.689  -2.294  1.00  0.00
ATOM    113  CD  ARG    34       0.816   4.928  -1.667  1.00  0.00
ATOM    114  NE  ARG    34      -0.367   4.607  -0.872  1.00  0.00
ATOM    115  CZ  ARG    34      -1.062   5.498  -0.172  1.00  0.00
ATOM    116  NH1 ARG    34      -2.125   5.115   0.520  1.00  0.00
ATOM    117  NH2 ARG    34      -0.692   6.772  -0.169  1.00  0.00
ATOM    118  O   ARG    34       4.286   3.232  -5.885  1.00  0.00
ATOM    119  C   ARG    34       4.453   3.322  -4.670  1.00  0.00
ATOM    120  N   GLN    35       5.548   3.842  -4.127  1.00  0.00
ATOM    121  CA  GLN    35       6.631   4.342  -4.958  1.00  0.00
ATOM    122  CB  GLN    35       7.781   4.854  -4.090  1.00  0.00
ATOM    123  CG  GLN    35       7.470   6.142  -3.346  1.00  0.00
ATOM    124  CD  GLN    35       8.579   6.548  -2.394  1.00  0.00
ATOM    125  OE1 GLN    35       9.559   5.826  -2.225  1.00  0.00
ATOM    126  NE2 GLN    35       8.426   7.711  -1.769  1.00  0.00
ATOM    127  O   GLN    35       7.321   3.446  -7.060  1.00  0.00
ATOM    128  C   GLN    35       7.167   3.237  -5.862  1.00  0.00
ATOM    129  N   GLU    36       7.432   2.062  -5.294  1.00  0.00
ATOM    130  CA  GLU    36       7.938   0.934  -6.075  1.00  0.00
ATOM    131  CB  GLU    36       8.161  -0.282  -5.175  1.00  0.00
ATOM    132  CG  GLU    36       9.336  -0.143  -4.222  1.00  0.00
ATOM    133  CD  GLU    36       9.469  -1.326  -3.283  1.00  0.00
ATOM    134  OE1 GLU    36       8.601  -2.222  -3.331  1.00  0.00
ATOM    135  OE2 GLU    36      10.441  -1.357  -2.499  1.00  0.00
ATOM    136  O   GLU    36       7.359   0.113  -8.251  1.00  0.00
ATOM    137  C   GLU    36       6.955   0.541  -7.172  1.00  0.00
ATOM    138  N   TYR    37       5.662   0.678  -6.890  1.00  0.00
ATOM    139  CA  TYR    37       4.637   0.336  -7.865  1.00  0.00
ATOM    140  CB  TYR    37       3.251   0.374  -7.219  1.00  0.00
ATOM    141  CG  TYR    37       2.122   0.054  -8.173  1.00  0.00
ATOM    142  CD1 TYR    37       1.843  -1.260  -8.529  1.00  0.00
ATOM    143  CD2 TYR    37       1.339   1.066  -8.713  1.00  0.00
ATOM    144  CE1 TYR    37       0.814  -1.562  -9.400  1.00  0.00
ATOM    145  CE2 TYR    37       0.305   0.782  -9.586  1.00  0.00
ATOM    146  CZ  TYR    37       0.048  -0.545  -9.926  1.00  0.00
ATOM    147  OH  TYR    37      -0.978  -0.844 -10.794  1.00  0.00
ATOM    148  O   TYR    37       4.610   0.949 -10.181  1.00  0.00
ATOM    149  C   TYR    37       4.673   1.333  -9.013  1.00  0.00
ATOM    150  N   LEU    38       4.771   2.615  -8.672  1.00  0.00
ATOM    151  CA  LEU    38       4.837   3.667  -9.676  1.00  0.00
ATOM    152  CB  LEU    38       4.942   5.040  -9.007  1.00  0.00
ATOM    153  CG  LEU    38       3.692   5.536  -8.279  1.00  0.00
ATOM    154  CD1 LEU    38       3.992   6.810  -7.505  1.00  0.00
ATOM    155  CD2 LEU    38       2.575   5.833  -9.269  1.00  0.00
ATOM    156  O   LEU    38       5.955   3.538 -11.785  1.00  0.00
ATOM    157  C   LEU    38       6.056   3.468 -10.568  1.00  0.00
ATOM    158  N   LYS    39       7.207   3.207  -9.956  1.00  0.00
ATOM    159  CA  LYS    39       8.436   3.010 -10.707  1.00  0.00
ATOM    160  CB  LYS    39       9.619   2.815  -9.758  1.00  0.00
ATOM    161  CG  LYS    39      10.021   4.072  -9.001  1.00  0.00
ATOM    162  CD  LYS    39      11.202   3.807  -8.081  1.00  0.00
ATOM    163  CE  LYS    39      11.588   5.057  -7.307  1.00  0.00
ATOM    164  NZ  LYS    39      12.722   4.803  -6.376  1.00  0.00
ATOM    165  O   LYS    39       8.861   1.842 -12.752  1.00  0.00
ATOM    166  C   LYS    39       8.383   1.791 -11.617  1.00  0.00
ATOM    167  N   GLY    40       7.809   0.696 -11.125  1.00  0.00
ATOM    168  CA  GLY    40       7.713  -0.531 -11.917  1.00  0.00
ATOM    169  O   GLY    40       7.201  -0.882 -14.235  1.00  0.00
ATOM    170  C   GLY    40       6.886  -0.323 -13.183  1.00  0.00
TER
END
