
#######################################################
#                                                     #
#                        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   15 (  125),  selected   15 , name T0335TS389_4-D1
# Molecule2: number of CA atoms   36 (  584),  selected   15 , name T0335_D1.pdb
# PARAMETERS: T0335TS389_4-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:    15        19 - 37          2.11     2.11
  LCS_AVERAGE:     41.67

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14        20 - 37          1.63     2.22
  LCS_AVERAGE:     37.04

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13        21 - 37          0.54     2.91
  LCS_AVERAGE:     32.41

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     A      19     A      19      3    4   15     3    3    3    4    5    6    6    9   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     G      20     G      20      3   14   15     3    3    3    4    5   13   14   14   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     V      21     V      21     13   14   15     3   12   13   13   13   13   14   14   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     I      22     I      22     13   14   15    12   12   13   13   13   13   14   14   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     T      23     T      23     13   14   15    12   12   13   13   13   13   14   14   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     E      24     E      24     13   14   15    12   12   13   13   13   13   14   14   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     E      25     E      25     13   14   15    12   12   13   13   13   13   14   14   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     E      26     E      26     13   14   15    12   12   13   13   13   13   14   14   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     K      27     K      27     13   14   15    12   12   13   13   13   13   14   14   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     Q      30     Q      30     13   14   15    12   12   13   13   13   13   14   14   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     Q      31     Q      31     13   14   15    12   12   13   13   13   13   14   14   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     K      32     K      32     13   14   15    12   12   13   13   13   13   14   14   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     L      33     L      33     13   14   15    12   12   13   13   13   13   14   14   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     R      34     R      34     13   14   15    12   12   13   13   13   13   14   14   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     Y      37     Y      37     13   14   15    12   12   13   13   13   13   14   14   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_AVERAGE  LCS_A:  37.04  (  32.41   37.04   41.67 )

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     12     12     13     13     13     13     14     14     15     15     15     15     15     15     15     15     15     15     15     15 
GDT PERCENT_CA  33.33  33.33  36.11  36.11  36.11  36.11  38.89  38.89  41.67  41.67  41.67  41.67  41.67  41.67  41.67  41.67  41.67  41.67  41.67  41.67
GDT RMS_LOCAL    0.35   0.35   0.54   0.54   0.54   0.54   1.63   1.63   2.11   2.11   2.11   2.11   2.11   2.11   2.11   2.11   2.11   2.11   2.11   2.11
GDT RMS_ALL_CA   3.09   3.09   2.91   2.91   2.91   2.91   2.22   2.22   2.11   2.11   2.11   2.11   2.11   2.11   2.11   2.11   2.11   2.11   2.11   2.11

#      Molecule1      Molecule2       DISTANCE
LGA    A      19      A      19          4.956
LGA    G      20      G      20          3.347
LGA    V      21      V      21          3.123
LGA    I      22      I      22          2.433
LGA    T      23      T      23          1.298
LGA    E      24      E      24          1.900
LGA    E      25      E      25          1.388
LGA    E      26      E      26          0.438
LGA    K      27      K      27          0.914
LGA    Q      30      Q      30          0.619
LGA    Q      31      Q      31          1.615
LGA    K      32      K      32          1.477
LGA    L      33      L      33          0.765
LGA    R      34      R      34          0.786
LGA    Y      37      Y      37          0.875

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   15   36    4.0     14    1.63    37.500    38.036     0.809

LGA_LOCAL      RMSD =  1.630  Number of atoms =   14  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  2.111  Number of atoms =   15 
Std_ALL_ATOMS  RMSD =  2.111  (standard rmsd on all 15 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.907086 * X  +   0.288233 * Y  +  -0.306783 * Z  +   2.195299
  Y_new =  -0.301613 * X  +   0.063357 * Y  +   0.951323 * Z  +  -6.306823
  Z_new =   0.293640 * X  +   0.955462 * Y  +   0.029465 * Z  +  -4.008826 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.539968   -1.601625  [ DEG:    88.2336    -91.7664 ]
  Theta =  -0.298032   -2.843560  [ DEG:   -17.0760   -162.9240 ]
  Phi   =  -2.820586    0.321007  [ DEG:  -161.6077     18.3923 ]
 
# 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_4-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0335TS389_4-D1.T0335_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   15   36   4.0   14   1.63  38.036     2.11
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS389_4-D1
PFRMAT TS
TARGET T0335
MODEL  4
PARENT N/A
ATOM      2  N   ALA    19      -8.566   3.572   5.128  1.00  0.00
ATOM      3  CA  ALA    19      -7.811   4.696   5.601  1.00  0.00
ATOM      4  CB  ALA    19      -8.091   5.922   4.745  1.00  0.00
ATOM      5  O   ALA    19      -7.615   5.788   7.754  1.00  0.00
ATOM      6  C   ALA    19      -8.214   4.984   7.041  1.00  0.00
ATOM      7  N   GLY    20      -9.267   4.307   7.471  1.00  0.00
ATOM      8  CA  GLY    20      -9.740   4.454   8.837  1.00  0.00
ATOM      9  O   GLY    20      -8.442   3.760  10.742  1.00  0.00
ATOM     10  C   GLY    20      -9.060   3.424   9.739  1.00  0.00
ATOM     11  N   VAL    21      -9.200   2.172   9.325  1.00  0.00
ATOM     12  CA  VAL    21      -8.655   1.011   9.973  1.00  0.00
ATOM     13  CB  VAL    21      -8.751  -0.236   9.072  1.00  0.00
ATOM     14  CG1 VAL    21      -7.982  -1.395   9.686  1.00  0.00
ATOM     15  CG2 VAL    21     -10.202  -0.657   8.901  1.00  0.00
ATOM     16  O   VAL    21      -6.737   1.006  11.371  1.00  0.00
ATOM     17  C   VAL    21      -7.217   1.250  10.295  1.00  0.00
ATOM     18  N   ILE    22      -6.503   1.659   9.294  1.00  0.00
ATOM     19  CA  ILE    22      -5.085   1.738   9.447  1.00  0.00
ATOM     20  CB  ILE    22      -4.371   1.758   8.082  1.00  0.00
ATOM     21  CG1 ILE    22      -4.784   2.996   7.283  1.00  0.00
ATOM     22  CG2 ILE    22      -4.729   0.521   7.275  1.00  0.00
ATOM     23  CD1 ILE    22      -3.973   3.207   6.023  1.00  0.00
ATOM     24  O   ILE    22      -4.738   4.025  10.105  1.00  0.00
ATOM     25  C   ILE    22      -4.395   2.875  10.144  1.00  0.00
ATOM     26  N   THR    23      -3.295   2.515  10.745  1.00  0.00
ATOM     27  CA  THR    23      -2.454   3.510  11.342  1.00  0.00
ATOM     28  CB  THR    23      -1.368   2.873  12.231  1.00  0.00
ATOM     29  CG2 THR    23      -2.004   2.032  13.326  1.00  0.00
ATOM     30  OG1 THR    23      -0.524   2.035  11.431  1.00  0.00
ATOM     31  O   THR    23      -1.547   3.934   9.134  1.00  0.00
ATOM     32  C   THR    23      -1.743   4.347  10.263  1.00  0.00
ATOM     33  N   GLU    24      -1.331   5.542  10.609  1.00  0.00
ATOM     34  CA  GLU    24      -0.600   6.393   9.697  1.00  0.00
ATOM     35  CB  GLU    24      -0.300   7.745  10.348  1.00  0.00
ATOM     36  CG  GLU    24      -1.522   8.629  10.529  1.00  0.00
ATOM     37  CD  GLU    24      -1.205   9.920  11.261  1.00  0.00
ATOM     38  OE1 GLU    24      -0.042  10.088  11.688  1.00  0.00
ATOM     39  OE2 GLU    24      -2.116  10.760  11.407  1.00  0.00
ATOM     40  O   GLU    24       1.234   5.808   8.200  1.00  0.00
ATOM     41  C   GLU    24       0.736   5.723   9.310  1.00  0.00
ATOM     42  N   GLU    25       1.295   4.960  10.218  1.00  0.00
ATOM     43  CA  GLU    25       2.525   4.229   9.991  1.00  0.00
ATOM     44  CB  GLU    25       2.942   3.476  11.256  1.00  0.00
ATOM     45  CG  GLU    25       4.253   2.714  11.122  1.00  0.00
ATOM     46  CD  GLU    25       4.650   2.009  12.404  1.00  0.00
ATOM     47  OE1 GLU    25       3.907   2.127  13.402  1.00  0.00
ATOM     48  OE2 GLU    25       5.703   1.338  12.410  1.00  0.00
ATOM     49  O   GLU    25       3.204   3.147   7.942  1.00  0.00
ATOM     50  C   GLU    25       2.374   3.204   8.867  1.00  0.00
ATOM     51  N   GLU    26       1.336   2.363   9.001  1.00  0.00
ATOM     52  CA  GLU    26       0.987   1.359   8.012  1.00  0.00
ATOM     53  CB  GLU    26      -0.289   0.622   8.423  1.00  0.00
ATOM     54  CG  GLU    26      -0.705  -0.481   7.464  1.00  0.00
ATOM     55  CD  GLU    26      -1.952  -1.211   7.921  1.00  0.00
ATOM     56  OE1 GLU    26      -2.485  -0.862   8.995  1.00  0.00
ATOM     57  OE2 GLU    26      -2.398  -2.133   7.204  1.00  0.00
ATOM     58  O   GLU    26       1.244   1.558   5.641  1.00  0.00
ATOM     59  C   GLU    26       0.753   2.031   6.649  1.00  0.00
ATOM     60  N   LYS    27      -0.033   3.122   6.615  1.00  0.00
ATOM     61  CA  LYS    27      -0.323   3.853   5.386  1.00  0.00
ATOM     62  CB  LYS    27      -1.109   5.129   5.693  1.00  0.00
ATOM     63  CG  LYS    27      -1.513   5.921   4.461  1.00  0.00
ATOM     64  CD  LYS    27      -2.350   7.134   4.832  1.00  0.00
ATOM     65  CE  LYS    27      -2.744   7.933   3.601  1.00  0.00
ATOM     66  NZ  LYS    27      -3.567   9.124   3.952  1.00  0.00
ATOM     67  O   LYS    27       1.163   4.004   3.492  1.00  0.00
ATOM     68  C   LYS    27       0.983   4.242   4.681  1.00  0.00
ATOM     72  N   GLN    30       2.790   1.438   3.170  1.00  0.00
ATOM     73  CA  GLN    30       2.038   0.997   2.010  1.00  0.00
ATOM     74  CB  GLN    30       0.539   0.977   2.317  1.00  0.00
ATOM     75  CG  GLN    30       0.117  -0.123   3.278  1.00  0.00
ATOM     76  CD  GLN    30      -1.350  -0.042   3.648  1.00  0.00
ATOM     77  OE1 GLN    30      -2.048   0.893   3.258  1.00  0.00
ATOM     78  NE2 GLN    30      -1.823  -1.026   4.405  1.00  0.00
ATOM     79  O   GLN    30       2.424   1.489  -0.295  1.00  0.00
ATOM     80  C   GLN    30       2.278   1.941   0.828  1.00  0.00
ATOM     81  N   GLN    31       2.349   3.242   1.052  1.00  0.00
ATOM     82  CA  GLN    31       2.609   4.225  -0.014  1.00  0.00
ATOM     83  CB  GLN    31       2.614   5.644   0.558  1.00  0.00
ATOM     84  CG  GLN    31       1.244   6.145   0.985  1.00  0.00
ATOM     85  CD  GLN    31       1.304   7.507   1.648  1.00  0.00
ATOM     86  OE1 GLN    31       2.385   8.053   1.875  1.00  0.00
ATOM     87  NE2 GLN    31       0.138   8.063   1.961  1.00  0.00
ATOM     88  O   GLN    31       4.191   3.932  -1.926  1.00  0.00
ATOM     89  C   GLN    31       4.002   3.959  -0.687  1.00  0.00
ATOM     90  N   LYS    32       4.985   3.689   0.174  1.00  0.00
ATOM     91  CA  LYS    32       6.337   3.377  -0.244  1.00  0.00
ATOM     92  CB  LYS    32       7.188   2.962   0.957  1.00  0.00
ATOM     93  CG  LYS    32       8.638   2.664   0.617  1.00  0.00
ATOM     94  CD  LYS    32       9.434   2.307   1.861  1.00  0.00
ATOM     95  CE  LYS    32      10.878   1.976   1.517  1.00  0.00
ATOM     96  NZ  LYS    32      11.678   1.649   2.730  1.00  0.00
ATOM     97  O   LYS    32       6.738   2.458  -2.375  1.00  0.00
ATOM     98  C   LYS    32       6.308   2.246  -1.237  1.00  0.00
ATOM     99  N   LEU    33       5.740   1.108  -0.812  1.00  0.00
ATOM    100  CA  LEU    33       5.552  -0.066  -1.663  1.00  0.00
ATOM    101  CB  LEU    33       4.686  -1.109  -0.954  1.00  0.00
ATOM    102  CG  LEU    33       5.334  -1.841   0.223  1.00  0.00
ATOM    103  CD1 LEU    33       4.311  -2.703   0.948  1.00  0.00
ATOM    104  CD2 LEU    33       6.460  -2.744  -0.260  1.00  0.00
ATOM    105  O   LEU    33       5.359  -0.034  -4.136  1.00  0.00
ATOM    106  C   LEU    33       4.846   0.271  -3.030  1.00  0.00
ATOM    107  N   ARG    34       3.668   0.943  -2.928  1.00  0.00
ATOM    108  CA  ARG    34       2.879   1.338  -4.051  1.00  0.00
ATOM    109  CB  ARG    34       1.694   2.193  -3.598  1.00  0.00
ATOM    110  CG  ARG    34       0.657   1.437  -2.784  1.00  0.00
ATOM    111  CD  ARG    34      -0.477   2.350  -2.346  1.00  0.00
ATOM    112  NE  ARG    34      -1.471   1.643  -1.542  1.00  0.00
ATOM    113  CZ  ARG    34      -2.524   2.223  -0.976  1.00  0.00
ATOM    114  NH1 ARG    34      -3.374   1.499  -0.261  1.00  0.00
ATOM    115  NH2 ARG    34      -2.724   3.525  -1.127  1.00  0.00
ATOM    116  O   ARG    34       3.963   1.804  -6.121  1.00  0.00
ATOM    117  C   ARG    34       3.815   2.127  -4.928  1.00  0.00
ATOM    121  N   TYR    37       5.922   0.001  -6.906  1.00  0.00
ATOM    122  CA  TYR    37       5.315  -0.653  -8.039  1.00  0.00
ATOM    123  CB  TYR    37       3.989  -1.300  -7.636  1.00  0.00
ATOM    124  CG  TYR    37       4.140  -2.452  -6.668  1.00  0.00
ATOM    125  CD1 TYR    37       3.976  -2.259  -5.302  1.00  0.00
ATOM    126  CD2 TYR    37       4.444  -3.730  -7.123  1.00  0.00
ATOM    127  CE1 TYR    37       4.111  -3.306  -4.409  1.00  0.00
ATOM    128  CE2 TYR    37       4.583  -4.787  -6.246  1.00  0.00
ATOM    129  CZ  TYR    37       4.413  -4.566  -4.878  1.00  0.00
ATOM    130  OH  TYR    37       4.548  -5.609  -3.993  1.00  0.00
ATOM    131  O   TYR    37       5.027  -0.100 -10.368  1.00  0.00
ATOM    132  C   TYR    37       5.009   0.292  -9.199  1.00  0.00
TER
END
