
#######################################################
#                                                     #
#                        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   43 (  172),  selected   17 , name T0335AL381_5
# Molecule2: number of CA atoms   42 (  691),  selected   17 , name T0335.pdb
# PARAMETERS: T0335AL381_5.T0335.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:    12        26 - 37          4.70     6.88
  LCS_AVERAGE:     27.87

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7        26 - 32          1.80    11.27
  LCS_AVERAGE:     12.89

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6        27 - 32          0.97    10.06
  LCS_AVERAGE:     10.36

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:   42
LCS_GDT     E      26     E      26      3    7   12     3    3    3    4    6    6    7    7    7    8    9   10   12   12   14   17   17   17   17   17 
LCS_GDT     K      27     K      27      6    7   12     4    5    5    6    6    6    7    7    8    9   10   11   12   13   15   17   17   17   17   17 
LCS_GDT     A      28     A      28      6    7   12     4    5    5    6    6    6    7    7    8    9   10   11   12   13   15   17   17   17   17   17 
LCS_GDT     E      29     E      29      6    7   12     4    5    5    6    6    6    7    7    8    9   10   11   12   13   15   17   17   17   17   17 
LCS_GDT     Q      30     Q      30      6    7   12     4    5    5    6    6    6    7    7    8    9   10   11   12   12   15   17   17   17   17   17 
LCS_GDT     Q      31     Q      31      6    7   12     3    5    5    6    6    6    7    7    8    9   10   11   12   13   15   17   17   17   17   17 
LCS_GDT     K      32     K      32      6    7   12     1    3    3    6    6    6    7    7    8    9   10   11   12   13   15   17   17   17   17   17 
LCS_GDT     L      33     L      33      3    3   12     0    3    3    3    3    5    5    7    8    9   10   11   12   13   15   17   17   17   17   17 
LCS_GDT     R      34     R      34      3    3   12     3    3    3    3    3    4    5    6    8    9   10   11   12   13   15   17   17   17   17   17 
LCS_GDT     Q      35     Q      35      3    4   12     3    3    3    3    3    4    7    8    8    9   10   11   12   13   15   17   17   17   17   17 
LCS_GDT     E      36     E      36      3    4   12     3    3    3    3    3    4    7    8    8    9   10   11   12   13   15   17   17   17   17   17 
LCS_GDT     Y      37     Y      37      3    4   12     3    3    3    3    3    4    7    8    8    9    9   11   12   13   15   17   17   17   17   17 
LCS_GDT     L      38     L      38      4    5   11     3    3    5    5    5    5    7    8    8    9    9   11   11   13   15   17   17   17   17   17 
LCS_GDT     K      39     K      39      4    5   11     3    3    5    5    5    5    7    8    8    9    9   11   11   13   15   17   17   17   17   17 
LCS_GDT     G      40     G      40      4    5   11     3    3    5    5    5    5    7    8    8    9    9   11   11   13   15   17   17   17   17   17 
LCS_GDT     F      41     F      41      4    5   11     3    3    5    5    5    5    7    8    8    9    9   11   11   13   15   17   17   17   17   17 
LCS_GDT     R      42     R      42      4    5   11     3    3    5    5    5    5    7    8    8    9    9   11   11   13   15   17   17   17   17   17 
LCS_AVERAGE  LCS_A:  17.04  (  10.36   12.89   27.87 )

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      4      5      5      6      6      6      7      8      8      9     10     11     12     13     15     17     17     17     17     17 
GDT PERCENT_CA   9.52  11.90  11.90  14.29  14.29  14.29  16.67  19.05  19.05  21.43  23.81  26.19  28.57  30.95  35.71  40.48  40.48  40.48  40.48  40.48
GDT RMS_LOCAL    0.13   0.34   0.34   0.97   0.97   0.97   1.80   3.16   3.16   3.60   4.16   4.47   4.70   5.47   5.78   6.10   6.10   6.10   6.10   6.10
GDT RMS_ALL_CA   9.89  10.20  10.20  10.06  10.06  10.06  11.27   8.81   8.81   8.10   7.03   6.91   6.88   6.17   6.18   6.10   6.10   6.10   6.10   6.10

#      Molecule1      Molecule2       DISTANCE
LGA    E      26      E      26         12.963
LGA    K      27      K      27         14.308
LGA    A      28      A      28         12.129
LGA    E      29      E      29         12.828
LGA    Q      30      Q      30         14.160
LGA    Q      31      Q      31         12.581
LGA    K      32      K      32          9.343
LGA    L      33      L      33          7.746
LGA    R      34      R      34          7.049
LGA    Q      35      Q      35          3.754
LGA    E      36      E      36          3.793
LGA    Y      37      Y      37          3.616
LGA    L      38      L      38          3.297
LGA    K      39      K      39          2.470
LGA    G      40      G      40          3.480
LGA    F      41      F      41          1.878
LGA    R      42      R      42          2.425

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   43   42    4.0      8    3.16    21.429    17.789     0.245

LGA_LOCAL      RMSD =  3.163  Number of atoms =    8  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  8.812  Number of atoms =   17 
Std_ALL_ATOMS  RMSD =  6.104  (standard rmsd on all 17 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.955428 * X  +  -0.090096 * Y  +  -0.281141 * Z  +  -5.723654
  Y_new =   0.286440 * X  +   0.052321 * Y  +   0.956668 * Z  + -34.413731
  Z_new =  -0.071483 * X  +  -0.994558 * Y  +   0.075797 * Z  + -36.612114 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.494732    1.646861  [ DEG:   -85.6418     94.3582 ]
  Theta =   0.071544    3.070049  [ DEG:     4.0991    175.9008 ]
  Phi   =   0.291276   -2.850317  [ DEG:    16.6889   -163.3111 ]
 
# 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: T0335AL381_5                                  
REMARK     2: T0335.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0335AL381_5.T0335.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   43   42   4.0    8   3.16  17.789     6.10
REMARK  ---------------------------------------------------------- 
MOLECULE T0335AL381_5
REMARK Aligment from pdb entry: 1qw7A
ATOM      1  N   GLU    26      -1.539  -2.266  19.526  1.00  0.00              
ATOM      2  CA  GLU    26      -0.335  -2.727  20.188  1.00  0.00              
ATOM      3  C   GLU    26       0.635  -3.499  19.337  1.00  0.00              
ATOM      4  O   GLU    26       1.423  -4.260  19.872  1.00  0.00              
ATOM      5  N   LYS    27       0.626  -3.290  18.024  1.00  0.00              
ATOM      6  CA  LYS    27       1.541  -4.026  17.161  1.00  0.00              
ATOM      7  C   LYS    27       2.539  -3.179  16.415  1.00  0.00              
ATOM      8  O   LYS    27       2.904  -3.503  15.302  1.00  0.00              
ATOM      9  N   ALA    28       2.999  -2.092  17.021  1.00  0.00              
ATOM     10  CA  ALA    28       3.952  -1.230  16.326  1.00  0.00              
ATOM     11  C   ALA    28       5.146  -2.000  15.797  1.00  0.00              
ATOM     12  O   ALA    28       5.627  -1.705  14.726  1.00  0.00              
ATOM     13  N   GLU    29       5.608  -3.010  16.531  1.00  0.00              
ATOM     14  CA  GLU    29       6.774  -3.796  16.113  1.00  0.00              
ATOM     15  C   GLU    29       6.563  -4.681  14.892  1.00  0.00              
ATOM     16  O   GLU    29       7.536  -5.162  14.308  1.00  0.00              
ATOM     17  N   GLN    30       5.301  -4.862  14.499  1.00  0.00              
ATOM     18  CA  GLN    30       4.927  -5.751  13.394  1.00  0.00              
ATOM     19  C   GLN    30       4.665  -5.033  12.089  1.00  0.00              
ATOM     20  O   GLN    30       4.364  -5.673  11.094  1.00  0.00              
ATOM     21  N   GLN    31       4.738  -3.718  12.113  1.00  0.00              
ATOM     22  CA  GLN    31       4.433  -2.922  10.921  1.00  0.00              
ATOM     23  C   GLN    31       5.636  -2.563  10.068  1.00  0.00              
ATOM     24  O   GLN    31       6.685  -2.203  10.597  1.00  0.00              
ATOM     25  N   LYS    32       5.473  -2.664   8.745  1.00  0.00              
ATOM     26  CA  LYS    32       6.512  -2.269   7.793  1.00  0.00              
ATOM     27  C   LYS    32       5.750  -1.375   6.798  1.00  0.00              
ATOM     28  O   LYS    32       4.649  -1.699   6.360  1.00  0.00              
ATOM     29  N   LEU    33       6.333  -0.239   6.460  1.00  0.00              
ATOM     30  CA  LEU    33       5.647   0.702   5.597  1.00  0.00              
ATOM     31  C   LEU    33       6.404   0.950   4.314  1.00  0.00              
ATOM     32  O   LEU    33       7.641   0.966   4.311  1.00  0.00              
ATOM     33  N   ARG    34       5.675   1.160   3.220  1.00  0.00              
ATOM     34  CA  ARG    34       6.334   1.450   1.951  1.00  0.00              
ATOM     35  C   ARG    34       5.385   2.134   0.957  1.00  0.00              
ATOM     36  O   ARG    34       4.238   2.409   1.306  1.00  0.00              
ATOM     37  N   GLN    35       5.875   2.424  -0.251  1.00  0.00              
ATOM     38  CA  GLN    35       5.105   3.144  -1.283  1.00  0.00              
ATOM     39  C   GLN    35       4.754   2.226  -2.436  1.00  0.00              
ATOM     40  O   GLN    35       3.843   2.516  -3.198  1.00  0.00              
ATOM     41  N   GLU    36       5.490   1.126  -2.593  1.00  0.00              
ATOM     42  CA  GLU    36       5.252   0.241  -3.735  1.00  0.00              
ATOM     43  C   GLU    36       5.293   1.117  -4.997  1.00  0.00              
ATOM     44  O   GLU    36       4.404   1.066  -5.846  1.00  0.00              
ATOM     45  N   TYR    37       6.336   1.938  -5.086  1.00  0.00              
ATOM     46  CA  TYR    37       6.546   2.821  -6.220  1.00  0.00              
ATOM     47  C   TYR    37       7.501   2.198  -7.256  1.00  0.00              
ATOM     48  O   TYR    37       8.009   1.100  -7.077  1.00  0.00              
ATOM     49  N   LEU    38       7.728   2.918  -8.346  1.00  0.00              
ATOM     50  CA  LEU    38       8.624   2.483  -9.412  1.00  0.00              
ATOM     51  C   LEU    38       8.913   3.691 -10.303  1.00  0.00              
ATOM     52  O   LEU    38       8.318   4.760 -10.114  1.00  0.00              
ATOM     53  N   LYS    39       9.823   3.526 -11.253  1.00  0.00              
ATOM     54  CA  LYS    39      10.219   4.628 -12.108  1.00  0.00              
ATOM     55  C   LYS    39       9.978   4.262 -13.553  1.00  0.00              
ATOM     56  O   LYS    39      10.055   5.106 -14.438  1.00  0.00              
ATOM     57  N   GLY    40       9.649   2.987 -13.756  1.00  0.00              
ATOM     58  CA  GLY    40       9.317   2.454 -15.073  1.00  0.00              
ATOM     59  C   GLY    40       8.263   1.381 -14.807  1.00  0.00              
ATOM     60  O   GLY    40       8.390   0.658 -13.820  1.00  0.00              
ATOM     61  N   PHE    41       7.253   1.240 -15.667  1.00  0.00              
ATOM     62  CA  PHE    41       6.172   0.263 -15.440  1.00  0.00              
ATOM     63  C   PHE    41       5.617  -0.237 -16.802  1.00  0.00              
ATOM     64  O   PHE    41       4.846   0.460 -17.476  1.00  0.00              
ATOM     65  N   ARG    42       6.017  -1.437 -17.218  1.00  0.00              
ATOM     66  CA  ARG    42       5.604  -1.965 -18.520  1.00  0.00              
ATOM     67  C   ARG    42       4.593  -3.109 -18.458  1.00  0.00              
ATOM     68  O   ARG    42       3.998  -3.465 -19.464  1.00  0.00              
ATOM     69  N   SER    43       4.415  -3.682 -17.277  1.00  0.00              
ATOM     70  CA  SER    43       3.514  -4.812 -17.108  1.00  0.00              
ATOM     71  C   SER    43       2.054  -4.425 -16.991  1.00  0.00              
ATOM     72  O   SER    43       1.220  -5.234 -16.563  1.00  0.00              
ATOM     73  N   SER    44       1.735  -3.198 -17.396  1.00  0.00              
ATOM     74  CA  SER    44       0.355  -2.726 -17.354  1.00  0.00              
ATOM     75  C   SER    44       0.035  -1.908 -18.604  1.00  0.00              
ATOM     76  O   SER    44       0.737  -2.026 -19.626  1.00  0.00              
ATOM     77  N   MET    45      -1.014  -1.088 -18.559  1.00  0.00              
ATOM     78  CA  MET    45      -1.336  -0.315 -19.756  1.00  0.00              
ATOM     79  C   MET    45      -0.210   0.708 -20.028  1.00  0.00              
ATOM     80  O   MET    45       0.553   1.065 -19.133  1.00  0.00              
ATOM     81  N   LYS    46      -0.107   1.155 -21.268  1.00  0.00              
ATOM     82  CA  LYS    46       0.925   2.112 -21.643  1.00  0.00              
ATOM     83  C   LYS    46       0.645   3.451 -20.975  1.00  0.00              
ATOM     84  O   LYS    46      -0.501   3.851 -20.810  1.00  0.00              
ATOM     85  N   ASN    47       1.701   4.124 -20.565  1.00  0.00              
ATOM     86  CA  ASN    47       1.557   5.420 -19.931  1.00  0.00              
ATOM     87  C   ASN    47       0.977   5.416 -18.510  1.00  0.00              
ATOM     88  O   ASN    47       0.625   6.465 -17.978  1.00  0.00              
ATOM     89  N   THR    48       0.899   4.241 -17.888  1.00  0.00              
ATOM     90  CA  THR    48       0.400   4.154 -16.517  1.00  0.00              
ATOM     91  C   THR    48       1.389   4.870 -15.577  1.00  0.00              
ATOM     92  O   THR    48       0.987   5.441 -14.556  1.00  0.00              
ATOM     93  N   LEU    49       2.675   4.835 -15.918  1.00  0.00              
ATOM     94  CA  LEU    49       3.695   5.495 -15.094  1.00  0.00              
ATOM     95  C   LEU    49       3.375   6.981 -15.024  1.00  0.00              
ATOM     96  O   LEU    49       3.484   7.600 -13.963  1.00  0.00              
ATOM     97  N   LYS    50       2.958   7.561 -16.144  1.00  0.00              
ATOM     98  CA  LYS    50       2.617   8.986 -16.156  1.00  0.00              
ATOM     99  C   LYS    50       1.431   9.322 -15.277  1.00  0.00              
ATOM    100  O   LYS    50       1.386  10.391 -14.675  1.00  0.00              
ATOM    101  N   SER    51       0.450   8.432 -15.248  1.00  0.00              
ATOM    102  CA  SER    51      -0.722   8.643 -14.426  1.00  0.00              
ATOM    103  C   SER    51      -0.322   8.544 -12.944  1.00  0.00              
ATOM    104  O   SER    51      -0.756   9.339 -12.111  1.00  0.00              
ATOM    105  N   VAL    52       0.514   7.576 -12.604  1.00  0.00              
ATOM    106  CA  VAL    52       0.928   7.433 -11.205  1.00  0.00              
ATOM    107  C   VAL    52       1.819   8.588 -10.774  1.00  0.00              
ATOM    108  O   VAL    52       1.692   9.093  -9.653  1.00  0.00              
ATOM    109  N   LYS    53       2.715   9.022 -11.655  1.00  0.00              
ATOM    110  CA  LYS    53       3.590  10.131 -11.288  1.00  0.00              
ATOM    111  C   LYS    53       2.776  11.398 -11.027  1.00  0.00              
ATOM    112  O   LYS    53       3.168  12.237 -10.219  1.00  0.00              
ATOM    113  N   ILE    54       1.640  11.543 -11.710  1.00  0.00              
ATOM    114  CA  ILE    54       0.796  12.703 -11.464  1.00  0.00              
ATOM    115  C   ILE    54       0.119  12.537 -10.128  1.00  0.00              
ATOM    116  O   ILE    54      -0.069  13.506  -9.403  1.00  0.00              
ATOM    117  N   ILE    55      -0.257  11.308  -9.799  1.00  0.00              
ATOM    118  CA  ILE    55      -0.917  11.032  -8.526  1.00  0.00              
ATOM    119  C   ILE    55      -0.001  11.265  -7.350  1.00  0.00              
ATOM    120  O   ILE    55      -0.396  11.862  -6.341  1.00  0.00              
ATOM    121  N   ASP    56       1.219  10.771  -7.473  1.00  0.00              
ATOM    122  CA  ASP    56       2.199  10.896  -6.400  1.00  0.00              
ATOM    123  C   ASP    56       3.544  11.415  -6.899  1.00  0.00              
ATOM    124  O   ASP    56       4.484  10.653  -7.081  1.00  0.00              
ATOM    125  N   PRO    57       3.647  12.729  -7.132  1.00  0.00              
ATOM    126  CA  PRO    57       4.886  13.349  -7.608  1.00  0.00              
ATOM    127  C   PRO    57       6.059  13.125  -6.665  1.00  0.00              
ATOM    128  O   PRO    57       7.215  13.177  -7.095  1.00  0.00              
ATOM    129  N   GLU    58       5.778  12.890  -5.382  1.00  0.00              
ATOM    130  CA  GLU    58       6.856  12.637  -4.423  1.00  0.00              
ATOM    131  C   GLU    58       7.475  11.256  -4.620  1.00  0.00              
ATOM    132  O   GLU    58       8.582  11.004  -4.172  1.00  0.00              
ATOM    133  N   GLY    59       6.736  10.356  -5.268  1.00  0.00              
ATOM    134  CA  GLY    59       7.259   9.026  -5.528  1.00  0.00              
ATOM    135  C   GLY    59       7.639   8.324  -4.237  1.00  0.00              
ATOM    136  O   GLY    59       6.848   8.296  -3.309  1.00  0.00              
ATOM    137  N   ASN    60       8.843   7.761  -4.168  1.00  0.00              
ATOM    138  CA  ASN    60       9.253   7.046  -2.965  1.00  0.00              
ATOM    139  C   ASN    60       9.394   7.908  -1.710  1.00  0.00              
ATOM    140  O   ASN    60       9.362   7.368  -0.578  1.00  0.00              
ATOM    141  N   ASP    61       9.573   9.223  -1.906  1.00  0.00              
ATOM    142  CA  ASP    61       9.710  10.168  -0.784  1.00  0.00              
ATOM    143  C   ASP    61       8.354  10.435  -0.104  1.00  0.00              
ATOM    144  O   ASP    61       8.276  11.095   0.947  1.00  0.00              
ATOM    145  N   VAL    62       7.281   9.886  -0.675  1.00  0.00              
ATOM    146  CA  VAL    62       5.943  10.066  -0.111  1.00  0.00              
ATOM    147  C   VAL    62       5.878   9.586   1.330  1.00  0.00              
ATOM    148  O   VAL    62       5.216  10.216   2.166  1.00  0.00              
ATOM    149  N   THR    63       6.544   8.482   1.659  1.00  0.00              
ATOM    150  CA  THR    63       6.455   8.013   3.046  1.00  0.00              
ATOM    151  C   THR    63       7.015   9.047   4.019  1.00  0.00              
ATOM    152  O   THR    63       6.302   9.520   4.881  1.00  0.00              
ATOM    153  N   PRO    64       8.298   9.420   3.881  1.00  0.00              
ATOM    154  CA  PRO    64       8.864  10.420   4.800  1.00  0.00              
ATOM    155  C   PRO    64       8.247  11.824   4.725  1.00  0.00              
ATOM    156  O   PRO    64       8.052  12.482   5.755  1.00  0.00              
ATOM    157  N   GLU    65       7.949  12.291   3.508  1.00  0.00              
ATOM    158  CA  GLU    65       7.389  13.626   3.316  1.00  0.00              
ATOM    159  C   GLU    65       5.919  13.821   3.693  1.00  0.00              
ATOM    160  O   GLU    65       5.563  14.869   4.230  1.00  0.00              
ATOM    161  N   LYS    66       5.068  12.824   3.441  1.00  0.00              
ATOM    162  CA  LYS    66       3.637  12.984   3.741  1.00  0.00              
ATOM    163  C   LYS    66       3.088  12.115   4.848  1.00  0.00              
ATOM    164  O   LYS    66       2.352  12.595   5.706  1.00  0.00              
ATOM    165  N   LEU    67       3.444  10.837   4.818  1.00  0.00              
ATOM    166  CA  LEU    67       2.942   9.870   5.785  1.00  0.00              
ATOM    167  C   LEU    67       3.472  10.008   7.224  1.00  0.00              
ATOM    168  O   LEU    67       2.687   9.976   8.192  1.00  0.00              
ATOM    169  N   LYS    68       4.787  10.156   7.382  1.00  0.00              
ATOM    170  CA  LYS    68       5.344  10.284   8.720  1.00  0.00              
ATOM    171  C   LYS    68       4.764  11.534   9.405  1.00  0.00              
ATOM    172  O   LYS    68       4.351  11.472  10.554  1.00  0.00              
END
