
#######################################################
#                                                     #
#                        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   34 (  136),  selected   29 , name T0309AL381_5
# Molecule2: number of CA atoms   62 (  501),  selected   29 , name T0309.pdb
# PARAMETERS: T0309AL381_5.T0309.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:    18        35 - 52          4.99    18.47
  LCS_AVERAGE:     23.47

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6        35 - 40          0.96    16.82
  LCS_AVERAGE:      6.73

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6        35 - 40          0.96    16.82
  LCS_AVERAGE:      6.34

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:   62
LCS_GDT     F      35     F      35      6    6   18     3    4    6    6    7    9   10   11   12   12   15   16   16   17   18   18   19   20   20   20 
LCS_GDT     K      36     K      36      6    6   18     4    4    6    6    7    9   10   11   12   12   15   16   16   17   18   18   19   20   20   20 
LCS_GDT     E      37     E      37      6    6   18     4    4    6    6    7    9   10   11   12   12   15   16   16   17   18   18   19   20   20   20 
LCS_GDT     I      38     I      38      6    6   18     4    4    6    6    7    8   10   11   12   12   15   16   16   17   18   18   19   20   20   20 
LCS_GDT     L      39     L      39      6    6   18     4    4    6    6    7    9   10   11   12   12   15   16   16   17   18   18   19   20   20   20 
LCS_GDT     S      40     S      40      6    6   18     4    4    6    6    7    9   10   11   12   12   15   16   16   17   18   18   19   20   20   20 
LCS_GDT     E      41     E      41      4    5   18     3    4    5    5    5    7    8   10   12   12   15   16   16   17   18   18   19   20   20   20 
LCS_GDT     F      42     F      42      4    5   18     4    4    5    6    7    9   10   11   12   12   15   16   16   17   18   18   19   20   20   20 
LCS_GDT     N      43     N      43      4    5   18     3    4    5    6    7    8    8    9   10   12   13   16   16   17   18   18   19   20   20   20 
LCS_GDT     G      44     G      44      4    5   18     3    4    4    4    5    6    7    9   10   12   13   14   14   16   18   18   19   20   20   20 
LCS_GDT     K      45     K      45      4    5   18     3    4    4    4    5    8    9   11   12   12   15   16   16   17   18   18   19   20   20   20 
LCS_GDT     N      46     N      46      3    5   18     3    3    3    4    5    8    9   11   12   12   15   16   16   17   18   18   19   20   20   20 
LCS_GDT     V      47     V      47      3    3   18     3    3    3    4    5    8    9   11   12   12   15   16   16   17   18   18   19   20   20   20 
LCS_GDT     S      48     S      48      3    3   18     3    3    3    4    4    5    8   11   12   12   15   16   16   17   18   18   19   20   20   20 
LCS_GDT     I      49     I      49      3    3   18     3    3    5    6    7    9   10   10   11   12   15   16   16   17   18   18   19   20   20   20 
LCS_GDT     T      50     T      50      3    3   18     4    4    5    6    7    9   10   10   11   12   15   16   16   17   18   18   19   20   20   20 
LCS_GDT     V      51     V      51      3    3   18     4    4    5    6    7    9   10   10   11   12   15   16   16   17   18   18   19   20   20   20 
LCS_GDT     K      52     K      52      3    3   18     0    3    3    3    4    5    5    8    8   11   12   13   14   17   18   18   19   20   20   20 
LCS_GDT     E      53     E      53      3    3    9     1    3    3    3    3    5    5    5    8    8    9   13   14   14   15   16   17   20   20   20 
LCS_GDT     E      54     E      54      3    3    8     0    3    3    3    3    3    4    8    8   10   12   13   14   14   16   18   19   20   20   20 
LCS_GDT     N      55     N      55      3    3    9     0    3    3    3    3    4    4    4    7    7    9    9    9    9   11   15   15   16   16   17 
LCS_GDT     E      56     E      56      3    3    9     0    3    3    3    4    4    4    5    7    8    9    9    9    9   11   13   14   14   15   15 
LCS_GDT     L      57     L      57      3    3    9     3    3    3    3    4    4    5    6    8    8    9    9   10   10   11   13   14   14   15   15 
LCS_GDT     P      58     P      58      3    3    9     3    3    3    3    4    5    5    6    8    8    9    9   10   10   11   13   14   14   15   15 
LCS_GDT     V      59     V      59      4    4    9     3    3    4    4    4    5    5    6    8    8    9    9   10   10   11   13   14   14   15   15 
LCS_GDT     K      60     K      60      4    4    9     3    3    4    4    4    5    5    6    8    8    9    9   10   10   11   13   14   14   15   15 
LCS_GDT     G      61     G      61      4    4    9     3    3    4    4    4    5    5    6    7    8    9    9   10   10   10   11   14   14   15   15 
LCS_GDT     V      62     V      62      4    4    9     3    3    4    4    4    5    5    6    8    8    9    9   10   10   11   13   14   14   15   15 
LCS_GDT     E      63     E      63      3    3    9     3    3    3    3    3    3    3    6    8    8    9    9   10   10   10   13   14   14   15   15 
LCS_AVERAGE  LCS_A:  12.18  (   6.34    6.73   23.47 )

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      4      6      6      7      9     10     11     12     12     15     16     16     17     18     18     19     20     20     20 
GDT PERCENT_CA   6.45   6.45   9.68   9.68  11.29  14.52  16.13  17.74  19.35  19.35  24.19  25.81  25.81  27.42  29.03  29.03  30.65  32.26  32.26  32.26
GDT RMS_LOCAL    0.27   0.27   0.96   0.96   1.40   2.16   2.34   3.05   3.29   3.29   4.12   4.32   4.32   4.73   4.99   4.99   5.44   5.75   5.75   5.75
GDT RMS_ALL_CA  16.99  16.99  16.82  16.82  17.61  17.76  17.54  17.14  16.25  16.25  16.66  17.16  17.16  18.30  18.47  18.47  18.59  19.13  19.13  19.13

#      Molecule1      Molecule2       DISTANCE
LGA    F      35      F      35          1.462
LGA    K      36      K      36          3.847
LGA    E      37      E      37          3.087
LGA    I      38      I      38          2.203
LGA    L      39      L      39          3.219
LGA    S      40      S      40          1.894
LGA    E      41      E      41          5.381
LGA    F      42      F      42          3.806
LGA    N      43      N      43          6.317
LGA    G      44      G      44          6.874
LGA    K      45      K      45          3.033
LGA    N      46      N      46          3.833
LGA    V      47      V      47          2.952
LGA    S      48      S      48          3.630
LGA    I      49      I      49          7.074
LGA    T      50      T      50          8.909
LGA    V      51      V      51          9.506
LGA    K      52      K      52         14.539
LGA    E      53      E      53         19.969
LGA    E      54      E      54         18.836
LGA    N      55      N      55         21.783
LGA    E      56      E      56         24.960
LGA    L      57      L      57         25.967
LGA    P      58      P      58         26.276
LGA    V      59      V      59         28.922
LGA    K      60      K      60         32.946
LGA    G      61      G      61         30.961
LGA    V      62      V      62         26.367
LGA    E      63      E      63         29.683

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   34   62    4.0     11    3.05    15.726    14.211     0.349

LGA_LOCAL      RMSD =  3.052  Number of atoms =   11  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 16.943  Number of atoms =   29 
Std_ALL_ATOMS  RMSD = 12.271  (standard rmsd on all 29 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.534577 * X  +   0.070296 * Y  +   0.842191 * Z  +   6.275183
  Y_new =  -0.824158 * X  +   0.177210 * Y  +  -0.537921 * Z  +  -4.402309
  Z_new =  -0.187058 * X  +  -0.981659 * Y  +  -0.036797 * Z  +   3.702874 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.608264    1.533329  [ DEG:   -92.1467     87.8533 ]
  Theta =   0.188167    2.953426  [ DEG:    10.7812    169.2188 ]
  Phi   =  -2.146210    0.995383  [ DEG:  -122.9688     57.0312 ]
 
# 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: T0309AL381_5                                  
REMARK     2: T0309.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0309AL381_5.T0309.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   34   62   4.0   11   3.05  14.211    12.27
REMARK  ---------------------------------------------------------- 
MOLECULE T0309AL381_5
REMARK Aligment from pdb entry: 1pn5A
ATOM      1  N   PHE    35      -1.619  -7.817  -6.106  1.00  0.00              
ATOM      2  CA  PHE    35      -2.437  -9.000  -5.831  1.00  0.00              
ATOM      3  C   PHE    35      -3.263  -8.709  -4.575  1.00  0.00              
ATOM      4  O   PHE    35      -4.480  -8.895  -4.550  1.00  0.00              
ATOM      5  N   LYS    36      -2.600  -8.162  -3.550  1.00  0.00              
ATOM      6  CA  LYS    36      -3.205  -7.795  -2.275  1.00  0.00              
ATOM      7  C   LYS    36      -3.998  -6.479  -2.346  1.00  0.00              
ATOM      8  O   LYS    36      -4.241  -5.860  -1.310  1.00  0.00              
ATOM      9  N   GLU    37      -4.360  -5.993  -3.535  1.00  0.00              
ATOM     10  CA  GLU    37      -5.310  -4.893  -3.702  1.00  0.00              
ATOM     11  C   GLU    37      -6.676  -5.434  -4.132  1.00  0.00              
ATOM     12  O   GLU    37      -7.689  -4.778  -3.891  1.00  0.00              
ATOM     13  N   ILE    38      -6.729  -6.619  -4.752  1.00  0.00              
ATOM     14  CA  ILE    38      -7.985  -7.209  -5.200  1.00  0.00              
ATOM     15  C   ILE    38      -8.840  -7.582  -3.977  1.00  0.00              
ATOM     16  O   ILE    38     -10.006  -7.181  -3.905  1.00  0.00              
ATOM     17  N   LEU    39      -8.251  -8.287  -3.002  1.00  0.00              
ATOM     18  CA  LEU    39      -8.944  -8.736  -1.798  1.00  0.00              
ATOM     19  C   LEU    39      -8.718  -7.789  -0.627  1.00  0.00              
ATOM     20  O   LEU    39      -7.681  -7.133  -0.505  1.00  0.00              
ATOM     21  N   SER    40      -9.705  -7.762   0.259  1.00  0.00              
ATOM     22  CA  SER    40      -9.853  -6.905   1.437  1.00  0.00              
ATOM     23  C   SER    40     -10.100  -7.823   2.632  1.00  0.00              
ATOM     24  O   SER    40      -9.866  -9.028   2.517  1.00  0.00              
ATOM     25  N   GLU    41     -10.496  -7.316   3.811  1.00  0.00              
ATOM     26  CA  GLU    41     -10.555  -8.151   5.026  1.00  0.00              
ATOM     27  C   GLU    41     -11.393  -9.415   4.836  1.00  0.00              
ATOM     28  O   GLU    41     -11.089 -10.400   5.506  1.00  0.00              
ATOM     29  N   PHE    42     -12.385  -9.399   3.940  1.00  0.00              
ATOM     30  CA  PHE    42     -13.292 -10.508   3.640  1.00  0.00              
ATOM     31  C   PHE    42     -12.541 -11.830   3.471  1.00  0.00              
ATOM     32  O   PHE    42     -13.053 -12.864   3.902  1.00  0.00              
ATOM     33  N   ASN    43     -11.326 -11.815   2.911  1.00  0.00              
ATOM     34  CA  ASN    43     -10.465 -12.986   2.904  1.00  0.00              
ATOM     35  C   ASN    43      -8.970 -12.661   3.079  1.00  0.00              
ATOM     36  O   ASN    43      -8.204 -13.576   3.340  1.00  0.00              
ATOM     37  N   GLY    44      -8.509 -11.401   3.044  1.00  0.00              
ATOM     38  CA  GLY    44      -7.120 -11.034   3.388  1.00  0.00              
ATOM     39  C   GLY    44      -6.779 -11.396   4.843  1.00  0.00              
ATOM     40  O   GLY    44      -5.653 -11.788   5.163  1.00  0.00              
ATOM     41  N   LYS    45      -7.746 -11.225   5.746  1.00  0.00              
ATOM     42  CA  LYS    45      -7.652 -11.729   7.120  1.00  0.00              
ATOM     43  C   LYS    45      -7.546 -13.242   7.103  1.00  0.00              
ATOM     44  O   LYS    45      -6.600 -13.755   7.685  1.00  0.00              
ATOM     45  N   ASN    46      -8.445 -13.955   6.439  1.00  0.00              
ATOM     46  CA  ASN    46      -8.348 -15.409   6.390  1.00  0.00              
ATOM     47  C   ASN    46      -7.010 -15.849   5.804  1.00  0.00              
ATOM     48  O   ASN    46      -6.391 -16.753   6.345  1.00  0.00              
ATOM     49  N   VAL    47      -6.481 -15.151   4.805  1.00  0.00              
ATOM     50  CA  VAL    47      -5.183 -15.437   4.232  1.00  0.00              
ATOM     51  C   VAL    47      -4.090 -15.399   5.300  1.00  0.00              
ATOM     52  O   VAL    47      -3.410 -16.398   5.517  1.00  0.00              
ATOM     53  N   SER    48      -3.911 -14.261   5.987  1.00  0.00              
ATOM     54  CA  SER    48      -2.854 -14.129   6.994  1.00  0.00              
ATOM     55  C   SER    48      -3.049 -15.100   8.176  1.00  0.00              
ATOM     56  O   SER    48      -2.079 -15.404   8.871  1.00  0.00              
ATOM     57  N   ILE    49      -4.285 -15.551   8.418  1.00  0.00              
ATOM     58  CA  ILE    49      -4.694 -16.504   9.422  1.00  0.00              
ATOM     59  C   ILE    49      -4.267 -17.917   9.006  1.00  0.00              
ATOM     60  O   ILE    49      -3.405 -18.502   9.655  1.00  0.00              
ATOM     61  N   THR    50      -4.840 -18.447   7.920  1.00  0.00              
ATOM     62  CA  THR    50      -4.619 -19.788   7.369  1.00  0.00              
ATOM     63  C   THR    50      -3.127 -20.084   7.206  1.00  0.00              
ATOM     64  O   THR    50      -2.650 -21.143   7.621  1.00  0.00              
ATOM     65  N   VAL    51      -2.382 -19.108   6.678  1.00  0.00              
ATOM     66  CA  VAL    51      -0.935 -19.026   6.634  1.00  0.00              
ATOM     67  C   VAL    51      -0.323 -19.496   7.950  1.00  0.00              
ATOM     68  O   VAL    51       0.483 -20.428   7.961  1.00  0.00              
ATOM     69  N   LYS    52      -0.673 -18.844   9.056  1.00  0.00              
ATOM     70  CA  LYS    52      -0.035 -19.067  10.341  1.00  0.00              
ATOM     71  C   LYS    52      -0.357 -20.449  10.914  1.00  0.00              
ATOM     72  O   LYS    52       0.374 -20.937  11.776  1.00  0.00              
ATOM     73  N   GLU    53      -1.437 -21.078  10.442  1.00  0.00              
ATOM     74  CA  GLU    53      -1.788 -22.442  10.813  1.00  0.00              
ATOM     75  C   GLU    53      -0.904 -23.421  10.041  1.00  0.00              
ATOM     76  O   GLU    53      -0.261 -24.290  10.634  1.00  0.00              
ATOM     77  N   GLU    54      -0.840 -23.261   8.712  1.00  0.00              
ATOM     78  CA  GLU    54      -0.067 -24.092   7.810  1.00  0.00              
ATOM     79  C   GLU    54       1.407 -24.031   8.201  1.00  0.00              
ATOM     80  O   GLU    54       2.035 -25.080   8.330  1.00  0.00              
ATOM     81  N   ASN    55      -7.781 -19.910  -7.079  1.00  0.00              
ATOM     82  CA  ASN    55      -7.056 -20.435  -8.229  1.00  0.00              
ATOM     83  C   ASN    55      -6.670 -19.310  -9.178  1.00  0.00              
ATOM     84  O   ASN    55      -5.614 -19.388  -9.790  1.00  0.00              
ATOM     85  N   GLU    56      -7.491 -18.259  -9.277  1.00  0.00              
ATOM     86  CA  GLU    56      -7.171 -17.090 -10.080  1.00  0.00              
ATOM     87  C   GLU    56      -5.846 -16.479  -9.632  1.00  0.00              
ATOM     88  O   GLU    56      -5.022 -16.161 -10.477  1.00  0.00              
ATOM     89  N   LEU    57      -5.596 -16.380  -8.325  1.00  0.00              
ATOM     90  CA  LEU    57      -4.395 -15.742  -7.799  1.00  0.00              
ATOM     91  C   LEU    57      -3.196 -16.631  -8.068  1.00  0.00              
ATOM     92  O   LEU    57      -2.189 -16.173  -8.596  1.00  0.00              
ATOM     93  N   PRO    58      -3.316 -17.915  -7.736  1.00  0.00              
ATOM     94  CA  PRO    58      -2.330 -18.938  -8.045  1.00  0.00              
ATOM     95  C   PRO    58      -2.006 -19.005  -9.546  1.00  0.00              
ATOM     96  O   PRO    58      -0.906 -19.431  -9.912  1.00  0.00              
ATOM     97  N   VAL    59      -2.948 -18.623 -10.412  1.00  0.00              
ATOM     98  CA  VAL    59      -2.756 -18.463 -11.842  1.00  0.00              
ATOM     99  C   VAL    59      -2.002 -17.157 -12.111  1.00  0.00              
ATOM    100  O   VAL    59      -0.887 -17.208 -12.612  1.00  0.00              
ATOM    101  N   LYS    60      -2.558 -15.999 -11.745  1.00  0.00              
ATOM    102  CA  LYS    60      -2.003 -14.655 -11.940  1.00  0.00              
ATOM    103  C   LYS    60      -0.543 -14.564 -11.467  1.00  0.00              
ATOM    104  O   LYS    60       0.306 -13.993 -12.158  1.00  0.00              
ATOM    105  N   GLY    61      -0.236 -15.168 -10.317  1.00  0.00              
ATOM    106  CA  GLY    61       1.087 -15.255  -9.711  1.00  0.00              
ATOM    107  C   GLY    61       2.116 -15.953 -10.603  1.00  0.00              
ATOM    108  O   GLY    61       3.310 -15.759 -10.392  1.00  0.00              
ATOM    109  N   VAL    62       1.680 -16.744 -11.586  1.00  0.00              
ATOM    110  CA  VAL    62       2.518 -17.594 -12.421  1.00  0.00              
ATOM    111  C   VAL    62       2.281 -17.353 -13.919  1.00  0.00              
ATOM    112  O   VAL    62       3.029 -17.865 -14.744  1.00  0.00              
ATOM    113  N   GLU    63       1.276 -16.559 -14.288  1.00  0.00              
ATOM    114  CA  GLU    63       0.767 -16.328 -15.641  1.00  0.00              
ATOM    115  C   GLU    63       1.753 -15.597 -16.564  1.00  0.00              
ATOM    116  O   GLU    63       1.411 -15.292 -17.706  1.00  0.00              
ATOM    117  N   MET    64       2.951 -15.262 -16.084  1.00  0.00              
ATOM    118  CA  MET    64       3.917 -14.473 -16.836  1.00  0.00              
ATOM    119  C   MET    64       3.441 -13.035 -17.069  1.00  0.00              
ATOM    120  O   MET    64       4.005 -12.342 -17.914  1.00  0.00              
ATOM    121  N   ALA    65       2.400 -12.581 -16.361  1.00  0.00              
ATOM    122  CA  ALA    65       1.573 -11.453 -16.786  1.00  0.00              
ATOM    123  C   ALA    65       1.640 -10.232 -15.871  1.00  0.00              
ATOM    124  O   ALA    65       1.370  -9.127 -16.335  1.00  0.00              
ATOM    125  N   GLY    66       1.972 -10.430 -14.594  1.00  0.00              
ATOM    126  CA  GLY    66       2.022  -9.359 -13.607  1.00  0.00              
ATOM    127  C   GLY    66       0.638  -8.787 -13.287  1.00  0.00              
ATOM    128  O   GLY    66       0.515  -7.573 -13.128  1.00  0.00              
ATOM    129  N   ASP    67      -0.379  -9.654 -13.148  1.00  0.00              
ATOM    130  CA  ASP    67      -1.806  -9.316 -13.165  1.00  0.00              
ATOM    131  C   ASP    67      -2.219  -8.844 -14.569  1.00  0.00              
ATOM    132  O   ASP    67      -1.477  -9.051 -15.525  1.00  0.00              
ATOM    133  N   PRO    68      -3.441  -8.329 -14.733  1.00  0.00              
ATOM    134  CA  PRO    68      -3.925  -7.823 -16.010  1.00  0.00              
ATOM    135  C   PRO    68      -5.070  -6.837 -15.755  1.00  0.00              
ATOM    136  O   PRO    68      -4.946  -5.658 -16.086  1.00  0.00              
END
