
#######################################################
#                                                     #
#                        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   24 (   96),  selected   24 , name T0309AL380_1
# Molecule2: number of CA atoms   62 (  501),  selected   24 , name T0309.pdb
# PARAMETERS: T0309AL380_1.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:    15        40 - 54          4.89    12.74
  LCS_AVERAGE:     21.77

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7        40 - 46          1.82    14.79
  LCS_AVERAGE:      8.13

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4        56 - 59          0.61    25.71
  LCS_AVERAGE:      5.11

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     S      40     S      40      3    7   15     3    4    5    5    6    8   10   10   11   12   13   13   13   14   14   15   16   16   17   18 
LCS_GDT     E      41     E      41      3    7   15     3    4    5    5    6    8   10   10   11   12   13   13   13   14   14   15   16   16   17   18 
LCS_GDT     F      42     F      42      3    7   15     3    4    5    5    6    8   10   10   11   12   13   13   13   14   14   15   16   16   17   18 
LCS_GDT     N      43     N      43      3    7   15     3    3    4    4    5    8   10   10   11   12   13   13   13   14   14   15   16   16   17   18 
LCS_GDT     G      44     G      44      3    7   15     3    3    5    5    6    8   10   10   11   12   13   13   13   14   14   15   16   16   17   18 
LCS_GDT     K      45     K      45      3    7   15     3    3    4    4    6    8   10   10   11   12   13   13   13   14   14   15   16   16   17   18 
LCS_GDT     N      46     N      46      3    7   15     3    4    5    5    6    8   10   10   11   12   13   13   13   14   14   15   16   16   17   18 
LCS_GDT     V      47     V      47      3    4   15     3    3    4    5    6    8   10   10   11   12   13   13   13   14   14   15   16   16   17   18 
LCS_GDT     S      48     S      48      3    4   15     1    3    4    5    6    8   10   10   11   12   13   13   13   14   14   15   16   16   17   18 
LCS_GDT     I      49     I      49      3    3   15     1    3    4    4    5    7   10   10   11   12   13   13   13   14   14   15   16   16   17   18 
LCS_GDT     T      50     T      50      3    3   15     0    3    3    3    3    3    6    9   10   12   13   13   13   14   14   15   16   16   17   18 
LCS_GDT     V      51     V      51      3    3   15     1    3    3    3    5    6    7    9   11   12   13   13   13   14   14   15   16   16   17   18 
LCS_GDT     K      52     K      52      3    3   15     3    3    3    3    3    3    6    7    9   11   13   13   13   14   14   15   16   16   17   18 
LCS_GDT     E      53     E      53      3    3   15     3    3    3    3    3    4    4    5    6    7    9   12   12   14   14   15   16   16   17   18 
LCS_GDT     E      54     E      54      3    4   15     3    3    3    3    3    4    5    5    6    7    8    9   12   13   13   15   16   16   17   18 
LCS_GDT     N      55     N      55      3    5   11     3    3    3    3    4    5    6    6    6    7    9    9   10   10   12   14   16   16   17   18 
LCS_GDT     E      56     E      56      4    5   11     3    4    4    4    5    5    6    7    7    8    9    9   10   10   12   12   13   16   17   18 
LCS_GDT     L      57     L      57      4    5   11     3    4    4    4    5    5    6    7    7    8    9    9   10   10   12   12   12   12   14   17 
LCS_GDT     P      58     P      58      4    5   11     3    4    4    4    5    5    6    7    7    8    9    9   10   10   12   12   12   13   14   18 
LCS_GDT     V      59     V      59      4    5   11     3    4    4    4    5    5    6    7    7    8    9    9   10   10   12   12   12   12   13   14 
LCS_GDT     K      60     K      60      3    5   11     3    3    3    4    5    5    6    7    7    8    9    9    9   10   12   12   12   12   13   14 
LCS_GDT     G      61     G      61      3    5   11     3    3    3    4    5    5    6    7    7    8    9    9    9   10   12   12   12   12   13   14 
LCS_GDT     V      62     V      62      3    5   11     3    3    3    4    5    5    6    7    7    8    9    9   10   10   12   12   12   12   13   14 
LCS_GDT     E      63     E      63      3    5   11     3    3    3    4    5    5    6    7    7    8    9    9   10   10   12   12   12   12   13   14 
LCS_AVERAGE  LCS_A:  11.67  (   5.11    8.13   21.77 )

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      3      4      5      5      6      8     10     10     11     12     13     13     13     14     14     15     16     16     17     18 
GDT PERCENT_CA   4.84   6.45   8.06   8.06   9.68  12.90  16.13  16.13  17.74  19.35  20.97  20.97  20.97  22.58  22.58  24.19  25.81  25.81  27.42  29.03
GDT RMS_LOCAL    0.11   0.46   0.87   0.87   1.33   2.12   2.62   2.62   3.05   3.30   3.73   3.73   3.73   4.29   4.29   4.89   5.40   5.40   5.91   6.75
GDT RMS_ALL_CA  30.59  14.66  15.84  15.84  15.59  15.33  13.89  13.89  14.07  13.65  13.74  13.74  13.74  13.44  13.44  12.74  12.65  12.65  12.42  11.71

#      Molecule1      Molecule2       DISTANCE
LGA    S      40      S      40          1.667
LGA    E      41      E      41          1.578
LGA    F      42      F      42          1.289
LGA    N      43      N      43          3.325
LGA    G      44      G      44          2.852
LGA    K      45      K      45          1.738
LGA    N      46      N      46          3.132
LGA    V      47      V      47          3.181
LGA    S      48      S      48          2.540
LGA    I      49      I      49          3.656
LGA    T      50      T      50          5.898
LGA    V      51      V      51          6.565
LGA    K      52      K      52          8.807
LGA    E      53      E      53         10.745
LGA    E      54      E      54         12.001
LGA    N      55      N      55         14.116
LGA    E      56      E      56         15.484
LGA    L      57      L      57         18.524
LGA    P      58      P      58         18.506
LGA    V      59      V      59         23.377
LGA    K      60      K      60         26.594
LGA    G      61      G      61         24.645
LGA    V      62      V      62         23.742
LGA    E      63      E      63         24.456

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   24   62    4.0     10    2.62    13.710    13.019     0.367

LGA_LOCAL      RMSD =  2.625  Number of atoms =   10  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 13.891  Number of atoms =   24 
Std_ALL_ATOMS  RMSD = 10.011  (standard rmsd on all 24 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.236877 * X  +   0.908092 * Y  +   0.345337 * Z  + -36.205574
  Y_new =  -0.743321 * X  +   0.398280 * Y  +  -0.537444 * Z  +  57.528553
  Z_new =  -0.625590 * X  +  -0.129388 * Y  +   0.769348 * Z  + -49.218170 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.166619    2.974973  [ DEG:    -9.5466    170.4534 ]
  Theta =   0.675887    2.465705  [ DEG:    38.7255    141.2745 ]
  Phi   =  -1.262297    1.879296  [ DEG:   -72.3243    107.6757 ]
 
# 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: T0309AL380_1                                  
REMARK     2: T0309.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0309AL380_1.T0309.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   24   62   4.0   10   2.62  13.019    10.01
REMARK  ---------------------------------------------------------- 
MOLECULE T0309AL380_1
REMARK Aligment from pdb entry: 2bdtA
ATOM      1  N   SER    40      -7.761  -5.549  -0.871  1.00  0.00              
ATOM      2  CA  SER    40      -8.910  -4.698  -0.594  1.00  0.00              
ATOM      3  C   SER    40     -10.187  -5.528  -0.461  1.00  0.00              
ATOM      4  O   SER    40     -11.154  -5.099   0.172  1.00  0.00              
ATOM      5  N   GLU    41     -10.188  -6.717  -1.053  1.00  0.00              
ATOM      6  CA  GLU    41     -11.349  -7.592  -0.970  1.00  0.00              
ATOM      7  C   GLU    41     -11.186  -8.702   0.070  1.00  0.00              
ATOM      8  O   GLU    41     -12.105  -9.488   0.285  1.00  0.00              
ATOM      9  N   PHE    42     -10.022  -8.777   0.710  1.00  0.00              
ATOM     10  CA  PHE    42      -9.807  -9.802   1.727  1.00  0.00              
ATOM     11  C   PHE    42     -10.236  -9.321   3.114  1.00  0.00              
ATOM     12  O   PHE    42     -10.500  -8.136   3.329  1.00  0.00              
ATOM     13  N   ASN    43     -10.317 -10.265   4.044  1.00  0.00              
ATOM     14  CA  ASN    43     -10.710  -9.989   5.421  1.00  0.00              
ATOM     15  C   ASN    43      -9.500 -10.173   6.328  1.00  0.00              
ATOM     16  O   ASN    43      -8.693 -11.071   6.112  1.00  0.00              
ATOM     17  N   GLY    44      -9.352  -9.313   7.348  1.00  0.00              
ATOM     18  CA  GLY    44      -8.223  -9.407   8.282  1.00  0.00              
ATOM     19  C   GLY    44      -8.247 -10.730   9.053  1.00  0.00              
ATOM     20  O   GLY    44      -7.228 -11.194   9.568  1.00  0.00              
ATOM     21  N   LYS    45      -9.426 -11.336   9.111  1.00  0.00              
ATOM     22  CA  LYS    45      -9.603 -12.598   9.802  1.00  0.00              
ATOM     23  C   LYS    45      -9.020 -13.745   8.961  1.00  0.00              
ATOM     24  O   LYS    45      -9.101 -14.911   9.338  1.00  0.00              
ATOM     25  N   ASN    46      -8.429 -13.396   7.820  1.00  0.00              
ATOM     26  CA  ASN    46      -7.819 -14.373   6.926  1.00  0.00              
ATOM     27  C   ASN    46      -6.326 -14.080   6.802  1.00  0.00              
ATOM     28  O   ASN    46      -5.645 -14.580   5.897  1.00  0.00              
ATOM     29  N   VAL    47      -5.825 -13.272   7.733  1.00  0.00              
ATOM     30  CA  VAL    47      -4.420 -12.891   7.760  1.00  0.00              
ATOM     31  C   VAL    47      -3.461 -14.071   7.597  1.00  0.00              
ATOM     32  O   VAL    47      -2.491 -13.971   6.848  1.00  0.00              
ATOM     33  N   SER    48      -3.721 -15.184   8.282  1.00  0.00              
ATOM     34  CA  SER    48      -2.839 -16.349   8.161  1.00  0.00              
ATOM     35  C   SER    48      -2.839 -16.973   6.765  1.00  0.00              
ATOM     36  O   SER    48      -1.840 -17.556   6.347  1.00  0.00              
ATOM     37  N   ILE    49      -3.946 -16.852   6.038  1.00  0.00              
ATOM     38  CA  ILE    49      -3.998 -17.405   4.689  1.00  0.00              
ATOM     39  C   ILE    49      -3.166 -16.532   3.760  1.00  0.00              
ATOM     40  O   ILE    49      -2.416 -17.038   2.927  1.00  0.00              
ATOM     41  N   THR    50      -3.314 -15.217   3.911  1.00  0.00              
ATOM     42  CA  THR    50      -2.573 -14.246   3.111  1.00  0.00              
ATOM     43  C   THR    50      -1.066 -14.476   3.229  1.00  0.00              
ATOM     44  O   THR    50      -0.370 -14.593   2.223  1.00  0.00              
ATOM     45  N   VAL    51      -0.567 -14.539   4.459  1.00  0.00              
ATOM     46  CA  VAL    51       0.858 -14.748   4.677  1.00  0.00              
ATOM     47  C   VAL    51       1.277 -16.145   4.217  1.00  0.00              
ATOM     48  O   VAL    51       2.442 -16.386   3.912  1.00  0.00              
ATOM     49  N   LYS    52       0.317 -17.060   4.174  1.00  0.00              
ATOM     50  CA  LYS    52       0.572 -18.428   3.748  1.00  0.00              
ATOM     51  C   LYS    52       0.752 -18.416   2.235  1.00  0.00              
ATOM     52  O   LYS    52       1.558 -19.161   1.684  1.00  0.00              
ATOM     53  N   GLU    53      -0.005 -17.555   1.568  1.00  0.00              
ATOM     54  CA  GLU    53       0.070 -17.459   0.125  1.00  0.00              
ATOM     55  C   GLU    53       1.366 -16.832  -0.359  1.00  0.00              
ATOM     56  O   GLU    53       2.131 -17.457  -1.095  1.00  0.00              
ATOM     57  N   GLU    54       1.610 -15.593   0.058  1.00  0.00              
ATOM     58  CA  GLU    54       2.811 -14.873  -0.348  1.00  0.00              
ATOM     59  C   GLU    54       4.088 -15.561   0.110  1.00  0.00              
ATOM     60  O   GLU    54       5.184 -15.185  -0.303  1.00  0.00              
ATOM     61  N   ASN    55       3.954 -16.584   0.945  1.00  0.00              
ATOM     62  CA  ASN    55       5.128 -17.303   1.422  1.00  0.00              
ATOM     63  C   ASN    55       5.566 -18.356   0.414  1.00  0.00              
ATOM     64  O   ASN    55       6.749 -18.670   0.306  1.00  0.00              
ATOM     65  N   GLU    56       4.608 -18.888  -0.335  1.00  0.00              
ATOM     66  CA  GLU    56       4.903 -19.928  -1.309  1.00  0.00              
ATOM     67  C   GLU    56       4.540 -19.556  -2.740  1.00  0.00              
ATOM     68  O   GLU    56       5.079 -20.127  -3.692  1.00  0.00              
ATOM     69  N   LEU    57       3.630 -18.598  -2.895  1.00  0.00              
ATOM     70  CA  LEU    57       3.214 -18.180  -4.226  1.00  0.00              
ATOM     71  C   LEU    57       4.453 -17.784  -5.032  1.00  0.00              
ATOM     72  O   LEU    57       5.234 -16.937  -4.610  1.00  0.00              
ATOM     73  N   PRO    58       4.647 -18.400  -6.205  1.00  0.00              
ATOM     74  CA  PRO    58       5.802 -18.112  -7.062  1.00  0.00              
ATOM     75  C   PRO    58       5.763 -16.788  -7.816  1.00  0.00              
ATOM     76  O   PRO    58       6.795 -16.310  -8.279  1.00  0.00              
ATOM     77  N   VAL    59       4.581 -16.195  -7.933  1.00  0.00              
ATOM     78  CA  VAL    59       4.441 -14.930  -8.649  1.00  0.00              
ATOM     79  C   VAL    59       5.326 -13.830  -8.057  1.00  0.00              
ATOM     80  O   VAL    59       5.769 -12.933  -8.772  1.00  0.00              
ATOM     81  N   LYS    60       5.581 -13.899  -6.755  1.00  0.00              
ATOM     82  CA  LYS    60       6.406 -12.889  -6.098  1.00  0.00              
ATOM     83  C   LYS    60       7.879 -13.284  -6.081  1.00  0.00              
ATOM     84  O   LYS    60       8.729 -12.505  -5.649  1.00  0.00              
ATOM     85  N   GLY    61       8.176 -14.485  -6.566  1.00  0.00              
ATOM     86  CA  GLY    61       9.540 -15.002  -6.571  1.00  0.00              
ATOM     87  C   GLY    61      10.555 -14.070  -7.230  1.00  0.00              
ATOM     88  O   GLY    61      11.709 -14.449  -7.442  1.00  0.00              
ATOM     89  N   VAL    62      10.122 -12.855  -7.551  1.00  0.00              
ATOM     90  CA  VAL    62      10.986 -11.852  -8.169  1.00  0.00              
ATOM     91  C   VAL    62      11.558 -12.368  -9.482  1.00  0.00              
ATOM     92  O   VAL    62      12.780 -12.528  -9.629  1.00  0.00              
ATOM     93  N   GLU    63      10.660 -12.629 -10.429  1.00  0.00              
ATOM     94  CA  GLU    63      11.027 -13.129 -11.750  1.00  0.00              
ATOM     95  C   GLU    63      12.218 -12.358 -12.323  1.00  0.00              
ATOM     96  O   GLU    63      13.320 -12.896 -12.433  1.00  0.00              
END
