
#######################################################
#                                                     #
#                        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   28 (  112),  selected   28 , name T0350AL381_1-D1
# Molecule2: number of CA atoms   91 ( 1511),  selected   28 , name T0350_D1.pdb
# PARAMETERS: T0350AL381_1-D1.T0350_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:    28        36 - 63          1.57     1.57
  LCS_AVERAGE:     30.77

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    28        36 - 63          1.57     1.57
  LCS_AVERAGE:     30.77

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17        36 - 52          0.83     2.09
  LCS_AVERAGE:     14.48

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:   91
LCS_GDT     S      36     S      36     17   28   28     8   15   19   23   26   28   28   28   28   28   28   28   28   28   28   28   28   28   28   28 
LCS_GDT     Y      37     Y      37     17   28   28     8   15   19   23   26   28   28   28   28   28   28   28   28   28   28   28   28   28   28   28 
LCS_GDT     T      38     T      38     17   28   28     8   15   19   23   26   28   28   28   28   28   28   28   28   28   28   28   28   28   28   28 
LCS_GDT     N      39     N      39     17   28   28     8   15   19   23   26   28   28   28   28   28   28   28   28   28   28   28   28   28   28   28 
LCS_GDT     L      40     L      40     17   28   28     6   15   19   23   26   28   28   28   28   28   28   28   28   28   28   28   28   28   28   28 
LCS_GDT     A      41     A      41     17   28   28     8   14   19   23   26   28   28   28   28   28   28   28   28   28   28   28   28   28   28   28 
LCS_GDT     E      42     E      42     17   28   28     8   15   19   23   26   28   28   28   28   28   28   28   28   28   28   28   28   28   28   28 
LCS_GDT     M      43     M      43     17   28   28     8   15   19   23   26   28   28   28   28   28   28   28   28   28   28   28   28   28   28   28 
LCS_GDT     V      44     V      44     17   28   28     8   15   19   23   26   28   28   28   28   28   28   28   28   28   28   28   28   28   28   28 
LCS_GDT     G      45     G      45     17   28   28     8   15   19   23   26   28   28   28   28   28   28   28   28   28   28   28   28   28   28   28 
LCS_GDT     E      46     E      46     17   28   28     8   15   19   23   26   28   28   28   28   28   28   28   28   28   28   28   28   28   28   28 
LCS_GDT     M      47     M      47     17   28   28     8   15   19   23   26   28   28   28   28   28   28   28   28   28   28   28   28   28   28   28 
LCS_GDT     N      48     N      48     17   28   28     8   15   19   23   26   28   28   28   28   28   28   28   28   28   28   28   28   28   28   28 
LCS_GDT     K      49     K      49     17   28   28     7   15   19   23   26   28   28   28   28   28   28   28   28   28   28   28   28   28   28   28 
LCS_GDT     L      50     L      50     17   28   28     8   15   19   23   26   28   28   28   28   28   28   28   28   28   28   28   28   28   28   28 
LCS_GDT     L      51     L      51     17   28   28     4   15   19   23   26   28   28   28   28   28   28   28   28   28   28   28   28   28   28   28 
LCS_GDT     E      52     E      52     17   28   28     6   14   19   23   26   28   28   28   28   28   28   28   28   28   28   28   28   28   28   28 
LCS_GDT     P      53     P      53     14   28   28     4    7   16   22   26   28   28   28   28   28   28   28   28   28   28   28   28   28   28   28 
LCS_GDT     S      54     S      54     12   28   28     4    5   16   22   26   28   28   28   28   28   28   28   28   28   28   28   28   28   28   28 
LCS_GDT     Q      55     Q      55      6   28   28     3    5    6   19   24   28   28   28   28   28   28   28   28   28   28   28   28   28   28   28 
LCS_GDT     V      56     V      56      6   28   28     3   11   19   23   26   28   28   28   28   28   28   28   28   28   28   28   28   28   28   28 
LCS_GDT     H      57     H      57      6   28   28     3    4    7   21   26   28   28   28   28   28   28   28   28   28   28   28   28   28   28   28 
LCS_GDT     L      58     L      58      6   28   28     3    7   14   23   26   28   28   28   28   28   28   28   28   28   28   28   28   28   28   28 
LCS_GDT     K      59     K      59      6   28   28     5    6   19   23   26   28   28   28   28   28   28   28   28   28   28   28   28   28   28   28 
LCS_GDT     F      60     F      60      6   28   28     5   14   19   23   26   28   28   28   28   28   28   28   28   28   28   28   28   28   28   28 
LCS_GDT     E      61     E      61      6   28   28     5   12   19   23   26   28   28   28   28   28   28   28   28   28   28   28   28   28   28   28 
LCS_GDT     L      62     L      62      6   28   28     5   12   19   23   26   28   28   28   28   28   28   28   28   28   28   28   28   28   28   28 
LCS_GDT     H      63     H      63      6   28   28     3    6   17   22   26   28   28   28   28   28   28   28   28   28   28   28   28   28   28   28 
LCS_AVERAGE  LCS_A:  25.34  (  14.48   30.77   30.77 )

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      8     15     19     23     26     28     28     28     28     28     28     28     28     28     28     28     28     28     28     28 
GDT PERCENT_CA   8.79  16.48  20.88  25.27  28.57  30.77  30.77  30.77  30.77  30.77  30.77  30.77  30.77  30.77  30.77  30.77  30.77  30.77  30.77  30.77
GDT RMS_LOCAL    0.32   0.69   0.92   1.16   1.41   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   1.57
GDT RMS_ALL_CA   2.13   2.32   1.92   1.67   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   1.57

#      Molecule1      Molecule2       DISTANCE
LGA    S      36      S      36          2.265
LGA    Y      37      Y      37          1.305
LGA    T      38      T      38          0.879
LGA    N      39      N      39          1.753
LGA    L      40      L      40          1.834
LGA    A      41      A      41          1.251
LGA    E      42      E      42          1.045
LGA    M      43      M      43          0.189
LGA    V      44      V      44          0.924
LGA    G      45      G      45          1.219
LGA    E      46      E      46          0.907
LGA    M      47      M      47          0.746
LGA    N      48      N      48          0.998
LGA    K      49      K      49          1.026
LGA    L      50      L      50          0.883
LGA    L      51      L      51          1.362
LGA    E      52      E      52          0.699
LGA    P      53      P      53          2.254
LGA    S      54      S      54          2.249
LGA    Q      55      Q      55          3.036
LGA    V      56      V      56          1.300
LGA    H      57      H      57          2.709
LGA    L      58      L      58          1.892
LGA    K      59      K      59          1.578
LGA    F      60      F      60          0.993
LGA    E      61      E      61          0.836
LGA    L      62      L      62          1.164
LGA    H      63      H      63          2.514

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   28   91    4.0     28    1.57    25.824    28.374     1.672

LGA_LOCAL      RMSD =  1.575  Number of atoms =   28  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  1.575  Number of atoms =   28 
Std_ALL_ATOMS  RMSD =  1.575  (standard rmsd on all 28 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.691370 * X  +  -0.537037 * Y  +   0.483320 * Z  +  22.493475
  Y_new =   0.722495 * X  +   0.511349 * Y  +  -0.465320 * Z  + -10.675773
  Z_new =   0.002749 * X  +   0.670905 * Y  +   0.741538 * Z  + -42.107872 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.735432   -2.406161  [ DEG:    42.1371   -137.8629 ]
  Theta =  -0.002749   -3.138844  [ DEG:    -0.1575   -179.8425 ]
  Phi   =   0.807409   -2.334184  [ DEG:    46.2611   -133.7389 ]
 
# 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: T0350AL381_1-D1                               
REMARK     2: T0350_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0350AL381_1-D1.T0350_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   28   91   4.0   28   1.57  28.374     1.57
REMARK  ---------------------------------------------------------- 
MOLECULE T0350AL381_1-D1
REMARK Aligment from pdb entry: 1t6sA
ATOM     57  N   SER    36      -2.167   7.458 -31.637  1.00  0.00              
ATOM     58  CA  SER    36      -1.721   8.510 -32.541  1.00  0.00              
ATOM     59  C   SER    36      -0.285   8.769 -32.041  1.00  0.00              
ATOM     60  O   SER    36       0.030   8.489 -30.881  1.00  0.00              
ATOM     61  N   TYR    37       0.608   9.267 -32.909  1.00  0.00              
ATOM     62  CA  TYR    37       1.985   9.526 -32.468  1.00  0.00              
ATOM     63  C   TYR    37       2.050  10.486 -31.286  1.00  0.00              
ATOM     64  O   TYR    37       2.933  10.387 -30.427  1.00  0.00              
ATOM     65  N   THR    38       1.090  11.399 -31.232  1.00  0.00              
ATOM     66  CA  THR    38       1.039  12.361 -30.159  1.00  0.00              
ATOM     67  C   THR    38       0.481  11.717 -28.888  1.00  0.00              
ATOM     68  O   THR    38       0.975  11.961 -27.781  1.00  0.00              
ATOM     69  N   ASN    39      -0.549  10.890 -29.049  1.00  0.00              
ATOM     70  CA  ASN    39      -1.154  10.205 -27.909  1.00  0.00              
ATOM     71  C   ASN    39      -0.150   9.263 -27.246  1.00  0.00              
ATOM     72  O   ASN    39      -0.087   9.186 -26.022  1.00  0.00              
ATOM     73  N   LEU    40       0.661   8.572 -28.049  1.00  0.00              
ATOM     74  CA  LEU    40       1.643   7.633 -27.498  1.00  0.00              
ATOM     75  C   LEU    40       2.707   8.349 -26.679  1.00  0.00              
ATOM     76  O   LEU    40       3.096   7.893 -25.602  1.00  0.00              
ATOM     77  N   ALA    41       3.195   9.465 -27.202  1.00  0.00              
ATOM     78  CA  ALA    41       4.221  10.227 -26.504  1.00  0.00              
ATOM     79  C   ALA    41       3.687  10.773 -25.186  1.00  0.00              
ATOM     80  O   ALA    41       4.423  10.867 -24.202  1.00  0.00              
ATOM     81  N   GLU    42       2.402  11.137 -25.186  1.00  0.00              
ATOM     82  CA  GLU    42       1.717  11.676 -24.003  1.00  0.00              
ATOM     83  C   GLU    42       1.594  10.601 -22.925  1.00  0.00              
ATOM     84  O   GLU    42       1.672  10.894 -21.735  1.00  0.00              
ATOM     85  N   MET    43       1.392   9.352 -23.343  1.00  0.00              
ATOM     86  CA  MET    43       1.273   8.250 -22.390  1.00  0.00              
ATOM     87  C   MET    43       2.656   7.987 -21.809  1.00  0.00              
ATOM     88  O   MET    43       2.805   7.739 -20.615  1.00  0.00              
ATOM     89  N   VAL    44       3.669   8.046 -22.665  1.00  0.00              
ATOM     90  CA  VAL    44       5.034   7.828 -22.229  1.00  0.00              
ATOM     91  C   VAL    44       5.443   8.929 -21.252  1.00  0.00              
ATOM     92  O   VAL    44       6.104   8.647 -20.259  1.00  0.00              
ATOM     93  N   GLY    45       5.047  10.175 -21.532  1.00  0.00              
ATOM     94  CA  GLY    45       5.365  11.297 -20.637  1.00  0.00              
ATOM     95  C   GLY    45       4.788  11.056 -19.244  1.00  0.00              
ATOM     96  O   GLY    45       5.460  11.316 -18.245  1.00  0.00              
ATOM     97  N   GLU    46       3.548  10.569 -19.176  1.00  0.00              
ATOM     98  CA  GLU    46       2.912  10.299 -17.885  1.00  0.00              
ATOM     99  C   GLU    46       3.703   9.265 -17.083  1.00  0.00              
ATOM    100  O   GLU    46       3.939   9.449 -15.886  1.00  0.00              
ATOM    101  N   MET    47       4.122   8.186 -17.746  1.00  0.00              
ATOM    102  CA  MET    47       4.903   7.156 -17.074  1.00  0.00              
ATOM    103  C   MET    47       6.190   7.800 -16.540  1.00  0.00              
ATOM    104  O   MET    47       6.537   7.624 -15.369  1.00  0.00              
ATOM    105  N   ASN    48       6.899   8.533 -17.394  1.00  0.00              
ATOM    106  CA  ASN    48       8.135   9.192 -16.965  1.00  0.00              
ATOM    107  C   ASN    48       7.860  10.141 -15.792  1.00  0.00              
ATOM    108  O   ASN    48       8.712  10.320 -14.919  1.00  0.00              
ATOM    109  N   LYS    49       6.673  10.745 -15.762  1.00  0.00              
ATOM    110  CA  LYS    49       6.337  11.622 -14.644  1.00  0.00              
ATOM    111  C   LYS    49       6.214  10.790 -13.362  1.00  0.00              
ATOM    112  O   LYS    49       6.674  11.214 -12.294  1.00  0.00              
ATOM    113  N   LEU    50       5.622   9.601 -13.462  1.00  0.00              
ATOM    114  CA  LEU    50       5.492   8.720 -12.296  1.00  0.00              
ATOM    115  C   LEU    50       6.853   8.220 -11.806  1.00  0.00              
ATOM    116  O   LEU    50       7.050   8.022 -10.601  1.00  0.00              
ATOM    117  N   LEU    51       7.779   7.995 -12.744  1.00  0.00              
ATOM    118  CA  LEU    51       9.134   7.530 -12.399  1.00  0.00              
ATOM    119  C   LEU    51       9.834   8.629 -11.607  1.00  0.00              
ATOM    120  O   LEU    51      10.505   8.367 -10.607  1.00  0.00              
ATOM    121  N   GLU    52       9.679   9.863 -12.071  1.00  0.00              
ATOM    122  CA  GLU    52      10.270  11.004 -11.388  1.00  0.00              
ATOM    123  C   GLU    52       9.656  11.146  -9.993  1.00  0.00              
ATOM    124  O   GLU    52      10.363  11.364  -9.017  1.00  0.00              
ATOM    125  N   PRO    53       8.338  10.997  -9.920  1.00  0.00              
ATOM    126  CA  PRO    53       7.575  11.118  -8.680  1.00  0.00              
ATOM    127  C   PRO    53       7.908  10.094  -7.592  1.00  0.00              
ATOM    128  O   PRO    53       8.008  10.448  -6.413  1.00  0.00              
ATOM    129  N   SER    54       8.064   8.833  -7.990  1.00  0.00              
ATOM    130  CA  SER    54       8.355   7.750  -7.058  1.00  0.00              
ATOM    131  C   SER    54       9.856   7.513  -6.834  1.00  0.00              
ATOM    132  O   SER    54      10.241   6.664  -6.034  1.00  0.00              
ATOM    133  N   GLN    55      10.700   8.262  -7.535  1.00  0.00              
ATOM    134  CA  GLN    55      12.131   8.126  -7.342  1.00  0.00              
ATOM    135  C   GLN    55      12.807   6.956  -8.031  1.00  0.00              
ATOM    136  O   GLN    55      13.760   6.392  -7.492  1.00  0.00              
ATOM    137  N   VAL    56      12.325   6.597  -9.218  1.00  0.00              
ATOM    138  CA  VAL    56      12.907   5.498  -9.991  1.00  0.00              
ATOM    139  C   VAL    56      14.214   5.963 -10.641  1.00  0.00              
ATOM    140  O   VAL    56      14.399   7.147 -10.921  1.00  0.00              
ATOM    141  N   HIS    57      15.120   5.023 -10.885  1.00  0.00              
ATOM    142  CA  HIS    57      16.422   5.350 -11.460  1.00  0.00              
ATOM    143  C   HIS    57      16.512   5.199 -12.978  1.00  0.00              
ATOM    144  O   HIS    57      17.604   5.222 -13.548  1.00  0.00              
ATOM    145  N   LEU    58      15.361   5.050 -13.626  1.00  0.00              
ATOM    146  CA  LEU    58      15.315   4.892 -15.075  1.00  0.00              
ATOM    147  C   LEU    58      14.213   5.740 -15.712  1.00  0.00              
ATOM    148  O   LEU    58      13.306   6.228 -15.026  1.00  0.00              
ATOM    149  N   LYS    59      14.303   5.907 -17.027  1.00  0.00              
ATOM    150  CA  LYS    59      13.326   6.698 -17.787  1.00  0.00              
ATOM    151  C   LYS    59      13.163   6.128 -19.175  1.00  0.00              
ATOM    152  O   LYS    59      14.084   5.509 -19.708  1.00  0.00              
ATOM    153  N   PHE    60      11.990   6.349 -19.760  1.00  0.00              
ATOM    154  CA  PHE    60      11.734   5.913 -21.124  1.00  0.00              
ATOM    155  C   PHE    60      12.163   7.050 -22.072  1.00  0.00              
ATOM    156  O   PHE    60      11.794   8.214 -21.888  1.00  0.00              
ATOM    157  N   GLU    61      12.956   6.688 -23.077  1.00  0.00              
ATOM    158  CA  GLU    61      13.472   7.613 -24.078  1.00  0.00              
ATOM    159  C   GLU    61      13.028   7.252 -25.500  1.00  0.00              
ATOM    160  O   GLU    61      13.036   6.077 -25.907  1.00  0.00              
ATOM    161  N   LEU    62      12.661   8.278 -26.256  1.00  0.00              
ATOM    162  CA  LEU    62      12.244   8.117 -27.639  1.00  0.00              
ATOM    163  C   LEU    62      13.488   8.315 -28.491  1.00  0.00              
ATOM    164  O   LEU    62      13.933   9.449 -28.687  1.00  0.00              
ATOM    165  N   HIS    63      14.063   7.222 -28.980  1.00  0.00              
ATOM    166  CA  HIS    63      15.258   7.322 -29.819  1.00  0.00              
ATOM    167  C   HIS    63      14.941   6.816 -31.222  1.00  0.00              
ATOM    168  O   HIS    63      14.637   5.640 -31.402  1.00  0.00              
END
