
#######################################################
#                                                     #
#                        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   29 (  116),  selected   23 , name T0300AL380_1
# Molecule2: number of CA atoms   89 (  695),  selected   23 , name T0300
# PARAMETERS: T0300AL380_1.T0300  -3  -ie  -d:4  -o1  -sda  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    23         9 - 31          0.61     0.61
  LCS_AVERAGE:     25.84

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    23         9 - 31          0.61     0.61
  LCS_AVERAGE:     25.84

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    23         9 - 31          0.61     0.61
  LCS_AVERAGE:     25.84

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:   89
LCS_GDT     T       9     T       9     23   23   23    10   22   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     Y      10     Y      10     23   23   23    10   22   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     E      11     E      11     23   23   23    10   22   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     E      12     E      12     23   23   23    16   22   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     M      13     M      13     23   23   23    16   22   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     V      14     V      14     23   23   23    16   22   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     K      15     K      15     23   23   23    16   22   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     E      16     E      16     23   23   23    16   22   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     V      17     V      17     23   23   23    15   22   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     E      18     E      18     23   23   23    11   22   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     R      19     R      19     23   23   23    14   22   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     L      20     L      20     23   23   23    16   22   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     K      21     K      21     23   23   23    16   22   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     L      22     L      22     23   23   23    16   22   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     E      23     E      23     23   23   23    16   22   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     N      24     N      24     23   23   23    16   22   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     K      25     K      25     23   23   23    16   22   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     T      26     T      26     23   23   23    16   22   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     L      27     L      27     23   23   23    16   22   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     K      28     K      28     23   23   23    16   22   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     Q      29     Q      29     23   23   23    16   22   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     K      30     K      30     23   23   23    16   22   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     V      31     V      31     23   23   23     3   20   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_AVERAGE  LCS_A:  25.84  (  25.84   25.84   25.84 )

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     16     22     23     23     23     23     23     23     23     23     23     23     23     23     23     23     23     23     23     23 
GDT PERCENT_CA  17.98  24.72  25.84  25.84  25.84  25.84  25.84  25.84  25.84  25.84  25.84  25.84  25.84  25.84  25.84  25.84  25.84  25.84  25.84  25.84
GDT RMS_LOCAL    0.30   0.56   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61
GDT RMS_ALL_CA   0.65   0.63   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61

#      Molecule1      Molecule2       DISTANCE
LGA    T       9      T       9          1.031
LGA    Y      10      Y      10          1.066
LGA    E      11      E      11          0.828
LGA    E      12      E      12          0.335
LGA    M      13      M      13          0.259
LGA    V      14      V      14          0.391
LGA    K      15      K      15          0.122
LGA    E      16      E      16          0.315
LGA    V      17      V      17          0.871
LGA    E      18      E      18          1.091
LGA    R      19      R      19          0.664
LGA    L      20      L      20          0.458
LGA    K      21      K      21          0.518
LGA    L      22      L      22          0.361
LGA    E      23      E      23          0.303
LGA    N      24      N      24          0.398
LGA    K      25      K      25          0.380
LGA    T      26      T      26          0.277
LGA    L      27      L      27          0.215
LGA    K      28      K      28          0.161
LGA    Q      29      Q      29          0.431
LGA    K      30      K      30          0.409
LGA    V      31      V      31          1.199

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   29   89    4.0     23    0.61    25.562    25.754     3.222

LGA_LOCAL      RMSD =  0.614  Number of atoms =   23  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  0.614  Number of atoms =   23 
Std_ALL_ATOMS  RMSD =  0.614  (standard rmsd on all 23 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.528610 * X  +  -0.824164 * Y  +  -0.203286 * Z  +  19.648890
  Y_new =  -0.709797 * X  +  -0.297800 * Y  +  -0.638360 * Z  +  23.766232
  Z_new =   0.465575 * X  +   0.481736 * Y  +  -0.742409 * Z  + -59.461689 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.566004   -0.575589  [ DEG:   147.0212    -32.9788 ]
  Theta =  -0.484284   -2.657309  [ DEG:   -27.7474   -152.2526 ]
  Phi   =  -0.930674    2.210919  [ DEG:   -53.3237    126.6763 ]
 
# 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: T0300AL380_1                                  
REMARK     2: T0300                                         
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0300AL380_1.T0300 -3 -ie -d:4 -o1 -sda 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   29   89   4.0   23   0.61  25.754     0.61
REMARK  ---------------------------------------------------------- 
MOLECULE T0300AL380_1
REMARK Aligment from pdb entry: 1debA
ATOM      1  N   THR     9      35.772  -0.917  -5.677  1.00  0.00              
ATOM      2  CA  THR     9      36.568  -1.563  -4.647  1.00  0.00              
ATOM      3  C   THR     9      37.505  -2.526  -5.374  1.00  0.00              
ATOM      4  O   THR     9      37.438  -2.681  -6.595  1.00  0.00              
ATOM      5  N   TYR    10      38.369  -3.186  -4.620  1.00  0.00              
ATOM      6  CA  TYR    10      39.289  -4.144  -5.204  1.00  0.00              
ATOM      7  C   TYR    10      38.487  -5.325  -5.768  1.00  0.00              
ATOM      8  O   TYR    10      38.847  -5.895  -6.798  1.00  0.00              
ATOM      9  N   GLU    11      37.400  -5.683  -5.090  1.00  0.00              
ATOM     10  CA  GLU    11      36.570  -6.799  -5.529  1.00  0.00              
ATOM     11  C   GLU    11      35.713  -6.478  -6.751  1.00  0.00              
ATOM     12  O   GLU    11      35.446  -7.343  -7.572  1.00  0.00              
ATOM     13  N   GLU    12      35.277  -5.237  -6.866  1.00  0.00              
ATOM     14  CA  GLU    12      34.478  -4.852  -8.010  1.00  0.00              
ATOM     15  C   GLU    12      35.358  -4.872  -9.253  1.00  0.00              
ATOM     16  O   GLU    12      34.931  -5.288 -10.326  1.00  0.00              
ATOM     17  N   MET    13      36.608  -4.463  -9.096  1.00  0.00              
ATOM     18  CA  MET    13      37.533  -4.468 -10.221  1.00  0.00              
ATOM     19  C   MET    13      37.784  -5.897 -10.645  1.00  0.00              
ATOM     20  O   MET    13      37.806  -6.217 -11.835  1.00  0.00              
ATOM     21  N   VAL    14      37.981  -6.756  -9.658  1.00  0.00              
ATOM     22  CA  VAL    14      38.249  -8.141  -9.962  1.00  0.00              
ATOM     23  C   VAL    14      37.122  -8.687 -10.813  1.00  0.00              
ATOM     24  O   VAL    14      37.359  -9.447 -11.743  1.00  0.00              
ATOM     25  N   LYS    15      35.892  -8.305 -10.500  1.00  0.00              
ATOM     26  CA  LYS    15      34.772  -8.776 -11.291  1.00  0.00              
ATOM     27  C   LYS    15      34.810  -8.216 -12.715  1.00  0.00              
ATOM     28  O   LYS    15      34.450  -8.904 -13.671  1.00  0.00              
ATOM     29  N   GLU    16      35.233  -6.965 -12.856  1.00  0.00              
ATOM     30  CA  GLU    16      35.308  -6.361 -14.179  1.00  0.00              
ATOM     31  C   GLU    16      36.325  -7.124 -15.011  1.00  0.00              
ATOM     32  O   GLU    16      36.072  -7.458 -16.170  1.00  0.00              
ATOM     33  N   VAL    17      37.472  -7.411 -14.403  1.00  0.00              
ATOM     34  CA  VAL    17      38.540  -8.115 -15.092  1.00  0.00              
ATOM     35  C   VAL    17      38.070  -9.480 -15.556  1.00  0.00              
ATOM     36  O   VAL    17      38.340  -9.882 -16.687  1.00  0.00              
ATOM     37  N   GLU    18      37.351 -10.190 -14.697  1.00  0.00              
ATOM     38  CA  GLU    18      36.843 -11.504 -15.062  1.00  0.00              
ATOM     39  C   GLU    18      35.927 -11.444 -16.289  1.00  0.00              
ATOM     40  O   GLU    18      36.031 -12.269 -17.191  1.00  0.00              
ATOM     41  N   ARG    19      35.029 -10.471 -16.321  1.00  0.00              
ATOM     42  CA  ARG    19      34.106 -10.345 -17.443  1.00  0.00              
ATOM     43  C   ARG    19      34.841  -9.832 -18.682  1.00  0.00              
ATOM     44  O   ARG    19      34.546 -10.239 -19.810  1.00  0.00              
ATOM     45  N   LEU    20      35.811  -8.950 -18.474  1.00  0.00              
ATOM     46  CA  LEU    20      36.578  -8.403 -19.595  1.00  0.00              
ATOM     47  C   LEU    20      37.407  -9.489 -20.281  1.00  0.00              
ATOM     48  O   LEU    20      37.461  -9.554 -21.507  1.00  0.00              
ATOM     49  N   LYS    21      38.042 -10.341 -19.479  1.00  0.00              
ATOM     50  CA  LYS    21      38.843 -11.448 -19.992  1.00  0.00              
ATOM     51  C   LYS    21      37.976 -12.431 -20.782  1.00  0.00              
ATOM     52  O   LYS    21      38.403 -12.996 -21.797  1.00  0.00              
ATOM     53  N   LEU    22      36.768 -12.682 -20.306  1.00  0.00              
ATOM     54  CA  LEU    22      35.941 -13.650 -21.019  1.00  0.00              
ATOM     55  C   LEU    22      35.501 -13.023 -22.338  1.00  0.00              
ATOM     56  O   LEU    22      35.551 -13.655 -23.391  1.00  0.00              
ATOM     57  N   GLU    23      35.114 -11.762 -22.280  1.00  0.00              
ATOM     58  CA  GLU    23      34.713 -11.047 -23.465  1.00  0.00              
ATOM     59  C   GLU    23      35.883 -11.070 -24.449  1.00  0.00              
ATOM     60  O   GLU    23      35.692 -11.407 -25.619  1.00  0.00              
ATOM     61  N   ASN    24      37.089 -10.738 -23.978  1.00  0.00              
ATOM     62  CA  ASN    24      38.265 -10.754 -24.844  1.00  0.00              
ATOM     63  C   ASN    24      38.460 -12.119 -25.452  1.00  0.00              
ATOM     64  O   ASN    24      38.819 -12.216 -26.608  1.00  0.00              
ATOM     65  N   LYS    25      38.243 -13.176 -24.680  1.00  0.00              
ATOM     66  CA  LYS    25      38.401 -14.519 -25.229  1.00  0.00              
ATOM     67  C   LYS    25      37.340 -14.793 -26.298  1.00  0.00              
ATOM     68  O   LYS    25      37.618 -15.440 -27.319  1.00  0.00              
ATOM     69  N   THR    26      36.129 -14.286 -26.080  1.00  0.00              
ATOM     70  CA  THR    26      35.062 -14.516 -27.042  1.00  0.00              
ATOM     71  C   THR    26      35.285 -13.726 -28.331  1.00  0.00              
ATOM     72  O   THR    26      35.066 -14.257 -29.424  1.00  0.00              
ATOM     73  N   LEU    27      35.730 -12.473 -28.204  1.00  0.00              
ATOM     74  CA  LEU    27      36.011 -11.658 -29.374  1.00  0.00              
ATOM     75  C   LEU    27      37.082 -12.347 -30.238  1.00  0.00              
ATOM     76  O   LEU    27      36.932 -12.428 -31.448  1.00  0.00              
ATOM     77  N   LYS    28      38.139 -12.869 -29.618  1.00  0.00              
ATOM     78  CA  LYS    28      39.188 -13.573 -30.361  1.00  0.00              
ATOM     79  C   LYS    28      38.625 -14.784 -31.090  1.00  0.00              
ATOM     80  O   LYS    28      39.003 -15.076 -32.217  1.00  0.00              
ATOM     81  N   GLN    29      37.734 -15.513 -30.424  1.00  0.00              
ATOM     82  CA  GLN    29      37.107 -16.683 -31.028  1.00  0.00              
ATOM     83  C   GLN    29      36.334 -16.247 -32.289  1.00  0.00              
ATOM     84  O   GLN    29      36.393 -16.890 -33.350  1.00  0.00              
ATOM     85  N   LYS    30      35.623 -15.135 -32.171  1.00  0.00              
ATOM     86  CA  LYS    30      34.839 -14.622 -33.280  1.00  0.00              
ATOM     87  C   LYS    30      35.697 -14.223 -34.462  1.00  0.00              
ATOM     88  O   LYS    30      35.395 -14.570 -35.590  1.00  0.00              
ATOM     89  N   VAL    31      36.757 -13.473 -34.195  1.00  0.00              
ATOM     90  CA  VAL    31      37.653 -13.007 -35.243  1.00  0.00              
ATOM     91  C   VAL    31      38.280 -14.216 -35.937  1.00  0.00              
ATOM     92  O   VAL    31      38.407 -14.265 -37.152  1.00  0.00              
ATOM     93  N   LYS    32      38.631 -15.206 -35.136  1.00  0.00              
ATOM     94  CA  LYS    32      39.237 -16.435 -35.603  1.00  0.00              
ATOM     95  C   LYS    32      38.252 -17.158 -36.524  1.00  0.00              
ATOM     96  O   LYS    32      38.618 -17.632 -37.597  1.00  0.00              
ATOM     97  N   SER    33      36.997 -17.224 -36.092  1.00  0.00              
ATOM     98  CA  SER    33      35.916 -17.873 -36.838  1.00  0.00              
ATOM     99  C   SER    33      35.757 -17.166 -38.181  1.00  0.00              
ATOM    100  O   SER    33      35.834 -17.768 -39.259  1.00  0.00              
ATOM    101  N   SER    34      35.552 -15.864 -38.094  1.00  0.00              
ATOM    102  CA  SER    34      35.335 -15.040 -39.257  1.00  0.00              
ATOM    103  C   SER    34      36.521 -14.961 -40.176  1.00  0.00              
ATOM    104  O   SER    34      36.361 -14.873 -41.397  1.00  0.00              
ATOM    105  N   GLY    35      37.714 -15.004 -39.606  1.00  0.00              
ATOM    106  CA  GLY    35      38.896 -14.951 -40.437  1.00  0.00              
ATOM    107  C   GLY    35      38.914 -16.247 -41.246  1.00  0.00              
ATOM    108  O   GLY    35      39.111 -16.209 -42.459  1.00  0.00              
ATOM    109  N   ALA    36      38.653 -17.382 -40.602  1.00  0.00              
ATOM    110  CA  ALA    36      38.626 -18.669 -41.307  1.00  0.00              
ATOM    111  C   ALA    36      37.514 -18.686 -42.372  1.00  0.00              
ATOM    112  O   ALA    36      37.662 -19.260 -43.479  1.00  0.00              
ATOM    113  N   VAL    37      36.393 -18.059 -42.036  1.00  0.00              
ATOM    114  CA  VAL    37      35.273 -17.980 -42.958  1.00  0.00              
ATOM    115  C   VAL    37      35.637 -17.183 -44.225  1.00  0.00              
ATOM    116  O   VAL    37      35.238 -17.553 -45.330  1.00  0.00              
END
103  C   SER    34      36.521 -14.961 -40.176  1.00  0.00              
ATOM    104  O   SER    34      36.361 -14.873 -41.397  1.00  0.00              
ATOM    105  N   GLY    35      37.714 -15.004 -39.606  1.00  0.00              
ATOM    106  CA  GLY    35      38.896 -14.951 -40.437  1.00  0.00              
ATOM    107  C   GLY    35      38.914 -16.247 -41.246  1.00  0.00              
ATOM    108  O   GLY    35      39.111 -16.209 -42.459  1.00  0.00              
ATOM    109  N   ALA    36      38.653 -17.382 -40.602  1.00  0.00              
ATOM    110  CA  ALA    36      38.626 -18.669 -41.307  1.00  0.00              
ATOM    111  C   ALA    36      37.514 -18.686 -42.372  1.00  0.00              
ATOM    112  O   ALA    36      37.662 -19.260 -43.479  1.00  0.00              
ATOM    113  N   VAL    37      36.393 -18.059 -42.036  1.00  0.00              
ATOM    114  CA  VAL    37      35.273 -17.980 -42.958  1.00  0.00              
ATOM    115  C   VAL    37      35.637 -17.183 -44.225  1.00  0.00              
ATOM    116  O   VAL    37      35.238 -17.553 -45.330  1.00  0.00              
END
