
#######################################################
#                                                     #
#                        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_2
# Molecule2: number of CA atoms   89 (  695),  selected   23 , name T0300
# PARAMETERS: T0300AL380_2.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          0.66     0.66
  LCS_AVERAGE:     25.84

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    23         9 - 31          0.66     0.66
  LCS_AVERAGE:     25.84

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    23         9 - 31          0.66     0.66
  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     7   13   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     7   21   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    16   21   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    17   21   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    14   21   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     7   21   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    17   21   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    17   21   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    17   21   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    17   21   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    17   21   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    17   21   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    17   21   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    17   21   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    17   21   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    17   21   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    17   21   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    17   21   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    17   21   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    17   21   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    17   21   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    17   21   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   21   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     17     21     23     23     23     23     23     23     23     23     23     23     23     23     23     23     23     23     23     23 
GDT PERCENT_CA  19.10  23.60  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    0.27   0.45   0.66   0.66   0.66   0.66   0.66   0.66   0.66   0.66   0.66   0.66   0.66   0.66   0.66   0.66   0.66   0.66   0.66   0.66
GDT RMS_ALL_CA   0.85   0.74   0.66   0.66   0.66   0.66   0.66   0.66   0.66   0.66   0.66   0.66   0.66   0.66   0.66   0.66   0.66   0.66   0.66   0.66

#      Molecule1      Molecule2       DISTANCE
LGA    T       9      T       9          1.603
LGA    Y      10      Y      10          1.162
LGA    E      11      E      11          0.669
LGA    E      12      E      12          0.448
LGA    M      13      M      13          0.260
LGA    V      14      V      14          0.635
LGA    K      15      K      15          0.249
LGA    E      16      E      16          0.668
LGA    V      17      V      17          1.075
LGA    E      18      E      18          0.841
LGA    R      19      R      19          0.260
LGA    L      20      L      20          0.339
LGA    K      21      K      21          0.461
LGA    L      22      L      22          0.312
LGA    E      23      E      23          0.206
LGA    N      24      N      24          0.301
LGA    K      25      K      25          0.198
LGA    T      26      T      26          0.141
LGA    L      27      L      27          0.105
LGA    K      28      K      28          0.212
LGA    Q      29      Q      29          0.536
LGA    K      30      K      30          0.423
LGA    V      31      V      31          1.151

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   29   89    4.0     23    0.66    25.281    25.665     3.036

LGA_LOCAL      RMSD =  0.658  Number of atoms =   23  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  0.657  Number of atoms =   23 
Std_ALL_ATOMS  RMSD =  0.658  (standard rmsd on all 23 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.432186 * X  +   0.895772 * Y  +  -0.103956 * Z  +  49.104252
  Y_new =   0.866351 * X  +   0.444433 * Y  +   0.227850 * Z  + -52.238358
  Z_new =   0.250303 * X  +   0.008411 * Y  +  -0.968131 * Z  + -45.638775 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   3.132905   -0.008688  [ DEG:   179.5022     -0.4978 ]
  Theta =  -0.252993   -2.888600  [ DEG:   -14.4954   -165.5046 ]
  Phi   =   2.033530   -1.108063  [ DEG:   116.5127    -63.4873 ]
 
# 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_2                                  
REMARK     2: T0300                                         
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0300AL380_2.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   0.66  25.665     0.66
REMARK  ---------------------------------------------------------- 
MOLECULE T0300AL380_2
REMARK Aligment from pdb entry: 1debB
ATOM      1  N   THR     9      35.151  -0.666  -6.051  1.00  0.00              
ATOM      2  CA  THR     9      35.732  -1.509  -5.014  1.00  0.00              
ATOM      3  C   THR     9      36.799  -2.454  -5.563  1.00  0.00              
ATOM      4  O   THR     9      36.938  -2.630  -6.778  1.00  0.00              
ATOM      5  N   TYR    10      37.540  -3.081  -4.657  1.00  0.00              
ATOM      6  CA  TYR    10      38.580  -4.005  -5.057  1.00  0.00              
ATOM      7  C   TYR    10      38.003  -5.268  -5.667  1.00  0.00              
ATOM      8  O   TYR    10      38.399  -5.656  -6.758  1.00  0.00              
ATOM      9  N   GLU    11      37.058  -5.915  -4.990  1.00  0.00              
ATOM     10  CA  GLU    11      36.507  -7.131  -5.571  1.00  0.00              
ATOM     11  C   GLU    11      35.791  -6.772  -6.867  1.00  0.00              
ATOM     12  O   GLU    11      35.580  -7.622  -7.736  1.00  0.00              
ATOM     13  N   GLU    12      35.445  -5.499  -7.010  1.00  0.00              
ATOM     14  CA  GLU    12      34.771  -5.039  -8.208  1.00  0.00              
ATOM     15  C   GLU    12      35.716  -4.874  -9.381  1.00  0.00              
ATOM     16  O   GLU    12      35.352  -5.180 -10.511  1.00  0.00              
ATOM     17  N   MET    13      36.925  -4.385  -9.135  1.00  0.00              
ATOM     18  CA  MET    13      37.876  -4.258 -10.230  1.00  0.00              
ATOM     19  C   MET    13      38.135  -5.712 -10.608  1.00  0.00              
ATOM     20  O   MET    13      38.318  -6.063 -11.771  1.00  0.00              
ATOM     21  N   VAL    14      38.087  -6.558  -9.587  1.00  0.00              
ATOM     22  CA  VAL    14      38.316  -7.983  -9.707  1.00  0.00              
ATOM     23  C   VAL    14      37.271  -8.697 -10.589  1.00  0.00              
ATOM     24  O   VAL    14      37.633  -9.535 -11.425  1.00  0.00              
ATOM     25  N   LYS    15      35.984  -8.378 -10.404  1.00  0.00              
ATOM     26  CA  LYS    15      34.898  -8.969 -11.206  1.00  0.00              
ATOM     27  C   LYS    15      35.064  -8.373 -12.599  1.00  0.00              
ATOM     28  O   LYS    15      34.738  -9.008 -13.600  1.00  0.00              
ATOM     29  N   GLU    16      35.628  -7.165 -12.657  1.00  0.00              
ATOM     30  CA  GLU    16      35.850  -6.495 -13.940  1.00  0.00              
ATOM     31  C   GLU    16      36.978  -7.133 -14.753  1.00  0.00              
ATOM     32  O   GLU    16      36.884  -7.208 -15.971  1.00  0.00              
ATOM     33  N   VAL    17      38.042  -7.597 -14.103  1.00  0.00              
ATOM     34  CA  VAL    17      39.102  -8.237 -14.867  1.00  0.00              
ATOM     35  C   VAL    17      38.491  -9.456 -15.551  1.00  0.00              
ATOM     36  O   VAL    17      38.517  -9.568 -16.788  1.00  0.00              
ATOM     37  N   GLU    18      37.886 -10.331 -14.731  1.00  0.00              
ATOM     38  CA  GLU    18      37.243 -11.584 -15.203  1.00  0.00              
ATOM     39  C   GLU    18      36.258 -11.335 -16.349  1.00  0.00              
ATOM     40  O   GLU    18      36.237 -12.091 -17.325  1.00  0.00              
ATOM     41  N   ARG    19      35.410 -10.321 -16.219  1.00  0.00              
ATOM     42  CA  ARG    19      34.395 -10.049 -17.244  1.00  0.00              
ATOM     43  C   ARG    19      35.053  -9.685 -18.573  1.00  0.00              
ATOM     44  O   ARG    19      34.714 -10.228 -19.637  1.00  0.00              
ATOM     45  N   LEU    20      35.980  -8.738 -18.504  1.00  0.00              
ATOM     46  CA  LEU    20      36.704  -8.304 -19.681  1.00  0.00              
ATOM     47  C   LEU    20      37.499  -9.451 -20.295  1.00  0.00              
ATOM     48  O   LEU    20      37.556  -9.576 -21.516  1.00  0.00              
ATOM     49  N   LYS    21      38.117 -10.292 -19.466  1.00  0.00              
ATOM     50  CA  LYS    21      38.878 -11.407 -20.018  1.00  0.00              
ATOM     51  C   LYS    21      37.949 -12.362 -20.754  1.00  0.00              
ATOM     52  O   LYS    21      38.276 -12.853 -21.832  1.00  0.00              
ATOM     53  N   LEU    22      36.779 -12.612 -20.190  1.00  0.00              
ATOM     54  CA  LEU    22      35.824 -13.504 -20.842  1.00  0.00              
ATOM     55  C   LEU    22      35.413 -12.901 -22.188  1.00  0.00              
ATOM     56  O   LEU    22      35.448 -13.576 -23.223  1.00  0.00              
ATOM     57  N   GLU    23      35.042 -11.626 -22.183  1.00  0.00              
ATOM     58  CA  GLU    23      34.635 -10.990 -23.423  1.00  0.00              
ATOM     59  C   GLU    23      35.753 -10.968 -24.473  1.00  0.00              
ATOM     60  O   GLU    23      35.499 -11.210 -25.631  1.00  0.00              
ATOM     61  N   ASN    24      36.986 -10.685 -24.069  1.00  0.00              
ATOM     62  CA  ASN    24      38.099 -10.644 -25.031  1.00  0.00              
ATOM     63  C   ASN    24      38.281 -12.003 -25.655  1.00  0.00              
ATOM     64  O   ASN    24      38.553 -12.133 -26.847  1.00  0.00              
ATOM     65  N   LYS    25      38.111 -13.022 -24.827  1.00  0.00              
ATOM     66  CA  LYS    25      38.228 -14.394 -25.277  1.00  0.00              
ATOM     67  C   LYS    25      37.174 -14.718 -26.358  1.00  0.00              
ATOM     68  O   LYS    25      37.492 -15.355 -27.350  1.00  0.00              
ATOM     69  N   THR    26      35.934 -14.258 -26.181  1.00  0.00              
ATOM     70  CA  THR    26      34.875 -14.529 -27.150  1.00  0.00              
ATOM     71  C   THR    26      35.111 -13.760 -28.432  1.00  0.00              
ATOM     72  O   THR    26      34.817 -14.241 -29.534  1.00  0.00              
ATOM     73  N   LEU    27      35.623 -12.549 -28.296  1.00  0.00              
ATOM     74  CA  LEU    27      35.871 -11.756 -29.476  1.00  0.00              
ATOM     75  C   LEU    27      36.945 -12.454 -30.305  1.00  0.00              
ATOM     76  O   LEU    27      36.802 -12.558 -31.521  1.00  0.00              
ATOM     77  N   LYS    28      37.994 -12.963 -29.659  1.00  0.00              
ATOM     78  CA  LYS    28      39.054 -13.661 -30.394  1.00  0.00              
ATOM     79  C   LYS    28      38.499 -14.856 -31.149  1.00  0.00              
ATOM     80  O   LYS    28      38.839 -15.067 -32.314  1.00  0.00              
ATOM     81  N   GLN    29      37.641 -15.628 -30.491  1.00  0.00              
ATOM     82  CA  GLN    29      37.047 -16.786 -31.145  1.00  0.00              
ATOM     83  C   GLN    29      36.226 -16.325 -32.364  1.00  0.00              
ATOM     84  O   GLN    29      36.222 -16.990 -33.422  1.00  0.00              
ATOM     85  N   LYS    30      35.543 -15.189 -32.209  1.00  0.00              
ATOM     86  CA  LYS    30      34.717 -14.640 -33.289  1.00  0.00              
ATOM     87  C   LYS    30      35.583 -14.155 -34.440  1.00  0.00              
ATOM     88  O   LYS    30      35.213 -14.321 -35.599  1.00  0.00              
ATOM     89  N   VAL    31      36.733 -13.556 -34.115  1.00  0.00              
ATOM     90  CA  VAL    31      37.652 -13.074 -35.143  1.00  0.00              
ATOM     91  C   VAL    31      38.169 -14.304 -35.883  1.00  0.00              
ATOM     92  O   VAL    31      38.345 -14.265 -37.095  1.00  0.00              
ATOM     93  N   LYS    32      38.395 -15.399 -35.156  1.00  0.00              
ATOM     94  CA  LYS    32      38.851 -16.630 -35.795  1.00  0.00              
ATOM     95  C   LYS    32      37.761 -17.205 -36.707  1.00  0.00              
ATOM     96  O   LYS    32      38.015 -17.466 -37.883  1.00  0.00              
ATOM     97  N   SER    33      36.550 -17.397 -36.181  1.00  0.00              
ATOM     98  CA  SER    33      35.483 -17.931 -37.018  1.00  0.00              
ATOM     99  C   SER    33      35.363 -17.032 -38.245  1.00  0.00              
ATOM    100  O   SER    33      35.322 -17.519 -39.369  1.00  0.00              
ATOM    101  N   SER    34      35.353 -15.721 -38.031  1.00  0.00              
ATOM    102  CA  SER    34      35.244 -14.791 -39.142  1.00  0.00              
ATOM    103  C   SER    34      36.399 -14.953 -40.116  1.00  0.00              
ATOM    104  O   SER    34      36.212 -14.861 -41.323  1.00  0.00              
ATOM    105  N   GLY    35      37.595 -15.199 -39.603  1.00  0.00              
ATOM    106  CA  GLY    35      38.770 -15.361 -40.460  1.00  0.00              
ATOM    107  C   GLY    35      38.565 -16.498 -41.477  1.00  0.00              
ATOM    108  O   GLY    35      38.846 -16.344 -42.668  1.00  0.00              
ATOM    109  N   ALA    36      38.069 -17.635 -40.990  1.00  0.00              
ATOM    110  CA  ALA    36      37.805 -18.805 -41.822  1.00  0.00              
ATOM    111  C   ALA    36      36.873 -18.510 -42.971  1.00  0.00              
ATOM    112  O   ALA    36      37.091 -18.979 -44.093  1.00  0.00              
ATOM    113  N   VAL    37      35.824 -17.745 -42.701  1.00  0.00              
ATOM    114  CA  VAL    37      34.869 -17.417 -43.749  1.00  0.00              
ATOM    115  C   VAL    37      35.496 -16.450 -44.749  1.00  0.00              
ATOM    116  O   VAL    37      35.283 -16.583 -45.963  1.00  0.00              
END
103  C   SER    34      36.399 -14.953 -40.116  1.00  0.00              
ATOM    104  O   SER    34      36.212 -14.861 -41.323  1.00  0.00              
ATOM    105  N   GLY    35      37.595 -15.199 -39.603  1.00  0.00              
ATOM    106  CA  GLY    35      38.770 -15.361 -40.460  1.00  0.00              
ATOM    107  C   GLY    35      38.565 -16.498 -41.477  1.00  0.00              
ATOM    108  O   GLY    35      38.846 -16.344 -42.668  1.00  0.00              
ATOM    109  N   ALA    36      38.069 -17.635 -40.990  1.00  0.00              
ATOM    110  CA  ALA    36      37.805 -18.805 -41.822  1.00  0.00              
ATOM    111  C   ALA    36      36.873 -18.510 -42.971  1.00  0.00              
ATOM    112  O   ALA    36      37.091 -18.979 -44.093  1.00  0.00              
ATOM    113  N   VAL    37      35.824 -17.745 -42.701  1.00  0.00              
ATOM    114  CA  VAL    37      34.869 -17.417 -43.749  1.00  0.00              
ATOM    115  C   VAL    37      35.496 -16.450 -44.749  1.00  0.00              
ATOM    116  O   VAL    37      35.283 -16.583 -45.963  1.00  0.00              
END
