
#######################################################
#                                                     #
#                        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   30 (  120),  selected   24 , name T0300AL381_2
# Molecule2: number of CA atoms   89 (  695),  selected   24 , name T0300
# PARAMETERS: T0300AL381_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          1.23     7.59
  LCS_AVERAGE:     24.77

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    23         9 - 31          1.23     7.59
  LCS_AVERAGE:     24.77

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    21        11 - 31          1.00     7.61
  LCS_AVERAGE:     22.24

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     15   23   23     4    7   10   19   21   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     Y      10     Y      10     19   23   23     4    8   19   22   22   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     E      11     E      11     21   23   23     4   11   19   22   22   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     E      12     E      12     21   23   23     9   16   19   22   22   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     M      13     M      13     21   23   23     9   16   19   22   22   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     V      14     V      14     21   23   23     4   16   19   22   22   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     K      15     K      15     21   23   23     9   16   19   22   22   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     E      16     E      16     21   23   23     9   16   19   22   22   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     V      17     V      17     21   23   23     9   16   19   22   22   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     E      18     E      18     21   23   23     6   16   19   22   22   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     R      19     R      19     21   23   23     9   16   19   22   22   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     L      20     L      20     21   23   23     6   16   19   22   22   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     K      21     K      21     21   23   23     9   16   19   22   22   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     L      22     L      22     21   23   23     9   16   19   22   22   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     E      23     E      23     21   23   23     9   16   19   22   22   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     N      24     N      24     21   23   23     7   16   19   22   22   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     K      25     K      25     21   23   23     7   16   19   22   22   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     T      26     T      26     21   23   23     7   16   19   22   22   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     L      27     L      27     21   23   23     9   16   19   22   22   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     K      28     K      28     21   23   23     5   15   19   22   22   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     Q      29     Q      29     21   23   23     5   13   19   22   22   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     K      30     K      30     21   23   23     7   16   19   22   22   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     V      31     V      31     21   23   23     4   10   16   22   22   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     E     101     E     101      0    0    0     0    0    0    0    0    0    0    0    0    0    0    5    7    7    8    8    8    8   10   10 
LCS_AVERAGE  LCS_A:  23.92  (  22.24   24.77   24.77 )

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      9     16     19     22     22     23     23     23     23     23     23     23     23     23     23     23     23     23     23     23 
GDT PERCENT_CA  10.11  17.98  21.35  24.72  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
GDT RMS_LOCAL    0.31   0.67   0.84   1.08   1.08   1.23   1.23   1.23   1.23   1.23   1.23   1.23   1.23   1.23   1.23   1.23   1.23   1.23   1.23   1.23
GDT RMS_ALL_CA   7.69   7.64   7.60   7.61   7.61   7.59   7.59   7.59   7.59   7.59   7.59   7.59   7.59   7.59   7.59   7.59   7.59   7.59   7.59   7.59

#      Molecule1      Molecule2       DISTANCE
LGA    T       9      T       9          2.779
LGA    Y      10      Y      10          1.585
LGA    E      11      E      11          1.355
LGA    E      12      E      12          0.755
LGA    M      13      M      13          1.145
LGA    V      14      V      14          1.341
LGA    K      15      K      15          0.417
LGA    E      16      E      16          0.784
LGA    V      17      V      17          1.644
LGA    E      18      E      18          1.683
LGA    R      19      R      19          0.597
LGA    L      20      L      20          0.809
LGA    K      21      K      21          1.104
LGA    L      22      L      22          1.025
LGA    E      23      E      23          0.439
LGA    N      24      N      24          0.443
LGA    K      25      K      25          0.377
LGA    T      26      T      26          0.314
LGA    L      27      L      27          0.425
LGA    K      28      K      28          0.989
LGA    Q      29      Q      29          1.531
LGA    K      30      K      30          0.845
LGA    V      31      V      31          2.106
LGA    E     101      E     101         36.731

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   30   89    4.0     23    1.23    23.596    24.465     1.733

LGA_LOCAL      RMSD =  1.227  Number of atoms =   23  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  7.593  Number of atoms =   24 
Std_ALL_ATOMS  RMSD =  7.252  (standard rmsd on all 24 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.232051 * X  +  -0.128473 * Y  +   0.964182 * Z  +  37.682236
  Y_new =  -0.185118 * X  +   0.978956 * Y  +   0.085889 * Z  +  -7.351784
  Z_new =  -0.954926 * X  +  -0.158557 * Y  +  -0.250950 * Z  + -24.302185 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.578098    0.563495  [ DEG:  -147.7141     32.2859 ]
  Theta =   1.269410    1.872182  [ DEG:    72.7319    107.2681 ]
  Phi   =  -2.468225    0.673368  [ DEG:  -141.4189     38.5811 ]
 
# 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: T0300AL381_2                                  
REMARK     2: T0300                                         
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0300AL381_2.T0300 -3 -ie -d:4 -o1 -sda 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   30   89   4.0   23   1.23  24.465     7.25
REMARK  ---------------------------------------------------------- 
MOLECULE T0300AL381_2
REMARK Aligment from pdb entry: 1u2uA
ATOM      1  N   THR     9      36.897  -0.030  -5.275  1.00  0.00              
ATOM      2  CA  THR     9      36.559  -0.957  -6.350  1.00  0.00              
ATOM      3  C   THR     9      37.507  -2.152  -6.378  1.00  0.00              
ATOM      4  O   THR     9      37.670  -2.804  -7.410  1.00  0.00              
ATOM      5  N   TYR    10      38.127  -2.430  -5.242  1.00  0.00              
ATOM      6  CA  TYR    10      39.057  -3.540  -5.123  1.00  0.00              
ATOM      7  C   TYR    10      38.348  -4.868  -5.331  1.00  0.00              
ATOM      8  O   TYR    10      38.872  -5.774  -5.981  1.00  0.00              
ATOM      9  N   GLU    11      37.145  -4.964  -4.809  1.00  0.00              
ATOM     10  CA  GLU    11      36.346  -6.158  -4.964  1.00  0.00              
ATOM     11  C   GLU    11      35.627  -6.120  -6.309  1.00  0.00              
ATOM     12  O   GLU    11      34.973  -7.082  -6.709  1.00  0.00              
ATOM     13  N   GLU    12      35.771  -4.991  -7.006  1.00  0.00              
ATOM     14  CA  GLU    12      35.161  -4.803  -8.309  1.00  0.00              
ATOM     15  C   GLU    12      36.106  -5.264  -9.413  1.00  0.00              
ATOM     16  O   GLU    12      35.674  -5.897 -10.375  1.00  0.00              
ATOM     17  N   MET    13      37.402  -4.958  -9.275  1.00  0.00              
ATOM     18  CA  MET    13      38.368  -5.376 -10.283  1.00  0.00              
ATOM     19  C   MET    13      38.348  -6.889 -10.423  1.00  0.00              
ATOM     20  O   MET    13      38.344  -7.422 -11.532  1.00  0.00              
ATOM     21  N   VAL    14      38.334  -7.576  -9.284  1.00  0.00              
ATOM     22  CA  VAL    14      38.311  -9.034  -9.279  1.00  0.00              
ATOM     23  C   VAL    14      37.199  -9.555 -10.179  1.00  0.00              
ATOM     24  O   VAL    14      37.287 -10.654 -10.724  1.00  0.00              
ATOM     25  N   LYS    15      36.157  -8.747 -10.333  1.00  0.00              
ATOM     26  CA  LYS    15      35.028  -9.113 -11.171  1.00  0.00              
ATOM     27  C   LYS    15      35.107  -8.398 -12.518  1.00  0.00              
ATOM     28  O   LYS    15      34.563  -8.870 -13.516  1.00  0.00              
ATOM     29  N   GLU    16      35.796  -7.259 -12.538  1.00  0.00              
ATOM     30  CA  GLU    16      35.953  -6.482 -13.762  1.00  0.00              
ATOM     31  C   GLU    16      36.832  -7.220 -14.767  1.00  0.00              
ATOM     32  O   GLU    16      36.756  -6.970 -15.969  1.00  0.00              
ATOM     33  N   VAL    17      37.662  -8.134 -14.268  1.00  0.00              
ATOM     34  CA  VAL    17      38.546  -8.906 -15.131  1.00  0.00              
ATOM     35  C   VAL    17      37.785 -10.065 -15.765  1.00  0.00              
ATOM     36  O   VAL    17      37.754 -10.204 -16.987  1.00  0.00              
ATOM     37  N   GLU    18      37.156 -10.883 -14.928  1.00  0.00              
ATOM     38  CA  GLU    18      36.380 -12.015 -15.414  1.00  0.00              
ATOM     39  C   GLU    18      35.301 -11.545 -16.386  1.00  0.00              
ATOM     40  O   GLU    18      34.836 -12.306 -17.233  1.00  0.00              
ATOM     41  N   ARG    19      34.914 -10.277 -16.255  1.00  0.00              
ATOM     42  CA  ARG    19      33.898  -9.691 -17.119  1.00  0.00              
ATOM     43  C   ARG    19      34.415  -9.569 -18.549  1.00  0.00              
ATOM     44  O   ARG    19      33.800 -10.076 -19.487  1.00  0.00              
ATOM     45  N   LEU    20      35.554  -8.897 -18.711  1.00  0.00              
ATOM     46  CA  LEU    20      36.148  -8.720 -20.030  1.00  0.00              
ATOM     47  C   LEU    20      36.834  -9.999 -20.491  1.00  0.00              
ATOM     48  O   LEU    20      36.657 -10.432 -21.626  1.00  0.00              
ATOM     49  N   LYS    21      37.618 -10.607 -19.604  1.00  0.00              
ATOM     50  CA  LYS    21      38.325 -11.842 -19.931  1.00  0.00              
ATOM     51  C   LYS    21      37.384 -12.854 -20.580  1.00  0.00              
ATOM     52  O   LYS    21      37.809 -13.690 -21.377  1.00  0.00              
ATOM     53  N   LEU    22      36.101 -12.765 -20.240  1.00  0.00              
ATOM     54  CA  LEU    22      35.098 -13.664 -20.797  1.00  0.00              
ATOM     55  C   LEU    22      34.638 -13.175 -22.167  1.00  0.00              
ATOM     56  O   LEU    22      34.316 -13.973 -23.046  1.00  0.00              
ATOM     57  N   GLU    23      34.616 -11.855 -22.341  1.00  0.00              
ATOM     58  CA  GLU    23      34.203 -11.254 -23.604  1.00  0.00              
ATOM     59  C   GLU    23      35.394 -11.117 -24.546  1.00  0.00              
ATOM     60  O   GLU    23      35.381 -11.640 -25.661  1.00  0.00              
ATOM     61  N   ASN    24      36.427 -10.415 -24.085  1.00  0.00              
ATOM     62  CA  ASN    24      37.635 -10.211 -24.875  1.00  0.00              
ATOM     63  C   ASN    24      38.115 -11.526 -25.488  1.00  0.00              
ATOM     64  O   ASN    24      38.643 -11.548 -26.601  1.00  0.00              
ATOM     65  N   LYS    25      37.926 -12.618 -24.756  1.00  0.00              
ATOM     66  CA  LYS    25      38.338 -13.937 -25.227  1.00  0.00              
ATOM     67  C   LYS    25      37.317 -14.515 -26.204  1.00  0.00              
ATOM     68  O   LYS    25      37.676 -15.221 -27.146  1.00  0.00              
ATOM     69  N   THR    26      36.044 -14.218 -25.970  1.00  0.00              
ATOM     70  CA  THR    26      34.973 -14.716 -26.826  1.00  0.00              
ATOM     71  C   THR    26      35.043 -14.091 -28.218  1.00  0.00              
ATOM     72  O   THR    26      34.629 -14.701 -29.203  1.00  0.00              
ATOM     73  N   LEU    27      35.564 -12.870 -28.291  1.00  0.00              
ATOM     74  CA  LEU    27      35.681 -12.166 -29.563  1.00  0.00              
ATOM     75  C   LEU    27      36.985 -12.516 -30.269  1.00  0.00              
ATOM     76  O   LEU    27      36.983 -12.895 -31.439  1.00  0.00              
ATOM     77  N   LYS    28      38.099 -12.383 -29.555  1.00  0.00              
ATOM     78  CA  LYS    28      39.414 -12.681 -30.120  1.00  0.00              
ATOM     79  C   LYS    28      39.417 -14.020 -30.855  1.00  0.00              
ATOM     80  O   LYS    28      40.188 -14.221 -31.793  1.00  0.00              
ATOM     81  N   GLN    29      38.555 -14.933 -30.423  1.00  0.00              
ATOM     82  CA  GLN    29      38.465 -16.252 -31.040  1.00  0.00              
ATOM     83  C   GLN    29      37.545 -16.230 -32.259  1.00  0.00              
ATOM     84  O   GLN    29      37.724 -17.009 -33.195  1.00  0.00              
ATOM     85  N   LYS    30      36.559 -15.340 -32.240  1.00  0.00              
ATOM     86  CA  LYS    30      35.613 -15.227 -33.346  1.00  0.00              
ATOM     87  C   LYS    30      36.118 -14.249 -34.401  1.00  0.00              
ATOM     88  O   LYS    30      35.884 -14.431 -35.595  1.00  0.00              
ATOM     89  N   VAL    31      36.813 -13.213 -33.950  1.00  0.00              
ATOM     90  CA  VAL    31      37.354 -12.200 -34.849  1.00  0.00              
ATOM     91  C   VAL    31      38.525 -12.753 -35.655  1.00  0.00              
ATOM     92  O   VAL    31      38.772 -12.327 -36.782  1.00  0.00              
ATOM     93  N   LYS    32      39.243 -13.704 -35.066  1.00  0.00              
ATOM     94  CA  LYS    32      40.389 -14.318 -35.724  1.00  0.00              
ATOM     95  C   LYS    32      39.974 -15.053 -36.997  1.00  0.00              
ATOM     96  O   LYS    32      40.807 -15.334 -37.859  1.00  0.00              
ATOM     97  N   SER    33      38.686 -15.369 -37.107  1.00  0.00              
ATOM     98  CA  SER    33      38.174 -16.078 -38.275  1.00  0.00              
ATOM     99  C   SER    33      37.284 -15.175 -39.127  1.00  0.00              
ATOM    100  O   SER    33      37.300 -15.257 -40.355  1.00  0.00              
ATOM    101  N   SER    34      36.506 -14.318 -38.471  1.00  0.00              
ATOM    102  CA  SER    34      35.608 -13.407 -39.177  1.00  0.00              
ATOM    103  C   SER    34      36.371 -12.551 -40.185  1.00  0.00              
ATOM    104  O   SER    34      36.128 -12.630 -41.390  1.00  0.00              
ATOM    105  N   GLY    35      37.292 -11.733 -39.687  1.00  0.00              
ATOM    106  CA  GLY    35      38.085 -10.861 -40.547  1.00  0.00              
ATOM    107  C   GLY    35      39.364 -11.558 -41.002  1.00  0.00              
ATOM    108  O   GLY    35      40.470 -11.084 -40.740  1.00  0.00              
ATOM    109  N   ALA    36      39.206 -12.686 -41.685  1.00  0.00              
ATOM    110  CA  ALA    36      40.349 -13.446 -42.178  1.00  0.00              
ATOM    111  C   ALA    36      40.959 -12.776 -43.404  1.00  0.00              
ATOM    112  O   ALA    36      42.179 -12.669 -43.525  1.00  0.00              
ATOM    113  N   VAL    37      40.100 -12.325 -44.314  1.00  0.00              
ATOM    114  CA  VAL    37      40.552 -11.663 -45.533  1.00  0.00              
ATOM    115  C   VAL    37      40.678 -10.158 -45.322  1.00  0.00              
ATOM    116  O   VAL    37      41.578  -9.517 -45.864  1.00  0.00              
ATOM    117  N   GLU   101      39.766  -9.600 -44.531  1.00  0.00              
ATOM    118  CA  GLU   101      39.791  -8.174 -44.264  1.00  0.00              
ATOM    119  C   GLU   101      40.749  -7.811 -43.146  1.00  0.00              
ATOM    120  O   GLU   101      40.346  -7.231 -42.139  1.00  0.00              
END
.861 -40.547  1.00  0.00              
ATOM    107  C   GLY    35      39.364 -11.558 -41.002  1.00  0.00              
ATOM    108  O   GLY    35      40.470 -11.084 -40.740  1.00  0.00              
ATOM    109  N   ALA    36      39.206 -12.686 -41.685  1.00  0.00              
ATOM    110  CA  ALA    36      40.349 -13.446 -42.178  1.00  0.00              
ATOM    111  C   ALA    36      40.959 -12.776 -43.404  1.00  0.00              
ATOM    112  O   ALA    36      42.179 -12.669 -43.525  1.00  0.00              
ATOM    113  N   VAL    37      40.100 -12.325 -44.314  1.00  0.00              
ATOM    114  CA  VAL    37      40.552 -11.663 -45.533  1.00  0.00              
ATOM    115  C   VAL    37      40.678 -10.158 -45.322  1.00  0.00              
ATOM    116  O   VAL    37      41.578  -9.517 -45.864  1.00  0.00              
ATOM    117  N   GLU   101      39.766  -9.600 -44.531  1.00  0.00              
ATOM    118  CA  GLU   101      39.791  -8.174 -44.264  1.00  0.00              
ATOM    119  C   GLU   101      40.749  -7.811 -43.146  1.00  0.00              
ATOM    120  O   GLU   101      40.346  -7.231 -42.139  1.00  0.00              
END
