
#######################################################
#                                                     #
#                        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   16 (  126),  selected   16 , name T0382TS009_2_1-D1
# Molecule2: number of CA atoms  119 (  920),  selected   16 , name T0382_D1.pdb
# PARAMETERS: T0382TS009_2_1-D1.T0382_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:    16         4 - 19          4.92     4.92
  LCS_AVERAGE:     13.45

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6         5 - 10          1.29     7.76
  LONGEST_CONTINUOUS_SEGMENT:     6        14 - 19          1.58    11.14
  LCS_AVERAGE:      4.78

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5         6 - 10          0.95     8.03
  LCS_AVERAGE:      3.52

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:  119
LCS_GDT     L       4     L       4      3    4   16     3    3    3    3    4    4    7    8    9   10   10   11   13   13   13   13   15   15   16   16 
LCS_GDT     D       5     D       5      4    6   16     3    4    4    7    7    7    8    9   11   12   12   14   15   15   15   15   15   15   16   16 
LCS_GDT     L       6     L       6      5    6   16     3    4    5    7    7    7    8    9   11   13   14   14   15   15   15   15   15   15   16   16 
LCS_GDT     H       7     H       7      5    6   16     3    4    5    7    7    7    8   10   12   13   14   14   15   15   15   15   15   15   16   16 
LCS_GDT     Q       8     Q       8      5    6   16     3    4    5    7    7    7    8   10   12   13   14   14   15   15   15   15   15   15   16   16 
LCS_GDT     M       9     M       9      5    6   16     3    4    5    7    7    7    8   10   12   13   14   14   15   15   15   15   15   15   16   16 
LCS_GDT     T      10     T      10      5    6   16     4    4    5    7    7    7    8   10   12   13   14   14   15   15   15   15   15   15   16   16 
LCS_GDT     T      11     T      11      4    5   16     4    4    4    4    6    7    8   10   12   13   14   14   15   15   15   15   15   15   16   16 
LCS_GDT     Q      12     Q      12      4    5   16     4    4    4    4    6    7    8   10   12   13   14   14   15   15   15   15   15   15   16   16 
LCS_GDT     D      13     D      13      4    5   16     4    4    4    7    7    7    8   10   12   13   14   14   15   15   15   15   15   15   16   16 
LCS_GDT     L      14     L      14      3    6   16     3    3    4    5    6    7    8   10   12   13   14   14   15   15   15   15   15   15   16   16 
LCS_GDT     V      15     V      15      4    6   16     4    4    4    5    6    7    8   10   12   13   14   14   15   15   15   15   15   15   16   16 
LCS_GDT     A      16     A      16      4    6   16     4    4    4    5    6    7    8   10   12   13   14   14   15   15   15   15   15   15   16   16 
LCS_GDT     L      17     L      17      4    6   16     4    4    4    5    6    7    8   10   11   12   14   14   15   15   15   15   15   15   16   16 
LCS_GDT     F      18     F      18      4    6   16     4    4    4    5    6    7    8   10   12   13   14   14   15   15   15   15   15   15   16   16 
LCS_GDT     A      19     A      19      4    6   16     0    3    4    5    6    7    8   10   12   13   14   14   15   15   15   15   15   15   16   16 
LCS_AVERAGE  LCS_A:   7.25  (   3.52    4.78   13.45 )

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      4      4      5      7      7      7      8     10     12     13     14     14     15     15     15     15     15     15     16     16 
GDT PERCENT_CA   3.36   3.36   4.20   5.88   5.88   5.88   6.72   8.40  10.08  10.92  11.76  11.76  12.61  12.61  12.61  12.61  12.61  12.61  13.45  13.45
GDT RMS_LOCAL    0.22   0.22   0.95   1.44   1.44   1.44   2.57   3.04   3.44   3.61   3.81   3.81   4.16   4.16   4.16   4.16   4.16   4.16   4.92   4.92
GDT RMS_ALL_CA  11.67  11.67   8.03   6.77   6.77   6.77   6.23   8.15   6.03   5.52   5.59   5.59   5.12   5.12   5.12   5.12   5.12   5.12   4.92   4.92

#      Molecule1      Molecule2       DISTANCE
LGA    L       4      L       4         19.309
LGA    D       5      D       5         13.155
LGA    L       6      L       6          8.172
LGA    H       7      H       7          7.100
LGA    Q       8      Q       8          7.112
LGA    M       9      M       9          4.271
LGA    T      10      T      10          3.220
LGA    T      11      T      11          2.222
LGA    Q      12      Q      12          3.729
LGA    D      13      D      13          3.159
LGA    L      14      L      14          3.768
LGA    V      15      V      15          2.206
LGA    A      16      A      16          2.107
LGA    L      17      L      17          3.898
LGA    F      18      F      18          2.297
LGA    A      19      A      19          3.956

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   16  119    4.0     10    3.04     7.563     7.155     0.318

LGA_LOCAL      RMSD =  3.044  Number of atoms =   10  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  7.206  Number of atoms =   16 
Std_ALL_ATOMS  RMSD =  4.921  (standard rmsd on all 16 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.269734 * X  +   0.492052 * Y  +   0.827725 * Z  +  -3.424936
  Y_new =   0.769286 * X  +   0.627127 * Y  +  -0.122114 * Z  +  40.871948
  Z_new =  -0.579175 * X  +   0.603818 * Y  +  -0.547686 * Z  + -29.996321 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.307487   -0.834106  [ DEG:   132.2092    -47.7908 ]
  Theta =   0.617716    2.523877  [ DEG:    35.3925    144.6075 ]
  Phi   =   1.908032   -1.233561  [ DEG:   109.3222    -70.6778 ]
 
# 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: T0382TS009_2_1-D1                             
REMARK     2: T0382_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0382TS009_2_1-D1.T0382_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   16  119   4.0   10   3.04   7.155     4.92
REMARK  ---------------------------------------------------------- 
MOLECULE T0382TS009_2_1-D1
REMARK PARENT number 1
PFRMAT TS                                                                       
TARGET T0382                                                                    
PARENT N/A                                                                      
ATOM     24  N   LEU     4      -9.484  38.159 -24.448  1.00  0.00              
ATOM     25  CA  LEU     4     -10.305  36.961 -24.570  1.00  0.00              
ATOM     26  C   LEU     4     -10.964  36.606 -23.242  1.00  0.00              
ATOM     27  O   LEU     4     -11.972  37.202 -22.860  1.00  0.00              
ATOM     28  CB  LEU     4     -11.369  37.147 -25.653  1.00  0.00              
ATOM     29  CG  LEU     4     -11.259  36.233 -26.875  1.00  0.00              
ATOM     30  CD1 LEU     4     -12.629  35.992 -27.490  1.00  0.00              
ATOM     31  CD2 LEU     4     -10.593  34.917 -26.505  1.00  0.00              
ATOM     32  N   ASP     5     -10.390  35.635 -22.540  1.00  0.00              
ATOM     33  CA  ASP     5     -10.921  35.201 -21.254  1.00  0.00              
ATOM     34  C   ASP     5     -10.596  36.207 -20.155  1.00  0.00              
ATOM     35  O   ASP     5     -11.314  37.190 -19.969  1.00  0.00              
ATOM     36  CB  ASP     5     -12.433  34.988 -21.344  1.00  0.00              
ATOM     37  CG  ASP     5     -12.813  33.522 -21.405  1.00  0.00              
ATOM     38  OD1 ASP     5     -13.443  33.030 -20.444  1.00  0.00              
ATOM     39  OD2 ASP     5     -12.481  32.864 -22.413  1.00  0.00              
ATOM     40  N   LEU     6      -9.511  35.954 -19.430  1.00  0.00              
ATOM     41  CA  LEU     6      -9.091  36.838 -18.349  1.00  0.00              
ATOM     42  C   LEU     6      -9.530  38.275 -18.608  1.00  0.00              
ATOM     43  O   LEU     6      -9.641  39.076 -17.680  1.00  0.00              
ATOM     44  CB  LEU     6      -9.649  36.350 -17.011  1.00  0.00              
ATOM     45  CG  LEU     6      -8.641  36.200 -15.869  1.00  0.00              
ATOM     46  CD1 LEU     6      -9.298  36.496 -14.530  1.00  0.00              
ATOM     47  CD2 LEU     6      -7.439  37.105 -16.093  1.00  0.00              
ATOM     48  N   HIS     7      -9.776  38.594 -19.874  1.00  0.00              
ATOM     49  CA  HIS     7     -10.204  39.934 -20.257  1.00  0.00              
ATOM     50  C   HIS     7     -11.265  40.469 -19.301  1.00  0.00              
ATOM     51  O   HIS     7     -10.967  41.272 -18.416  1.00  0.00              
ATOM     52  CB  HIS     7      -9.007  40.886 -20.301  1.00  0.00              
ATOM     53  CG  HIS     7      -8.921  41.690 -21.561  1.00  0.00              
ATOM     54  ND1 HIS     7      -9.493  41.280 -22.747  1.00  0.00              
ATOM     55  CD2 HIS     7      -8.329  42.879 -21.821  1.00  0.00              
ATOM     56  CE1 HIS     7      -9.256  42.184 -23.681  1.00  0.00              
ATOM     57  NE2 HIS     7      -8.553  43.164 -23.147  1.00  0.00              
ATOM     58  N   GLN     8     -12.501  40.020 -19.484  1.00  0.00              
ATOM     59  CA  GLN     8     -13.607  40.452 -18.639  1.00  0.00              
ATOM     60  C   GLN     8     -13.697  39.606 -17.373  1.00  0.00              
ATOM     61  O   GLN     8     -13.854  40.134 -16.273  1.00  0.00              
ATOM     62  CB  GLN     8     -13.457  41.931 -18.274  1.00  0.00              
ATOM     63  CG  GLN     8     -14.735  42.740 -18.420  1.00  0.00              
ATOM     64  CD  GLN     8     -14.615  44.132 -17.831  1.00  0.00              
ATOM     65  OE1 GLN     8     -15.602  44.857 -17.723  1.00  0.00              
ATOM     66  NE2 GLN     8     -13.400  44.507 -17.447  1.00  0.00              
ATOM     67  N   MET     9     -13.597  38.291 -17.538  1.00  0.00              
ATOM     68  CA  MET     9     -13.668  37.370 -16.410  1.00  0.00              
ATOM     69  C   MET     9     -13.846  38.122 -15.094  1.00  0.00              
ATOM     70  O   MET     9     -14.552  37.662 -14.197  1.00  0.00              
ATOM     71  CB  MET     9     -14.809  36.371 -16.604  1.00  0.00              
ATOM     72  CG  MET     9     -14.393  35.077 -17.284  1.00  0.00              
ATOM     73  SD  MET     9     -15.785  34.198 -18.019  1.00  0.00              
ATOM     74  CE  MET     9     -14.947  32.802 -18.765  1.00  0.00              
ATOM     75  N   THR    10     -13.203  39.280 -14.989  1.00  0.00              
ATOM     76  CA  THR    10     -13.292  40.115 -13.757  1.00  0.00              
ATOM     77  C   THR    10     -14.667  39.997 -13.108  1.00  0.00              
ATOM     78  O   THR    10     -14.790  40.023 -11.883  1.00  0.00              
ATOM     79  CB  THR    10     -12.214  39.723 -12.729  1.00  0.00              
ATOM     80  OG1 THR    10     -11.573  38.511 -13.145  1.00  0.00              
ATOM     81  CG2 THR    10     -11.174  40.825 -12.601  1.00  0.00              
ATOM     82  N   THR    11     -15.698  39.866 -13.936  1.00  0.00              
ATOM     83  CA  THR    11     -17.096  39.741 -13.434  1.00  0.00             
ATOM     84  C   THR    11     -17.199  38.672 -12.351  1.00  0.00             
ATOM     85  O   THR    11     -17.824  38.885 -11.313  1.00  0.00             
ATOM     86  CB  THR    11     -17.617  41.077 -12.874  1.00  0.00             
ATOM     87  OG1 THR    11     -16.527  41.997 -12.732  1.00  0.00             
ATOM     88  CG2 THR    11     -18.660  41.674 -13.805  1.00  0.00             
ATOM     89  N   GLN    12     -16.580  37.522 -12.601  1.00  0.00             
ATOM     90  CA  GLN    12     -16.601  36.418 -11.648  1.00  0.00             
ATOM     91  C   GLN    12     -16.328  36.909 -10.230  1.00  0.00             
ATOM     92  O   GLN    12     -16.739  36.280  -9.255  1.00  0.00             
ATOM     93  CB  GLN    12     -17.944  35.689 -11.703  1.00  0.00             
ATOM     94  CG  GLN    12     -17.833  34.176 -11.612  1.00  0.00             
ATOM     95  CD  GLN    12     -19.164  33.480 -11.816  1.00  0.00             
ATOM     96  OE1 GLN    12     -19.213  32.278 -12.079  1.00  0.00             
ATOM     97  NE2 GLN    12     -20.249  34.235 -11.695  1.00  0.00             
ATOM     98  N   ASP    13     -15.632  38.036 -10.123  1.00  0.00             
ATOM     99  CA  ASP    13     -15.302  38.613  -8.825  1.00  0.00             
ATOM    100  C   ASP    13     -15.836  37.749  -7.686  1.00  0.00             
ATOM    101  O   ASP    13     -15.727  38.112  -6.516  1.00  0.00             
ATOM    102  CB  ASP    13     -13.790  38.790  -8.685  1.00  0.00             
ATOM    103  CG  ASP    13     -13.383  40.244  -8.545  1.00  0.00             
ATOM    104  OD1 ASP    13     -12.530  40.542  -7.683  1.00  0.00             
ATOM    105  OD2 ASP    13     -13.920  41.085  -9.296  1.00  0.00             
ATOM    106  N   LEU    14     -16.413  36.606  -8.038  1.00  0.00             
ATOM    107  CA  LEU    14     -16.965  35.689  -7.049  1.00  0.00             
ATOM    108  C   LEU    14     -16.690  36.178  -5.630  1.00  0.00             
ATOM    109  O   LEU    14     -16.211  35.423  -4.784  1.00  0.00             
ATOM    110  CB  LEU    14     -18.470  35.512  -7.260  1.00  0.00             
ATOM    111  CG  LEU    14     -18.903  34.274  -8.050  1.00  0.00             
ATOM    112  CD1 LEU    14     -19.952  33.487  -7.283  1.00  0.00             
ATOM    113  CD2 LEU    14     -17.702  33.399  -8.378  1.00  0.00             
ATOM    114  N   VAL    15     -16.997  37.446  -5.377  1.00  0.00             
ATOM    115  CA  VAL    15     -16.779  38.052  -4.033  1.00  0.00             
ATOM    116  C   VAL    15     -17.358  37.171  -2.931  1.00  0.00             
ATOM    117  O   VAL    15     -16.785  37.060  -1.846  1.00  0.00             
ATOM    118  CB  VAL    15     -15.282  38.286  -3.756  1.00  0.00             
ATOM    119  CG1 VAL    15     -14.923  39.748  -3.973  1.00  0.00             
ATOM    120  CG2 VAL    15     -14.429  37.384  -4.634  1.00  0.00             
ATOM    121  N   ALA    16     -18.496  36.548  -3.216  1.00  0.00             
ATOM    122  CA  ALA    16     -19.155  35.677  -2.250  1.00  0.00             
ATOM    123  C   ALA    16     -18.330  35.544  -0.973  1.00  0.00             
ATOM    124  O   ALA    16     -18.668  36.123   0.059  1.00  0.00             
ATOM    125  CB  ALA    16     -20.544  36.201  -1.923  1.00  0.00             
ATOM    126  N   LEU    17     -17.246  34.777  -1.052  1.00  0.00             
ATOM    127  CA  LEU    17     -16.372  34.568   0.095  1.00  0.00             
ATOM    128  C   LEU    17     -15.958  35.894   0.722  1.00  0.00             
ATOM    129  O   LEU    17     -16.485  36.292   1.761  1.00  0.00             
ATOM    130  CB  LEU    17     -17.059  33.684   1.138  1.00  0.00             
ATOM    131  CG  LEU    17     -16.306  32.420   1.557  1.00  0.00             
ATOM    132  CD1 LEU    17     -16.653  32.037   2.988  1.00  0.00             
ATOM    133  CD2 LEU    17     -14.804  32.611   1.397  1.00  0.00             
ATOM    134  N   PHE    18     -15.010  36.575   0.086  1.00  0.00             
ATOM    135  CA  PHE    18     -14.523  37.857   0.580  1.00  0.00             
ATOM    136  C   PHE    18     -15.464  38.992   0.188  1.00  0.00             
ATOM    137  O   PHE    18     -16.670  38.790   0.046  1.00  0.00             
ATOM    138  CB  PHE    18     -14.353  37.815   2.100  1.00  0.00             
ATOM    139  CG  PHE    18     -12.932  37.990   2.556  1.00  0.00             
ATOM    140  CD1 PHE    18     -11.970  38.489   1.695  1.00  0.00             
ATOM    141  CD2 PHE    18     -12.558  37.654   3.845  1.00  0.00             
ATOM    142  CE1 PHE    18     -10.663  38.650   2.115  1.00  0.00             
ATOM    143  CE2 PHE    18     -11.251  37.813   4.264  1.00  0.00             
ATOM    144  CZ  PHE    18     -10.305  38.309   3.405  1.00  0.00             
ATOM    145  N   ALA    19     -14.904  40.185   0.016  1.00  0.00             
ATOM    146  CA  ALA    19     -15.691  41.354  -0.359  1.00  0.00             
ATOM    147  C   ALA    19     -15.100  42.047  -1.582  1.00  0.00             
ATOM    148  O   ALA    19     -13.958  41.791  -1.961  1.00  0.00             
ATOM    149  CB  ALA    19     -17.135  40.956  -0.628  1.00  0.00             
TER
END
