
#######################################################
#                                                     #
#                        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 (  137),  selected   16 , name T0378TS389_4-D1
# Molecule2: number of CA atoms   89 (  716),  selected   16 , name T0378_D1.pdb
# PARAMETERS: T0378TS389_4-D1.T0378_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:    12        70 - 81          4.77     8.23
  LCS_AVERAGE:     12.78

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7        70 - 76          1.99    11.02
  LONGEST_CONTINUOUS_SEGMENT:     7        71 - 77          1.59    11.25
  LCS_AVERAGE:      6.32

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6        71 - 76          0.84    11.80
  LCS_AVERAGE:      4.92

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     I       7     I       7      4    4    9     0    4    4    5    5    5    7    8    9   11   11   11   12   14   15   15   15   16   16   16 
LCS_GDT     K       8     K       8      4    4    9     3    4    4    6    7    7    8    8    9   11   11   11   12   13   15   15   15   16   16   16 
LCS_GDT     F       9     F       9      4    4    9     3    4    4    6    7    7    8    8    9   11   11   11   12   14   15   15   15   16   16   16 
LCS_GDT     L      10     L      10      4    4   11     3    4    4    6    7    7    8    8    9   11   11   11   12   14   15   15   15   16   16   16 
LCS_GDT     F      70     F      70      3    7   12     3    3    3    3    3    5    7    8   10   10   10   11   11   14   15   15   15   16   16   16 
LCS_GDT     D      71     D      71      6    7   12     3    4    6    6    6    7    7    8   10   10   10   11   11   14   15   15   15   16   16   16 
LCS_GDT     F      72     F      72      6    7   12     3    5    6    6    6    7    7    8   10   10   10   11   12   14   15   15   15   16   16   16 
LCS_GDT     K      73     K      73      6    7   12     3    5    6    6    6    7    7    8   10   11   11   11   12   14   15   15   15   16   16   16 
LCS_GDT     R      74     R      74      6    7   12     3    5    6    6    7    7    8    8   10   11   11   11   12   14   15   15   15   16   16   16 
LCS_GDT     I      75     I      75      6    7   12     3    5    6    6    6    7    8    8   10   11   11   11   12   14   15   15   15   16   16   16 
LCS_GDT     S      76     S      76      6    7   12     3    5    6    6    7    7    8    8   10   11   11   11   12   14   15   15   15   16   16   16 
LCS_GDT     T      77     T      77      3    7   12     3    3    4    5    6    7    7    8   10   10   10   11   12   14   15   15   15   16   16   16 
LCS_GDT     Q      78     Q      78      3    5   12     3    3    3    4    5    5    7    8   10   11   11   11   12   14   15   15   15   16   16   16 
LCS_GDT     T      79     T      79      3    5   12     3    3    3    6    7    7    8    8   10   11   11   11   12   14   15   15   15   16   16   16 
LCS_GDT     T      80     T      80      3    5   12     3    3    3    6    7    7    8    8    9   11   11   11   12   14   15   15   15   16   16   16 
LCS_GDT     P      81     P      81      3    3   12     3    3    3    3    3    5    5    5    6    6   10   11   11   13   13   14   15   16   16   16 
LCS_AVERAGE  LCS_A:   8.01  (   4.92    6.32   12.78 )

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      3      5      6      6      7      7      8      8     10     11     11     11     12     14     15     15     15     16     16     16 
GDT PERCENT_CA   3.37   5.62   6.74   6.74   7.87   7.87   8.99   8.99  11.24  12.36  12.36  12.36  13.48  15.73  16.85  16.85  16.85  17.98  17.98  17.98
GDT RMS_LOCAL    0.02   0.48   0.84   0.84   1.82   1.59   2.16   2.16   3.60   3.34   3.34   3.34   3.74   5.34   5.30   5.30   5.30   5.58   5.58   5.58
GDT RMS_ALL_CA   9.91  11.15  11.80  11.80   6.02  11.25   6.08   6.08   9.13   5.85   5.85   5.85   5.97   5.77   5.65   5.65   5.65   5.58   5.58   5.58

#      Molecule1      Molecule2       DISTANCE
LGA    I       7      I       7          4.892
LGA    K       8      K       8          1.885
LGA    F       9      F       9          1.604
LGA    L      10      L      10          1.956
LGA    F      70      F      70         11.722
LGA    D      71      D      71         11.266
LGA    F      72      F      72          8.824
LGA    K      73      K      73          6.673
LGA    R      74      R      74          1.803
LGA    I      75      I      75          3.492
LGA    S      76      S      76          1.110
LGA    T      77      T      77          7.635
LGA    Q      78      Q      78          6.329
LGA    T      79      T      79          2.677
LGA    T      80      T      80          1.886
LGA    P      81      P      81          6.744

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   16   89    4.0      8    2.16     9.551     8.943     0.354

LGA_LOCAL      RMSD =  2.161  Number of atoms =    8  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  6.082  Number of atoms =   16 
Std_ALL_ATOMS  RMSD =  5.580  (standard rmsd on all 16 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.874104 * X  +  -0.114738 * Y  +  -0.471993 * Z  +  17.098957
  Y_new =   0.266937 * X  +  -0.925287 * Y  +  -0.269423 * Z  +  28.497995
  Z_new =  -0.405816 * X  +  -0.361496 * Y  +   0.839425 * Z  +  35.681950 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.406644    2.734949  [ DEG:   -23.2990    156.7010 ]
  Theta =   0.417872    2.723721  [ DEG:    23.9423    156.0577 ]
  Phi   =   2.845204   -0.296389  [ DEG:   163.0182    -16.9818 ]
 
# 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: T0378TS389_4-D1                               
REMARK     2: T0378_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0378TS389_4-D1.T0378_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   16   89   4.0    8   2.16   8.943     5.58
REMARK  ---------------------------------------------------------- 
MOLECULE T0378TS389_4-D1
PFRMAT TS
TARGET T0378
MODEL  4
PARENT N/A
ATOM      2  N   ILE     7       7.634  33.076  56.233  1.00  0.00
ATOM      3  CA  ILE     7       7.514  34.361  55.550  1.00  0.00
ATOM      4  CB  ILE     7       7.523  35.532  56.548  1.00  0.00
ATOM      5  CG1 ILE     7       6.247  35.523  57.393  1.00  0.00
ATOM      6  CG2 ILE     7       7.602  36.861  55.809  1.00  0.00
ATOM      7  CD1 ILE     7       6.286  36.475  58.569  1.00  0.00
ATOM      8  O   ILE     7       8.488  35.318  53.598  1.00  0.00
ATOM      9  C   ILE     7       8.654  34.600  54.575  1.00  0.00
ATOM     10  N   LYS     8       9.805  33.990  54.819  1.00  0.00
ATOM     11  CA  LYS     8      10.936  34.209  53.933  1.00  0.00
ATOM     12  CB  LYS     8      12.222  34.395  54.740  1.00  0.00
ATOM     13  CG  LYS     8      12.246  35.656  55.590  1.00  0.00
ATOM     14  CD  LYS     8      13.547  35.776  56.364  1.00  0.00
ATOM     15  CE  LYS     8      13.573  37.039  57.209  1.00  0.00
ATOM     16  NZ  LYS     8      14.866  37.199  57.928  1.00  0.00
ATOM     17  O   LYS     8      10.728  33.084  51.823  1.00  0.00
ATOM     18  C   LYS     8      11.207  33.071  52.956  1.00  0.00
ATOM     19  N   PHE     9      11.993  32.101  53.406  1.00  0.00
ATOM     20  CA  PHE     9      12.365  30.960  52.593  1.00  0.00
ATOM     21  CB  PHE     9      12.931  29.841  53.471  1.00  0.00
ATOM     22  CG  PHE     9      13.405  28.645  52.695  1.00  0.00
ATOM     23  CD1 PHE     9      14.642  28.651  52.073  1.00  0.00
ATOM     24  CD2 PHE     9      12.615  27.513  52.588  1.00  0.00
ATOM     25  CE1 PHE     9      15.079  27.551  51.360  1.00  0.00
ATOM     26  CE2 PHE     9      13.052  26.413  51.874  1.00  0.00
ATOM     27  CZ  PHE     9      14.278  26.429  51.263  1.00  0.00
ATOM     28  O   PHE     9      11.150  30.362  50.616  1.00  0.00
ATOM     29  C   PHE     9      11.156  30.416  51.843  1.00  0.00
ATOM     30  N   LEU    10      10.133  30.034  52.599  1.00  0.00
ATOM     31  CA  LEU    10       8.904  29.476  52.060  1.00  0.00
ATOM     32  CB  LEU    10       7.847  29.345  53.158  1.00  0.00
ATOM     33  CG  LEU    10       6.493  28.778  52.731  1.00  0.00
ATOM     34  CD1 LEU    10       6.643  27.350  52.227  1.00  0.00
ATOM     35  CD2 LEU    10       5.520  28.771  53.901  1.00  0.00
ATOM     36  O   LEU    10       8.020  29.810  49.853  1.00  0.00
ATOM     37  C   LEU    10       8.273  30.318  50.943  1.00  0.00
ATOM     38  N   PHE    70       8.033  31.595  51.222  1.00  0.00
ATOM     39  CA  PHE    70       7.416  32.527  50.271  1.00  0.00
ATOM     40  CB  PHE    70       7.133  33.872  50.945  1.00  0.00
ATOM     41  CG  PHE    70       6.484  34.879  50.040  1.00  0.00
ATOM     42  CD1 PHE    70       5.132  34.798  49.747  1.00  0.00
ATOM     43  CD2 PHE    70       7.223  35.906  49.481  1.00  0.00
ATOM     44  CE1 PHE    70       4.535  35.727  48.913  1.00  0.00
ATOM     45  CE2 PHE    70       6.625  36.833  48.648  1.00  0.00
ATOM     46  CZ  PHE    70       5.287  36.747  48.364  1.00  0.00
ATOM     47  O   PHE    70       7.750  32.840  47.920  1.00  0.00
ATOM     48  C   PHE    70       8.272  32.833  49.038  1.00  0.00
ATOM     49  N   ASP    71       9.568  33.088  49.216  1.00  0.00
ATOM     50  CA  ASP    71      10.404  33.382  48.055  1.00  0.00
ATOM     51  CB  ASP    71      11.806  33.807  48.497  1.00  0.00
ATOM     52  CG  ASP    71      11.830  35.197  49.098  1.00  0.00
ATOM     53  OD1 ASP    71      10.827  35.927  48.952  1.00  0.00
ATOM     54  OD2 ASP    71      12.854  35.559  49.717  1.00  0.00
ATOM     55  O   ASP    71      10.567  32.309  45.913  1.00  0.00
ATOM     56  C   ASP    71      10.557  32.167  47.130  1.00  0.00
ATOM     57  N   PHE    72      10.676  30.973  47.700  1.00  0.00
ATOM     58  CA  PHE    72      10.819  29.775  46.890  1.00  0.00
ATOM     59  CB  PHE    72      11.055  28.551  47.778  1.00  0.00
ATOM     60  CG  PHE    72      11.206  27.267  47.013  1.00  0.00
ATOM     61  CD1 PHE    72      12.401  26.951  46.391  1.00  0.00
ATOM     62  CD2 PHE    72      10.151  26.376  46.915  1.00  0.00
ATOM     63  CE1 PHE    72      12.540  25.770  45.688  1.00  0.00
ATOM     64  CE2 PHE    72      10.291  25.193  46.212  1.00  0.00
ATOM     65  CZ  PHE    72      11.479  24.890  45.600  1.00  0.00
ATOM     66  O   PHE    72       9.648  29.062  44.884  1.00  0.00
ATOM     67  C   PHE    72       9.564  29.500  46.040  1.00  0.00
ATOM     68  N   LYS    73       8.394  29.738  46.616  1.00  0.00
ATOM     69  CA  LYS    73       7.177  29.462  45.874  1.00  0.00
ATOM     70  CB  LYS    73       5.963  29.493  46.806  1.00  0.00
ATOM     71  CG  LYS    73       5.900  28.327  47.780  1.00  0.00
ATOM     72  CD  LYS    73       4.671  28.416  48.669  1.00  0.00
ATOM     73  CE  LYS    73       4.627  27.270  49.667  1.00  0.00
ATOM     74  NZ  LYS    73       3.440  27.357  50.561  1.00  0.00
ATOM     75  O   LYS    73       6.595  30.243  43.720  1.00  0.00
ATOM     76  C   LYS    73       7.044  30.525  44.823  1.00  0.00
ATOM     77  N   ARG    74       7.420  31.747  45.165  1.00  0.00
ATOM     78  CA  ARG    74       7.329  32.836  44.195  1.00  0.00
ATOM     79  CB  ARG    74       7.947  34.113  44.767  1.00  0.00
ATOM     80  CG  ARG    74       7.801  35.329  43.865  1.00  0.00
ATOM     81  CD  ARG    74       8.546  36.528  44.430  1.00  0.00
ATOM     82  NE  ARG    74       9.994  36.321  44.434  1.00  0.00
ATOM     83  CZ  ARG    74      10.767  36.434  43.360  1.00  0.00
ATOM     84  NH1 ARG    74      12.073  36.227  43.459  1.00  0.00
ATOM     85  NH2 ARG    74      10.232  36.755  42.191  1.00  0.00
ATOM     86  O   ARG    74       7.577  32.644  41.818  1.00  0.00
ATOM     87  C   ARG    74       8.073  32.451  42.927  1.00  0.00
ATOM     88  N   ILE    75       9.267  31.905  43.096  1.00  0.00
ATOM     89  CA  ILE    75      10.073  31.468  41.974  1.00  0.00
ATOM     90  CB  ILE    75      11.510  31.127  42.412  1.00  0.00
ATOM     91  CG1 ILE    75      12.247  32.391  42.859  1.00  0.00
ATOM     92  CG2 ILE    75      12.284  30.501  41.261  1.00  0.00
ATOM     93  CD1 ILE    75      13.566  32.118  43.548  1.00  0.00
ATOM     94  O   ILE    75       9.555  30.090  40.058  1.00  0.00
ATOM     95  C   ILE    75       9.518  30.218  41.290  1.00  0.00
ATOM     96  N   SER    76       8.972  29.292  42.085  1.00  0.00
ATOM     97  CA  SER    76       8.417  28.081  41.524  1.00  0.00
ATOM     98  CB  SER    76       7.920  27.155  42.636  1.00  0.00
ATOM     99  OG  SER    76       6.827  27.733  43.330  1.00  0.00
ATOM    100  O   SER    76       6.967  27.756  39.622  1.00  0.00
ATOM    101  C   SER    76       7.246  28.442  40.613  1.00  0.00
ATOM    102  N   THR    77       6.575  29.525  40.965  1.00  0.00
ATOM    103  CA  THR    77       5.413  29.992  40.200  1.00  0.00
ATOM    104  CB  THR    77       4.652  31.100  40.952  1.00  0.00
ATOM    105  CG2 THR    77       4.150  30.587  42.294  1.00  0.00
ATOM    106  OG1 THR    77       5.525  32.214  41.179  1.00  0.00
ATOM    107  O   THR    77       4.894  30.792  37.997  1.00  0.00
ATOM    108  C   THR    77       5.772  30.571  38.838  1.00  0.00
ATOM    109  N   GLN    78       7.057  30.825  38.607  1.00  0.00
ATOM    110  CA  GLN    78       7.497  31.330  37.316  1.00  0.00
ATOM    111  CB  GLN    78       8.495  32.475  37.503  1.00  0.00
ATOM    112  CG  GLN    78       7.939  33.665  38.267  1.00  0.00
ATOM    113  CD  GLN    78       6.749  34.297  37.575  1.00  0.00
ATOM    114  OE1 GLN    78       6.789  34.576  36.376  1.00  0.00
ATOM    115  NE2 GLN    78       5.678  34.523  38.331  1.00  0.00
ATOM    116  O   GLN    78       8.640  30.443  35.414  1.00  0.00
ATOM    117  C   GLN    78       8.181  30.205  36.509  1.00  0.00
ATOM    118  N   THR    79       8.254  28.989  37.036  1.00  0.00
ATOM    119  CA  THR    79       8.909  27.917  36.285  1.00  0.00
ATOM    120  CB  THR    79       9.061  26.643  37.135  1.00  0.00
ATOM    121  CG2 THR    79       9.749  25.549  36.335  1.00  0.00
ATOM    122  OG1 THR    79       9.848  26.932  38.298  1.00  0.00
ATOM    123  O   THR    79       6.911  27.395  35.083  1.00  0.00
ATOM    124  C   THR    79       8.134  27.523  35.032  1.00  0.00
ATOM    125  N   THR    80       8.846  27.336  33.917  1.00  0.00
ATOM    126  CA  THR    80       8.239  27.013  32.622  1.00  0.00
ATOM    127  CB  THR    80       8.834  27.873  31.490  1.00  0.00
ATOM    128  CG2 THR    80       8.200  27.508  30.157  1.00  0.00
ATOM    129  OG1 THR    80       8.587  29.259  31.758  1.00  0.00
ATOM    130  O   THR    80       9.663  25.148  32.090  1.00  0.00
ATOM    131  C   THR    80       8.509  25.535  32.325  1.00  0.00
ATOM    132  N   PRO    81       7.476  24.685  32.356  1.00  0.00
ATOM    133  CA  PRO    81       7.724  23.268  32.082  1.00  0.00
ATOM    134  CB  PRO    81       6.471  22.566  32.609  1.00  0.00
ATOM    135  CG  PRO    81       5.382  23.576  32.453  1.00  0.00
ATOM    136  CD  PRO    81       6.014  24.913  32.722  1.00  0.00
ATOM    137  O   PRO    81       8.402  21.933  30.203  1.00  0.00
ATOM    138  C   PRO    81       7.916  22.998  30.585  1.00  0.00
TER
END
