
#######################################################
#                                                     #
#                        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   14 (  122),  selected   14 , name T0358TS389_5
# Molecule2: number of CA atoms   66 ( 1047),  selected   14 , name T0358.pdb
# PARAMETERS: T0358TS389_5.T0358.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:    14        40 - 58          4.99     4.99
  LCS_AVERAGE:     21.21

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8        43 - 55          1.96     6.07
  LCS_AVERAGE:      9.52

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4        45 - 50          0.89     6.12
  LCS_AVERAGE:      4.98

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:   66
LCS_GDT     V      40     V      40      3    3   14     3    4    4    4    4    4    6    7    7    9   11   12   12   13   14   14   14   14   14   14 
LCS_GDT     V      41     V      41      3    5   14     3    4    4    4    4    5    6    7    7   10   11   12   12   13   14   14   14   14   14   14 
LCS_GDT     R      42     R      42      3    5   14     3    4    4    4    4    5    6    7    7    8   11   12   12   13   14   14   14   14   14   14 
LCS_GDT     D      43     D      43      3    8   14     1    3    3    5    7    8    8    8    9   10   11   12   12   13   14   14   14   14   14   14 
LCS_GDT     E      45     E      45      4    8   14     3    3    4    6    7    8    8    8    9   10   11   12   12   13   14   14   14   14   14   14 
LCS_GDT     G      46     G      46      4    8   14     3    3    4    6    7    8    8    8    9   10   11   12   12   13   14   14   14   14   14   14 
LCS_GDT     R      47     R      47      4    8   14     3    3    4    6    7    8    8    8    9   10   11   12   12   13   14   14   14   14   14   14 
LCS_GDT     W      50     W      50      4    8   14     3    3    4    6    7    8    8    8    9   10   11   12   12   13   14   14   14   14   14   14 
LCS_GDT     R      51     R      51      3    8   14     3    3    4    5    6    8    8    8    9   10   11   12   12   13   14   14   14   14   14   14 
LCS_GDT     A      52     A      52      3    8   14     3    3    4    6    7    8    8    8    9   10   11   12   12   13   14   14   14   14   14   14 
LCS_GDT     F      55     F      55      3    8   14     1    3    4    6    7    8    8    8    9   10   11   12   12   13   14   14   14   14   14   14 
LCS_GDT     E      56     E      56      3    5   14     3    4    4    5    5    6    6    8    9   10   11   12   12   13   14   14   14   14   14   14 
LCS_GDT     P      57     P      57      3    3   14     3    3    3    3    3    4    4    4    6    7    7    7   12   13   14   14   14   14   14   14 
LCS_GDT     D      58     D      58      3    3   14     3    3    3    3    5    6    6    6    8    8    8    9   11   13   14   14   14   14   14   14 
LCS_AVERAGE  LCS_A:  11.90  (   4.98    9.52   21.21 )

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      4      4      6      7      8      8      8      9     10     11     12     12     13     14     14     14     14     14     14 
GDT PERCENT_CA   4.55   6.06   6.06   9.09  10.61  12.12  12.12  12.12  13.64  15.15  16.67  18.18  18.18  19.70  21.21  21.21  21.21  21.21  21.21  21.21
GDT RMS_LOCAL    0.02   0.57   0.57   1.38   1.72   1.96   1.96   1.96   2.62   3.13   3.53   3.80   3.80   4.49   4.99   4.99   4.99   4.99   4.99   4.99
GDT RMS_ALL_CA  25.81   8.05   8.05   6.11   5.90   6.07   6.07   6.07   5.68   5.56   5.58   5.55   5.55   5.17   4.99   4.99   4.99   4.99   4.99   4.99

#      Molecule1      Molecule2       DISTANCE
LGA    V      40      V      40          7.302
LGA    V      41      V      41          7.011
LGA    R      42      R      42          7.700
LGA    D      43      D      43          2.641
LGA    E      45      E      45          1.214
LGA    G      46      G      46          1.133
LGA    R      47      R      47          1.162
LGA    W      50      W      50          2.072
LGA    R      51      R      51          2.884
LGA    A      52      A      52          0.929
LGA    F      55      F      55          2.473
LGA    E      56      E      56          6.319
LGA    P      57      P      57         11.106
LGA    D      58      D      58         12.684

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   14   66    4.0      8    1.96    12.121    11.811     0.389

LGA_LOCAL      RMSD =  1.958  Number of atoms =    8  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  6.075  Number of atoms =   14 
Std_ALL_ATOMS  RMSD =  4.985  (standard rmsd on all 14 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.413495 * X  +  -0.345380 * Y  +   0.842458 * Z  +  -8.880599
  Y_new =   0.373904 * X  +  -0.779235 * Y  +  -0.502980 * Z  +  13.058688
  Z_new =   0.830191 * X  +   0.522978 * Y  +  -0.193071 * Z  +   2.454561 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.924451   -1.217142  [ DEG:   110.2629    -69.7371 ]
  Theta =  -0.979451   -2.162142  [ DEG:   -56.1184   -123.8816 ]
  Phi   =   0.735160   -2.406433  [ DEG:    42.1216   -137.8784 ]
 
# 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: T0358TS389_5                                  
REMARK     2: T0358.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0358TS389_5.T0358.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   14   66   4.0    8   1.96  11.811     4.99
REMARK  ---------------------------------------------------------- 
MOLECULE T0358TS389_5
PFRMAT TS
TARGET T0358
MODEL  5
PARENT N/A
ATOM      2  N   VAL    40      -3.098  -6.614   2.664  1.00  0.00
ATOM      3  CA  VAL    40      -4.059  -5.937   1.776  1.00  0.00
ATOM      4  CB  VAL    40      -3.526  -4.569   1.307  1.00  0.00
ATOM      5  CG1 VAL    40      -4.439  -3.980   0.243  1.00  0.00
ATOM      6  CG2 VAL    40      -3.458  -3.595   2.473  1.00  0.00
ATOM      7  O   VAL    40      -5.462  -7.147   0.257  1.00  0.00
ATOM      8  C   VAL    40      -4.320  -6.791   0.550  1.00  0.00
ATOM      9  N   VAL    41      -3.247  -7.167  -0.125  1.00  0.00
ATOM     10  CA  VAL    41      -3.346  -7.963  -1.343  1.00  0.00
ATOM     11  CB  VAL    41      -1.956  -8.275  -1.927  1.00  0.00
ATOM     12  CG1 VAL    41      -1.230  -6.990  -2.292  1.00  0.00
ATOM     13  CG2 VAL    41      -1.111  -9.035  -0.916  1.00  0.00
ATOM     14  O   VAL    41      -4.579  -9.931  -2.072  1.00  0.00
ATOM     15  C   VAL    41      -4.041  -9.319  -1.135  1.00  0.00
ATOM     16  N   ARG    42      -4.024  -9.774   0.112  1.00  0.00
ATOM     17  CA  ARG    42      -4.505 -11.076   0.516  1.00  0.00
ATOM     18  CB  ARG    42      -3.669 -11.622   1.675  1.00  0.00
ATOM     19  CG  ARG    42      -2.216 -11.889   1.319  1.00  0.00
ATOM     20  CD  ARG    42      -1.440 -12.411   2.518  1.00  0.00
ATOM     21  NE  ARG    42      -0.035 -12.655   2.198  1.00  0.00
ATOM     22  CZ  ARG    42       0.907 -12.894   3.103  1.00  0.00
ATOM     23  NH1 ARG    42       2.159 -13.105   2.720  1.00  0.00
ATOM     24  NH2 ARG    42       0.596 -12.922   4.392  1.00  0.00
ATOM     25  O   ARG    42      -6.662 -12.018   1.081  1.00  0.00
ATOM     26  C   ARG    42      -5.971 -10.999   0.973  1.00  0.00
ATOM     27  N   ASP    43      -6.439  -9.789   1.261  1.00  0.00
ATOM     28  CA  ASP    43      -7.734  -9.598   1.927  1.00  0.00
ATOM     29  CB  ASP    43      -7.768  -8.254   2.660  1.00  0.00
ATOM     30  CG  ASP    43      -6.913  -8.254   3.913  1.00  0.00
ATOM     31  OD1 ASP    43      -6.503  -9.348   4.354  1.00  0.00
ATOM     32  OD2 ASP    43      -6.654  -7.159   4.454  1.00  0.00
ATOM     33  O   ASP    43      -8.796  -9.663  -0.235  1.00  0.00
ATOM     34  C   ASP    43      -8.943  -9.604   0.986  1.00  0.00
ATOM     35  N   GLU    45     -10.131  -9.539   1.584  1.00  0.00
ATOM     36  CA  GLU    45     -11.381  -9.369   0.840  1.00  0.00
ATOM     37  CB  GLU    45     -12.564  -9.902   1.651  1.00  0.00
ATOM     38  CG  GLU    45     -12.556 -11.410   1.846  1.00  0.00
ATOM     39  CD  GLU    45     -13.668 -11.888   2.756  1.00  0.00
ATOM     40  OE1 GLU    45     -14.426 -11.035   3.266  1.00  0.00
ATOM     41  OE2 GLU    45     -13.785 -13.113   2.960  1.00  0.00
ATOM     42  O   GLU    45     -12.674  -7.570  -0.115  1.00  0.00
ATOM     43  C   GLU    45     -11.667  -7.890   0.519  1.00  0.00
ATOM     44  N   GLY    46     -10.758  -7.007   0.942  1.00  0.00
ATOM     45  CA  GLY    46     -10.954  -5.559   0.914  1.00  0.00
ATOM     46  O   GLY    46     -12.120  -5.847   2.990  1.00  0.00
ATOM     47  C   GLY    46     -11.874  -5.100   2.040  1.00  0.00
ATOM     48  N   ARG    47     -12.402  -3.878   1.941  1.00  0.00
ATOM     49  CA  ARG    47     -13.437  -3.440   2.864  1.00  0.00
ATOM     50  CB  ARG    47     -14.069  -4.641   3.568  1.00  0.00
ATOM     51  CG  ARG    47     -14.873  -5.548   2.651  1.00  0.00
ATOM     52  CD  ARG    47     -15.454  -6.728   3.411  1.00  0.00
ATOM     53  NE  ARG    47     -16.201  -7.628   2.536  1.00  0.00
ATOM     54  CZ  ARG    47     -16.762  -8.765   2.936  1.00  0.00
ATOM     55  NH1 ARG    47     -17.423  -9.520   2.071  1.00  0.00
ATOM     56  NH2 ARG    47     -16.660  -9.144   4.205  1.00  0.00
ATOM     57  O   ARG    47     -13.825  -2.139   4.799  1.00  0.00
ATOM     58  C   ARG    47     -13.000  -2.510   3.973  1.00  0.00
ATOM     62  N   TRP    50      -7.373   2.024   4.407  1.00  0.00
ATOM     63  CA  TRP    50      -5.928   1.938   4.639  1.00  0.00
ATOM     64  CB  TRP    50      -5.249   1.153   3.515  1.00  0.00
ATOM     65  CG  TRP    50      -3.779   0.967   3.714  1.00  0.00
ATOM     66  CD1 TRP    50      -2.774   1.674   3.117  1.00  0.00
ATOM     67  CD2 TRP    50      -3.143   0.012   4.574  1.00  0.00
ATOM     68  CE2 TRP    50      -1.751   0.197   4.446  1.00  0.00
ATOM     69  CE3 TRP    50      -3.612  -0.981   5.438  1.00  0.00
ATOM     70  NE1 TRP    50      -1.551   1.219   3.550  1.00  0.00
ATOM     71  CZ2 TRP    50      -0.827  -0.572   5.148  1.00  0.00
ATOM     72  CZ3 TRP    50      -2.692  -1.743   6.134  1.00  0.00
ATOM     73  CH2 TRP    50      -1.315  -1.537   5.987  1.00  0.00
ATOM     74  O   TRP    50      -5.150   3.991   3.656  1.00  0.00
ATOM     75  C   TRP    50      -5.342   3.345   4.686  1.00  0.00
ATOM     76  N   ARG    51      -5.037   3.806   5.891  1.00  0.00
ATOM     77  CA  ARG    51      -4.446   5.108   6.107  1.00  0.00
ATOM     78  CB  ARG    51      -4.703   5.583   7.538  1.00  0.00
ATOM     79  CG  ARG    51      -6.167   5.854   7.848  1.00  0.00
ATOM     80  CD  ARG    51      -6.362   6.226   9.309  1.00  0.00
ATOM     81  NE  ARG    51      -6.133   5.090  10.198  1.00  0.00
ATOM     82  CZ  ARG    51      -6.013   5.189  11.518  1.00  0.00
ATOM     83  NH1 ARG    51      -5.807   4.099  12.246  1.00  0.00
ATOM     84  NH2 ARG    51      -6.099   6.373  12.106  1.00  0.00
ATOM     85  O   ARG    51      -2.293   4.061   6.393  1.00  0.00
ATOM     86  C   ARG    51      -2.935   4.973   5.861  1.00  0.00
ATOM     87  N   ALA    52      -2.374   5.855   5.040  1.00  0.00
ATOM     88  CA  ALA    52      -0.969   5.740   4.640  1.00  0.00
ATOM     89  CB  ALA    52      -0.865   5.384   3.164  1.00  0.00
ATOM     90  O   ALA    52      -0.816   8.120   4.653  1.00  0.00
ATOM     91  C   ALA    52      -0.244   7.057   4.871  1.00  0.00
ATOM     95  N   PHE    55       4.410   9.271   1.211  1.00  0.00
ATOM     96  CA  PHE    55       5.041   8.533   0.126  1.00  0.00
ATOM     97  CB  PHE    55       6.480   8.166   0.492  1.00  0.00
ATOM     98  CG  PHE    55       7.188   7.365  -0.563  1.00  0.00
ATOM     99  CD1 PHE    55       7.719   7.982  -1.681  1.00  0.00
ATOM    100  CD2 PHE    55       7.324   5.993  -0.437  1.00  0.00
ATOM    101  CE1 PHE    55       8.371   7.246  -2.653  1.00  0.00
ATOM    102  CE2 PHE    55       7.975   5.256  -1.407  1.00  0.00
ATOM    103  CZ  PHE    55       8.497   5.877  -2.511  1.00  0.00
ATOM    104  O   PHE    55       3.965   7.000  -1.378  1.00  0.00
ATOM    105  C   PHE    55       4.322   7.224  -0.222  1.00  0.00
ATOM    106  N   GLU    56       4.097   6.391   0.790  1.00  0.00
ATOM    107  CA  GLU    56       3.337   5.157   0.665  1.00  0.00
ATOM    108  CB  GLU    56       3.157   4.496   2.035  1.00  0.00
ATOM    109  CG  GLU    56       2.423   3.168   1.993  1.00  0.00
ATOM    110  CD  GLU    56       2.320   2.515   3.359  1.00  0.00
ATOM    111  OE1 GLU    56       2.845   3.093   4.334  1.00  0.00
ATOM    112  OE2 GLU    56       1.716   1.427   3.452  1.00  0.00
ATOM    113  O   GLU    56       1.486   4.624  -0.737  1.00  0.00
ATOM    114  C   GLU    56       1.947   5.400   0.083  1.00  0.00
ATOM    115  N   PRO    57       1.278   6.462   0.535  1.00  0.00
ATOM    116  CA  PRO    57      -0.072   6.806   0.063  1.00  0.00
ATOM    117  CB  PRO    57      -0.506   7.949   0.984  1.00  0.00
ATOM    118  CG  PRO    57       0.771   8.496   1.526  1.00  0.00
ATOM    119  CD  PRO    57       1.721   7.334   1.610  1.00  0.00
ATOM    120  O   PRO    57      -0.947   6.922  -2.136  1.00  0.00
ATOM    121  C   PRO    57      -0.043   7.242  -1.391  1.00  0.00
ATOM    122  N   ASP    58       1.007   7.959  -1.791  1.00  0.00
ATOM    123  CA  ASP    58       1.198   8.344  -3.190  1.00  0.00
ATOM    124  CB  ASP    58       2.496   9.135  -3.356  1.00  0.00
ATOM    125  CG  ASP    58       2.624   9.762  -4.731  1.00  0.00
ATOM    126  OD1 ASP    58       1.653   9.684  -5.512  1.00  0.00
ATOM    127  OD2 ASP    58       3.696  10.333  -5.026  1.00  0.00
ATOM    128  O   ASP    58       0.514   6.923  -5.003  1.00  0.00
ATOM    129  C   ASP    58       1.266   7.075  -4.045  1.00  0.00
TER
END
