
#######################################################
#                                                     #
#                        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   18 (  145),  selected   18 , name T0378TS021_1-D1
# Molecule2: number of CA atoms   89 (  716),  selected   18 , name T0378_D1.pdb
# PARAMETERS: T0378TS021_1-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:    14        73 - 86          4.88     9.01
  LONGEST_CONTINUOUS_SEGMENT:    14        74 - 87          4.94     8.15
  LCS_AVERAGE:     15.23

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9        80 - 88          1.74    12.64
  LCS_AVERAGE:      7.93

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5        80 - 84          0.37    13.42
  LCS_AVERAGE:      4.56

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     F      72     F      72      3    4    8     0    3    3    3    3    4    4    4    5    6    8    9    9    9   11   12   12   13   13   14 
LCS_GDT     K      73     K      73      3    4   14     0    3    3    3    3    4    5    5    5    6    8    9    9    9   11   14   15   16   16   16 
LCS_GDT     R      74     R      74      3    5   14     3    3    4    5    5    5    6    9    9   11   12   12   12   13   13   14   15   16   16   16 
LCS_GDT     I      75     I      75      4    5   14     3    4    4    5    6    8   10   10   10   11   12   12   12   13   13   14   15   16   16   16 
LCS_GDT     S      76     S      76      4    5   14     3    4    4    5    6    8   10   10   10   11   12   12   12   13   13   14   15   16   16   16 
LCS_GDT     T      77     T      77      4    6   14     3    4    4    5    7    8   10   10   10   11   12   12   12   13   13   14   15   16   16   16 
LCS_GDT     Q      78     Q      78      4    6   14     3    4    4    5    7    8   10   10   10   11   12   12   12   13   13   14   15   16   16   16 
LCS_GDT     T      79     T      79      4    6   14     3    3    4    5    7    8   10   10   10   11   12   12   12   13   13   14   15   16   16   16 
LCS_GDT     T      80     T      80      5    9   14     4    5    6    7    8    9   10   10   10   11   12   12   12   13   13   14   15   16   16   16 
LCS_GDT     P      81     P      81      5    9   14     4    5    6    7    8    9   10   10   10   11   12   12   12   13   13   14   15   16   16   16 
LCS_GDT     Q      82     Q      82      5    9   14     4    5    6    7    8    9   10   10   10   11   12   12   12   13   13   14   15   16   16   16 
LCS_GDT     P      83     P      83      5    9   14     4    5    6    7    8    9   10   10   10   11   12   12   12   13   13   14   14   16   16   16 
LCS_GDT     L      84     L      84      5    9   14     4    5    6    7    8    9   10   10   10   11   12   12   12   13   13   14   15   16   16   16 
LCS_GDT     M      85     M      85      4    9   14     1    4    5    6    8    9    9   10   10   10   12   12   12   13   13   14   15   16   16   16 
LCS_GDT     A      86     A      86      4    9   14     3    4    6    7    8    9    9   10   10   10   11   12   12   13   13   14   15   16   16   16 
LCS_GDT     V      87     V      87      4    9   14     3    4    4    7    8    9    9   10   10   10   11   12   12   13   13   14   15   16   16   16 
LCS_GDT     F      88     F      88      4    9   13     3    4    4    7    8    9    9   10   10   10   11   12   12   13   13   14   15   16   16   16 
LCS_GDT     D      89     D      89      3    5   13     3    3    4    5    5    7    7    8    9   10   11   12   12   12   12   12   12   14   14   16 
LCS_AVERAGE  LCS_A:   9.24  (   4.56    7.93   15.23 )

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      5      6      7      8      9     10     10     10     11     12     12     12     13     13     14     15     16     16     16 
GDT PERCENT_CA   4.49   5.62   6.74   7.87   8.99  10.11  11.24  11.24  11.24  12.36  13.48  13.48  13.48  14.61  14.61  15.73  16.85  17.98  17.98  17.98
GDT RMS_LOCAL    0.18   0.37   0.99   1.24   1.51   1.74   2.57   2.57   2.57   3.24   3.59   3.59   3.59   4.13   4.13   4.94   5.58   5.87   5.87   5.87
GDT RMS_ALL_CA  13.40  13.42  13.09  12.81  12.73  12.64  11.84  11.84  11.84  11.49  10.50  10.50  10.50   9.25   9.25   8.15   7.19   7.28   7.28   7.28

#      Molecule1      Molecule2       DISTANCE
LGA    F      72      F      72         15.468
LGA    K      73      K      73         13.387
LGA    R      74      R      74          8.694
LGA    I      75      I      75          2.611
LGA    S      76      S      76          3.048
LGA    T      77      T      77          2.660
LGA    Q      78      Q      78          1.207
LGA    T      79      T      79          2.833
LGA    T      80      T      80          0.926
LGA    P      81      P      81          3.157
LGA    Q      82      Q      82          1.588
LGA    P      83      P      83          3.650
LGA    L      84      L      84          2.591
LGA    M      85      M      85          7.580
LGA    A      86      A      86         12.280
LGA    V      87      V      87         18.903
LGA    F      88      F      88         23.196
LGA    D      89      D      89         29.310

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   18   89    4.0     10    2.57    10.112     9.867     0.375

LGA_LOCAL      RMSD =  2.570  Number of atoms =   10  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 11.839  Number of atoms =   18 
Std_ALL_ATOMS  RMSD =  6.918  (standard rmsd on all 18 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.320735 * X  +  -0.941586 * Y  +   0.102688 * Z  +   4.091266
  Y_new =   0.757929 * X  +   0.190121 * Y  +  -0.624017 * Z  +  44.856060
  Z_new =   0.568043 * X  +   0.277974 * Y  +   0.774634 * Z  +  25.941059 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.344533   -2.797059  [ DEG:    19.7403   -160.2597 ]
  Theta =  -0.604125   -2.537467  [ DEG:   -34.6138   -145.3862 ]
  Phi   =   1.170474   -1.971118  [ DEG:    67.0632   -112.9368 ]
 
# 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: T0378TS021_1-D1                               
REMARK     2: T0378_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0378TS021_1-D1.T0378_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   18   89   4.0   10   2.57   9.867     6.92
REMARK  ---------------------------------------------------------- 
MOLECULE T0378TS021_1-D1
PFRMAT TS
TARGET T0378
MODEL 1
PARENT N/A
ATOM      1  N   PHE    72       6.161  30.356  57.147  1.00 31.84       1SG   2
ATOM      2  CA  PHE    72       7.447  30.403  56.411  1.00 31.84       1SG   3
ATOM      3  CB  PHE    72       8.051  28.991  56.288  1.00 31.84       1SG   4
ATOM      4  CG  PHE    72       8.420  28.502  57.648  1.00 31.84       1SG   5
ATOM      5  CD1 PHE    72       7.484  27.886  58.448  1.00 31.84       1SG   6
ATOM      6  CD2 PHE    72       9.702  28.657  58.119  1.00 31.84       1SG   7
ATOM      7  CE1 PHE    72       7.828  27.433  59.701  1.00 31.84       1SG   8
ATOM      8  CE2 PHE    72      10.052  28.206  59.369  1.00 31.84       1SG   9
ATOM      9  CZ  PHE    72       9.112  27.594  60.163  1.00 31.84       1SG  10
ATOM     10  C   PHE    72       7.224  30.930  55.035  1.00 31.84       1SG  11
ATOM     11  O   PHE    72       6.181  30.685  54.429  1.00 31.84       1SG  12
ATOM     12  N   LYS    73       8.198  31.696  54.511  1.00 75.57       1SG  13
ATOM     13  CA  LYS    73       8.020  32.221  53.194  1.00 75.57       1SG  14
ATOM     14  CB  LYS    73       7.835  33.746  53.179  1.00 75.57       1SG  15
ATOM     15  CG  LYS    73       7.289  34.293  51.861  1.00 75.57       1SG  16
ATOM     16  CD  LYS    73       6.731  35.711  51.995  1.00 75.57       1SG  17
ATOM     17  CE  LYS    73       6.005  36.215  50.746  1.00 75.57       1SG  18
ATOM     18  NZ  LYS    73       5.327  37.496  51.042  1.00 75.57       1SG  19
ATOM     19  C   LYS    73       9.249  31.897  52.412  1.00 75.57       1SG  20
ATOM     20  O   LYS    73      10.352  32.316  52.759  1.00 75.57       1SG  21
ATOM     21  N   ARG    74       9.082  31.117  51.330  1.00125.75       1SG  22
ATOM     22  CA  ARG    74      10.205  30.765  50.519  1.00125.75       1SG  23
ATOM     23  CB  ARG    74      10.711  29.342  50.818  1.00125.75       1SG  24
ATOM     24  CG  ARG    74      11.227  29.189  52.254  1.00125.75       1SG  25
ATOM     25  CD  ARG    74      11.381  27.737  52.713  1.00125.75       1SG  26
ATOM     26  NE  ARG    74      12.461  27.114  51.901  1.00125.75       1SG  27
ATOM     27  CZ  ARG    74      12.788  25.806  52.109  1.00125.75       1SG  28
ATOM     28  NH1 ARG    74      12.139  25.088  53.072  1.00125.75       1SG  29
ATOM     29  NH2 ARG    74      13.762  25.217  51.354  1.00125.75       1SG  30
ATOM     30  C   ARG    74       9.707  30.786  49.114  1.00125.75       1SG  31
ATOM     31  O   ARG    74       8.573  30.385  48.852  1.00125.75       1SG  32
ATOM     32  N   ILE    75      10.524  31.282  48.165  1.00 97.38       1SG  33
ATOM     33  CA  ILE    75      10.043  31.275  46.818  1.00 97.38       1SG  34
ATOM     34  CB  ILE    75       9.806  32.645  46.250  1.00 97.38       1SG  35
ATOM     35  CG2 ILE    75      11.163  33.344  46.065  1.00 97.38       1SG  36
ATOM     36  CG1 ILE    75       8.975  32.541  44.961  1.00 97.38       1SG  37
ATOM     37  CD1 ILE    75       8.406  33.883  44.507  1.00 97.38       1SG  38
ATOM     38  C   ILE    75      11.042  30.584  45.951  1.00 97.38       1SG  39
ATOM     39  O   ILE    75      12.245  30.820  46.054  1.00 97.38       1SG  40
ATOM     40  N   SER    76      10.561  29.674  45.083  1.00 41.84       1SG  41
ATOM     41  CA  SER    76      11.456  29.014  44.183  1.00 41.84       1SG  42
ATOM     42  CB  SER    76      11.757  27.554  44.573  1.00 41.84       1SG  43
ATOM     43  OG  SER    76      12.387  27.500  45.844  1.00 41.84       1SG  44
ATOM     44  C   SER    76      10.784  28.980  42.849  1.00 41.84       1SG  45
ATOM     45  O   SER    76       9.613  28.617  42.742  1.00 41.84       1SG  46
ATOM     46  N   THR    77      11.521  29.363  41.790  1.00128.71       1SG  47
ATOM     47  CA  THR    77      10.973  29.337  40.468  1.00128.71       1SG  48
ATOM     48  CB  THR    77      11.765  30.132  39.474  1.00128.71       1SG  49
ATOM     49  OG1 THR    77      13.072  29.592  39.347  1.00128.71       1SG  50
ATOM     50  CG2 THR    77      11.843  31.592  39.956  1.00128.71       1SG  51
ATOM     51  C   THR    77      11.027  27.915  40.028  1.00128.71       1SG  52
ATOM     52  O   THR    77      11.862  27.139  40.485  1.00128.71       1SG  53
ATOM     53  N   GLN    78      10.117  27.525  39.127  1.00124.42       1SG  54
ATOM     54  CA  GLN    78      10.110  26.175  38.666  1.00124.42       1SG  55
ATOM     55  CB  GLN    78       8.849  25.377  39.049  1.00124.42       1SG  56
ATOM     56  CG  GLN    78       9.009  23.864  38.859  1.00124.42       1SG  57
ATOM     57  CD  GLN    78       7.670  23.194  39.116  1.00124.42       1SG  58
ATOM     58  OE1 GLN    78       6.620  23.815  38.969  1.00124.42       1SG  59
ATOM     59  NE2 GLN    78       7.709  21.893  39.510  1.00124.42       1SG  60
ATOM     60  C   GLN    78      10.169  26.275  37.186  1.00124.42       1SG  61
ATOM     61  O   GLN    78      10.730  27.221  36.636  1.00124.42       1SG  62
ATOM     62  N   THR    79       9.558  25.301  36.498  1.00156.20       1SG  63
ATOM     63  CA  THR    79       9.558  25.315  35.074  1.00156.20       1SG  64
ATOM     64  CB  THR    79       9.226  23.962  34.501  1.00156.20       1SG  65
ATOM     65  OG1 THR    79      10.103  22.990  35.052  1.00156.20       1SG  66
ATOM     66  CG2 THR    79       9.424  23.972  32.974  1.00156.20       1SG  67
ATOM     67  C   THR    79       8.486  26.304  34.742  1.00156.20       1SG  68
ATOM     68  O   THR    79       8.135  27.136  35.575  1.00156.20       1SG  69
ATOM     69  N   THR    80       7.966  26.312  33.511  1.00103.63       1SG  70
ATOM     70  CA  THR    80       6.987  27.309  33.244  1.00103.63       1SG  71
ATOM     71  CB  THR    80       6.555  27.332  31.802  1.00103.63       1SG  72
ATOM     72  OG1 THR    80       7.676  27.571  30.967  1.00103.63       1SG  73
ATOM     73  CG2 THR    80       5.502  28.436  31.604  1.00103.63       1SG  74
ATOM     74  C   THR    80       5.795  27.101  34.139  1.00103.63       1SG  75
ATOM     75  O   THR    80       5.378  28.072  34.760  1.00103.63       1SG  76
ATOM     76  N   PRO    81       5.242  25.913  34.288  1.00166.04       1SG  77
ATOM     77  CA  PRO    81       4.050  25.767  35.107  1.00166.04       1SG  78
ATOM     78  CD  PRO    81       5.218  24.991  33.160  1.00166.04       1SG  79
ATOM     79  CB  PRO    81       3.338  24.513  34.602  1.00166.04       1SG  80
ATOM     80  CG  PRO    81       3.812  24.372  33.150  1.00166.04       1SG  81
ATOM     81  C   PRO    81       4.288  25.698  36.590  1.00166.04       1SG  82
ATOM     82  O   PRO    81       5.428  25.500  37.005  1.00166.04       1SG  83
ATOM     83  N   GLN    82       3.219  25.860  37.411  1.00231.12       1SG  84
ATOM     84  CA  GLN    82       3.371  25.728  38.834  1.00231.12       1SG  85
ATOM     85  CB  GLN    82       2.785  26.843  39.720  1.00231.12       1SG  86
ATOM     86  CG  GLN    82       3.696  28.060  39.881  1.00231.12       1SG  87
ATOM     87  CD  GLN    82       3.235  28.807  41.130  1.00231.12       1SG  88
ATOM     88  OE1 GLN    82       2.042  28.906  41.414  1.00231.12       1SG  89
ATOM     89  NE2 GLN    82       4.219  29.319  41.917  1.00231.12       1SG  90
ATOM     90  C   GLN    82       2.743  24.461  39.313  1.00231.12       1SG  91
ATOM     91  O   GLN    82       1.878  23.834  38.694  1.00231.12       1SG  92
ATOM     92  N   PRO    83       3.257  24.119  40.459  1.00154.01       1SG  93
ATOM     93  CA  PRO    83       2.910  22.925  41.181  1.00154.01       1SG  94
ATOM     94  CD  PRO    83       4.599  24.574  40.786  1.00154.01       1SG  95
ATOM     95  CB  PRO    83       4.006  22.732  42.228  1.00154.01       1SG  96
ATOM     96  CG  PRO    83       5.222  23.460  41.641  1.00154.01       1SG  97
ATOM     97  C   PRO    83       1.556  22.951  41.811  1.00154.01       1SG  98
ATOM     98  O   PRO    83       1.200  21.931  42.399  1.00154.01       1SG  99
ATOM     99  N   LEU    84       0.802  24.071  41.717  1.00246.98       1SG 100
ATOM    100  CA  LEU    84      -0.446  24.188  42.428  1.00246.98       1SG 101
ATOM    101  CB  LEU    84      -1.259  25.446  42.075  1.00246.98       1SG 102
ATOM    102  CG  LEU    84      -0.599  26.738  42.595  1.00246.98       1SG 103
ATOM    103  CD1 LEU    84      -1.459  27.975  42.311  1.00246.98       1SG 104
ATOM    104  CD2 LEU    84      -0.233  26.608  44.081  1.00246.98       1SG 105
ATOM    105  C   LEU    84      -1.293  22.978  42.204  1.00246.98       1SG 106
ATOM    106  O   LEU    84      -1.735  22.670  41.099  1.00246.98       1SG 107
ATOM    107  N   MET    85      -1.486  22.258  43.323  1.00144.30       1SG 108
ATOM    108  CA  MET    85      -2.140  20.991  43.440  1.00144.30       1SG 109
ATOM    109  CB  MET    85      -1.982  20.430  44.861  1.00144.30       1SG 110
ATOM    110  CG  MET    85      -2.524  19.018  45.068  1.00144.30       1SG 111
ATOM    111  SD  MET    85      -2.300  18.401  46.765  1.00144.30       1SG 112
ATOM    112  CE  MET    85      -2.950  16.743  46.419  1.00144.30       1SG 113
ATOM    113  C   MET    85      -3.597  21.067  43.134  1.00144.30       1SG 114
ATOM    114  O   MET    85      -4.109  20.195  42.433  1.00144.30       1SG 115
ATOM    115  N   ALA    86      -4.297  22.110  43.625  1.00216.05       1SG 116
ATOM    116  CA  ALA    86      -5.727  22.120  43.495  1.00216.05       1SG 117
ATOM    117  CB  ALA    86      -6.393  23.378  44.083  1.00216.05       1SG 118
ATOM    118  C   ALA    86      -6.099  21.996  42.054  1.00216.05       1SG 119
ATOM    119  O   ALA    86      -5.771  22.839  41.221  1.00216.05       1SG 120
ATOM    120  N   VAL    87      -6.820  20.902  41.752  1.00165.39       1SG 121
ATOM    121  CA  VAL    87      -7.220  20.549  40.424  1.00165.39       1SG 122
ATOM    122  CB  VAL    87      -7.979  19.256  40.363  1.00165.39       1SG 123
ATOM    123  CG1 VAL    87      -7.061  18.129  40.861  1.00165.39       1SG 124
ATOM    124  CG2 VAL    87      -9.280  19.411  41.171  1.00165.39       1SG 125
ATOM    125  C   VAL    87      -8.129  21.616  39.952  1.00165.39       1SG 126
ATOM    126  O   VAL    87      -8.163  21.936  38.764  1.00165.39       1SG 127
ATOM    127  N   PHE    88      -8.862  22.203  40.915  1.00252.20       1SG 128
ATOM    128  CA  PHE    88      -9.888  23.172  40.681  1.00252.20       1SG 129
ATOM    129  CB  PHE    88     -10.324  23.920  41.953  1.00252.20       1SG 130
ATOM    130  CG  PHE    88     -11.652  24.546  41.683  1.00252.20       1SG 131
ATOM    131  CD1 PHE    88     -12.803  23.820  41.879  1.00252.20       1SG 132
ATOM    132  CD2 PHE    88     -11.765  25.841  41.242  1.00252.20       1SG 133
ATOM    133  CE1 PHE    88     -14.033  24.383  41.637  1.00252.20       1SG 134
ATOM    134  CE2 PHE    88     -12.992  26.412  40.996  1.00252.20       1SG 135
ATOM    135  CZ  PHE    88     -14.136  25.678  41.191  1.00252.20       1SG 136
ATOM    136  C   PHE    88      -9.391  24.170  39.696  1.00252.20       1SG 137
ATOM    137  O   PHE    88      -8.203  24.482  39.626  1.00252.20       1SG 138
ATOM    138  N   ASP    89     -10.325  24.648  38.868  1.00102.71       1SG 139
ATOM    139  CA  ASP    89     -10.050  25.566  37.811  1.00102.71       1SG 140
ATOM    140  CB  ASP    89     -11.232  25.811  36.864  1.00102.71       1SG 141
ATOM    141  CG  ASP    89     -11.245  24.641  35.888  1.00102.71       1SG 142
ATOM    142  OD1 ASP    89     -10.277  23.832  35.924  1.00102.71       1SG 143
ATOM    143  OD2 ASP    89     -12.214  24.541  35.090  1.00102.71       1SG 144
ATOM    144  C   ASP    89      -9.583  26.869  38.365  1.00102.71       1SG 145
ATOM    145  O   ASP    89      -9.022  27.686  37.637  1.00102.71       1SG 146
TER
END
