
#######################################################
#                                                     #
#                        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   15 (  116),  selected   15 , name T0356TS213_1_2-D1
# Molecule2: number of CA atoms  124 (  963),  selected   15 , name T0356_D1.pdb
# PARAMETERS: T0356TS213_1_2-D1.T0356_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:    15       333 - 347         2.98     2.98
  LCS_AVERAGE:     12.10

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11       336 - 346         1.10     4.30
  LCS_AVERAGE:      7.58

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10       336 - 345         0.73     4.57
  LCS_AVERAGE:      6.45

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:  124
LCS_GDT     G     333     G     333      3    3   15     0    3    3    3    4   10   12   12   14   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     V     334     V     334      3    4   15     0    3    3    3    4    5   12   12   14   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     A     335     A     335      3    4   15     1    3    3    3    4    5    8   12   14   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     L     336     L     336     10   11   15     4   10   10   11   11   11   12   12   14   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     N     337     N     337     10   11   15     5   10   10   11   11   11   11   12   14   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     E     338     E     338     10   11   15     5   10   10   11   11   11   12   12   14   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     V     339     V     339     10   11   15     5   10   10   11   11   11   12   12   14   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     F     340     F     340     10   11   15     6   10   10   11   11   11   12   12   14   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     V     341     V     341     10   11   15     6   10   10   11   11   11   12   12   14   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     P     342     P     342     10   11   15     6   10   10   11   11   11   12   12   14   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     I     343     I     343     10   11   15     6   10   10   11   11   11   12   12   14   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     L     344     L     344     10   11   15     6   10   10   11   11   11   12   12   14   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     Q     345     Q     345     10   11   15     6   10   10   11   11   11   12   12   14   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     K     346     K     346      8   11   15     4    5    7   11   11   11   12   12   14   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     Q     347     Q     347      3    9   15     0    3    3    3    5    6    8    9   11   15   15   15   15   15   15   15   15   15   15   15 
LCS_AVERAGE  LCS_A:   8.71  (   6.45    7.58   12.10 )

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      6     10     10     11     11     11     12     12     14     15     15     15     15     15     15     15     15     15     15     15 
GDT PERCENT_CA   4.84   8.06   8.06   8.87   8.87   8.87   9.68   9.68  11.29  12.10  12.10  12.10  12.10  12.10  12.10  12.10  12.10  12.10  12.10  12.10
GDT RMS_LOCAL    0.24   0.73   0.73   1.10   1.10   1.10   2.23   2.01   2.69   2.98   2.98   2.98   2.98   2.98   2.98   2.98   2.98   2.98   2.98   2.98
GDT RMS_ALL_CA   4.68   4.57   4.57   4.30   4.30   4.30   3.14   3.49   3.11   2.98   2.98   2.98   2.98   2.98   2.98   2.98   2.98   2.98   2.98   2.98

#      Molecule1      Molecule2       DISTANCE
LGA    G     333      G     333          3.973
LGA    V     334      V     334          5.481
LGA    A     335      A     335          5.874
LGA    L     336      L     336          2.070
LGA    N     337      N     337          3.260
LGA    E     338      E     338          2.410
LGA    V     339      V     339          0.834
LGA    F     340      F     340          2.049
LGA    V     341      V     341          1.043
LGA    P     342      P     342          0.561
LGA    I     343      I     343          1.251
LGA    L     344      L     344          0.589
LGA    Q     345      Q     345          0.856
LGA    K     346      K     346          2.222
LGA    Q     347      Q     347          7.245

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   15  124    4.0     12    2.01     9.677     9.408     0.568

LGA_LOCAL      RMSD =  2.012  Number of atoms =   12  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.341  Number of atoms =   15 
Std_ALL_ATOMS  RMSD =  2.979  (standard rmsd on all 15 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.828129 * X  +   0.449592 * Y  +  -0.334768 * Z  +  20.982235
  Y_new =  -0.298480 * X  +  -0.151825 * Y  +  -0.942263 * Z  + 137.858063
  Z_new =  -0.474459 * X  +   0.880237 * Y  +   0.008464 * Z  +  73.969452 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.561182   -1.580411  [ DEG:    89.4491    -90.5509 ]
  Theta =   0.494350    2.647243  [ DEG:    28.3242    151.6758 ]
  Phi   =  -0.345934    2.795659  [ DEG:   -19.8205    160.1795 ]
 
# 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: T0356TS213_1_2-D1                             
REMARK     2: T0356_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0356TS213_1_2-D1.T0356_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   15  124   4.0   12   2.01   9.408     2.98
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS213_1_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0356
PARENT 1oi2_A 2iu4_A
ATOM      1  N   GLY   333      64.055  65.431  75.478  1.00 10.94       1SG   2
ATOM      2  CA  GLY   333      62.618  65.654  75.204  1.00 10.94       1SG   3
ATOM      3  C   GLY   333      62.343  65.555  73.741  1.00 10.94       1SG   4
ATOM      4  O   GLY   333      63.221  65.214  72.952  1.00 10.94       1SG   5
ATOM      5  N   VAL   334      61.090  65.852  73.350  1.00 93.00       1SG   6
ATOM      6  CA  VAL   334      60.712  65.798  71.971  1.00 93.00       1SG   7
ATOM      7  CB  VAL   334      59.229  65.727  71.749  1.00 93.00       1SG   8
ATOM      8  CG1 VAL   334      58.700  64.417  72.357  1.00 93.00       1SG   9
ATOM      9  CG2 VAL   334      58.587  66.996  72.332  1.00 93.00       1SG  10
ATOM     10  C   VAL   334      61.206  67.050  71.329  1.00 93.00       1SG  11
ATOM     11  O   VAL   334      61.417  68.060  71.997  1.00 93.00       1SG  12
ATOM     12  N   ALA   335      61.432  66.995  70.004  1.00 28.75       1SG  13
ATOM     13  CA  ALA   335      61.917  68.139  69.295  1.00 28.75       1SG  14
ATOM     14  CB  ALA   335      62.259  67.850  67.822  1.00 28.75       1SG  15
ATOM     15  C   ALA   335      60.846  69.177  69.324  1.00 28.75       1SG  16
ATOM     16  O   ALA   335      59.666  68.875  69.494  1.00 28.75       1SG  17
ATOM     17  N   LEU   336      61.263  70.449  69.182  1.00 40.20       1SG  18
ATOM     18  CA  LEU   336      60.369  71.568  69.224  1.00 40.20       1SG  19
ATOM     19  CB  LEU   336      61.119  72.908  69.308  1.00 40.20       1SG  20
ATOM     20  CG  LEU   336      62.015  73.011  70.556  1.00 40.20       1SG  21
ATOM     21  CD1 LEU   336      62.680  74.391  70.665  1.00 40.20       1SG  22
ATOM     22  CD2 LEU   336      61.250  72.607  71.826  1.00 40.20       1SG  23
ATOM     23  C   LEU   336      59.557  71.565  67.968  1.00 40.20       1SG  24
ATOM     24  O   LEU   336      60.006  71.092  66.925  1.00 40.20       1SG  25
ATOM     25  N   ASN   337      58.316  72.090  68.054  1.00 72.56       1SG  26
ATOM     26  CA  ASN   337      57.426  72.123  66.927  1.00 72.56       1SG  27
ATOM     27  CB  ASN   337      56.037  72.694  67.272  1.00 72.56       1SG  28
ATOM     28  CG  ASN   337      56.194  74.138  67.729  1.00 72.56       1SG  29
ATOM     29  OD1 ASN   337      56.926  74.434  68.670  1.00 72.56       1SG  30
ATOM     30  ND2 ASN   337      55.485  75.072  67.039  1.00 72.56       1SG  31
ATOM     31  C   ASN   337      58.029  72.983  65.867  1.00 72.56       1SG  32
ATOM     32  O   ASN   337      57.987  72.643  64.686  1.00 72.56       1SG  33
ATOM     33  N   GLU   338      58.613  74.129  66.260  1.00 85.06       1SG  34
ATOM     34  CA  GLU   338      59.198  74.979  65.271  1.00 85.06       1SG  35
ATOM     35  CB  GLU   338      59.665  76.350  65.790  1.00 85.06       1SG  36
ATOM     36  CG  GLU   338      60.787  76.317  66.822  1.00 85.06       1SG  37
ATOM     37  CD  GLU   338      61.171  77.767  67.086  1.00 85.06       1SG  38
ATOM     38  OE1 GLU   338      60.519  78.669  66.493  1.00 85.06       1SG  39
ATOM     39  OE2 GLU   338      62.121  77.995  67.882  1.00 85.06       1SG  40
ATOM     40  C   GLU   338      60.359  74.257  64.679  1.00 85.06       1SG  41
ATOM     41  O   GLU   338      60.665  74.412  63.504  1.00 85.06       1SG  42
ATOM     42  N   VAL   339      61.076  73.447  65.467  1.00 29.29       1SG  43
ATOM     43  CA  VAL   339      62.160  72.739  64.855  1.00 29.29       1SG  44
ATOM     44  CB  VAL   339      62.910  71.888  65.837  1.00 29.29       1SG  45
ATOM     45  CG1 VAL   339      63.976  71.076  65.083  1.00 29.29       1SG  46
ATOM     46  CG2 VAL   339      63.478  72.803  66.934  1.00 29.29       1SG  47
ATOM     47  C   VAL   339      61.567  71.832  63.821  1.00 29.29       1SG  48
ATOM     48  O   VAL   339      62.078  71.707  62.708  1.00 29.29       1SG  49
ATOM     49  N   PHE   340      60.438  71.198  64.180  1.00101.85       1SG  50
ATOM     50  CA  PHE   340      59.761  70.214  63.387  1.00101.85       1SG  51
ATOM     51  CB  PHE   340      58.533  69.669  64.146  1.00101.85       1SG  52
ATOM     52  CG  PHE   340      57.905  68.543  63.400  1.00101.85       1SG  53
ATOM     53  CD1 PHE   340      58.464  67.287  63.439  1.00101.85       1SG  54
ATOM     54  CD2 PHE   340      56.743  68.734  62.687  1.00101.85       1SG  55
ATOM     55  CE1 PHE   340      57.885  66.242  62.761  1.00101.85       1SG  56
ATOM     56  CE2 PHE   340      56.159  67.690  62.006  1.00101.85       1SG  57
ATOM     57  CZ  PHE   340      56.732  66.442  62.041  1.00101.85       1SG  58
ATOM     58  C   PHE   340      59.290  70.810  62.094  1.00101.85       1SG  59
ATOM     59  O   PHE   340      59.510  70.233  61.028  1.00101.85       1SG  60
ATOM     60  N   VAL   341      58.634  71.987  62.138  1.00 59.70       1SG  61
ATOM     61  CA  VAL   341      58.078  72.496  60.918  1.00 59.70       1SG  62
ATOM     62  CB  VAL   341      57.160  73.670  61.124  1.00 59.70       1SG  63
ATOM     63  CG1 VAL   341      56.676  74.158  59.748  1.00 59.70       1SG  64
ATOM     64  CG2 VAL   341      56.030  73.247  62.077  1.00 59.70       1SG  65
ATOM     65  C   VAL   341      59.156  72.816  59.915  1.00 59.70       1SG  66
ATOM     66  O   VAL   341      59.085  72.321  58.791  1.00 59.70       1SG  67
ATOM     67  N   PRO   342      60.165  73.590  60.232  1.00115.35       1SG  68
ATOM     68  CA  PRO   342      61.180  73.772  59.237  1.00115.35       1SG  69
ATOM     69  CD  PRO   342      59.899  74.873  60.868  1.00115.35       1SG  70
ATOM     70  CB  PRO   342      62.013  74.965  59.687  1.00115.35       1SG  71
ATOM     71  CG  PRO   342      60.962  75.859  60.357  1.00115.35       1SG  72
ATOM     72  C   PRO   342      61.973  72.570  58.866  1.00115.35       1SG  73
ATOM     73  O   PRO   342      62.585  72.608  57.805  1.00115.35       1SG  74
ATOM     74  N   ILE   343      62.053  71.511  59.687  1.00 92.71       1SG  75
ATOM     75  CA  ILE   343      62.820  70.433  59.140  1.00 92.71       1SG  76
ATOM     76  CB  ILE   343      63.057  69.281  60.082  1.00 92.71       1SG  77
ATOM     77  CG2 ILE   343      63.914  69.794  61.251  1.00 92.71       1SG  78
ATOM     78  CG1 ILE   343      61.741  68.608  60.504  1.00 92.71       1SG  79
ATOM     79  CD1 ILE   343      61.941  67.232  61.138  1.00 92.71       1SG  80
ATOM     80  C   ILE   343      62.067  69.923  57.954  1.00 92.71       1SG  81
ATOM     81  O   ILE   343      62.632  69.710  56.883  1.00 92.71       1SG  82
ATOM     82  N   LEU   344      60.745  69.743  58.117  1.00 68.01       1SG  83
ATOM     83  CA  LEU   344      59.963  69.205  57.048  1.00 68.01       1SG  84
ATOM     84  CB  LEU   344      58.535  68.859  57.496  1.00 68.01       1SG  85
ATOM     85  CG  LEU   344      58.513  67.870  58.679  1.00 68.01       1SG  86
ATOM     86  CD1 LEU   344      57.081  67.416  58.997  1.00 68.01       1SG  87
ATOM     87  CD2 LEU   344      59.478  66.694  58.456  1.00 68.01       1SG  88
ATOM     88  C   LEU   344      59.892  70.168  55.894  1.00 68.01       1SG  89
ATOM     89  O   LEU   344      60.071  69.763  54.748  1.00 68.01       1SG  90
ATOM     90  N   GLN   345      59.585  71.457  56.159  1.00170.67       1SG  91
ATOM     91  CA  GLN   345      59.440  72.459  55.127  1.00170.67       1SG  92
ATOM     92  CB  GLN   345      58.673  73.700  55.613  1.00170.67       1SG  93
ATOM     93  CG  GLN   345      58.533  74.798  54.554  1.00170.67       1SG  94
ATOM     94  CD  GLN   345      57.690  74.276  53.398  1.00170.67       1SG  95
ATOM     95  OE1 GLN   345      57.863  73.143  52.952  1.00170.67       1SG  96
ATOM     96  NE2 GLN   345      56.753  75.125  52.895  1.00170.67       1SG  97
ATOM     97  C   GLN   345      60.735  72.958  54.541  1.00170.67       1SG  98
ATOM     98  O   GLN   345      60.845  73.101  53.324  1.00170.67       1SG  99
ATOM     99  N   LYS   346      61.740  73.192  55.412  1.00306.70       1SG 100
ATOM    100  CA  LYS   346      62.999  73.880  55.212  1.00306.70       1SG 101
ATOM    101  CB  LYS   346      64.253  73.130  55.706  1.00306.70       1SG 102
ATOM    102  CG  LYS   346      65.484  74.025  55.848  1.00306.70       1SG 103
ATOM    103  CD  LYS   346      66.620  73.382  56.649  1.00306.70       1SG 104
ATOM    104  CE  LYS   346      66.259  73.085  58.109  1.00306.70       1SG 105
ATOM    105  NZ  LYS   346      66.085  74.346  58.864  1.00306.70       1SG 106
ATOM    106  C   LYS   346      63.243  74.317  53.807  1.00306.70       1SG 107
ATOM    107  O   LYS   346      63.309  73.515  52.877  1.00306.70       1SG 108
ATOM    108  N   GLN   347      63.367  75.651  53.642  1.00326.90       1SG 109
ATOM    109  CA  GLN   347      63.660  76.265  52.383  1.00326.90       1SG 110
ATOM    110  CB  GLN   347      62.433  76.804  51.634  1.00326.90       1SG 111
ATOM    111  CG  GLN   347      62.823  77.538  50.348  1.00326.90       1SG 112
ATOM    112  CD  GLN   347      61.614  78.310  49.838  1.00326.90       1SG 113
ATOM    113  OE1 GLN   347      61.621  79.540  49.808  1.00326.90       1SG 114
ATOM    114  NE2 GLN   347      60.547  77.574  49.425  1.00326.90       1SG 115
ATOM    115  C   GLN   347      64.486  77.476  52.673  1.00326.90       1SG 116
ATOM    116  O   GLN   347      64.346  78.100  53.724  1.00326.90       1SG 117
TER
END
