
#######################################################
#                                                     #
#                        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 T0356TS212_1_2-D1
# Molecule2: number of CA atoms  124 (  963),  selected   15 , name T0356_D1.pdb
# PARAMETERS: T0356TS212_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         2.85     2.85
  LCS_AVERAGE:     12.10

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12       336 - 347         1.97     3.78
  LCS_AVERAGE:      8.23

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10       336 - 345         0.81     4.50
  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   13   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     V     334     V     334      3    3   15     0    3    6    7    8   10   12   13   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     A     335     A     335      3    3   15     1    3    3    3    4    9   11   13   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     L     336     L     336     10   12   15     6    9   10   11   11   11   12   13   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     N     337     N     337     10   12   15     6    9   10   11   11   11   11   13   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     E     338     E     338     10   12   15     6    9   10   11   11   11   12   13   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     V     339     V     339     10   12   15     6    9   10   11   11   11   12   13   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     F     340     F     340     10   12   15     6    9   10   11   11   11   12   13   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     V     341     V     341     10   12   15     6    9   10   11   11   11   12   13   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     P     342     P     342     10   12   15     6    9   10   11   11   11   12   13   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     I     343     I     343     10   12   15     6    8   10   11   11   11   12   13   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     L     344     L     344     10   12   15     6    9   10   11   11   11   12   13   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     Q     345     Q     345     10   12   15     6    9   10   11   11   11   12   13   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     K     346     K     346      8   12   15     0    5    9   11   11   11   12   13   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     Q     347     Q     347      3   12   15     0    3    3    3    3    6    9   11   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_AVERAGE  LCS_A:   8.92  (   6.45    8.23   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      9     10     11     11     11     12     13     15     15     15     15     15     15     15     15     15     15     15     15 
GDT PERCENT_CA   4.84   7.26   8.06   8.87   8.87   8.87   9.68  10.48  12.10  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    0.28   0.76   0.81   1.05   1.05   1.05   2.19   2.41   2.85   2.85   2.85   2.85   2.85   2.85   2.85   2.85   2.85   2.85   2.85   2.85
GDT RMS_ALL_CA   4.96   4.58   4.50   4.14   4.14   4.14   2.99   2.96   2.85   2.85   2.85   2.85   2.85   2.85   2.85   2.85   2.85   2.85   2.85   2.85

#      Molecule1      Molecule2       DISTANCE
LGA    G     333      G     333          3.032
LGA    V     334      V     334          3.092
LGA    A     335      A     335          3.958
LGA    L     336      L     336          3.550
LGA    N     337      N     337          4.957
LGA    E     338      E     338          3.307
LGA    V     339      V     339          0.729
LGA    F     340      F     340          2.714
LGA    V     341      V     341          1.847
LGA    P     342      P     342          0.654
LGA    I     343      I     343          1.670
LGA    L     344      L     344          0.768
LGA    Q     345      Q     345          1.172
LGA    K     346      K     346          1.170
LGA    Q     347      Q     347          5.588

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   15  124    4.0     13    2.41     9.677     9.587     0.517

LGA_LOCAL      RMSD =  2.415  Number of atoms =   13  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  2.962  Number of atoms =   15 
Std_ALL_ATOMS  RMSD =  2.854  (standard rmsd on all 15 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.887236 * X  +  -0.013093 * Y  +  -0.461130 * Z  +  31.222286
  Y_new =  -0.461139 * X  +   0.002501 * Y  +  -0.887325 * Z  + 143.544617
  Z_new =   0.012771 * X  +   0.999911 * Y  +  -0.003819 * Z  +  44.659298 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.574615   -1.566977  [ DEG:    90.2188    -89.7812 ]
  Theta =  -0.012771   -3.128822  [ DEG:    -0.7317   -179.2683 ]
  Phi   =  -0.479320    2.662272  [ DEG:   -27.4630    152.5370 ]
 
# 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: T0356TS212_1_2-D1                             
REMARK     2: T0356_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0356TS212_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   13   2.41   9.587     2.85
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS212_1_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0356
PARENT 1oi2_A
ATOM      1  N   GLY   333      61.474  66.469  76.522  1.00 12.64       1SG   2
ATOM      2  CA  GLY   333      60.413  67.381  76.039  1.00 12.64       1SG   3
ATOM      3  C   GLY   333      60.314  67.298  74.556  1.00 12.64       1SG   4
ATOM      4  O   GLY   333      61.306  67.060  73.865  1.00 12.64       1SG   5
ATOM      5  N   VAL   334      59.099  67.511  74.024  1.00 37.17       1SG   6
ATOM      6  CA  VAL   334      58.895  67.432  72.610  1.00 37.17       1SG   7
ATOM      7  CB  VAL   334      57.450  67.462  72.214  1.00 37.17       1SG   8
ATOM      8  CG1 VAL   334      57.347  67.410  70.681  1.00 37.17       1SG   9
ATOM      9  CG2 VAL   334      56.745  66.301  72.930  1.00 37.17       1SG  10
ATOM     10  C   VAL   334      59.576  68.606  71.992  1.00 37.17       1SG  11
ATOM     11  O   VAL   334      59.788  69.631  72.638  1.00 37.17       1SG  12
ATOM     12  N   ALA   335      59.972  68.458  70.717  1.00 28.32       1SG  13
ATOM     13  CA  ALA   335      60.640  69.518  70.029  1.00 28.32       1SG  14
ATOM     14  CB  ALA   335      61.137  69.123  68.627  1.00 28.32       1SG  15
ATOM     15  C   ALA   335      59.670  70.640  69.870  1.00 28.32       1SG  16
ATOM     16  O   ALA   335      58.456  70.447  69.909  1.00 28.32       1SG  17
ATOM     17  N   LEU   336      60.216  71.858  69.716  1.00125.21       1SG  18
ATOM     18  CA  LEU   336      59.437  73.048  69.557  1.00125.21       1SG  19
ATOM     19  CB  LEU   336      60.268  74.336  69.676  1.00125.21       1SG  20
ATOM     20  CG  LEU   336      59.447  75.630  69.509  1.00125.21       1SG  21
ATOM     21  CD1 LEU   336      58.398  75.785  70.621  1.00125.21       1SG  22
ATOM     22  CD2 LEU   336      60.369  76.855  69.380  1.00125.21       1SG  23
ATOM     23  C   LEU   336      58.835  73.032  68.192  1.00125.21       1SG  24
ATOM     24  O   LEU   336      59.311  72.348  67.290  1.00125.21       1SG  25
ATOM     25  N   ASN   337      57.747  73.806  68.024  1.00 74.25       1SG  26
ATOM     26  CA  ASN   337      57.033  73.888  66.785  1.00 74.25       1SG  27
ATOM     27  CB  ASN   337      55.825  74.836  66.866  1.00 74.25       1SG  28
ATOM     28  CG  ASN   337      56.350  76.227  67.199  1.00 74.25       1SG  29
ATOM     29  OD1 ASN   337      57.104  76.412  68.153  1.00 74.25       1SG  30
ATOM     30  ND2 ASN   337      55.951  77.238  66.383  1.00 74.25       1SG  31
ATOM     31  C   ASN   337      57.961  74.426  65.752  1.00 74.25       1SG  32
ATOM     32  O   ASN   337      57.919  74.014  64.594  1.00 74.25       1SG  33
ATOM     33  N   GLU   338      58.834  75.365  66.154  1.00105.16       1SG  34
ATOM     34  CA  GLU   338      59.754  75.953  65.232  1.00105.16       1SG  35
ATOM     35  CB  GLU   338      60.687  76.970  65.905  1.00105.16       1SG  36
ATOM     36  CG  GLU   338      61.718  77.571  64.951  1.00105.16       1SG  37
ATOM     37  CD  GLU   338      61.019  78.601  64.079  1.00105.16       1SG  38
ATOM     38  OE1 GLU   338      59.784  78.779  64.238  1.00105.16       1SG  39
ATOM     39  OE2 GLU   338      61.720  79.225  63.236  1.00105.16       1SG  40
ATOM     40  C   GLU   338      60.618  74.870  64.674  1.00105.16       1SG  41
ATOM     41  O   GLU   338      60.905  74.852  63.481  1.00105.16       1SG  42
ATOM     42  N   VAL   339      61.061  73.922  65.514  1.00 28.09       1SG  43
ATOM     43  CA  VAL   339      61.929  72.904  65.000  1.00 28.09       1SG  44
ATOM     44  CB  VAL   339      62.336  71.907  66.044  1.00 28.09       1SG  45
ATOM     45  CG1 VAL   339      63.149  70.795  65.360  1.00 28.09       1SG  46
ATOM     46  CG2 VAL   339      63.091  72.638  67.167  1.00 28.09       1SG  47
ATOM     47  C   VAL   339      61.190  72.146  63.946  1.00 28.09       1SG  48
ATOM     48  O   VAL   339      61.714  71.898  62.862  1.00 28.09       1SG  49
ATOM     49  N   PHE   340      59.930  71.775  64.238  1.00 53.20       1SG  50
ATOM     50  CA  PHE   340      59.160  70.990  63.319  1.00 53.20       1SG  51
ATOM     51  CB  PHE   340      57.755  70.634  63.836  1.00 53.20       1SG  52
ATOM     52  CG  PHE   340      57.872  69.579  64.880  1.00 53.20       1SG  53
ATOM     53  CD1 PHE   340      58.169  69.902  66.183  1.00 53.20       1SG  54
ATOM     54  CD2 PHE   340      57.667  68.258  64.547  1.00 53.20       1SG  55
ATOM     55  CE1 PHE   340      58.273  68.918  67.139  1.00 53.20       1SG  56
ATOM     56  CE2 PHE   340      57.769  67.269  65.496  1.00 53.20       1SG  57
ATOM     57  CZ  PHE   340      58.074  67.601  66.795  1.00 53.20       1SG  58
ATOM     58  C   PHE   340      58.949  71.736  62.037  1.00 53.20       1SG  59
ATOM     59  O   PHE   340      59.175  71.184  60.962  1.00 53.20       1SG  60
ATOM     60  N   VAL   341      58.519  73.011  62.101  1.00131.36       1SG  61
ATOM     61  CA  VAL   341      58.210  73.642  60.850  1.00131.36       1SG  62
ATOM     62  CB  VAL   341      57.457  74.947  60.997  1.00131.36       1SG  63
ATOM     63  CG1 VAL   341      55.985  74.576  61.237  1.00131.36       1SG  64
ATOM     64  CG2 VAL   341      57.964  75.728  62.223  1.00131.36       1SG  65
ATOM     65  C   VAL   341      59.395  73.707  59.917  1.00131.36       1SG  66
ATOM     66  O   VAL   341      59.266  73.180  58.813  1.00131.36       1SG  67
ATOM     67  N   PRO   342      60.545  74.257  60.217  1.00111.84       1SG  68
ATOM     68  CA  PRO   342      61.570  74.129  59.221  1.00111.84       1SG  69
ATOM     69  CD  PRO   342      60.596  75.591  60.792  1.00111.84       1SG  70
ATOM     70  CB  PRO   342      62.637  75.165  59.558  1.00111.84       1SG  71
ATOM     71  CG  PRO   342      61.812  76.302  60.176  1.00111.84       1SG  72
ATOM     72  C   PRO   342      62.096  72.749  59.015  1.00111.84       1SG  73
ATOM     73  O   PRO   342      62.545  72.456  57.908  1.00111.84       1SG  74
ATOM     74  N   ILE   343      62.069  71.876  60.036  1.00119.82       1SG  75
ATOM     75  CA  ILE   343      62.635  70.584  59.798  1.00119.82       1SG  76
ATOM     76  CB  ILE   343      62.709  69.727  61.039  1.00119.82       1SG  77
ATOM     77  CG2 ILE   343      61.291  69.497  61.584  1.00119.82       1SG  78
ATOM     78  CG1 ILE   343      63.484  68.431  60.749  1.00119.82       1SG  79
ATOM     79  CD1 ILE   343      64.971  68.653  60.485  1.00119.82       1SG  80
ATOM     80  C   ILE   343      61.815  69.884  58.760  1.00119.82       1SG  81
ATOM     81  O   ILE   343      62.352  69.335  57.800  1.00119.82       1SG  82
ATOM     82  N   LEU   344      60.479  69.906  58.917  1.00125.00       1SG  83
ATOM     83  CA  LEU   344      59.634  69.226  57.985  1.00125.00       1SG  84
ATOM     84  CB  LEU   344      58.158  69.129  58.409  1.00125.00       1SG  85
ATOM     85  CG  LEU   344      57.883  68.117  59.538  1.00125.00       1SG  86
ATOM     86  CD1 LEU   344      58.594  68.505  60.843  1.00125.00       1SG  87
ATOM     87  CD2 LEU   344      56.374  67.896  59.723  1.00125.00       1SG  88
ATOM     88  C   LEU   344      59.687  69.899  56.663  1.00125.00       1SG  89
ATOM     89  O   LEU   344      59.630  69.225  55.639  1.00125.00       1SG  90
ATOM     90  N   GLN   345      59.764  71.243  56.631  1.00281.08       1SG  91
ATOM     91  CA  GLN   345      59.764  71.856  55.339  1.00281.08       1SG  92
ATOM     92  CB  GLN   345      58.544  72.768  55.110  1.00281.08       1SG  93
ATOM     93  CG  GLN   345      58.500  73.991  56.031  1.00281.08       1SG  94
ATOM     94  CD  GLN   345      57.238  74.785  55.725  1.00281.08       1SG  95
ATOM     95  OE1 GLN   345      57.022  75.871  56.260  1.00281.08       1SG  96
ATOM     96  NE2 GLN   345      56.368  74.218  54.848  1.00281.08       1SG  97
ATOM     97  C   GLN   345      60.989  72.692  55.181  1.00281.08       1SG  98
ATOM     98  O   GLN   345      61.218  73.641  55.926  1.00281.08       1SG  99
ATOM     99  N   LYS   346      61.835  72.337  54.202  1.00239.55       1SG 100
ATOM    100  CA  LYS   346      62.956  73.173  53.905  1.00239.55       1SG 101
ATOM    101  CB  LYS   346      64.272  72.805  54.619  1.00239.55       1SG 102
ATOM    102  CG  LYS   346      64.354  73.347  56.049  1.00239.55       1SG 103
ATOM    103  CD  LYS   346      65.539  72.814  56.859  1.00239.55       1SG 104
ATOM    104  CE  LYS   346      65.608  73.378  58.281  1.00239.55       1SG 105
ATOM    105  NZ  LYS   346      66.781  72.826  58.996  1.00239.55       1SG 106
ATOM    106  C   LYS   346      63.198  73.067  52.443  1.00239.55       1SG 107
ATOM    107  O   LYS   346      63.377  71.975  51.907  1.00239.55       1SG 108
ATOM    108  N   GLN   347      63.182  74.220  51.752  1.00282.07       1SG 109
ATOM    109  CA  GLN   347      63.468  74.195  50.354  1.00282.07       1SG 110
ATOM    110  CB  GLN   347      62.361  74.828  49.488  1.00282.07       1SG 111
ATOM    111  CG  GLN   347      62.164  76.332  49.701  1.00282.07       1SG 112
ATOM    112  CD  GLN   347      63.014  77.067  48.673  1.00282.07       1SG 113
ATOM    113  OE1 GLN   347      63.434  76.487  47.673  1.00282.07       1SG 114
ATOM    114  NE2 GLN   347      63.267  78.380  48.919  1.00282.07       1SG 115
ATOM    115  C   GLN   347      64.724  74.980  50.202  1.00282.07       1SG 116
ATOM    116  O   GLN   347      64.785  76.155  50.560  1.00282.07       1SG 117
TER
END
