
#######################################################
#                                                     #
#                        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   12 (   98),  selected   12 , name T0363TS186_4-D1
# Molecule2: number of CA atoms   46 (  372),  selected   12 , name T0363_D1.pdb
# PARAMETERS: T0363TS186_4-D1.T0363_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:    10        39 - 55          4.90     6.51
  LONGEST_CONTINUOUS_SEGMENT:    10        47 - 56          3.08     7.69
  LCS_AVERAGE:     21.56

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6        47 - 52          0.45     8.13
  LCS_AVERAGE:      9.42

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6        47 - 52          0.45     8.13
  LCS_AVERAGE:      9.06

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:   46
LCS_GDT     V      38     V      38      0    0    9     3    3    3    3    3    3    3    3    3    4    6    7    8    9   10   10   10   11   12   12 
LCS_GDT     Q      39     Q      39      0    0   10     3    3    3    3    3    3    3    3    3    4    6    7    8    9   10   10   10   11   12   12 
LCS_GDT     I      47     I      47      6    6   10     5    6    6    6    6    8    8    8    9   10   10   10   10   10   10   10   10   11   12   12 
LCS_GDT     L      48     L      48      6    6   10     5    6    6    6    6    8    8    8    9   10   10   10   10   10   10   10   10   11   12   12 
LCS_GDT     S      49     S      49      6    6   10     5    6    6    6    6    8    8    8    9   10   10   10   10   10   10   10   10   11   12   12 
LCS_GDT     Q      50     Q      50      6    6   10     5    6    6    6    6    6    7    8    9   10   10   10   10   10   10   10   10   11   12   12 
LCS_GDT     F      51     F      51      6    6   10     5    6    6    6    6    6    7    7    9   10   10   10   10   10   10   10   10   11   12   12 
LCS_GDT     P      52     P      52      6    6   10     4    6    6    6    6    8    8    8    9   10   10   10   10   10   10   10   10   11   12   12 
LCS_GDT     E      53     E      53      4    4   10     3    4    4    5    6    8    8    8    9   10   10   10   10   10   10   10   10   11   12   12 
LCS_GDT     I      54     I      54      4    4   10     3    4    4    5    6    8    8    8    9   10   10   10   10   10   10   10   10   11   12   12 
LCS_GDT     D      55     D      55      3    4   10     3    4    4    5    6    8    8    8    9   10   10   10   10   10   10   10   10   11   12   12 
LCS_GDT     L      56     L      56      3    4   10     3    3    4    5    5    8    8    8    9   10   10   10   10   10   10   10   10   11   12   12 
LCS_AVERAGE  LCS_A:  13.35  (   9.06    9.42   21.56 )

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      5      6      6      6      6      8      8      8      9     10     10     10     10     10     10     10     10     11     12     12 
GDT PERCENT_CA  10.87  13.04  13.04  13.04  13.04  17.39  17.39  17.39  19.57  21.74  21.74  21.74  21.74  21.74  21.74  21.74  21.74  23.91  26.09  26.09
GDT RMS_LOCAL    0.18   0.45   0.45   0.45   0.45   2.28   2.28   2.28   2.73   3.08   3.08   3.08   3.08   3.08   3.08   3.08   3.08   5.14   5.97   5.97
GDT RMS_ALL_CA   8.34   8.13   8.13   8.13   8.13   7.33   7.33   7.33   7.50   7.69   7.69   7.69   7.69   7.69   7.69   7.69   7.69   6.44   5.97   5.97

#      Molecule1      Molecule2       DISTANCE
LGA    V      38      V      38         18.589
LGA    Q      39      Q      39         16.427
LGA    I      47      I      47          1.499
LGA    L      48      L      48          2.690
LGA    S      49      S      49          2.590
LGA    Q      50      Q      50          4.279
LGA    F      51      F      51          4.951
LGA    P      52      P      52          2.467
LGA    E      53      E      53          1.797
LGA    I      54      I      54          2.188
LGA    D      55      D      55          3.680
LGA    L      56      L      56          2.831

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   12   46    4.0      8    2.28    16.304    15.332     0.336

LGA_LOCAL      RMSD =  2.284  Number of atoms =    8  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  7.692  Number of atoms =   12 
Std_ALL_ATOMS  RMSD =  5.969  (standard rmsd on all 12 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.839556 * X  +  -0.202154 * Y  +  -0.504261 * Z  + -57.979168
  Y_new =   0.525017 * X  +   0.540503 * Y  +   0.657430 * Z  + -113.389946
  Z_new =   0.139652 * X  +  -0.816695 * Y  +   0.559917 * Z  +  13.666533 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.969808    2.171784  [ DEG:   -55.5659    124.4341 ]
  Theta =  -0.140110   -3.001482  [ DEG:    -8.0277   -171.9723 ]
  Phi   =   0.558851   -2.582741  [ DEG:    32.0198   -147.9802 ]
 
# 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: T0363TS186_4-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0363TS186_4-D1.T0363_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   12   46   4.0    8   2.28  15.332     5.97
REMARK  ---------------------------------------------------------- 
MOLECULE T0363TS186_4-D1
PFRMAT TS
TARGET T0363
MODEL  4
PARENT 1vqy_B
ATOM      1  N   VAL    38      34.944   9.347  -3.320  1.00  0.00
ATOM      2  CA  VAL    38      36.123  10.200  -3.480  1.00  0.00
ATOM      3  C   VAL    38      35.788  11.679  -3.346  1.00  0.00
ATOM      4  O   VAL    38      36.621  12.464  -2.900  1.00  0.00
ATOM      5  CB  VAL    38      36.774  10.010  -4.863  1.00  0.00
ATOM      6  CG1 VAL    38      37.870  11.041  -5.081  1.00  0.00
ATOM      7  CG2 VAL    38      37.387   8.624  -4.977  1.00  0.00
ATOM      8  N   GLN    39      34.579  12.055  -3.735  1.00  0.00
ATOM      9  CA  GLN    39      34.110  13.436  -3.567  1.00  0.00
ATOM     10  C   GLN    39      33.865  13.742  -2.079  1.00  0.00
ATOM     11  O   GLN    39      34.308  14.771  -1.566  1.00  0.00
ATOM     12  CB  GLN    39      32.801  13.654  -4.328  1.00  0.00
ATOM     13  CG  GLN    39      32.953  13.640  -5.841  1.00  0.00
ATOM     14  CD  GLN    39      31.621  13.710  -6.560  1.00  0.00
ATOM     15  OE1 GLN    39      30.562  13.665  -5.934  1.00  0.00
ATOM     16  NE2 GLN    39      31.669  13.822  -7.883  1.00  0.00
ATOM     17  N   ILE    47      33.172  12.832  -1.393  1.00  0.00
ATOM     18  CA  ILE    47      32.987  12.912   0.061  1.00  0.00
ATOM     19  C   ILE    47      34.327  13.090   0.769  1.00  0.00
ATOM     20  O   ILE    47      34.509  14.026   1.534  1.00  0.00
ATOM     21  CB  ILE    47      32.329  11.636   0.618  1.00  0.00
ATOM     22  CG1 ILE    47      30.896  11.506   0.098  1.00  0.00
ATOM     23  CG2 ILE    47      32.289  11.676   2.138  1.00  0.00
ATOM     24  CD1 ILE    47      30.271  10.153   0.361  1.00  0.00
ATOM     25  N   LEU    48      35.249  12.169   0.499  1.00  0.00
ATOM     26  CA  LEU    48      36.574  12.186   1.085  1.00  0.00
ATOM     27  C   LEU    48      37.366  13.454   0.815  1.00  0.00
ATOM     28  O   LEU    48      38.074  13.952   1.699  1.00  0.00
ATOM     29  CB  LEU    48      37.367  10.984   0.579  1.00  0.00
ATOM     30  CG  LEU    48      36.969   9.648   1.191  1.00  0.00
ATOM     31  CD1 LEU    48      37.853   8.555   0.585  1.00  0.00
ATOM     32  CD2 LEU    48      37.038   9.668   2.755  1.00  0.00
ATOM     33  N   SER    49      37.248  13.962  -0.410  1.00  0.00
ATOM     34  CA  SER    49      37.998  15.126  -0.846  1.00  0.00
ATOM     35  C   SER    49      37.530  16.365  -0.103  1.00  0.00
ATOM     36  O   SER    49      38.344  17.183   0.327  1.00  0.00
ATOM     37  CB  SER    49      37.804  15.357  -2.346  1.00  0.00
ATOM     38  OG  SER    49      38.370  14.301  -3.102  1.00  0.00
ATOM     39  N   GLN    50      36.223  16.517   0.015  1.00  0.00
ATOM     40  CA  GLN    50      35.666  17.602   0.813  1.00  0.00
ATOM     41  C   GLN    50      36.157  17.583   2.259  1.00  0.00
ATOM     42  O   GLN    50      36.532  18.621   2.803  1.00  0.00
ATOM     43  CB  GLN    50      34.139  17.510   0.851  1.00  0.00
ATOM     44  CG  GLN    50      33.464  17.843  -0.469  1.00  0.00
ATOM     45  CD  GLN    50      31.963  17.631  -0.427  1.00  0.00
ATOM     46  OE1 GLN    50      31.423  17.146   0.568  1.00  0.00
ATOM     47  NE2 GLN    50      31.285  17.996  -1.507  1.00  0.00
ATOM     48  N   PHE    51      36.172  16.410   2.873  1.00  0.00
ATOM     49  CA  PHE    51      36.570  16.325   4.261  1.00  0.00
ATOM     50  C   PHE    51      38.082  16.576   4.371  1.00  0.00
ATOM     51  O   PHE    51      38.512  17.435   5.151  1.00  0.00
ATOM     52  CB  PHE    51      36.251  14.939   4.826  1.00  0.00
ATOM     53  CG  PHE    51      34.802  14.745   5.174  1.00  0.00
ATOM     54  CD1 PHE    51      33.948  14.093   4.301  1.00  0.00
ATOM     55  CD2 PHE    51      34.294  15.214   6.373  1.00  0.00
ATOM     56  CE1 PHE    51      32.615  13.915   4.621  1.00  0.00
ATOM     57  CE2 PHE    51      32.962  15.034   6.693  1.00  0.00
ATOM     58  CZ  PHE    51      32.123  14.388   5.822  1.00  0.00
ATOM     59  N   PRO    52      38.870  15.872   3.561  1.00  0.00
ATOM     60  CA  PRO    52      40.336  16.064   3.513  1.00  0.00
ATOM     61  C   PRO    52      40.738  17.537   3.394  1.00  0.00
ATOM     62  O   PRO    52      41.506  18.059   4.213  1.00  0.00
ATOM     63  CB  PRO    52      40.772  15.283   2.271  1.00  0.00
ATOM     64  CG  PRO    52      39.783  14.171   2.164  1.00  0.00
ATOM     65  CD  PRO    52      38.446  14.767   2.509  1.00  0.00
ATOM     66  N   GLU    53      40.183  18.195   2.374  1.00  0.00
ATOM     67  CA  GLU    53      40.606  19.528   1.962  1.00  0.00
ATOM     68  C   GLU    53      39.975  20.695   2.729  1.00  0.00
ATOM     69  O   GLU    53      40.563  21.773   2.785  1.00  0.00
ATOM     70  CB  GLU    53      40.335  19.695   0.477  1.00  0.00
ATOM     71  CG  GLU    53      41.108  18.704  -0.405  1.00  0.00
ATOM     72  CD  GLU    53      41.052  19.064  -1.889  1.00  0.00
ATOM     73  OE1 GLU    53      40.297  19.983  -2.270  1.00  0.00
ATOM     74  OE2 GLU    53      41.764  18.423  -2.685  1.00  0.00
ATOM     75  N   ILE    54      38.798  20.489   3.323  1.00  0.00
ATOM     76  CA  ILE    54      38.093  21.563   4.037  1.00  0.00
ATOM     77  C   ILE    54      37.558  21.173   5.415  1.00  0.00
ATOM     78  O   ILE    54      37.865  21.832   6.404  1.00  0.00
ATOM     79  CB  ILE    54      36.871  22.061   3.243  1.00  0.00
ATOM     80  CG1 ILE    54      37.308  22.639   1.897  1.00  0.00
ATOM     81  CG2 ILE    54      36.137  23.145   4.019  1.00  0.00
ATOM     82  CD1 ILE    54      36.157  22.983   0.976  1.00  0.00
ATOM     83  N   ASP    55      36.770  20.105   5.479  1.00  0.00
ATOM     84  CA  ASP    55      35.909  19.860   6.626  1.00  0.00
ATOM     85  C   ASP    55      36.589  19.520   7.932  1.00  0.00
ATOM     86  O   ASP    55      36.226  20.050   8.976  1.00  0.00
ATOM     87  CB  ASP    55      34.971  18.684   6.349  1.00  0.00
ATOM     88  CG  ASP    55      33.871  19.034   5.367  1.00  0.00
ATOM     89  OD1 ASP    55      33.684  20.237   5.089  1.00  0.00
ATOM     90  OD2 ASP    55      33.197  18.105   4.874  1.00  0.00
ATOM     91  N   LEU    56      37.590  18.652   7.864  1.00  0.00
ATOM     92  CA  LEU    56      38.271  18.181   9.063  1.00  0.00
ATOM     93  C   LEU    56      39.111  19.304   9.716  1.00  0.00
ATOM     94  O   LEU    56      39.292  19.327  10.944  1.00  0.00
ATOM     95  CB  LEU    56      39.214  17.025   8.724  1.00  0.00
ATOM     96  CG  LEU    56      38.553  15.717   8.287  1.00  0.00
ATOM     97  CD1 LEU    56      39.598  14.710   7.835  1.00  0.00
ATOM     98  CD2 LEU    56      37.766  15.102   9.435  1.00  0.00
TER
END
