
#######################################################
#                                                     #
#                        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   23 (  114),  selected   23 , name T0321TS102_3-D1
# Molecule2: number of CA atoms   96 (  710),  selected   23 , name T0321_D1.pdb
# PARAMETERS: T0321TS102_3-D1.T0321_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:    20        69 - 88          4.91     6.53
  LCS_AVERAGE:     20.34

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11        78 - 88          1.95    10.63
  LCS_AVERAGE:      9.47

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9        78 - 86          0.35     9.56
  LCS_AVERAGE:      7.29

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:   96
LCS_GDT     S      69     S      69      3    3   20     0    3    3    3    4    5    5    7   10   14   16   17   18   19   19   21   22   22   22   23 
LCS_GDT     W      70     W      70      3    3   20     3    3    4    4    5    7    8   11   13   14   16   17   18   19   19   21   22   22   22   23 
LCS_GDT     N      71     N      71      3    7   20     3    3    3    3    6    8    9   12   14   14   16   17   18   19   19   21   22   22   22   23 
LCS_GDT     Y      72     Y      72      6    7   20     3    4    6    6    6    8    9   11   14   14   16   17   18   19   19   21   22   22   22   23 
LCS_GDT     V      73     V      73      6    7   20     4    4    6    6    8    8   10   12   14   14   16   17   18   19   19   21   22   22   22   23 
LCS_GDT     E      74     E      74      6    7   20     4    4    6    6    8    8   10   12   14   14   15   16   18   19   19   21   22   22   22   23 
LCS_GDT     A      75     A      75      6    7   20     4    4    6    6    8    8   10   12   14   14   16   17   18   19   19   21   22   22   22   23 
LCS_GDT     S      76     S      76      6    7   20     4    4    6    6    8    8   10   12   14   14   16   17   18   19   19   21   22   22   22   23 
LCS_GDT     I      77     I      77      6   10   20     1    3    6    6    6    8   10   12   14   14   16   17   18   19   19   21   22   22   22   23 
LCS_GDT     G      78     G      78      9   11   20     9    9    9    9    9   10   12   14   14   14   16   17   18   19   19   21   22   22   22   23 
LCS_GDT     L      79     L      79      9   11   20     9    9    9    9    9   10   13   14   14   14   15   16   16   18   19   20   22   22   22   23 
LCS_GDT     A      80     A      80      9   11   20     9    9    9    9    9   10   13   14   14   14   15   16   17   18   19   21   22   22   22   23 
LCS_GDT     A      81     A      81      9   11   20     9    9    9    9    9   11   13   14   14   14   16   17   18   19   19   21   22   22   22   23 
LCS_GDT     I      82     I      82      9   11   20     9    9    9    9    9   11   13   14   14   14   16   17   18   19   19   21   22   22   22   23 
LCS_GDT     N      83     N      83      9   11   20     9    9    9    9    9   11   13   14   14   14   15   16   18   19   19   21   22   22   22   23 
LCS_GDT     A      84     A      84      9   11   20     9    9    9    9    9   11   13   14   14   14   16   17   18   19   19   21   22   22   22   23 
LCS_GDT     Y      85     Y      85      9   11   20     9    9    9    9    9   11   13   14   14   14   16   17   18   19   19   21   22   22   22   23 
LCS_GDT     Y      86     Y      86      9   11   20     9    9    9    9    9   11   13   14   14   14   16   17   18   19   19   21   22   22   22   23 
LCS_GDT     N      87     N      87      7   11   20     5    7    7    8    9   11   13   14   14   14   16   17   18   19   19   21   22   22   22   23 
LCS_GDT     N      88     N      88      7   11   20     5    7    7    8    9   11   13   14   14   14   16   17   18   19   19   21   22   22   22   23 
LCS_GDT     P      89     P      89      7   10   17     5    7    7    8    9   11   13   14   14   14   16   17   18   19   19   21   22   22   22   23 
LCS_GDT     Q      90     Q      90      7   10   16     4    7    7    8    9   11   13   14   14   14   14   15   15   15   15   15   18   21   22   23 
LCS_GDT     V      91     V      91      7   10   16     4    7    7    8    9   11   13   14   14   14   14   15   16   17   18   21   22   22   22   23 
LCS_AVERAGE  LCS_A:  12.36  (   7.29    9.47   20.34 )

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      9      9      9      9      9     11     13     14     14     14     16     17     18     19     19     21     22     22     22     23 
GDT PERCENT_CA   9.37   9.37   9.37   9.37   9.37  11.46  13.54  14.58  14.58  14.58  16.67  17.71  18.75  19.79  19.79  21.87  22.92  22.92  22.92  23.96
GDT RMS_LOCAL    0.35   0.35   0.35   0.35   0.35   2.15   2.59   2.73   2.73   2.73   3.97   4.14   4.30   4.51   4.51   5.36   5.60   5.60   5.60   6.02
GDT RMS_ALL_CA   9.56   9.56   9.56   9.56   9.56  15.35  13.30  12.45  12.45  12.45   6.18   6.13   6.18   6.22   6.22   6.07   6.09   6.09   6.09   6.02

#      Molecule1      Molecule2       DISTANCE
LGA    S      69      S      69         17.965
LGA    W      70      W      70         21.387
LGA    N      71      N      71         24.997
LGA    Y      72      Y      72         25.092
LGA    V      73      V      73         20.424
LGA    E      74      E      74         18.161
LGA    A      75      A      75         18.136
LGA    S      76      S      76         15.805
LGA    I      77      I      77         10.143
LGA    G      78      G      78          3.610
LGA    L      79      L      79          2.649
LGA    A      80      A      80          2.004
LGA    A      81      A      81          0.865
LGA    I      82      I      82          1.375
LGA    N      83      N      83          2.130
LGA    A      84      A      84          3.383
LGA    Y      85      Y      85          3.769
LGA    Y      86      Y      86          3.598
LGA    N      87      N      87          2.602
LGA    N      88      N      88          0.948
LGA    P      89      P      89          2.963
LGA    Q      90      Q      90          3.402
LGA    V      91      V      91          2.519

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   23   96    4.0     14    2.73    13.802    12.463     0.495

LGA_LOCAL      RMSD =  2.728  Number of atoms =   14  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 12.454  Number of atoms =   23 
Std_ALL_ATOMS  RMSD =  6.016  (standard rmsd on all 23 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.353341 * X  +   0.927705 * Y  +  -0.120474 * Z  + -11.562321
  Y_new =   0.181396 * X  +  -0.058393 * Y  +  -0.981675 * Z  +  47.585377
  Z_new =  -0.917739 * X  +  -0.368720 * Y  +  -0.147649 * Z  +  85.539047 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.951679    1.189914  [ DEG:  -111.8230     68.1770 ]
  Theta =   1.162351    1.979242  [ DEG:    66.5978    113.4022 ]
  Phi   =   2.667305   -0.474288  [ DEG:   152.8253    -27.1747 ]
 
# 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: T0321TS102_3-D1                               
REMARK     2: T0321_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0321TS102_3-D1.T0321_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   23   96   4.0   14   2.73  12.463     6.02
REMARK  ---------------------------------------------------------- 
MOLECULE T0321TS102_3-D1
PFRMAT TS
TARGET T0321
MODEL 3
PARENT 1uar_A
ATOM      1  N   SER    69     -24.581  53.215  53.003  1.00  1.00
ATOM      2  CA  SER    69     -23.481  52.421  53.621  1.00  1.00
ATOM      3  C   SER    69     -23.997  51.123  54.210  1.00  1.00
ATOM      4  O   SER    69     -25.127  50.711  53.933  1.00  1.00
ATOM      5  CB  SER    69     -22.867  53.256  54.760  1.00  1.00
ATOM      6  N   TRP    70     -23.172  50.471  55.023  1.00  1.00
ATOM      7  CA  TRP    70     -23.570  49.215  55.651  1.00  1.00
ATOM      8  C   TRP    70     -24.728  49.457  56.613  1.00  1.00
ATOM      9  O   TRP    70     -24.934  50.580  57.082  1.00  1.00
ATOM     10  CB  TRP    70     -22.403  48.598  56.434  1.00  1.00
ATOM     11  N   ASN    71     -25.477  48.401  56.905  1.00  1.00
ATOM     12  CA  ASN    71     -26.601  48.499  57.833  1.00  1.00
ATOM     13  C   ASN    71     -26.076  48.602  59.262  1.00  1.00
ATOM     14  O   ASN    71     -26.638  49.322  60.096  1.00  1.00
ATOM     15  CB  ASN    71     -27.503  47.279  57.698  1.00  1.00
ATOM     16  N   TYR    72     -24.988  47.884  59.531  1.00  1.00
ATOM     17  CA  TYR    72     -24.381  47.868  60.854  1.00  1.00
ATOM     18  C   TYR    72     -22.892  48.155  60.833  1.00  1.00
ATOM     19  O   TYR    72     -22.075  47.291  61.168  1.00  1.00
ATOM     20  CB  TYR    72     -24.644  46.517  61.523  1.00  1.00
ATOM     21  N   VAL    73     -22.509  49.380  60.450  1.00  1.00
ATOM     22  CA  VAL    73     -21.081  49.707  60.418  1.00  1.00
ATOM     23  C   VAL    73     -20.478  49.674  61.819  1.00  1.00
ATOM     24  O   VAL    73     -19.262  49.551  61.976  1.00  1.00
ATOM     25  CB  VAL    73     -21.065  51.110  59.822  1.00  1.00
ATOM     26  N   GLU    74     -21.325  49.764  62.845  1.00  1.00
ATOM     27  CA  GLU    74     -20.816  49.764  64.209  1.00  1.00
ATOM     28  C   GLU    74     -20.207  48.439  64.657  1.00  1.00
ATOM     29  O   GLU    74     -19.484  48.401  65.657  1.00  1.00
ATOM     30  CB  GLU    74     -21.901  50.212  65.209  1.00  1.00
ATOM     31  N   ALA    75     -20.478  47.353  63.930  1.00  1.00
ATOM     32  CA  ALA    75     -19.893  46.068  64.306  1.00  1.00
ATOM     33  C   ALA    75     -18.623  45.781  63.505  1.00  1.00
ATOM     34  O   ALA    75     -18.044  44.705  63.621  1.00  1.00
ATOM     35  CB  ALA    75     -20.888  44.877  64.133  1.00  1.00
ATOM     36  N   SER    76     -18.200  46.748  62.695  1.00  1.00
ATOM     37  CA  SER    76     -16.984  46.603  61.899  1.00  1.00
ATOM     38  C   SER    76     -15.993  47.689  62.327  1.00  1.00
ATOM     39  O   SER    76     -16.297  48.880  62.232  1.00  1.00
ATOM     40  CB  SER    76     -17.323  46.744  60.408  1.00  1.00
ATOM     41  N   ILE    77     -14.817  47.293  62.810  1.00  1.00
ATOM     42  CA  ILE    77     -13.819  48.274  63.227  1.00  1.00
ATOM     43  C   ILE    77     -12.591  48.239  62.323  1.00  1.00
ATOM     44  O   ILE    77     -12.245  47.199  61.757  1.00  1.00
ATOM     45  CB  ILE    77     -13.370  48.059  64.694  1.00  1.00
ATOM     46  N   GLY    78     -11.933  49.385  62.195  1.00  1.00
ATOM     47  CA  GLY    78     -10.751  49.494  61.352  1.00  1.00
ATOM     48  C   GLY    78      -9.495  49.103  62.118  1.00  1.00
ATOM     49  O   GLY    78      -9.503  48.990  63.344  1.00  1.00
ATOM     50  N   LEU    79      -8.403  48.893  61.395  1.00  1.00
ATOM     51  CA  LEU    79      -7.162  48.542  62.067  1.00  1.00
ATOM     52  C   LEU    79      -6.727  49.716  62.939  1.00  1.00
ATOM     53  O   LEU    79      -6.113  49.522  63.988  1.00  1.00
ATOM     54  CB  LEU    79      -6.057  48.194  61.058  1.00  1.00
ATOM     55  N   ALA    80      -7.057  50.932  62.505  1.00  1.00
ATOM     56  CA  ALA    80      -6.717  52.130  63.265  1.00  1.00
ATOM     57  C   ALA    80      -7.465  52.104  64.597  1.00  1.00
ATOM     58  O   ALA    80      -6.878  52.350  65.652  1.00  1.00
ATOM     59  CB  ALA    80      -7.109  53.391  62.487  1.00  1.00
ATOM     60  N   ALA    81      -8.761  51.810  64.532  1.00  1.00
ATOM     61  CA  ALA    81      -9.604  51.745  65.727  1.00  1.00
ATOM     62  C   ALA    81      -9.024  50.754  66.727  1.00  1.00
ATOM     63  O   ALA    81      -8.885  51.056  67.913  1.00  1.00
ATOM     64  CB  ALA    81     -11.031  51.321  65.347  1.00  1.00
ATOM     65  N   ILE    82      -8.662  49.571  66.245  1.00  1.00
ATOM     66  CA  ILE    82      -8.116  48.554  67.122  1.00  1.00
ATOM     67  C   ILE    82      -6.813  49.010  67.776  1.00  1.00
ATOM     68  O   ILE    82      -6.650  48.867  68.986  1.00  1.00
ATOM     69  CB  ILE    82      -7.918  47.233  66.352  1.00  1.00
ATOM     70  N   ASN    83      -5.897  49.584  67.000  1.00  1.00
ATOM     71  CA  ASN    83      -4.636  50.021  67.580  1.00  1.00
ATOM     72  C   ASN    83      -4.837  51.097  68.645  1.00  1.00
ATOM     73  O   ASN    83      -4.073  51.171  69.604  1.00  1.00
ATOM     74  CB  ASN    83      -3.668  50.531  66.502  1.00  1.00
ATOM     75  N   ALA    84      -5.871  51.918  68.491  1.00  1.00
ATOM     76  CA  ALA    84      -6.142  52.973  69.462  1.00  1.00
ATOM     77  C   ALA    84      -6.988  52.507  70.652  1.00  1.00
ATOM     78  O   ALA    84      -7.315  53.295  71.545  1.00  1.00
ATOM     79  CB  ALA    84      -6.798  54.169  68.767  1.00  1.00
ATOM     80  N   TYR    85      -7.326  51.223  70.678  1.00  1.00
ATOM     81  CA  TYR    85      -8.111  50.679  71.785  1.00  1.00
ATOM     82  C   TYR    85      -7.394  49.504  72.442  1.00  1.00
ATOM     83  O   TYR    85      -7.999  48.740  73.191  1.00  1.00
ATOM     84  CB  TYR    85      -9.493  50.243  71.289  1.00  1.00
ATOM     85  N   TYR    86      -6.099  49.369  72.167  1.00  1.00
ATOM     86  CA  TYR    86      -5.305  48.275  72.720  1.00  1.00
ATOM     87  C   TYR    86      -5.217  48.286  74.241  1.00  1.00
ATOM     88  O   TYR    86      -4.877  47.272  74.850  1.00  1.00
ATOM     89  CB  TYR    86      -3.893  48.290  72.138  1.00  1.00
ATOM     90  N   ASN    87      -5.518  49.428  74.850  1.00  1.00
ATOM     91  CA  ASN    87      -5.469  49.546  76.303  1.00  1.00
ATOM     92  C   ASN    87      -6.833  49.889  76.898  1.00  1.00
ATOM     93  O   ASN    87      -6.933  50.235  78.077  1.00  1.00
ATOM     94  CB  ASN    87      -4.445  50.612  76.710  1.00  1.00
ATOM     95  N   ASN    88      -7.881  49.803  76.082  1.00  1.00
ATOM     96  CA  ASN    88      -9.231  50.093  76.556  1.00  1.00
ATOM     97  C   ASN    88      -9.592  48.965  77.516  1.00  1.00
ATOM     98  O   ASN    88      -9.575  47.791  77.139  1.00  1.00
ATOM     99  CB  ASN    88     -10.219  50.120  75.384  1.00  1.00
ATOM    100  N   PRO    89      -9.905  49.299  78.777  1.00  1.00
ATOM    101  CA  PRO    89     -10.256  48.255  79.746  1.00  1.00
ATOM    102  C   PRO    89     -11.502  47.444  79.392  1.00  1.00
ATOM    103  O   PRO    89     -11.689  46.330  79.886  1.00  1.00
ATOM    104  CB  PRO    89     -10.409  49.036  81.053  1.00  1.00
ATOM    105  N   GLN    90     -12.347  47.997  78.531  1.00  1.00
ATOM    106  CA  GLN    90     -13.573  47.318  78.132  1.00  1.00
ATOM    107  C   GLN    90     -13.426  46.556  76.820  1.00  1.00
ATOM    108  O   GLN    90     -14.396  46.000  76.329  1.00  1.00
ATOM    109  CB  GLN    90     -14.713  48.331  77.998  1.00  1.00
ATOM    110  N   VAL    91     -12.218  46.526  76.265  1.00  1.00
ATOM    111  CA  VAL    91     -11.977  45.835  74.993  1.00  1.00
ATOM    112  C   VAL    91     -11.107  44.583  75.134  1.00  1.00
ATOM    113  O   VAL    91     -10.078  44.599  75.806  1.00  1.00
ATOM    114  CB  VAL    91     -11.290  46.777  73.967  1.00  1.00
TER
END
