
#######################################################
#                                                     #
#                        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   28 (  112),  selected   28 , name T0363TS383_3-D1
# Molecule2: number of CA atoms   46 (  372),  selected   28 , name T0363_D1.pdb
# PARAMETERS: T0363TS383_3-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:    28        27 - 56          4.34     4.34
  LCS_AVERAGE:     60.87

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15        36 - 52          1.97     5.97
  LCS_AVERAGE:     26.71

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9        36 - 44          0.58     5.74
  LCS_AVERAGE:     13.12

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     L      27     L      27      3    9   28     0    3    4    5    8   13   16   17   19   21   24   26   27   28   28   28   28   28   28   28 
LCS_GDT     K      28     K      28      6    9   28     3    5    6    8    8   13   16   16   19   21   24   26   27   28   28   28   28   28   28   28 
LCS_GDT     S      29     S      29      6    9   28     4    5    6    8   13   13   16   17   19   21   24   26   27   28   28   28   28   28   28   28 
LCS_GDT     F      30     F      30      6    9   28     4    5    6    8   13   13   16   17   19   21   24   26   27   28   28   28   28   28   28   28 
LCS_GDT     Q      31     Q      31      6    9   28     4    6    9   11   13   13   16   17   19   21   24   26   27   28   28   28   28   28   28   28 
LCS_GDT     V      32     V      32      6    9   28     4    5    9   11   13   13   16   17   19   21   24   26   27   28   28   28   28   28   28   28 
LCS_GDT     D      33     D      33      6    9   28     3    5    8   11   13   13   16   17   19   21   24   26   27   28   28   28   28   28   28   28 
LCS_GDT     E      34     E      34      3   11   28     1    3    7    7    9   12   16   16   17   19   21   24   27   28   28   28   28   28   28   28 
LCS_GDT     G      35     G      35      3   11   28     3    3    6    8    9   13   16   16   19   21   24   26   27   28   28   28   28   28   28   28 
LCS_GDT     I      36     I      36      9   15   28     5    8    9   10   15   16   17   18   19   21   24   26   27   28   28   28   28   28   28   28 
LCS_GDT     T      37     T      37      9   15   28     8    8    9   11   15   16   17   18   19   21   24   26   27   28   28   28   28   28   28   28 
LCS_GDT     V      38     V      38      9   15   28     8    8    9   11   15   16   17   18   19   21   24   26   27   28   28   28   28   28   28   28 
LCS_GDT     Q      39     Q      39      9   15   28     8    8    9   11   15   16   17   18   19   21   24   26   27   28   28   28   28   28   28   28 
LCS_GDT     T      40     T      40      9   15   28     8    8    9   11   15   16   17   18   19   21   24   26   27   28   28   28   28   28   28   28 
LCS_GDT     A      41     A      41      9   15   28     8    8    9   11   15   16   17   18   19   21   24   26   27   28   28   28   28   28   28   28 
LCS_GDT     I      42     I      42      9   15   28     8    8    9   11   15   16   17   18   19   21   24   26   27   28   28   28   28   28   28   28 
LCS_GDT     T      43     T      43      9   15   28     8    8    9   11   15   16   17   18   19   21   24   26   27   28   28   28   28   28   28   28 
LCS_GDT     Q      44     Q      44      9   15   28     8    8    9   11   13   14   17   18   19   21   24   26   27   28   28   28   28   28   28   28 
LCS_GDT     I      47     I      47      5   15   28     4    5    6   10   15   16   17   18   19   21   24   26   27   28   28   28   28   28   28   28 
LCS_GDT     L      48     L      48      5   15   28     4    5    9   10   15   16   17   18   19   21   24   26   27   28   28   28   28   28   28   28 
LCS_GDT     S      49     S      49      5   15   28     4    5    6    9   15   16   17   18   19   21   24   26   27   28   28   28   28   28   28   28 
LCS_GDT     Q      50     Q      50      5   15   28     4    5    6   10   15   16   17   18   19   21   24   26   27   28   28   28   28   28   28   28 
LCS_GDT     F      51     F      51      5   15   28     4    4    6   10   15   16   17   18   19   21   24   26   27   28   28   28   28   28   28   28 
LCS_GDT     P      52     P      52      4   15   28     4    4    6   10   15   16   17   18   19   21   24   26   27   28   28   28   28   28   28   28 
LCS_GDT     E      53     E      53      4   14   28     4    5    6   10   15   16   17   18   19   21   24   26   27   28   28   28   28   28   28   28 
LCS_GDT     I      54     I      54      4   12   28     4    4    6   10   13   16   17   18   19   21   24   26   27   28   28   28   28   28   28   28 
LCS_GDT     D      55     D      55      3    5   28     3    3    3    4    5    5   10   18   19   21   24   26   27   28   28   28   28   28   28   28 
LCS_GDT     L      56     L      56      3    3   28     3    3    3    8    8    8    9   12   17   17   23   24   27   28   28   28   28   28   28   28 
LCS_AVERAGE  LCS_A:  33.57  (  13.12   26.71   60.87 )

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      8      8      9     11     15     16     17     18     19     21     24     26     27     28     28     28     28     28     28     28 
GDT PERCENT_CA  17.39  17.39  19.57  23.91  32.61  34.78  36.96  39.13  41.30  45.65  52.17  56.52  58.70  60.87  60.87  60.87  60.87  60.87  60.87  60.87
GDT RMS_LOCAL    0.31   0.31   0.58   1.11   1.89   1.95   2.09   2.29   2.97   3.21   3.71   4.00   4.18   4.34   4.34   4.34   4.34   4.34   4.34   4.34
GDT RMS_ALL_CA   5.73   5.73   5.74   6.96   6.68   6.95   6.66   6.51   4.80   4.77   4.56   4.40   4.37   4.34   4.34   4.34   4.34   4.34   4.34   4.34

#      Molecule1      Molecule2       DISTANCE
LGA    L      27      L      27          8.997
LGA    K      28      K      28         13.045
LGA    S      29      S      29         11.624
LGA    F      30      F      30         11.455
LGA    Q      31      Q      31         11.316
LGA    V      32      V      32          9.998
LGA    D      33      D      33         11.328
LGA    E      34      E      34          9.134
LGA    G      35      G      35          8.505
LGA    I      36      I      36          2.583
LGA    T      37      T      37          2.337
LGA    V      38      V      38          1.453
LGA    Q      39      Q      39          1.812
LGA    T      40      T      40          1.062
LGA    A      41      A      41          1.410
LGA    I      42      I      42          2.416
LGA    T      43      T      43          1.306
LGA    Q      44      Q      44          3.402
LGA    I      47      I      47          3.113
LGA    L      48      L      48          2.598
LGA    S      49      S      49          3.154
LGA    Q      50      Q      50          2.543
LGA    F      51      F      51          1.906
LGA    P      52      P      52          1.411
LGA    E      53      E      53          1.204
LGA    I      54      I      54          2.095
LGA    D      55      D      55          3.813
LGA    L      56      L      56          6.104

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   28   46    4.0     18    2.29    35.326    35.081     0.752

LGA_LOCAL      RMSD =  2.293  Number of atoms =   18  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  6.452  Number of atoms =   28 
Std_ALL_ATOMS  RMSD =  4.343  (standard rmsd on all 28 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.790134 * X  +   0.609567 * Y  +   0.064164 * Z  +  21.606754
  Y_new =  -0.496210 * X  +  -0.697603 * Y  +   0.516842 * Z  +  47.315273
  Z_new =   0.359811 * X  +   0.376536 * Y  +   0.853673 * Z  +  -8.487332 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.415409   -2.726184  [ DEG:    23.8012   -156.1988 ]
  Theta =  -0.368065   -2.773528  [ DEG:   -21.0886   -158.9114 ]
  Phi   =  -2.580833    0.560760  [ DEG:  -147.8708     32.1292 ]
 
# 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: T0363TS383_3-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0363TS383_3-D1.T0363_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   28   46   4.0   18   2.29  35.081     4.34
REMARK  ---------------------------------------------------------- 
MOLECULE T0363TS383_3-D1
PFRMAT TS
TARGET T0363
MODEL 3
PARENT 1fm0D
ATOM      1  N   LEU    27      29.653  25.655   0.846  1.00  0.00
ATOM      2  CA  LEU    27      28.213  25.570   0.630  1.00  0.00
ATOM      3  C   LEU    27      27.528  25.706   1.992  1.00  0.00
ATOM      4  O   LEU    27      28.122  25.375   3.020  1.00  0.00
ATOM      5  N   LYS    28      26.277  26.176   1.998  1.00  0.00
ATOM      6  CA  LYS    28      25.499  26.333   3.229  1.00  0.00
ATOM      7  C   LYS    28      24.745  25.055   3.633  1.00  0.00
ATOM      8  O   LYS    28      24.399  24.877   4.823  1.00  0.00
ATOM      9  N   SER    29      24.490  24.172   2.664  1.00  0.00
ATOM     10  CA  SER    29      23.622  23.016   2.883  1.00  0.00
ATOM     11  C   SER    29      23.782  22.006   1.759  1.00  0.00
ATOM     12  O   SER    29      24.002  22.400   0.603  1.00  0.00
ATOM     13  N   PHE    30      23.640  20.722   2.078  1.00  0.00
ATOM     14  CA  PHE    30      23.643  19.665   1.053  1.00  0.00
ATOM     15  C   PHE    30      22.844  18.447   1.534  1.00  0.00
ATOM     16  O   PHE    30      22.458  18.359   2.699  1.00  0.00
ATOM     17  N   GLN    31      22.558  17.521   0.624  1.00  0.00
ATOM     18  CA  GLN    31      21.794  16.308   0.938  1.00  0.00
ATOM     19  C   GLN    31      22.647  15.062   0.750  1.00  0.00
ATOM     20  O   GLN    31      23.478  15.017  -0.164  1.00  0.00
ATOM     21  N   VAL    32      22.439  14.062   1.609  1.00  0.00
ATOM     22  CA  VAL    32      23.125  12.775   1.530  1.00  0.00
ATOM     23  C   VAL    32      22.116  11.620   1.716  1.00  0.00
ATOM     24  O   VAL    32      21.125  11.748   2.430  1.00  0.00
ATOM     25  N   ASP    33      22.328  10.485   1.054  1.00  0.00
ATOM     26  CA  ASP    33      21.447   9.334   1.279  1.00  0.00
ATOM     27  C   ASP    33      21.516   8.886   2.757  1.00  0.00
ATOM     28  O   ASP    33      22.483   9.182   3.467  1.00  0.00
ATOM     29  N   GLU    34      22.508   6.352   4.416  1.00  0.00
ATOM     30  CA  GLU    34      23.340   5.152   4.500  1.00  0.00
ATOM     31  C   GLU    34      24.457   5.240   5.538  1.00  0.00
ATOM     32  O   GLU    34      25.532   4.689   5.313  1.00  0.00
ATOM     33  N   GLY    35      24.234   5.938   6.646  1.00  0.00
ATOM     34  CA  GLY    35      25.258   6.031   7.685  1.00  0.00
ATOM     35  C   GLY    35      24.642   5.790   9.067  1.00  0.00
ATOM     36  O   GLY    35      23.625   6.394   9.403  1.00  0.00
ATOM     37  N   ILE    36      25.248   4.901   9.860  1.00  0.00
ATOM     38  CA  ILE    36      24.679   4.550  11.168  1.00  0.00
ATOM     39  C   ILE    36      24.675   5.668  12.227  1.00  0.00
ATOM     40  O   ILE    36      23.757   5.726  13.035  1.00  0.00
ATOM     41  N   THR    37      25.667   6.555  12.188  1.00  0.00
ATOM     42  CA  THR    37      25.832   7.606  13.203  1.00  0.00
ATOM     43  C   THR    37      26.319   8.929  12.619  1.00  0.00
ATOM     44  O   THR    37      26.759   8.995  11.464  1.00  0.00
ATOM     45  N   VAL    38      26.245   9.980  13.443  1.00  0.00
ATOM     46  CA  VAL    38      26.808  11.285  13.087  1.00  0.00
ATOM     47  C   VAL    38      28.306  11.143  12.715  1.00  0.00
ATOM     48  O   VAL    38      28.783  11.744  11.744  1.00  0.00
ATOM     49  N   GLN    39      29.062  10.382  13.512  1.00  0.00
ATOM     50  CA  GLN    39      30.504  10.190  13.242  1.00  0.00
ATOM     51  C   GLN    39      30.775   9.545  11.876  1.00  0.00
ATOM     52  O   GLN    39      31.694   9.967  11.161  1.00  0.00
ATOM     53  N   THR    40      30.006   8.517  11.519  1.00  0.00
ATOM     54  CA  THR    40      30.167   7.883  10.201  1.00  0.00
ATOM     55  C   THR    40      29.899   8.881   9.064  1.00  0.00
ATOM     56  O   THR    40      30.616   8.891   8.062  1.00  0.00
ATOM     57  N   ALA    41      28.857   9.714   9.225  1.00  0.00
ATOM     58  CA  ALA    41      28.577  10.784   8.252  1.00  0.00
ATOM     59  C   ALA    41      29.739  11.817   8.183  1.00  0.00
ATOM     60  O   ALA    41      30.166  12.207   7.094  1.00  0.00
ATOM     61  N   ILE    42      30.235  12.253   9.345  1.00  0.00
ATOM     62  CA  ILE    42      31.366  13.197   9.413  1.00  0.00
ATOM     63  C   ILE    42      32.582  12.651   8.635  1.00  0.00
ATOM     64  O   ILE    42      33.203  13.364   7.813  1.00  0.00
ATOM     65  N   THR    43      32.913  11.376   8.860  1.00  0.00
ATOM     66  CA  THR    43      34.069  10.747   8.170  1.00  0.00
ATOM     67  C   THR    43      33.849  10.711   6.638  1.00  0.00
ATOM     68  O   THR    43      34.764  10.967   5.860  1.00  0.00
ATOM     69  N   GLN    44      32.641  10.337   6.207  1.00  0.00
ATOM     70  CA  GLN    44      32.315  10.316   4.774  1.00  0.00
ATOM     71  C   GLN    44      32.494  11.695   4.120  1.00  0.00
ATOM     72  O   GLN    44      33.091  11.812   3.033  1.00  0.00
ATOM     73  N   ILE    47      31.969  12.734   4.774  1.00  0.00
ATOM     74  CA  ILE    47      32.069  14.088   4.219  1.00  0.00
ATOM     75  C   ILE    47      33.527  14.604   4.224  1.00  0.00
ATOM     76  O   ILE    47      33.978  15.241   3.246  1.00  0.00
ATOM     77  N   LEU    48      34.277  14.324   5.302  1.00  0.00
ATOM     78  CA  LEU    48      35.690  14.723   5.375  1.00  0.00
ATOM     79  C   LEU    48      36.520  14.108   4.235  1.00  0.00
ATOM     80  O   LEU    48      37.517  14.696   3.783  1.00  0.00
ATOM     81  N   SER    49      36.115  12.928   3.758  1.00  0.00
ATOM     82  CA  SER    49      36.866  12.218   2.744  1.00  0.00
ATOM     83  C   SER    49      36.649  12.750   1.326  1.00  0.00
ATOM     84  O   SER    49      37.317  12.266   0.401  1.00  0.00
ATOM     85  N   GLN    50      35.769  13.750   1.147  1.00  0.00
ATOM     86  CA  GLN    50      35.451  14.255  -0.206  1.00  0.00
ATOM     87  C   GLN    50      36.532  15.138  -0.824  1.00  0.00
ATOM     88  O   GLN    50      36.683  15.155  -2.059  1.00  0.00
ATOM     89  N   PHE    51      37.275  15.869   0.011  1.00  0.00
ATOM     90  CA  PHE    51      38.343  16.765  -0.445  1.00  0.00
ATOM     91  C   PHE    51      39.222  17.238   0.702  1.00  0.00
ATOM     92  O   PHE    51      38.841  17.118   1.858  1.00  0.00
ATOM     93  N   PRO    52      40.373  17.844   0.385  1.00  0.00
ATOM     94  CA  PRO    52      41.276  18.350   1.411  1.00  0.00
ATOM     95  C   PRO    52      40.630  19.503   2.208  1.00  0.00
ATOM     96  O   PRO    52      40.850  19.608   3.415  1.00  0.00
ATOM     97  N   GLU    53      39.837  20.353   1.542  1.00  0.00
ATOM     98  CA  GLU    53      39.134  21.454   2.232  1.00  0.00
ATOM     99  C   GLU    53      38.059  20.912   3.179  1.00  0.00
ATOM    100  O   GLU    53      37.907  21.423   4.292  1.00  0.00
ATOM    101  N   ILE    54      37.288  19.915   2.728  1.00  0.00
ATOM    102  CA  ILE    54      36.260  19.301   3.581  1.00  0.00
ATOM    103  C   ILE    54      36.903  18.599   4.799  1.00  0.00
ATOM    104  O   ILE    54      36.375  18.660   5.903  1.00  0.00
ATOM    105  N   ASP    55      38.070  17.966   4.599  1.00  0.00
ATOM    106  CA  ASP    55      38.775  17.318   5.721  1.00  0.00
ATOM    107  C   ASP    55      39.237  18.341   6.773  1.00  0.00
ATOM    108  O   ASP    55      39.084  18.129   7.978  1.00  0.00
ATOM    109  N   LEU    56      39.792  19.465   6.319  1.00  0.00
ATOM    110  CA  LEU    56      40.231  20.497   7.244  1.00  0.00
ATOM    111  C   LEU    56      39.059  21.071   8.052  1.00  0.00
ATOM    112  O   LEU    56      39.161  21.275   9.269  1.00  0.00
TER
END
