
#######################################################
#                                                     #
#                        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   27 (  108),  selected   27 , name T0363TS383_5-D1
# Molecule2: number of CA atoms   46 (  372),  selected   27 , name T0363_D1.pdb
# PARAMETERS: T0363TS383_5-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:    27        14 - 56          4.47     4.47
  LCS_AVERAGE:     58.70

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17        28 - 45          1.99     4.99
  LCS_AVERAGE:     25.85

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11        35 - 45          0.43     6.56
  LCS_AVERAGE:     14.65

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     N      14     N      14      4    4   27     3    6   13   16   21   21   22   23   24   24   24   24   24   25   25   25   25   26   27   27 
LCS_GDT     I      15     I      15      4    4   27     4    8   13   16   21   21   22   23   24   24   24   24   24   25   25   25   25   26   27   27 
LCS_GDT     E      16     E      16      4    4   27     4    8   13   16   21   21   22   23   24   24   24   24   24   25   25   25   25   26   27   27 
LCS_GDT     I      17     I      17      4    4   27     4    8   13   16   21   21   22   23   24   24   24   24   24   25   25   25   25   26   27   27 
LCS_GDT     P      22     P      22      0    0   27     0    0    0    0    0    1    1    1    2    2    3    5    6   12   16   23   25   26   27   27 
LCS_GDT     E      23     E      23      0    0   27     0    0    0    0    0    0    0    1    2    2    2    3    3    9   13   16   24   26   27   27 
LCS_GDT     K      28     K      28      5   17   27     4    8   13   16   21   21   22   23   24   24   24   24   24   25   25   25   25   26   27   27 
LCS_GDT     S      29     S      29      5   17   27     4    8   13   16   21   21   22   23   24   24   24   24   24   25   25   25   25   26   27   27 
LCS_GDT     F      30     F      30      5   17   27     4    8   13   16   21   21   22   23   24   24   24   24   24   25   25   25   25   26   27   27 
LCS_GDT     Q      31     Q      31      5   17   27     4    8   13   16   21   21   22   23   24   24   24   24   24   25   25   25   25   26   27   27 
LCS_GDT     V      32     V      32      5   17   27     3    5   10   15   21   21   22   23   24   24   24   24   24   25   25   25   25   26   27   27 
LCS_GDT     D      33     D      33      4   17   27     0    3    5   12   14   19   22   23   24   24   24   24   24   25   25   25   25   26   27   27 
LCS_GDT     G      35     G      35     11   17   27     9   11   11   12   21   21   22   23   24   24   24   24   24   25   25   25   25   26   27   27 
LCS_GDT     I      36     I      36     11   17   27     9   11   13   16   21   21   22   23   24   24   24   24   24   25   25   25   25   26   27   27 
LCS_GDT     T      37     T      37     11   17   27     9   11   13   16   21   21   22   23   24   24   24   24   24   25   25   25   25   26   27   27 
LCS_GDT     V      38     V      38     11   17   27     9   11   13   16   21   21   22   23   24   24   24   24   24   25   25   25   25   26   27   27 
LCS_GDT     Q      39     Q      39     11   17   27     9   11   13   16   21   21   22   23   24   24   24   24   24   25   25   25   25   26   27   27 
LCS_GDT     T      40     T      40     11   17   27     9   11   13   16   21   21   22   23   24   24   24   24   24   25   25   25   25   26   27   27 
LCS_GDT     A      41     A      41     11   17   27     9   11   11   16   21   21   22   23   24   24   24   24   24   25   25   25   25   26   27   27 
LCS_GDT     I      42     I      42     11   17   27     9   11   11   15   21   21   22   23   24   24   24   24   24   25   25   25   25   26   27   27 
LCS_GDT     T      43     T      43     11   17   27     9   11   11   16   21   21   22   23   24   24   24   24   24   25   25   25   25   26   27   27 
LCS_GDT     Q      44     Q      44     11   17   27     9   11   11   16   21   21   22   23   24   24   24   24   24   25   25   25   25   26   27   27 
LCS_GDT     S      45     S      45     11   17   27     5   11   11   12   15   18   22   23   24   24   24   24   24   25   25   25   25   26   27   27 
LCS_GDT     E      53     E      53      4    4   27     3    4    4    4    4    7    9    9    9   15   17   24   24   25   25   25   25   26   27   27 
LCS_GDT     I      54     I      54      4    4   27     3    4    4    7    9   13   22   23   24   24   24   24   24   25   25   25   25   26   27   27 
LCS_GDT     D      55     D      55      4    4   27     3    4   10   15   21   21   22   23   24   24   24   24   24   25   25   25   25   26   27   27 
LCS_GDT     L      56     L      56      4    4   27     4    8   13   16   21   21   22   23   24   24   24   24   24   25   25   25   25   26   27   27 
LCS_AVERAGE  LCS_A:  33.06  (  14.65   25.85   58.70 )

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     11     13     16     21     21     22     23     24     24     24     24     24     25     25     25     25     26     27     27 
GDT PERCENT_CA  19.57  23.91  28.26  34.78  45.65  45.65  47.83  50.00  52.17  52.17  52.17  52.17  52.17  54.35  54.35  54.35  54.35  56.52  58.70  58.70
GDT RMS_LOCAL    0.27   0.43   1.09   1.29   1.68   1.68   1.83   2.00   2.18   2.18   2.18   2.18   2.18   2.77   2.77   2.77   2.77   3.71   4.47   4.47
GDT RMS_ALL_CA   6.32   6.56   4.70   4.71   4.70   4.70   4.76   4.79   4.75   4.75   4.75   4.75   4.75   4.75   4.75   4.75   4.75   4.55   4.47   4.47

#      Molecule1      Molecule2       DISTANCE
LGA    N      14      N      14          1.606
LGA    I      15      I      15          1.544
LGA    E      16      E      16          2.279
LGA    I      17      I      17          2.416
LGA    P      22      P      22         13.562
LGA    E      23      E      23         15.364
LGA    K      28      K      28          2.852
LGA    S      29      S      29          2.391
LGA    F      30      F      30          0.815
LGA    Q      31      Q      31          0.908
LGA    V      32      V      32          2.295
LGA    D      33      D      33          3.932
LGA    G      35      G      35          2.382
LGA    I      36      I      36          0.917
LGA    T      37      T      37          0.635
LGA    V      38      V      38          0.758
LGA    Q      39      Q      39          1.093
LGA    T      40      T      40          0.910
LGA    A      41      A      41          1.487
LGA    I      42      I      42          1.943
LGA    T      43      T      43          1.717
LGA    Q      44      Q      44          1.739
LGA    S      45      S      45          3.657
LGA    E      53      E      53          9.737
LGA    I      54      I      54          4.900
LGA    D      55      D      55          2.455
LGA    L      56      L      56          0.327

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   27   46    4.0     23    2.00    40.761    39.404     1.095

LGA_LOCAL      RMSD =  2.001  Number of atoms =   23  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  4.837  Number of atoms =   27 
Std_ALL_ATOMS  RMSD =  4.467  (standard rmsd on all 27 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.436297 * X  +   0.095230 * Y  +  -0.894749 * Z  +  45.711548
  Y_new =   0.710909 * X  +   0.646054 * Y  +  -0.277891 * Z  + -12.517587
  Z_new =   0.551592 * X  +  -0.757328 * Y  +  -0.349571 * Z  +  19.415293 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.003242    1.138350  [ DEG:  -114.7773     65.2227 ]
  Theta =  -0.584272   -2.557321  [ DEG:   -33.4763   -146.5237 ]
  Phi   =   2.121241   -1.020352  [ DEG:   121.5381    -58.4619 ]
 
# 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_5-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0363TS383_5-D1.T0363_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   27   46   4.0   23   2.00  39.404     4.47
REMARK  ---------------------------------------------------------- 
MOLECULE T0363TS383_5-D1
PFRMAT TS
TARGET T0363
MODEL 5
PARENT 2cu3A
ATOM      1  N   ASN    14      15.010   7.562   5.423  1.00  0.00
ATOM      2  CA  ASN    14      16.389   7.942   5.011  1.00  0.00
ATOM      3  C   ASN    14      16.830   9.173   5.800  1.00  0.00
ATOM      4  O   ASN    14      16.018   9.855   6.431  1.00  0.00
ATOM      5  N   ILE    15      18.131   9.435   5.777  1.00  0.00
ATOM      6  CA  ILE    15      18.709  10.597   6.442  1.00  0.00
ATOM      7  C   ILE    15      19.141  11.484   5.287  1.00  0.00
ATOM      8  O   ILE    15      19.675  10.986   4.295  1.00  0.00
ATOM      9  N   GLU    16      18.898  12.785   5.390  1.00  0.00
ATOM     10  CA  GLU    16      19.281  13.690   4.313  1.00  0.00
ATOM     11  C   GLU    16      20.625  14.330   4.581  1.00  0.00
ATOM     12  O   GLU    16      20.815  15.034   5.574  1.00  0.00
ATOM     13  N   ILE    17      21.565  14.050   3.687  1.00  0.00
ATOM     14  CA  ILE    17      22.941  14.537   3.782  1.00  0.00
ATOM     15  C   ILE    17      23.305  15.461   2.606  1.00  0.00
ATOM     16  O   ILE    17      23.426  15.059   1.457  1.00  0.00
ATOM     17  N   PRO    22      23.435  16.762   2.928  1.00  0.00
ATOM     18  CA  PRO    22      23.739  17.739   1.884  1.00  0.00
ATOM     19  C   PRO    22      22.733  17.694   0.726  1.00  0.00
ATOM     20  O   PRO    22      23.077  17.841  -0.438  1.00  0.00
ATOM     21  N   GLU    23      21.458  17.432   1.076  1.00  0.00
ATOM     22  CA  GLU    23      20.407  17.537   0.067  1.00  0.00
ATOM     23  C   GLU    23      20.101  16.203  -0.631  1.00  0.00
ATOM     24  O   GLU    23      19.283  16.122  -1.539  1.00  0.00
ATOM     25  N   LYS    28      20.815  15.136  -0.213  1.00  0.00
ATOM     26  CA  LYS    28      20.555  13.822  -0.788  1.00  0.00
ATOM     27  C   LYS    28      20.168  12.801   0.285  1.00  0.00
ATOM     28  O   LYS    28      20.654  12.815   1.408  1.00  0.00
ATOM     29  N   SER    29      19.221  11.919  -0.087  1.00  0.00
ATOM     30  CA  SER    29      18.767  10.864   0.806  1.00  0.00
ATOM     31  C   SER    29      19.809   9.749   0.929  1.00  0.00
ATOM     32  O   SER    29      20.295   9.198  -0.050  1.00  0.00
ATOM     33  N   PHE    30      20.179   9.451   2.187  1.00  0.00
ATOM     34  CA  PHE    30      21.173   8.409   2.415  1.00  0.00
ATOM     35  C   PHE    30      20.814   7.536   3.619  1.00  0.00
ATOM     36  O   PHE    30      20.353   8.003   4.652  1.00  0.00
ATOM     37  N   GLN    31      21.008   6.215   3.443  1.00  0.00
ATOM     38  CA  GLN    31      20.719   5.251   4.497  1.00  0.00
ATOM     39  C   GLN    31      21.741   5.347   5.629  1.00  0.00
ATOM     40  O   GLN    31      22.678   4.565   5.733  1.00  0.00
ATOM     41  N   VAL    32      21.554   6.373   6.479  1.00  0.00
ATOM     42  CA  VAL    32      22.555   6.652   7.502  1.00  0.00
ATOM     43  C   VAL    32      22.036   6.378   8.917  1.00  0.00
ATOM     44  O   VAL    32      22.744   6.513   9.905  1.00  0.00
ATOM     45  N   ASP    33      20.741   6.017   8.999  1.00  0.00
ATOM     46  CA  ASP    33      20.156   5.758  10.310  1.00  0.00
ATOM     47  C   ASP    33      21.015   4.795  11.131  1.00  0.00
ATOM     48  O   ASP    33      21.491   3.777  10.646  1.00  0.00
ATOM     49  N   GLY    35      21.220   5.128  12.402  1.00  0.00
ATOM     50  CA  GLY    35      22.008   4.279  13.274  1.00  0.00
ATOM     51  C   GLY    35      23.467   4.673  13.385  1.00  0.00
ATOM     52  O   GLY    35      24.129   4.337  14.369  1.00  0.00
ATOM     53  N   ILE    36      23.972   5.377  12.375  1.00  0.00
ATOM     54  CA  ILE    36      25.361   5.825  12.362  1.00  0.00
ATOM     55  C   ILE    36      25.483   7.162  13.082  1.00  0.00
ATOM     56  O   ILE    36      24.518   7.920  13.163  1.00  0.00
ATOM     57  N   THR    37      26.666   7.444  13.617  1.00  0.00
ATOM     58  CA  THR    37      26.907   8.712  14.298  1.00  0.00
ATOM     59  C   THR    37      27.508   9.681  13.290  1.00  0.00
ATOM     60  O   THR    37      28.048   9.264  12.263  1.00  0.00
ATOM     61  N   VAL    38      27.424  10.974  13.585  1.00  0.00
ATOM     62  CA  VAL    38      27.980  11.980  12.691  1.00  0.00
ATOM     63  C   VAL    38      29.478  11.772  12.469  1.00  0.00
ATOM     64  O   VAL    38      29.967  11.915  11.351  1.00  0.00
ATOM     65  N   GLN    39      30.206  11.429  13.527  1.00  0.00
ATOM     66  CA  GLN    39      31.642  11.197  13.389  1.00  0.00
ATOM     67  C   GLN    39      31.907  10.089  12.381  1.00  0.00
ATOM     68  O   GLN    39      32.794  10.201  11.541  1.00  0.00
ATOM     69  N   THR    40      31.137   9.011  12.480  1.00  0.00
ATOM     70  CA  THR    40      31.295   7.888  11.570  1.00  0.00
ATOM     71  C   THR    40      31.021   8.356  10.149  1.00  0.00
ATOM     72  O   THR    40      31.775   8.049   9.231  1.00  0.00
ATOM     73  N   ALA    41      29.943   9.115   9.974  1.00  0.00
ATOM     74  CA  ALA    41      29.582   9.624   8.659  1.00  0.00
ATOM     75  C   ALA    41      30.657  10.547   8.090  1.00  0.00
ATOM     76  O   ALA    41      31.015  10.441   6.914  1.00  0.00
ATOM     77  N   ILE    42      31.173  11.447   8.922  1.00  0.00
ATOM     78  CA  ILE    42      32.198  12.385   8.471  1.00  0.00
ATOM     79  C   ILE    42      33.475  11.671   8.029  1.00  0.00
ATOM     80  O   ILE    42      34.133  12.094   7.073  1.00  0.00
ATOM     81  N   THR    43      33.823  10.591   8.720  1.00  0.00
ATOM     82  CA  THR    43      35.020   9.836   8.371  1.00  0.00
ATOM     83  C   THR    43      34.810   9.126   7.041  1.00  0.00
ATOM     84  O   THR    43      35.740   8.996   6.250  1.00  0.00
ATOM     85  N   GLN    44      33.583   8.677   6.793  1.00  0.00
ATOM     86  CA  GLN    44      33.266   7.983   5.551  1.00  0.00
ATOM     87  C   GLN    44      33.229   8.957   4.380  1.00  0.00
ATOM     88  O   GLN    44      33.274   8.543   3.224  1.00  0.00
ATOM     89  N   SER    45      33.144  10.250   4.691  1.00  0.00
ATOM     90  CA  SER    45      33.109  11.305   3.681  1.00  0.00
ATOM     91  C   SER    45      34.525  11.826   3.418  1.00  0.00
ATOM     92  O   SER    45      34.754  12.545   2.450  1.00  0.00
ATOM     93  N   GLU    53      35.463  11.473   4.295  1.00  0.00
ATOM     94  CA  GLU    53      36.835  11.931   4.140  1.00  0.00
ATOM     95  C   GLU    53      36.944  13.400   4.509  1.00  0.00
ATOM     96  O   GLU    53      37.828  14.110   4.041  1.00  0.00
ATOM     97  N   ILE    54      36.032  13.855   5.361  1.00  0.00
ATOM     98  CA  ILE    54      35.998  15.245   5.796  1.00  0.00
ATOM     99  C   ILE    54      37.030  15.612   6.862  1.00  0.00
ATOM    100  O   ILE    54      37.364  14.809   7.725  1.00  0.00
ATOM    101  N   ASP    55      37.543  16.834   6.766  1.00  0.00
ATOM    102  CA  ASP    55      38.507  17.368   7.720  1.00  0.00
ATOM    103  C   ASP    55      37.640  17.996   8.808  1.00  0.00
ATOM    104  O   ASP    55      37.046  19.051   8.598  1.00  0.00
ATOM    105  N   LEU    56      37.559  17.343   9.961  1.00  0.00
ATOM    106  CA  LEU    56      36.722  17.827  11.056  1.00  0.00
ATOM    107  C   LEU    56      36.976  19.262  11.484  1.00  0.00
ATOM    108  O   LEU    56      36.030  20.018  11.685  1.00  0.00
TER
END
