
#######################################################
#                                                     #
#                        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   17 (   85),  selected   17 , name T0381TS102_4-D1
# Molecule2: number of CA atoms   61 (  477),  selected   17 , name T0381_D1.pdb
# PARAMETERS: T0381TS102_4-D1.T0381_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:    17        46 - 63          3.27     3.27
  LCS_AVERAGE:     27.87

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15        48 - 63          1.59     3.86
  LCS_AVERAGE:     22.47

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11        53 - 63          0.20     4.09
  LCS_AVERAGE:     13.69

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:   61
LCS_GDT     T      46     T      46      3    4   17     3    3    3    4    4    5    7    7    8    9    9   14   16   17   17   17   17   17   17   17 
LCS_GDT     D      47     D      47      3    4   17     3    3    3    4    4    4    7    9   12   15   16   16   16   17   17   17   17   17   17   17 
LCS_GDT     L      48     L      48      3   15   17     3    7   12   13   13   15   15   15   15   15   16   16   16   17   17   17   17   17   17   17 
LCS_GDT     T      49     T      49      4   15   17     3    3    4    6   13   15   15   15   15   15   16   16   16   17   17   17   17   17   17   17 
LCS_GDT     R      50     R      50      4   15   17     3    3    5   13   13   15   15   15   15   15   16   16   16   17   17   17   17   17   17   17 
LCS_GDT     A      51     A      51      4   15   17     3    3    5    7   12   15   15   15   15   15   16   16   16   17   17   17   17   17   17   17 
LCS_GDT     A      53     A      53     11   15   17    11   11   12   13   13   15   15   15   15   15   16   16   16   17   17   17   17   17   17   17 
LCS_GDT     R      54     R      54     11   15   17    11   11   12   13   13   15   15   15   15   15   16   16   16   17   17   17   17   17   17   17 
LCS_GDT     R      55     R      55     11   15   17    11   11   12   13   13   15   15   15   15   15   16   16   16   17   17   17   17   17   17   17 
LCS_GDT     F      56     F      56     11   15   17    11   11   12   13   13   15   15   15   15   15   16   16   16   17   17   17   17   17   17   17 
LCS_GDT     L      57     L      57     11   15   17    11   11   12   13   13   15   15   15   15   15   16   16   16   17   17   17   17   17   17   17 
LCS_GDT     L      58     L      58     11   15   17    11   11   12   13   13   15   15   15   15   15   16   16   16   17   17   17   17   17   17   17 
LCS_GDT     T      59     T      59     11   15   17    11   11   12   13   13   15   15   15   15   15   16   16   16   17   17   17   17   17   17   17 
LCS_GDT     L      60     L      60     11   15   17    11   11   12   13   13   15   15   15   15   15   16   16   16   17   17   17   17   17   17   17 
LCS_GDT     V      61     V      61     11   15   17    11   11   12   13   13   15   15   15   15   15   16   16   16   17   17   17   17   17   17   17 
LCS_GDT     E      62     E      62     11   15   17    11   11   12   13   13   15   15   15   15   15   16   16   16   17   17   17   17   17   17   17 
LCS_GDT     L      63     L      63     11   15   17    11   11   12   13   13   15   15   15   15   15   16   16   16   17   17   17   17   17   17   17 
LCS_AVERAGE  LCS_A:  21.34  (  13.69   22.47   27.87 )

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     11     11     12     13     13     15     15     15     15     15     16     16     16     17     17     17     17     17     17     17 
GDT PERCENT_CA  18.03  18.03  19.67  21.31  21.31  24.59  24.59  24.59  24.59  24.59  26.23  26.23  26.23  27.87  27.87  27.87  27.87  27.87  27.87  27.87
GDT RMS_LOCAL    0.20   0.20   0.58   0.95   0.89   1.59   1.59   1.59   1.59   1.59   2.45   2.45   2.45   3.27   3.27   3.27   3.27   3.27   3.27   3.27
GDT RMS_ALL_CA   4.09   4.09   3.79   3.67   3.86   3.86   3.86   3.86   3.86   3.86   3.46   3.46   3.46   3.27   3.27   3.27   3.27   3.27   3.27   3.27

#      Molecule1      Molecule2       DISTANCE
LGA    T      46      T      46         11.862
LGA    D      47      D      47          8.657
LGA    L      48      L      48          2.039
LGA    T      49      T      49          2.979
LGA    R      50      R      50          2.275
LGA    A      51      A      51          3.683
LGA    A      53      A      53          0.567
LGA    R      54      R      54          1.015
LGA    R      55      R      55          1.171
LGA    F      56      F      56          0.876
LGA    L      57      L      57          0.552
LGA    L      58      L      58          0.770
LGA    T      59      T      59          0.674
LGA    L      60      L      60          0.525
LGA    V      61      V      61          0.639
LGA    E      62      E      62          0.590
LGA    L      63      L      63          0.687

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   17   61    4.0     15    1.59    22.951    23.204     0.885

LGA_LOCAL      RMSD =  1.594  Number of atoms =   15  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.864  Number of atoms =   17 
Std_ALL_ATOMS  RMSD =  3.269  (standard rmsd on all 17 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.242245 * X  +  -0.206428 * Y  +  -0.948001 * Z  +  -3.508970
  Y_new =   0.946989 * X  +   0.262826 * Y  +   0.184756 * Z  +  -9.037574
  Z_new =   0.211021 * X  +  -0.942502 * Y  +   0.259153 * Z  +  20.091391 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.302464    1.839128  [ DEG:   -74.6257    105.3743 ]
  Theta =  -0.212619   -2.928973  [ DEG:   -12.1822   -167.8178 ]
  Phi   =   1.320361   -1.821231  [ DEG:    75.6511   -104.3489 ]
 
# 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: T0381TS102_4-D1                               
REMARK     2: T0381_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0381TS102_4-D1.T0381_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   17   61   4.0   15   1.59  23.204     3.27
REMARK  ---------------------------------------------------------- 
MOLECULE T0381TS102_4-D1
PFRMAT TS
TARGET T0381
MODEL 4
PARENT 1ysp_A
ATOM      1  N   THR    46      -2.879  66.943  18.476  1.00  1.00
ATOM      2  CA  THR    46      -3.019  66.044  19.667  1.00  1.00
ATOM      3  C   THR    46      -1.814  66.033  20.613  1.00  1.00
ATOM      4  O   THR    46      -0.651  66.207  20.208  1.00  1.00
ATOM      5  CB  THR    46      -3.360  64.610  19.245  1.00  1.00
ATOM      6  N   ASP    47      -2.144  65.795  21.878  1.00  1.00
ATOM      7  CA  ASP    47      -1.235  65.760  23.001  1.00  1.00
ATOM      8  C   ASP    47      -0.264  64.575  22.961  1.00  1.00
ATOM      9  O   ASP    47       0.886  64.747  23.323  1.00  1.00
ATOM     10  CB  ASP    47      -2.043  65.707  24.303  1.00  1.00
ATOM     11  N   LEU    48      -0.729  63.392  22.555  1.00  1.00
ATOM     12  CA  LEU    48       0.160  62.214  22.430  1.00  1.00
ATOM     13  C   LEU    48       1.329  62.516  21.489  1.00  1.00
ATOM     14  O   LEU    48       2.483  62.225  21.813  1.00  1.00
ATOM     15  CB  LEU    48      -0.613  60.947  21.975  1.00  1.00
ATOM     16  N   THR    49       1.031  63.090  20.331  1.00  1.00
ATOM     17  CA  THR    49       2.059  63.363  19.313  1.00  1.00
ATOM     18  C   THR    49       2.995  64.487  19.813  1.00  1.00
ATOM     19  O   THR    49       4.212  64.430  19.632  1.00  1.00
ATOM     20  CB  THR    49       1.439  63.585  17.895  1.00  1.00
ATOM     21  N   ARG    50       2.428  65.493  20.473  1.00  1.00
ATOM     22  CA  ARG    50       3.273  66.581  20.994  1.00  1.00
ATOM     23  C   ARG    50       4.298  66.082  22.030  1.00  1.00
ATOM     24  O   ARG    50       5.485  66.425  21.953  1.00  1.00
ATOM     25  CB  ARG    50       2.410  67.703  21.559  1.00  1.00
ATOM     26  N   ALA    51       3.857  65.212  22.944  1.00  1.00
ATOM     27  CA  ALA    51       4.775  64.663  23.984  1.00  1.00
ATOM     28  C   ALA    51       5.744  63.695  23.360  1.00  1.00
ATOM     29  O   ALA    51       6.913  63.623  23.776  1.00  1.00
ATOM     30  CB  ALA    51       4.026  63.911  25.078  1.00  1.00
ATOM     31  N   ALA    53       5.225  62.874  22.442  1.00  1.00
ATOM     32  CA  ALA    53       6.054  61.883  21.760  1.00  1.00
ATOM     33  C   ALA    53       7.125  62.602  20.951  1.00  1.00
ATOM     34  O   ALA    53       8.265  62.177  20.955  1.00  1.00
ATOM     35  CB  ALA    53       5.199  61.048  20.832  1.00  1.00
ATOM     36  N   ARG    54       6.748  63.683  20.264  1.00  1.00
ATOM     37  CA  ARG    54       7.677  64.392  19.389  1.00  1.00
ATOM     38  C   ARG    54       8.949  64.783  20.144  1.00  1.00
ATOM     39  O   ARG    54      10.080  64.617  19.610  1.00  1.00
ATOM     40  CB  ARG    54       7.011  65.631  18.752  1.00  1.00
ATOM     41  N   ARG    55       8.765  65.306  21.370  1.00  1.00
ATOM     42  CA  ARG    55       9.868  65.700  22.237  1.00  1.00
ATOM     43  C   ARG    55      10.786  64.539  22.633  1.00  1.00
ATOM     44  O   ARG    55      12.013  64.633  22.576  1.00  1.00
ATOM     45  CB  ARG    55       9.311  66.433  23.547  1.00  1.00
ATOM     46  N   PHE    56      10.170  63.433  23.034  1.00  1.00
ATOM     47  CA  PHE    56      10.938  62.292  23.497  1.00  1.00
ATOM     48  C   PHE    56      11.600  61.552  22.329  1.00  1.00
ATOM     49  O   PHE    56      12.707  60.980  22.489  1.00  1.00
ATOM     50  CB  PHE    56      10.049  61.355  24.329  1.00  1.00
ATOM     51  N   LEU    57      10.954  61.593  21.181  1.00  1.00
ATOM     52  CA  LEU    57      11.527  60.979  19.948  1.00  1.00
ATOM     53  C   LEU    57      12.737  61.769  19.445  1.00  1.00
ATOM     54  O   LEU    57      13.754  61.214  19.021  1.00  1.00
ATOM     55  CB  LEU    57      10.466  60.873  18.877  1.00  1.00
ATOM     56  N   LEU    58      12.624  63.101  19.486  1.00  1.00
ATOM     57  CA  LEU    58      13.785  63.936  19.137  1.00  1.00
ATOM     58  C   LEU    58      14.952  63.677  20.090  1.00  1.00
ATOM     59  O   LEU    58      16.100  63.555  19.634  1.00  1.00
ATOM     60  CB  LEU    58      13.408  65.427  19.009  1.00  1.00
ATOM     61  N   THR    59      14.655  63.490  21.380  1.00  1.00
ATOM     62  CA  THR    59      15.648  63.060  22.364  1.00  1.00
ATOM     63  C   THR    59      16.333  61.671  22.073  1.00  1.00
ATOM     64  O   THR    59      17.565  61.520  22.157  1.00  1.00
ATOM     65  CB  THR    59      15.066  63.142  23.773  1.00  1.00
ATOM     66  N   LEU    60      15.534  60.674  21.717  1.00  1.00
ATOM     67  CA  LEU    60      16.113  59.390  21.296  1.00  1.00
ATOM     68  C   LEU    60      16.968  59.534  20.036  1.00  1.00
ATOM     69  O   LEU    60      18.004  58.892  19.926  1.00  1.00
ATOM     70  CB  LEU    60      14.986  58.378  21.015  1.00  1.00
ATOM     71  N   VAL    61      16.531  60.337  19.082  1.00  1.00
ATOM     72  CA  VAL    61      17.292  60.552  17.854  1.00  1.00
ATOM     73  C   VAL    61      18.639  61.197  18.199  1.00  1.00
ATOM     74  O   VAL    61      19.697  60.727  17.754  1.00  1.00
ATOM     75  CB  VAL    61      16.511  61.389  16.864  1.00  1.00
ATOM     76  N   GLU    62      18.592  62.240  19.036  1.00  1.00
ATOM     77  CA  GLU    62      19.799  62.862  19.588  1.00  1.00
ATOM     78  C   GLU    62      20.727  61.845  20.263  1.00  1.00
ATOM     79  O   GLU    62      21.945  61.868  20.037  1.00  1.00
ATOM     80  CB  GLU    62      19.418  63.947  20.632  1.00  1.00
ATOM     81  N   LEU    63      20.174  60.987  21.121  1.00  1.00
ATOM     82  CA  LEU    63      21.022  60.043  21.865  1.00  1.00
ATOM     83  C   LEU    63      21.538  58.877  20.988  1.00  1.00
ATOM     84  O   LEU    63      22.603  58.315  21.268  1.00  1.00
ATOM     85  CB  LEU    63      20.310  59.489  23.092  1.00  1.00
TER
END
