
#######################################################
#                                                     #
#                        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   13 (   52),  selected   13 , name T0378AL316_5-D1
# Molecule2: number of CA atoms   89 (  716),  selected   13 , name T0378_D1.pdb
# PARAMETERS: T0378AL316_5-D1.T0378_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:    11        57 - 67          5.00     6.09
  LCS_AVERAGE:     12.01

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5        58 - 62          1.57    11.33
  LCS_AVERAGE:      4.32

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4        58 - 61          0.38    11.51
  LCS_AVERAGE:      3.72

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:   89
LCS_GDT     S      56     S      56      3    3   10     3    3    3    4    5    6    7    7    7    8   10   10   11   12   12   12   13   13   13   13 
LCS_GDT     T      57     T      57      3    3   11     3    3    3    4    5    6    7    7    7    8   10   10   11   12   12   12   13   13   13   13 
LCS_GDT     P      58     P      58      4    5   11     4    4    4    4    5    6    7    7    7    8   10   10   11   12   12   12   13   13   13   13 
LCS_GDT     H      59     H      59      4    5   11     4    4    4    4    5    6    6    6    7    8    9    9   10   12   12   12   13   13   13   13 
LCS_GDT     D      60     D      60      4    5   11     4    4    4    4    5    6    6    6    7    8    9    9   10   11   11   12   13   13   13   13 
LCS_GDT     A      61     A      61      4    5   11     4    4    4    4    5    6    6    6    7    8    9   10   11   12   12   12   13   13   13   13 
LCS_GDT     E      62     E      62      3    5   11     3    3    3    3    5    6    7    7    7    8   10   10   11   12   12   12   13   13   13   13 
LCS_GDT     V      63     V      63      3    4   11     3    3    3    4    5    6    7    7    7    8   10   10   11   12   12   12   13   13   13   13 
LCS_GDT     V      64     V      64      3    3   11     3    3    3    3    5    6    7    7    7    7   10   10   11   12   12   12   13   13   13   13 
LCS_GDT     E      65     E      65      3    3   11     3    3    3    4    5    6    7    7    7    8   10   10   11   12   12   12   13   13   13   13 
LCS_GDT     L      66     L      66      3    3   11     3    3    3    4    4    5    6    6    7    8   10   10   11   12   12   12   13   13   13   13 
LCS_GDT     P      67     P      67      3    3   11     0    3    3    4    4    5    6    6    7    8   10   10   11   12   12   12   13   13   13   13 
LCS_GDT     E      68     E      68      3    3    8     0    3    3    3    4    4    6    6    7    8   10   10   11   12   12   12   13   13   13   13 
LCS_AVERAGE  LCS_A:   6.68  (   3.72    4.32   12.01 )

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      4      4      4      4      5      6      7      7      7      8     10     10     11     12     12     12     13     13     13     13 
GDT PERCENT_CA   4.49   4.49   4.49   4.49   5.62   6.74   7.87   7.87   7.87   8.99  11.24  11.24  12.36  13.48  13.48  13.48  14.61  14.61  14.61  14.61
GDT RMS_LOCAL    0.38   0.38   0.38   0.38   1.60   2.15   2.53   2.53   2.53   3.35   4.02   4.02   4.55   4.97   4.97   4.97   5.49   5.49   5.49   5.49
GDT RMS_ALL_CA  11.51  11.51  11.51  11.51   7.37   9.53   6.54   6.54   6.54   6.47   5.99   5.99   5.76   5.57   5.57   5.57   5.49   5.49   5.49   5.49

#      Molecule1      Molecule2       DISTANCE
LGA    S      56      S      56          1.761
LGA    T      57      T      57          1.019
LGA    P      58      P      58          2.059
LGA    H      59      H      59          8.157
LGA    D      60      D      60         10.859
LGA    A      61      A      61          7.681
LGA    E      62      E      62          3.476
LGA    V      63      V      63          2.312
LGA    V      64      V      64          2.704
LGA    E      65      E      65          3.441
LGA    L      66      L      66          8.407
LGA    P      67      P      67          9.852
LGA    E      68      E      68         10.009

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   13   89    4.0      7    2.53     7.584     6.994     0.266

LGA_LOCAL      RMSD =  2.534  Number of atoms =    7  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  6.542  Number of atoms =   13 
Std_ALL_ATOMS  RMSD =  5.493  (standard rmsd on all 13 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.459133 * X  +  -0.885808 * Y  +  -0.067393 * Z  +  11.625484
  Y_new =  -0.883120 * X  +   0.446872 * Y  +   0.142847 * Z  +  49.400635
  Z_new =  -0.096419 * X  +   0.125102 * Y  +  -0.987448 * Z  +  64.084770 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   3.015572   -0.126020  [ DEG:   172.7796     -7.2204 ]
  Theta =   0.096569    3.045024  [ DEG:     5.5330    174.4670 ]
  Phi   =  -2.050236    1.091357  [ DEG:  -117.4699     62.5301 ]
 
# 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: T0378AL316_5-D1                               
REMARK     2: T0378_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0378AL316_5-D1.T0378_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   13   89   4.0    7   2.53   6.994     5.49
REMARK  ---------------------------------------------------------- 
MOLECULE T0378AL316_5-D1
REMARK Aligment from pdb entry: 1v2x_A
ATOM      1  N   SER    56      -3.138  14.553  52.448  1.00  0.00              
ATOM      2  CA  SER    56      -3.908  15.345  51.441  1.00  0.00              
ATOM      3  C   SER    56      -4.351  16.705  51.970  1.00  0.00              
ATOM      4  O   SER    56      -4.209  17.718  51.283  1.00  0.00              
ATOM      5  N   THR    57      -4.904  16.731  53.180  1.00  0.00              
ATOM      6  CA  THR    57      -5.354  17.995  53.744  1.00  0.00              
ATOM      7  C   THR    57      -4.164  18.708  54.385  1.00  0.00              
ATOM      8  O   THR    57      -4.194  19.913  54.618  1.00  0.00              
ATOM      9  N   PRO    58      -3.105  17.963  54.664  1.00  0.00              
ATOM     10  CA  PRO    58      -1.915  18.563  55.248  1.00  0.00              
ATOM     11  C   PRO    58      -1.276  19.386  54.122  1.00  0.00              
ATOM     12  O   PRO    58      -0.723  20.471  54.329  1.00  0.00              
ATOM     13  N   HIS    59      -1.393  18.843  52.917  1.00  0.00              
ATOM     14  CA  HIS    59      -0.869  19.441  51.700  1.00  0.00              
ATOM     15  C   HIS    59      -1.723  20.625  51.245  1.00  0.00              
ATOM     16  O   HIS    59      -1.215  21.624  50.732  1.00  0.00              
ATOM     17  N   ASP    60      -3.027  20.519  51.457  1.00  0.00              
ATOM     18  CA  ASP    60      -3.932  21.561  51.015  1.00  0.00              
ATOM     19  C   ASP    60      -4.511  22.375  52.184  1.00  0.00              
ATOM     20  O   ASP    60      -4.359  23.595  52.236  1.00  0.00              
ATOM     21  N   ALA    61      -5.135  21.699  53.139  1.00  0.00              
ATOM     22  CA  ALA    61      -5.739  22.377  54.281  1.00  0.00              
ATOM     23  C   ALA    61      -4.738  23.236  55.035  1.00  0.00              
ATOM     24  O   ALA    61      -5.116  24.218  55.660  1.00  0.00              
ATOM     25  N   GLU    62      -3.462  22.888  54.965  1.00  0.00              
ATOM     26  CA  GLU    62      -2.466  23.660  55.692  1.00  0.00              
ATOM     27  C   GLU    62      -1.652  24.617  54.831  1.00  0.00              
ATOM     28  O   GLU    62      -1.995  25.790  54.694  1.00  0.00              
ATOM     29  N   VAL    63      -0.564  24.104  54.269  1.00  0.00              
ATOM     30  CA  VAL    63       0.330  24.887  53.441  1.00  0.00              
ATOM     31  C   VAL    63      -0.460  25.757  52.470  1.00  0.00              
ATOM     32  O   VAL    63      -0.341  26.979  52.480  1.00  0.00              
ATOM     33  N   VAL    64      -1.278  25.105  51.649  1.00  0.00              
ATOM     34  CA  VAL    64      -2.096  25.766  50.646  1.00  0.00              
ATOM     35  C   VAL    64      -2.934  26.930  51.191  1.00  0.00              
ATOM     36  O   VAL    64      -2.852  28.044  50.681  1.00  0.00              
ATOM     37  N   GLU    65      -3.724  26.663  52.226  1.00  0.00              
ATOM     38  CA  GLU    65      -4.603  27.660  52.851  1.00  0.00              
ATOM     39  C   GLU    65      -3.864  28.801  53.556  1.00  0.00              
ATOM     40  O   GLU    65      -4.243  29.963  53.394  1.00  0.00              
ATOM     41  N   LEU    66      -2.824  28.497  54.332  1.00  0.00              
ATOM     42  CA  LEU    66      -2.104  29.570  55.014  1.00  0.00              
ATOM     43  C   LEU    66      -1.366  30.487  54.030  1.00  0.00              
ATOM     44  O   LEU    66      -1.318  31.697  54.223  1.00  0.00              
ATOM     45  N   PRO    67      -0.791  29.920  52.975  1.00  0.00              
ATOM     46  CA  PRO    67      -0.079  30.725  51.996  1.00  0.00              
ATOM     47  C   PRO    67      -1.018  31.694  51.254  1.00  0.00              
ATOM     48  O   PRO    67      -0.658  32.842  50.952  1.00  0.00              
ATOM     49  N   GLU    68      -2.220  31.231  50.937  1.00  0.00              
ATOM     50  CA  GLU    68      -3.133  32.088  50.205  1.00  0.00              
ATOM     51  C   GLU    68      -3.623  33.137  51.160  1.00  0.00              
ATOM     52  O   GLU    68      -3.814  34.281  50.768  1.00  0.00              
END
