
#######################################################
#                                                     #
#                        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   10 (   40),  selected   10 , name T0299AL243_2-D2
# Molecule2: number of CA atoms   89 (  757),  selected   10 , name T0299_D2.pdb
# PARAMETERS: T0299AL243_2-D2.T0299_D2.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:    10        79 - 88          1.08     1.08
  LCS_AVERAGE:     11.24

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10        79 - 88          1.08     1.08
  LCS_AVERAGE:     11.24

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9        80 - 88          0.94     1.15
  LCS_AVERAGE:      9.55

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     L      79     L      79      4   10   10     3    4    4   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     E      80     E      80      9   10   10     3    4    9   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     D      81     D      81      9   10   10     5    8    9   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     F      82     F      82      9   10   10     5    8    9   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     E      83     E      83      9   10   10     5    8    9   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     A      84     A      84      9   10   10     5    8    9   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     E      85     E      85      9   10   10     5    8    9   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     L      86     L      86      9   10   10     5    8    9   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     E      87     E      87      9   10   10     5    8    9   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     N      88     N      88      9   10   10     5    8    9   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10 
LCS_AVERAGE  LCS_A:  10.67  (   9.55   11.24   11.24 )

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      5      8      9     10     10     10     10     10     10     10     10     10     10     10     10     10     10     10     10     10 
GDT PERCENT_CA   5.62   8.99  10.11  11.24  11.24  11.24  11.24  11.24  11.24  11.24  11.24  11.24  11.24  11.24  11.24  11.24  11.24  11.24  11.24  11.24
GDT RMS_LOCAL    0.24   0.65   0.94   1.08   1.08   1.08   1.08   1.08   1.08   1.08   1.08   1.08   1.08   1.08   1.08   1.08   1.08   1.08   1.08   1.08
GDT RMS_ALL_CA   1.35   1.36   1.15   1.08   1.08   1.08   1.08   1.08   1.08   1.08   1.08   1.08   1.08   1.08   1.08   1.08   1.08   1.08   1.08   1.08

#      Molecule1      Molecule2       DISTANCE
LGA    L      79      L      79          1.668
LGA    E      80      E      80          1.539
LGA    D      81      D      81          1.134
LGA    F      82      F      82          0.860
LGA    E      83      E      83          1.448
LGA    A      84      A      84          1.312
LGA    E      85      E      85          0.647
LGA    L      86      L      86          0.263
LGA    E      87      E      87          0.415
LGA    N      88      N      88          0.135

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   10   89    4.0     10    1.08    10.674    10.975     0.847

LGA_LOCAL      RMSD =  1.080  Number of atoms =   10  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  1.080  Number of atoms =   10 
Std_ALL_ATOMS  RMSD =  1.080  (standard rmsd on all 10 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.181893 * X  +  -0.738813 * Y  +   0.648899 * Z  +  -8.754354
  Y_new =  -0.669220 * X  +  -0.576511 * Y  +  -0.468806 * Z  + 109.108215
  Z_new =   0.720457 * X  +  -0.348984 * Y  +  -0.599292 * Z  + -38.248711 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.614270    0.527323  [ DEG:  -149.7866     30.2134 ]
  Theta =  -0.804462   -2.337131  [ DEG:   -46.0923   -133.9077 ]
  Phi   =  -1.305409    1.836184  [ DEG:   -74.7944    105.2056 ]
 
# 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: T0299AL243_2-D2                               
REMARK     2: T0299_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0299AL243_2-D2.T0299_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   10   89   4.0   10   1.08  10.975     1.08
REMARK  ---------------------------------------------------------- 
MOLECULE T0299AL243_2-D2
REMARK Aligment from pdb entry: 1k1wA
ATOM    181  N   LEU    79     -10.469  54.513  -5.629  1.00  0.00              
ATOM    182  CA  LEU    79     -10.835  54.887  -4.265  1.00  0.00              
ATOM    183  C   LEU    79     -10.747  56.408  -4.205  1.00  0.00              
ATOM    184  O   LEU    79      -9.753  56.993  -4.616  1.00  0.00              
ATOM    185  N   GLU    80     -11.791  57.060  -3.683  1.00  0.00              
ATOM    186  CA  GLU    80     -11.899  58.514  -3.549  1.00  0.00              
ATOM    187  C   GLU    80     -10.798  59.089  -2.684  1.00  0.00              
ATOM    188  O   GLU    80     -11.052  59.567  -1.583  1.00  0.00              
ATOM    189  N   ASP    81      -9.573  59.057  -3.179  1.00  0.00              
ATOM    190  CA  ASP    81      -8.453  59.554  -2.396  1.00  0.00              
ATOM    191  C   ASP    81      -7.258  59.623  -3.306  1.00  0.00              
ATOM    192  O   ASP    81      -6.230  60.193  -2.956  1.00  0.00              
ATOM    193  N   PHE    82      -7.396  59.024  -4.480  1.00  0.00              
ATOM    194  CA  PHE    82      -6.324  59.058  -5.457  1.00  0.00              
ATOM    195  C   PHE    82      -6.352  60.464  -6.066  1.00  0.00              
ATOM    196  O   PHE    82      -5.413  60.898  -6.737  1.00  0.00              
ATOM    197  N   GLU    83      -7.440  61.179  -5.812  1.00  0.00              
ATOM    198  CA  GLU    83      -7.582  62.518  -6.346  1.00  0.00              
ATOM    199  C   GLU    83      -6.415  63.379  -5.877  1.00  0.00              
ATOM    200  O   GLU    83      -5.721  63.974  -6.689  1.00  0.00              
ATOM    201  N   ALA    84      -6.196  63.425  -4.566  1.00  0.00              
ATOM    202  CA  ALA    84      -5.103  64.201  -3.987  1.00  0.00              
ATOM    203  C   ALA    84      -3.758  63.826  -4.626  1.00  0.00              
ATOM    204  O   ALA    84      -3.005  64.701  -5.049  1.00  0.00              
ATOM    205  N   GLU    85      -3.464  62.530  -4.699  1.00  0.00              
ATOM    206  CA  GLU    85      -2.197  62.065  -5.264  1.00  0.00              
ATOM    207  C   GLU    85      -2.043  62.473  -6.722  1.00  0.00              
ATOM    208  O   GLU    85      -1.054  63.104  -7.109  1.00  0.00              
ATOM    209  N   LEU    86      -3.031  62.106  -7.529  1.00  0.00              
ATOM    210  CA  LEU    86      -3.022  62.430  -8.942  1.00  0.00              
ATOM    211  C   LEU    86      -2.804  63.928  -9.171  1.00  0.00              
ATOM    212  O   LEU    86      -2.074  64.325 -10.073  1.00  0.00              
ATOM    213  N   GLU    87      -3.424  64.754  -8.341  1.00  0.00              
ATOM    214  CA  GLU    87      -3.294  66.199  -8.458  1.00  0.00              
ATOM    215  C   GLU    87      -1.890  66.688  -8.154  1.00  0.00              
ATOM    216  O   GLU    87      -1.369  67.568  -8.848  1.00  0.00              
ATOM    217  N   ASN    88      -1.286  66.121  -7.109  1.00  0.00              
ATOM    218  CA  ASN    88       0.055  66.496  -6.706  1.00  0.00              
ATOM    219  C   ASN    88       1.018  65.999  -7.753  1.00  0.00              
ATOM    220  O   ASN    88       2.089  66.566  -7.931  1.00  0.00              
END
