
#######################################################
#                                                     #
#                        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   16 (   64),  selected   16 , name T0372AL044_3-D2
# Molecule2: number of CA atoms  172 ( 1400),  selected   16 , name T0372_D2.pdb
# PARAMETERS: T0372AL044_3-D2.T0372_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:    14       120 - 133         4.58     5.34
  LCS_AVERAGE:      7.92

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9       125 - 133         0.65    10.31
  LCS_AVERAGE:      4.25

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9       125 - 133         0.65    10.31
  LCS_AVERAGE:      3.85

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:  172
LCS_GDT     R     118     R     118      4    5   11     4    4    4    4    5    5    6    7    8   10   13   14   14   15   15   16   16   16   16   16 
LCS_GDT     A     119     A     119      4    5   11     4    4    4    4    5    5    6    7    8    9   10   12   13   15   15   16   16   16   16   16 
LCS_GDT     Y     120     Y     120      4    5   14     4    4    4    4    5    5    6    7    8    9   10   12   12   15   15   16   16   16   16   16 
LCS_GDT     A     121     A     121      4    5   14     4    4    4    4    5    5    6    7    8   10   12   14   14   15   15   16   16   16   16   16 
LCS_GDT     D     122     D     122      3    5   14     3    3    3    3    5    5    6    7   10   12   13   14   14   15   15   16   16   16   16   16 
LCS_GDT     Y     123     Y     123      3    3   14     3    3    3    3    3    5    6    7   10   12   13   14   14   15   15   16   16   16   16   16 
LCS_GDT     I     124     I     124      3    8   14     3    3    3    3    4    4    8   10   10   12   13   14   14   15   15   16   16   16   16   16 
LCS_GDT     Y     125     Y     125      9    9   14     6    8    9    9    9    9    9   10   10   12   13   14   14   15   15   16   16   16   16   16 
LCS_GDT     L     126     L     126      9    9   14     7    8    9    9    9    9    9   10   10   12   13   14   14   15   15   16   16   16   16   16 
LCS_GDT     R     127     R     127      9    9   14     7    8    9    9    9    9    9   10   10   12   13   14   14   15   15   16   16   16   16   16 
LCS_GDT     S     128     S     128      9    9   14     7    8    9    9    9    9    9   10   10   12   13   14   14   15   15   16   16   16   16   16 
LCS_GDT     D     129     D     129      9    9   14     7    8    9    9    9    9    9   10   10   12   13   14   14   15   15   16   16   16   16   16 
LCS_GDT     L     130     L     130      9    9   14     7    8    9    9    9    9    9   10   10   12   13   14   14   15   15   16   16   16   16   16 
LCS_GDT     A     131     A     131      9    9   14     7    8    9    9    9    9    9   10   10   12   13   14   14   15   15   16   16   16   16   16 
LCS_GDT     T     132     T     132      9    9   14     7    8    9    9    9    9    9   10   10   12   13   14   14   15   15   16   16   16   16   16 
LCS_GDT     L     133     L     133      9    9   14     3    8    9    9    9    9    9   10   10   12   13   14   14   14   15   16   16   16   16   16 
LCS_AVERAGE  LCS_A:   5.34  (   3.85    4.25    7.92 )

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      7      8      9      9      9      9      9     10     10     12     13     14     14     15     15     16     16     16     16     16 
GDT PERCENT_CA   4.07   4.65   5.23   5.23   5.23   5.23   5.23   5.81   5.81   6.98   7.56   8.14   8.14   8.72   8.72   9.30   9.30   9.30   9.30   9.30
GDT RMS_LOCAL    0.29   0.49   0.65   0.65   0.65   0.65   0.65   2.04   2.04   3.50   3.87   4.11   4.11   5.10   4.74   5.12   5.12   5.12   5.12   5.12
GDT RMS_ALL_CA  10.93  10.28  10.31  10.31  10.31  10.31  10.31   8.69   8.69   5.94   5.58   5.47   5.47   5.28   5.21   5.12   5.12   5.12   5.12   5.12

#      Molecule1      Molecule2       DISTANCE
LGA    R     118      R     118         14.028
LGA    A     119      A     119         19.314
LGA    Y     120      Y     120         16.511
LGA    A     121      A     121          9.722
LGA    D     122      D     122          9.967
LGA    Y     123      Y     123          9.216
LGA    I     124      I     124          3.994
LGA    Y     125      Y     125          2.176
LGA    L     126      L     126          1.614
LGA    R     127      R     127          0.740
LGA    S     128      S     128          1.255
LGA    D     129      D     129          1.893
LGA    L     130      L     130          1.097
LGA    A     131      A     131          1.435
LGA    T     132      T     132          3.517
LGA    L     133      L     133          3.506

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   16  172    4.0     10    2.04     6.250     5.706     0.467

LGA_LOCAL      RMSD =  2.039  Number of atoms =   10  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  8.581  Number of atoms =   16 
Std_ALL_ATOMS  RMSD =  5.118  (standard rmsd on all 16 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.157183 * X  +   0.539125 * Y  +   0.827429 * Z  + -10.203963
  Y_new =  -0.981037 * X  +   0.010965 * Y  +  -0.193508 * Z  +  56.948551
  Z_new =  -0.113398 * X  +  -0.842155 * Y  +   0.527178 * Z  +  26.131411 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.011487    2.130105  [ DEG:   -57.9540    122.0460 ]
  Theta =   0.113642    3.027951  [ DEG:     6.5112    173.4888 ]
  Phi   =  -1.729667    1.411926  [ DEG:   -99.1026     80.8974 ]
 
# 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: T0372AL044_3-D2                               
REMARK     2: T0372_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0372AL044_3-D2.T0372_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   16  172   4.0   10   2.04   5.706     5.12
REMARK  ---------------------------------------------------------- 
MOLECULE T0372AL044_3-D2
REMARK Aligment from pdb entry: 1sqe_A
ATOM    149  N   ARG   118      19.374  51.530  15.208  1.00  0.00              
ATOM    150  CA  ARG   118      20.720  52.025  15.501  1.00  0.00              
ATOM    151  C   ARG   118      20.787  52.439  16.963  1.00  0.00              
ATOM    152  O   ARG   118      21.798  52.218  17.631  1.00  0.00              
ATOM    153  N   ALA   119      19.702  53.041  17.447  1.00  0.00              
ATOM    154  CA  ALA   119      19.607  53.476  18.835  1.00  0.00              
ATOM    155  C   ALA   119      19.821  52.275  19.719  1.00  0.00              
ATOM    156  O   ALA   119      20.571  52.331  20.684  1.00  0.00              
ATOM    157  N   TYR   120      19.147  51.180  19.378  1.00  0.00              
ATOM    158  CA  TYR   120      19.259  49.940  20.139  1.00  0.00              
ATOM    159  C   TYR   120      20.697  49.409  20.137  1.00  0.00              
ATOM    160  O   TYR   120      21.219  49.017  21.178  1.00  0.00              
ATOM    161  N   ALA   121      21.326  49.386  18.963  1.00  0.00              
ATOM    162  CA  ALA   121      22.694  48.901  18.850  1.00  0.00              
ATOM    163  C   ALA   121      23.634  49.744  19.710  1.00  0.00              
ATOM    164  O   ALA   121      24.557  49.218  20.326  1.00  0.00              
ATOM    165  N   ASP   122      23.391  51.051  19.751  1.00  0.00              
ATOM    166  CA  ASP   122      24.220  51.947  20.550  1.00  0.00              
ATOM    167  C   ASP   122      24.096  51.567  22.019  1.00  0.00              
ATOM    168  O   ASP   122      25.061  51.633  22.777  1.00  0.00              
ATOM    169  N   TYR   123      22.890  51.175  22.414  1.00  0.00              
ATOM    170  CA  TYR   123      22.620  50.744  23.779  1.00  0.00              
ATOM    171  C   TYR   123      23.476  49.510  24.079  1.00  0.00              
ATOM    172  O   TYR   123      24.120  49.420  25.126  1.00  0.00              
ATOM    173  N   ILE   124      23.490  48.569  23.143  1.00  0.00              
ATOM    174  CA  ILE   124      24.270  47.348  23.306  1.00  0.00              
ATOM    175  C   ILE   124      25.763  47.638  23.436  1.00  0.00              
ATOM    176  O   ILE   124      26.469  46.955  24.171  1.00  0.00              
ATOM    177  N   TYR   125      26.234  48.656  22.721  1.00  0.00              
ATOM    178  CA  TYR   125      27.652  49.030  22.734  1.00  0.00              
ATOM    179  C   TYR   125      28.000  50.113  23.759  1.00  0.00              
ATOM    180  O   TYR   125      29.127  50.599  23.790  1.00  0.00              
ATOM    181  N   LEU   126      27.043  50.484  24.597  1.00  0.00              
ATOM    182  CA  LEU   126      27.279  51.524  25.591  1.00  0.00              
ATOM    183  C   LEU   126      27.975  51.023  26.849  1.00  0.00              
ATOM    184  O   LEU   126      28.061  49.818  27.103  1.00  0.00              
ATOM    185  N   ARG   127      28.475  51.964  27.641  1.00  0.00              
ATOM    186  CA  ARG   127      29.141  51.605  28.871  1.00  0.00              
ATOM    187  C   ARG   127      28.102  51.191  29.897  1.00  0.00              
ATOM    188  O   ARG   127      28.331  50.259  30.659  1.00  0.00              
ATOM    189  N   SER   128      26.952  51.867  29.910  1.00  0.00              
ATOM    190  CA  SER   128      25.892  51.518  30.859  1.00  0.00              
ATOM    191  C   SER   128      25.439  50.079  30.651  1.00  0.00              
ATOM    192  O   SER   128      24.998  49.422  31.592  1.00  0.00              
ATOM    193  N   ASP   129      25.545  49.599  29.415  1.00  0.00              
ATOM    194  CA  ASP   129      25.169  48.228  29.096  1.00  0.00              
ATOM    195  C   ASP   129      26.292  47.308  29.570  1.00  0.00              
ATOM    196  O   ASP   129      26.037  46.269  30.182  1.00  0.00              
ATOM    197  N   LEU   130      27.532  47.700  29.281  1.00  0.00              
ATOM    198  CA  LEU   130      28.699  46.922  29.683  1.00  0.00              
ATOM    199  C   LEU   130      28.762  46.822  31.203  1.00  0.00              
ATOM    200  O   LEU   130      28.897  45.730  31.754  1.00  0.00              
ATOM    201  N   ALA   131      28.674  47.965  31.875  1.00  0.00              
ATOM    202  CA  ALA   131      28.699  47.991  33.333  1.00  0.00              
ATOM    203  C   ALA   131      27.657  47.002  33.858  1.00  0.00              
ATOM    204  O   ALA   131      27.970  46.130  34.672  1.00  0.00              
ATOM    205  N   THR   132      26.421  47.135  33.383  1.00  0.00              
ATOM    206  CA  THR   132      25.347  46.235  33.789  1.00  0.00              
ATOM    207  C   THR   132      25.714  44.858  33.252  1.00  0.00              
ATOM    208  O   THR   132      26.846  44.649  32.812  1.00  0.00              
ATOM    209  N   LEU   133      24.774  43.918  33.277  1.00  0.00              
ATOM    210  CA  LEU   133      25.060  42.576  32.769  1.00  0.00              
ATOM    211  C   LEU   133      26.303  41.991  33.438  1.00  0.00              
ATOM    212  O   LEU   133      27.417  42.106  32.913  1.00  0.00              
END
