
#######################################################
#                                                     #
#                        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   19 (   76),  selected   19 , name T0372AL044_4-D2
# Molecule2: number of CA atoms  172 ( 1400),  selected   19 , name T0372_D2.pdb
# PARAMETERS: T0372AL044_4-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:    16       121 - 136         4.63     5.79
  LCS_AVERAGE:      9.03

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9       125 - 133         2.00     8.21
  LCS_AVERAGE:      3.89

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       127 - 132         0.98     8.81
  LONGEST_CONTINUOUS_SEGMENT:     6       128 - 133         0.86     7.71
  LCS_AVERAGE:      2.42

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    9     4    4    4    4    5    5    6    6    6    7    8   12   15   16   17   18   18   18   19   19 
LCS_GDT     A     119     A     119      4    5   15     4    4    4    4    5    5    6    6    6    7    7    9   13   15   15   18   18   18   19   19 
LCS_GDT     Y     120     Y     120      4    5   15     4    4    4    4    5    5    6    6    6    7    7    9   11   13   15   16   16   16   19   19 
LCS_GDT     A     121     A     121      4    5   16     4    4    4    4    5    5    6    6    6    7   10   12   13   15   17   18   18   18   19   19 
LCS_GDT     D     122     D     122      3    5   16     3    3    3    3    5    5    6    9   11   13   14   14   15   16   17   18   18   18   19   19 
LCS_GDT     Y     123     Y     123      3    3   16     3    3    3    3    4    5    6    9   11   13   14   14   15   16   17   18   18   18   19   19 
LCS_GDT     I     124     I     124      3    3   16     3    3    3    3    4    5    8    9   11   13   14   14   15   16   17   18   18   18   19   19 
LCS_GDT     Y     125     Y     125      3    9   16     3    4    5    7    8    8    9    9   11   13   14   14   15   16   17   18   18   18   19   19 
LCS_GDT     L     126     L     126      3    9   16     3    3    3    7    8    8    9    9   10   11   13   13   15   16   17   18   18   18   19   19 
LCS_GDT     R     127     R     127      6    9   16     3    4    7    7    7    8    9    9   11   13   14   14   15   16   17   18   18   18   19   19 
LCS_GDT     S     128     S     128      6    9   16     3    5    7    7    8    8    9    9   11   13   14   14   15   16   17   18   18   18   19   19 
LCS_GDT     D     129     D     129      6    9   16     4    5    7    7    8    8    9    9   11   13   14   14   15   16   17   18   18   18   19   19 
LCS_GDT     L     130     L     130      6    9   16     4    5    7    7    8    8    9    9   11   13   14   14   15   16   17   18   18   18   19   19 
LCS_GDT     A     131     A     131      6    9   16     4    5    7    7    8    8    9    9   11   13   14   14   15   16   17   18   18   18   19   19 
LCS_GDT     T     132     T     132      6    9   16     4    5    7    7    8    8    9    9   11   13   14   14   15   16   17   18   18   18   19   19 
LCS_GDT     L     133     L     133      6    9   16     3    5    7    7    8    8    9    9   11   11   14   14   15   16   17   18   18   18   19   19 
LCS_GDT     K     134     K     134      3    5   16     3    4    4    5    6    7    7    9   11   13   14   14   15   16   17   18   18   18   19   19 
LCS_GDT     G     135     G     135      3    5   16     1    4    4    5    6    7    7    9   11   13   14   14   15   16   17   18   18   18   19   19 
LCS_GDT     K     136     K     136      0    5   16     2    4    4    5    6    6    7    9   11   13   14   14   15   16   17   18   18   18   19   19 
LCS_AVERAGE  LCS_A:   5.11  (   2.42    3.89    9.03 )

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      5      7      7      8      8      9      9     11     13     14     14     15     16     17     18     18     18     19     19 
GDT PERCENT_CA   2.33   2.91   4.07   4.07   4.65   4.65   5.23   5.23   6.40   7.56   8.14   8.14   8.72   9.30   9.88  10.47  10.47  10.47  11.05  11.05
GDT RMS_LOCAL    0.17   0.49   1.09   1.09   1.51   1.51   2.00   2.00   3.40   3.93   4.07   4.07   4.30   4.57   4.80   5.18   5.18   5.18   5.52   5.52
GDT RMS_ALL_CA  17.11   8.19   8.29   8.29   8.39   8.39   8.21   8.21   6.67   5.76   5.77   5.77   5.82   5.74   5.72   5.55   5.55   5.55   5.52   5.52

#      Molecule1      Molecule2       DISTANCE
LGA    R     118      R     118         10.322
LGA    A     119      A     119         13.948
LGA    Y     120      Y     120         12.836
LGA    A     121      A     121          9.617
LGA    D     122      D     122          9.318
LGA    Y     123      Y     123          8.803
LGA    I     124      I     124          5.894
LGA    Y     125      Y     125          2.018
LGA    L     126      L     126          2.541
LGA    R     127      R     127          3.657
LGA    S     128      S     128          0.894
LGA    D     129      D     129          2.164
LGA    L     130      L     130          1.818
LGA    A     131      A     131          1.188
LGA    T     132      T     132          0.658
LGA    L     133      L     133          1.205
LGA    K     134      K     134          8.632
LGA    G     135      G     135         12.391
LGA    K     136      K     136         16.096

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   19  172    4.0      9    2.00     5.669     5.393     0.429

LGA_LOCAL      RMSD =  2.000  Number of atoms =    9  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  8.209  Number of atoms =   19 
Std_ALL_ATOMS  RMSD =  5.517  (standard rmsd on all 19 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.681923 * X  +   0.121651 * Y  +   0.721236 * Z  +  43.301937
  Y_new =   0.721722 * X  +  -0.048164 * Y  +   0.690506 * Z  +  -0.954028
  Z_new =   0.118739 * X  +   0.991404 * Y  +  -0.054954 * Z  + -14.224928 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.626171   -1.515422  [ DEG:    93.1727    -86.8273 ]
  Theta =  -0.119019   -3.022573  [ DEG:    -6.8193   -173.1807 ]
  Phi   =   2.327848   -0.813744  [ DEG:   133.3759    -46.6241 ]
 
# 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_4-D2                               
REMARK     2: T0372_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0372AL044_4-D2.T0372_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   19  172   4.0    9   2.00   5.393     5.52
REMARK  ---------------------------------------------------------- 
MOLECULE T0372AL044_4-D2
REMARK Aligment from pdb entry: 1lq9_A
ATOM    157  N   ARG   118      23.883  46.222  15.391  1.00  0.00              
ATOM    158  CA  ARG   118      23.926  47.630  15.732  1.00  0.00              
ATOM    159  C   ARG   118      23.163  47.930  16.997  1.00  0.00              
ATOM    160  O   ARG   118      23.623  48.696  17.871  1.00  0.00              
ATOM    161  N   ALA   119      21.957  47.341  17.155  1.00  0.00              
ATOM    162  CA  ALA   119      21.172  47.620  18.351  1.00  0.00              
ATOM    163  C   ALA   119      21.905  47.142  19.581  1.00  0.00              
ATOM    164  O   ALA   119      21.890  47.776  20.636  1.00  0.00              
ATOM    165  N   TYR   120      22.515  45.957  19.489  1.00  0.00              
ATOM    166  CA  TYR   120      23.295  45.415  20.612  1.00  0.00              
ATOM    167  C   TYR   120      24.418  46.394  20.974  1.00  0.00              
ATOM    168  O   TYR   120      24.654  46.697  22.137  1.00  0.00              
ATOM    169  N   ALA   121      25.166  46.864  19.963  1.00  0.00              
ATOM    170  CA  ALA   121      26.313  47.725  20.212  1.00  0.00              
ATOM    171  C   ALA   121      25.888  49.067  20.816  1.00  0.00              
ATOM    172  O   ALA   121      26.530  49.580  21.743  1.00  0.00              
ATOM    173  N   ASP   122      24.834  49.675  20.261  1.00  0.00              
ATOM    174  CA  ASP   122      24.388  50.990  20.697  1.00  0.00              
ATOM    175  C   ASP   122      23.682  50.951  22.021  1.00  0.00              
ATOM    176  O   ASP   122      23.917  51.820  22.855  1.00  0.00              
ATOM    177  N   TYR   123      22.758  49.984  22.126  1.00  0.00              
ATOM    178  CA  TYR   123      21.856  50.037  23.264  1.00  0.00              
ATOM    179  C   TYR   123      22.271  49.147  24.405  1.00  0.00              
ATOM    180  O   TYR   123      21.685  49.142  25.516  1.00  0.00              
ATOM    181  N   ILE   124      23.314  48.338  24.226  1.00  0.00              
ATOM    182  CA  ILE   124      23.836  47.505  25.273  1.00  0.00              
ATOM    183  C   ILE   124      25.307  47.811  25.536  1.00  0.00              
ATOM    184  O   ILE   124      25.638  48.388  26.567  1.00  0.00              
ATOM    185  N   TYR   125      26.168  47.501  24.573  1.00  0.00              
ATOM    186  CA  TYR   125      27.610  47.638  24.737  1.00  0.00              
ATOM    187  C   TYR   125      28.052  49.045  25.073  1.00  0.00              
ATOM    188  O   TYR   125      29.006  49.233  25.873  1.00  0.00              
ATOM    189  N   LEU   126      27.414  50.041  24.471  1.00  0.00              
ATOM    190  CA  LEU   126      27.817  51.443  24.669  1.00  0.00              
ATOM    191  C   LEU   126      27.183  52.093  25.892  1.00  0.00              
ATOM    192  O   LEU   126      27.569  53.218  26.285  1.00  0.00              
ATOM    193  N   ARG   127      26.238  51.426  26.533  1.00  0.00              
ATOM    194  CA  ARG   127      25.600  51.956  27.739  1.00  0.00              
ATOM    195  C   ARG   127      26.468  51.531  28.901  1.00  0.00              
ATOM    196  O   ARG   127      26.738  50.329  29.056  1.00  0.00              
ATOM    197  N   SER   128      26.951  52.439  29.752  1.00  0.00              
ATOM    198  CA  SER   128      27.761  52.074  30.906  1.00  0.00              
ATOM    199  C   SER   128      27.045  51.123  31.854  1.00  0.00              
ATOM    200  O   SER   128      27.688  50.418  32.640  1.00  0.00              
ATOM    201  N   ASP   129      25.716  51.047  31.831  1.00  0.00              
ATOM    202  CA  ASP   129      24.991  50.067  32.645  1.00  0.00              
ATOM    203  C   ASP   129      25.399  48.659  32.282  1.00  0.00              
ATOM    204  O   ASP   129      25.299  47.768  33.120  1.00  0.00              
ATOM    205  N   LEU   130      25.904  48.362  31.067  1.00  0.00              
ATOM    206  CA  LEU   130      26.362  47.008  30.744  1.00  0.00              
ATOM    207  C   LEU   130      27.624  46.730  31.551  1.00  0.00              
ATOM    208  O   LEU   130      27.831  45.573  31.954  1.00  0.00              
ATOM    209  N   ALA   131      28.440  47.736  31.842  1.00  0.00              
ATOM    210  CA  ALA   131      29.655  47.507  32.650  1.00  0.00              
ATOM    211  C   ALA   131      29.255  47.321  34.097  1.00  0.00              
ATOM    212  O   ALA   131      29.794  46.476  34.822  1.00  0.00              
ATOM    213  N   THR   132      28.182  48.026  34.542  1.00  0.00              
ATOM    214  CA  THR   132      27.693  47.808  35.916  1.00  0.00              
ATOM    215  C   THR   132      27.101  46.412  36.054  1.00  0.00              
ATOM    216  O   THR   132      27.291  45.749  37.070  1.00  0.00              
ATOM    217  N   LEU   133      26.391  45.940  35.012  1.00  0.00              
ATOM    218  CA  LEU   133      25.821  44.605  35.035  1.00  0.00              
ATOM    219  C   LEU   133      26.947  43.578  35.021  1.00  0.00              
ATOM    220  O   LEU   133      26.917  42.577  35.785  1.00  0.00              
ATOM    221  N   LYS   134      27.989  43.783  34.213  1.00  0.00              
ATOM    222  CA  LYS   134      29.132  42.890  34.202  1.00  0.00              
ATOM    223  C   LYS   134      29.759  42.857  35.594  1.00  0.00              
ATOM    224  O   LYS   134      30.031  41.759  36.097  1.00  0.00              
ATOM    225  N   GLY   135      29.921  44.009  36.252  1.00  0.00              
ATOM    226  CA  GLY   135      30.460  43.971  37.597  1.00  0.00              
ATOM    227  C   GLY   135      29.577  43.155  38.533  1.00  0.00              
ATOM    228  O   GLY   135      30.074  42.378  39.361  1.00  0.00              
ATOM    229  N   LYS   136      29.956  39.482  37.975  1.00  0.00              
ATOM    230  CA  LYS   136      31.298  39.030  38.321  1.00  0.00              
ATOM    231  C   LYS   136      31.472  38.908  39.825  1.00  0.00              
ATOM    232  O   LYS   136      32.464  38.316  40.284  1.00  0.00              
END
