
#######################################################
#                                                     #
#                        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   11 (   44),  selected   11 , name T0372AL044_1-D2
# Molecule2: number of CA atoms  172 ( 1400),  selected   11 , name T0372_D2.pdb
# PARAMETERS: T0372AL044_1-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:    11       118 - 142         4.96     4.96
  LCS_AVERAGE:      6.40

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       118 - 122         1.29    14.73
  LCS_AVERAGE:      2.33

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       118 - 121         0.18    13.26
  LCS_AVERAGE:      1.80

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    5    5    5    6    7    7    8    9   10   10   11   11   11   11   11   11   11 
LCS_GDT     A     119     A     119      4    5   11     4    4    4    5    5    5    6    7    7    8    9   10   10   11   11   11   11   11   11   11 
LCS_GDT     Y     120     Y     120      4    5   11     4    4    4    5    5    5    6    7    7    8    9   10   10   11   11   11   11   11   11   11 
LCS_GDT     A     121     A     121      4    5   11     4    4    4    5    5    5    6    7    7    8    9   10   10   11   11   11   11   11   11   11 
LCS_GDT     D     122     D     122      3    5   11     3    3    4    5    5    5    6    7    7    8    9   10   10   11   11   11   11   11   11   11 
LCS_GDT     Y     123     Y     123      3    3   11     3    3    4    4    4    5    6    7    7    8    9   10   10   11   11   11   11   11   11   11 
LCS_GDT     I     124     I     124      3    4   11     3    3    3    4    4    4    5    7    7    8    9   10   10   11   11   11   11   11   11   11 
LCS_GDT     Y     125     Y     125      3    4   11     0    3    3    3    4    4    4    5    7    8    9   10   10   11   11   11   11   11   11   11 
LCS_GDT     L     126     L     126      3    4   11     1    3    3    3    4    4    4    5    7    8    9   10   10   11   11   11   11   11   11   11 
LCS_GDT     R     127     R     127      3    4   11     0    3    3    3    4    4    4    5    7    8    9   10   10   11   11   11   11   11   11   11 
LCS_GDT     R     142     R     142      0    0   11     2    3    4    4    4    5    5    6    7    8    9    9   10   11   11   11   11   11   11   11 
LCS_AVERAGE  LCS_A:   3.51  (   1.80    2.33    6.40 )

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      5      5      5      6      7      7      8      9     10     10     11     11     11     11     11     11     11 
GDT PERCENT_CA   2.33   2.33   2.33   2.91   2.91   2.91   3.49   4.07   4.07   4.65   5.23   5.81   5.81   6.40   6.40   6.40   6.40   6.40   6.40   6.40
GDT RMS_LOCAL    0.18   0.18   0.18   1.29   1.29   1.29   2.30   2.93   2.93   3.44   4.02   4.30   4.30   4.96   4.96   4.96   4.96   4.96   4.96   4.96
GDT RMS_ALL_CA  13.26  13.26  13.26  14.73  14.73  14.73  11.87  10.58  10.58  10.89  10.91  10.53  10.53   4.96   4.96   4.96   4.96   4.96   4.96   4.96

#      Molecule1      Molecule2       DISTANCE
LGA    R     118      R     118          3.068
LGA    A     119      A     119          2.965
LGA    Y     120      Y     120          3.655
LGA    A     121      A     121          1.895
LGA    D     122      D     122          3.974
LGA    Y     123      Y     123          1.735
LGA    I     124      I     124          3.651
LGA    Y     125      Y     125          6.734
LGA    L     126      L     126          8.289
LGA    R     127      R     127          7.755
LGA    R     142      R     142         28.344

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   11  172    4.0      7    2.93     3.924     3.504     0.231

LGA_LOCAL      RMSD =  2.929  Number of atoms =    7  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  9.746  Number of atoms =   11 
Std_ALL_ATOMS  RMSD =  4.959  (standard rmsd on all 11 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.782491 * X  +  -0.591817 * Y  +  -0.193548 * Z  +  27.625124
  Y_new =   0.193154 * X  +  -0.064795 * Y  +   0.979027 * Z  +  20.198338
  Z_new =  -0.591946 * X  +  -0.803464 * Y  +   0.063610 * Z  +  25.831947 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.491791    1.649801  [ DEG:   -85.4733     94.5267 ]
  Theta =   0.633471    2.508121  [ DEG:    36.2952    143.7048 ]
  Phi   =   0.242007   -2.899585  [ DEG:    13.8660   -166.1340 ]
 
# 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_1-D2                               
REMARK     2: T0372_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0372AL044_1-D2.T0372_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   11  172   4.0    7   2.93   3.504     4.96
REMARK  ---------------------------------------------------------- 
MOLECULE T0372AL044_1-D2
REMARK Aligment from pdb entry: 2go8_A
ATOM    133  N   ARG   118      26.730  41.126   8.106  1.00  0.00              
ATOM    134  CA  ARG   118      25.554  41.204   8.933  1.00  0.00              
ATOM    135  C   ARG   118      25.775  40.793  10.380  1.00  0.00              
ATOM    136  O   ARG   118      25.027  41.223  11.245  1.00  0.00              
ATOM    137  N   ALA   119      26.783  39.965  10.643  1.00  0.00              
ATOM    138  CA  ALA   119      27.074  39.497  11.993  1.00  0.00              
ATOM    139  C   ALA   119      27.779  40.580  12.777  1.00  0.00              
ATOM    140  O   ALA   119      27.719  40.616  13.996  1.00  0.00              
ATOM    141  N   TYR   120      28.414  41.482  12.046  1.00  0.00              
ATOM    142  CA  TYR   120      29.167  42.585  12.617  1.00  0.00              
ATOM    143  C   TYR   120      28.232  43.725  12.971  1.00  0.00              
ATOM    144  O   TYR   120      28.551  44.542  13.825  1.00  0.00              
ATOM    145  N   ALA   121      27.081  43.786  12.306  1.00  0.00              
ATOM    146  CA  ALA   121      26.116  44.855  12.560  1.00  0.00              
ATOM    147  C   ALA   121      25.245  44.595  13.783  1.00  0.00              
ATOM    148  O   ALA   121      24.724  45.518  14.383  1.00  0.00              
ATOM    149  N   ASP   122      25.067  43.330  14.135  1.00  0.00              
ATOM    150  CA  ASP   122      24.271  42.963  15.294  1.00  0.00              
ATOM    151  C   ASP   122      25.182  42.959  16.477  1.00  0.00              
ATOM    152  O   ASP   122      24.797  42.625  17.591  1.00  0.00              
ATOM    153  N   TYR   123      26.432  43.265  16.214  1.00  0.00              
ATOM    154  CA  TYR   123      27.365  43.330  17.290  1.00  0.00              
ATOM    155  C   TYR   123      27.514  44.798  17.576  1.00  0.00              
ATOM    156  O   TYR   123      27.340  45.220  18.707  1.00  0.00              
ATOM    157  N   ILE   124      27.841  45.581  16.562  1.00  0.00              
ATOM    158  CA  ILE   124      27.947  46.998  16.775  1.00  0.00              
ATOM    159  C   ILE   124      26.586  47.432  17.312  1.00  0.00              
ATOM    160  O   ILE   124      26.503  48.415  18.037  1.00  0.00              
ATOM    161  N   TYR   125      25.537  46.677  16.978  1.00  0.00              
ATOM    162  CA  TYR   125      24.171  46.999  17.400  1.00  0.00              
ATOM    163  C   TYR   125      23.818  46.749  18.872  1.00  0.00              
ATOM    164  O   TYR   125      23.244  47.629  19.525  1.00  0.00              
ATOM    165  N   LEU   126      24.138  45.567  19.394  1.00  0.00              
ATOM    166  CA  LEU   126      23.823  45.240  20.791  1.00  0.00              
ATOM    167  C   LEU   126      24.742  45.947  21.785  1.00  0.00              
ATOM    168  O   LEU   126      24.525  45.923  23.001  1.00  0.00              
ATOM    169  N   ARG   127      25.705  46.651  21.229  1.00  0.00              
ATOM    170  CA  ARG   127      26.712  47.328  21.987  1.00  0.00              
ATOM    171  C   ARG   127      26.269  48.616  22.677  1.00  0.00              
ATOM    172  O   ARG   127      25.435  49.381  22.181  1.00  0.00              
ATOM    173  N   ARG   142      41.942  56.477  24.368  1.00  0.00              
ATOM    174  CA  ARG   142      42.775  56.379  23.181  1.00  0.00              
ATOM    175  C   ARG   142      43.299  57.687  22.653  1.00  0.00              
ATOM    176  O   ARG   142      42.536  58.591  22.341  1.00  0.00              
END
