
#######################################################
#                                                     #
#                        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 T0356AL044_1-D3
# Molecule2: number of CA atoms  120 (  972),  selected   11 , name T0356_D3.pdb
# PARAMETERS: T0356AL044_1-D3.T0356_D3.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       348 - 357         4.34     5.66
  LCS_AVERAGE:      8.18

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       348 - 352         1.20    11.80
  LCS_AVERAGE:      3.71

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       348 - 351         0.35    11.93
  LONGEST_CONTINUOUS_SEGMENT:     4       351 - 354         0.97     7.59
  LONGEST_CONTINUOUS_SEGMENT:     4       355 - 358         0.66    12.27
  LCS_AVERAGE:      3.33

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:  120
LCS_GDT     F     348     F     348      4    5   10     4    4    4    5    5    5    7    8    8    8    8    9   10   10   10   10   10   10   11   11 
LCS_GDT     P     349     P     349      4    5   10     4    4    4    5    5    5    7    8    8    8    8    9   10   10   10   10   10   10   11   11 
LCS_GDT     E     350     E     350      4    5   10     4    4    4    5    5    5    7    8    8    8    8    9   10   10   10   10   10   10   11   11 
LCS_GDT     I     351     I     351      4    5   10     4    4    4    5    5    5    7    8    8    8    8    9   10   10   10   10   10   10   11   11 
LCS_GDT     V     352     V     352      4    5   10     3    3    4    5    5    5    7    8    8    8    8    9   10   10   10   10   10   10   11   11 
LCS_GDT     D     353     D     353      4    4   10     3    3    4    4    4    5    7    8    8    8    8    9   10   10   10   10   10   10   11   11 
LCS_GDT     F     354     F     354      4    4   10     2    3    4    4    4    5    7    8    8    8    8    9   10   10   10   10   10   10   11   11 
LCS_GDT     Y     355     Y     355      4    4   10     2    4    4    4    4    4    6    8    8    8    8    9   10   10   10   10   10   10   11   11 
LCS_GDT     L     356     L     356      4    4   10     1    4    4    4    4    4    5    6    7    8    8    9   10   10   10   10   10   10   11   11 
LCS_GDT     P     357     P     357      4    4   10     1    4    4    4    4    4    4    5    6    7    7    9   10   10   10   10   10   10   11   11 
LCS_GDT     P     358     P     358      4    4    8     0    4    4    4    4    4    4    4    4    5    5    6    8    8    9   10   10   10   11   11 
LCS_AVERAGE  LCS_A:   5.08  (   3.33    3.71    8.18 )

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      7      8      8      8      8      9     10     10     10     10     10     10     11     11 
GDT PERCENT_CA   3.33   3.33   3.33   4.17   4.17   4.17   5.83   6.67   6.67   6.67   6.67   7.50   8.33   8.33   8.33   8.33   8.33   8.33   9.17   9.17
GDT RMS_LOCAL    0.35   0.35   0.35   1.20   1.20   1.20   2.95   3.11   3.11   3.11   3.11   3.83   4.34   4.34   4.34   4.34   4.34   4.34   5.33   5.33
GDT RMS_ALL_CA  11.93  11.93  11.93  11.80  11.80  11.80   7.48   7.19   7.19   7.19   7.19   6.17   5.66   5.66   5.66   5.66   5.66   5.66   5.33   5.33

#      Molecule1      Molecule2       DISTANCE
LGA    F     348      F     348          3.118
LGA    P     349      P     349          3.472
LGA    E     350      E     350          3.193
LGA    I     351      I     351          2.908
LGA    V     352      V     352          3.299
LGA    D     353      D     353          2.493
LGA    F     354      F     354          3.260
LGA    Y     355      Y     355          3.804
LGA    L     356      L     356          9.006
LGA    P     357      P     357          9.729
LGA    P     358      P     358         16.863

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   11  120    4.0      8    3.11     5.625     5.113     0.249

LGA_LOCAL      RMSD =  3.115  Number of atoms =    8  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  7.024  Number of atoms =   11 
Std_ALL_ATOMS  RMSD =  5.332  (standard rmsd on all 11 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.955150 * X  +   0.181897 * Y  +  -0.233671 * Z  +  90.117882
  Y_new =   0.003472 * X  +  -0.782168 * Y  +  -0.623058 * Z  + 127.628685
  Z_new =  -0.296102 * X  +  -0.595925 * Y  +   0.746456 * Z  +  32.962559 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.673727    2.467866  [ DEG:   -38.6017    141.3983 ]
  Theta =   0.300609    2.840983  [ DEG:    17.2236    162.7764 ]
  Phi   =   3.137957   -0.003635  [ DEG:   179.7917     -0.2083 ]
 
# 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: T0356AL044_1-D3                               
REMARK     2: T0356_D3.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0356AL044_1-D3.T0356_D3.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   11  120   4.0    8   3.11   5.113     5.33
REMARK  ---------------------------------------------------------- 
MOLECULE T0356AL044_1-D3
REMARK Aligment from pdb entry: 1jwq_A
ATOM    209  N   PHE   348      56.693  71.711  51.408  1.00  0.00              
ATOM    210  CA  PHE   348      57.219  72.528  52.495  1.00  0.00              
ATOM    211  C   PHE   348      56.054  73.123  53.285  1.00  0.00              
ATOM    212  O   PHE   348      56.066  73.146  54.521  1.00  0.00              
ATOM    213  N   PRO   349      55.038  73.587  52.566  1.00  0.00              
ATOM    214  CA  PRO   349      53.863  74.157  53.208  1.00  0.00              
ATOM    215  C   PRO   349      53.201  73.102  54.094  1.00  0.00              
ATOM    216  O   PRO   349      52.809  73.394  55.218  1.00  0.00              
ATOM    217  N   GLU   350      53.081  71.877  53.588  1.00  0.00              
ATOM    218  CA  GLU   350      52.466  70.801  54.362  1.00  0.00              
ATOM    219  C   GLU   350      53.268  70.531  55.637  1.00  0.00              
ATOM    220  O   GLU   350      52.697  70.332  56.707  1.00  0.00              
ATOM    221  N   ILE   351      54.591  70.526  55.520  1.00  0.00              
ATOM    222  CA  ILE   351      55.426  70.293  56.685  1.00  0.00              
ATOM    223  C   ILE   351      55.106  71.285  57.790  1.00  0.00              
ATOM    224  O   ILE   351      55.018  70.926  58.964  1.00  0.00              
ATOM    225  N   VAL   352      54.922  72.545  57.410  1.00  0.00              
ATOM    226  CA  VAL   352      54.611  73.602  58.367  1.00  0.00              
ATOM    227  C   VAL   352      53.193  73.460  58.905  1.00  0.00              
ATOM    228  O   VAL   352      52.959  73.543  60.112  1.00  0.00              
ATOM    229  N   ASP   353      52.254  73.241  57.995  1.00  0.00              
ATOM    230  CA  ASP   353      50.854  73.088  58.362  1.00  0.00              
ATOM    231  C   ASP   353      50.645  71.895  59.285  1.00  0.00              
ATOM    232  O   ASP   353      49.939  71.993  60.289  1.00  0.00              
ATOM    233  N   PHE   354      51.258  70.768  58.943  1.00  0.00              
ATOM    234  CA  PHE   354      51.124  69.564  59.752  1.00  0.00              
ATOM    235  C   PHE   354      51.753  69.745  61.124  1.00  0.00              
ATOM    236  O   PHE   354      51.153  69.386  62.131  1.00  0.00              
ATOM    237  N   TYR   355      52.958  70.306  61.167  1.00  0.00              
ATOM    238  CA  TYR   355      53.637  70.504  62.443  1.00  0.00              
ATOM    239  C   TYR   355      52.876  71.450  63.361  1.00  0.00              
ATOM    240  O   TYR   355      52.754  71.196  64.561  1.00  0.00              
ATOM    241  N   LEU   356      52.371  72.542  62.797  1.00  0.00              
ATOM    242  CA  LEU   356      51.636  73.527  63.578  1.00  0.00              
ATOM    243  C   LEU   356      50.190  73.114  63.822  1.00  0.00              
ATOM    244  O   LEU   356      49.451  73.803  64.523  1.00  0.00              
ATOM    245  N   PRO   357      49.802  71.985  63.237  1.00  0.00              
ATOM    246  CA  PRO   357      48.460  71.443  63.401  1.00  0.00              
ATOM    247  C   PRO   357      47.379  72.484  63.115  1.00  0.00              
ATOM    248  O   PRO   357      46.490  72.723  63.933  1.00  0.00              
ATOM    249  N   PRO   358      47.465  73.104  61.942  1.00  0.00              
ATOM    250  CA  PRO   358      46.488  74.110  61.539  1.00  0.00              
ATOM    251  C   PRO   358      45.794  73.715  60.238  1.00  0.00              
ATOM    252  O   PRO   358      45.453  74.572  59.422  1.00  0.00              
END
