
#######################################################
#                                                     #
#                        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_2-D3
# Molecule2: number of CA atoms  120 (  972),  selected   11 , name T0356_D3.pdb
# PARAMETERS: T0356AL044_2-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:     9       348 - 356         4.31     6.90
  LONGEST_CONTINUOUS_SEGMENT:     9       350 - 358         4.43     6.64
  LCS_AVERAGE:      7.50

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       351 - 356         1.98     6.51
  LONGEST_CONTINUOUS_SEGMENT:     6       353 - 358         1.42     9.19
  LCS_AVERAGE:      4.77

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       354 - 358         0.71     9.83
  LCS_AVERAGE:      3.71

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    9     3    4    4    4    5    5    6    7    7    7    8    9    9    9    9    9    9   10   11   11 
LCS_GDT     P     349     P     349      4    5    9     3    4    4    4    5    5    5    7    7    7    8    8    8    9    9    9    9   10   11   11 
LCS_GDT     E     350     E     350      4    5    9     3    4    4    4    5    5    5    7    7    7    8    8    8    9    9    9    9   10   11   11 
LCS_GDT     I     351     I     351      4    6    9     3    4    4    5    5    6    6    7    8    8    8    9    9    9    9    9    9   10   11   11 
LCS_GDT     V     352     V     352      4    6    9     3    4    4    5    5    6    7    7    8    8    8    9    9    9    9    9    9   10   11   11 
LCS_GDT     D     353     D     353      4    6    9     3    4    4    5    6    6    7    7    8    8    8    9    9    9    9    9    9   10   11   11 
LCS_GDT     F     354     F     354      5    6    9     4    4    5    5    6    6    7    7    8    8    8    9    9    9    9    9    9   10   11   11 
LCS_GDT     Y     355     Y     355      5    6    9     3    4    5    5    6    6    7    7    8    8    8    9    9    9    9    9    9   10   11   11 
LCS_GDT     L     356     L     356      5    6    9     4    4    5    5    6    6    7    7    8    8    8    9    9    9    9    9    9   10   11   11 
LCS_GDT     P     357     P     357      5    6    9     4    4    5    5    6    6    7    7    8    8    8    9    9    9    9    9    9   10   11   11 
LCS_GDT     P     358     P     358      5    6    9     4    4    5    5    6    6    7    7    8    8    8    9    9    9    9    9    9   10   11   11 
LCS_AVERAGE  LCS_A:   5.33  (   3.71    4.77    7.50 )

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      5      5      6      6      7      7      8      8      8      9      9      9      9      9      9     10     11     11 
GDT PERCENT_CA   3.33   3.33   4.17   4.17   5.00   5.00   5.83   5.83   6.67   6.67   6.67   7.50   7.50   7.50   7.50   7.50   7.50   8.33   9.17   9.17
GDT RMS_LOCAL    0.40   0.40   0.71   0.71   1.42   1.42   2.20   2.20   2.78   2.78   2.78   4.02   4.02   4.02   4.02   4.02   4.02   4.96   5.57   5.57
GDT RMS_ALL_CA   9.63   9.63   9.83   9.83   9.19   9.19   8.31   8.31   7.31   7.31   7.31   5.93   5.93   5.93   5.93   5.93   5.93   5.71   5.57   5.57

#      Molecule1      Molecule2       DISTANCE
LGA    F     348      F     348         16.125
LGA    P     349      P     349         16.201
LGA    E     350      E     350         12.731
LGA    I     351      I     351          6.405
LGA    V     352      V     352          3.850
LGA    D     353      D     353          1.903
LGA    F     354      F     354          1.209
LGA    Y     355      Y     355          2.224
LGA    L     356      L     356          0.981
LGA    P     357      P     357          1.839
LGA    P     358      P     358          2.175

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   11  120    4.0      7    2.20     5.208     5.411     0.304

LGA_LOCAL      RMSD =  2.201  Number of atoms =    7  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  8.309  Number of atoms =   11 
Std_ALL_ATOMS  RMSD =  5.573  (standard rmsd on all 11 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.841823 * X  +  -0.408675 * Y  +   0.352588 * Z  + 108.340027
  Y_new =   0.202875 * X  +   0.365767 * Y  +   0.908326 * Z  +  42.946060
  Z_new =  -0.500176 * X  +   0.836181 * Y  +  -0.225001 * Z  +  87.263100 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.833652   -1.307940  [ DEG:   105.0605    -74.9395 ]
  Theta =   0.523802    2.617791  [ DEG:    30.0116    149.9884 ]
  Phi   =   2.905107   -0.236485  [ DEG:   166.4504    -13.5496 ]
 
# 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_2-D3                               
REMARK     2: T0356_D3.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0356AL044_2-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    7   2.20   5.411     5.57
REMARK  ---------------------------------------------------------- 
MOLECULE T0356AL044_2-D3
REMARK Aligment from pdb entry: 1xov_A
ATOM    213  N   PHE   348      44.401  68.388  62.036  1.00  0.00              
ATOM    214  CA  PHE   348      44.597  69.703  61.465  1.00  0.00              
ATOM    215  C   PHE   348      45.790  70.391  62.120  1.00  0.00              
ATOM    216  O   PHE   348      46.629  70.991  61.453  1.00  0.00              
ATOM    217  N   PRO   349      45.905  70.266  63.440  1.00  0.00              
ATOM    218  CA  PRO   349      47.018  70.905  64.139  1.00  0.00              
ATOM    219  C   PRO   349      48.348  70.286  63.715  1.00  0.00              
ATOM    220  O   PRO   349      49.298  71.008  63.446  1.00  0.00              
ATOM    221  N   GLU   350      48.409  68.965  63.619  1.00  0.00              
ATOM    222  CA  GLU   350      49.657  68.310  63.179  1.00  0.00              
ATOM    223  C   GLU   350      49.962  68.594  61.716  1.00  0.00              
ATOM    224  O   GLU   350      51.126  68.768  61.316  1.00  0.00              
ATOM    225  N   ILE   351      48.920  68.650  60.897  1.00  0.00              
ATOM    226  CA  ILE   351      49.134  69.029  59.492  1.00  0.00              
ATOM    227  C   ILE   351      49.638  70.435  59.295  1.00  0.00              
ATOM    228  O   ILE   351      50.489  70.704  58.411  1.00  0.00              
ATOM    229  N   VAL   352      49.147  71.362  60.113  1.00  0.00              
ATOM    230  CA  VAL   352      49.597  72.724  60.031  1.00  0.00              
ATOM    231  C   VAL   352      51.009  72.913  60.562  1.00  0.00              
ATOM    232  O   VAL   352      51.828  73.654  59.990  1.00  0.00              
ATOM    233  N   ASP   353      51.304  72.259  61.679  1.00  0.00              
ATOM    234  CA  ASP   353      52.559  72.557  62.375  1.00  0.00              
ATOM    235  C   ASP   353      53.688  71.585  62.082  1.00  0.00              
ATOM    236  O   ASP   353      54.857  71.911  62.323  1.00  0.00              
ATOM    237  N   PHE   354      53.366  70.399  61.602  1.00  0.00              
ATOM    238  CA  PHE   354      54.358  69.361  61.365  1.00  0.00              
ATOM    239  C   PHE   354      54.872  68.726  62.643  1.00  0.00              
ATOM    240  O   PHE   354      55.892  68.045  62.620  1.00  0.00              
ATOM    241  N   TYR   355      54.164  68.920  63.762  1.00  0.00              
ATOM    242  CA  TYR   355      54.605  68.417  65.058  1.00  0.00              
ATOM    243  C   TYR   355      53.502  67.631  65.734  1.00  0.00              
ATOM    244  O   TYR   355      52.363  68.069  65.767  1.00  0.00              
ATOM    245  N   LEU   356      53.849  66.467  66.261  1.00  0.00              
ATOM    246  CA  LEU   356      52.883  65.599  66.912  1.00  0.00              
ATOM    247  C   LEU   356      52.364  66.273  68.178  1.00  0.00              
ATOM    248  O   LEU   356      53.140  66.833  68.933  1.00  0.00              
ATOM    249  N   PRO   357      51.050  66.239  68.395  1.00  0.00              
ATOM    250  CA  PRO   357      50.482  66.919  69.552  1.00  0.00              
ATOM    251  C   PRO   357      50.761  66.110  70.809  1.00  0.00              
ATOM    252  O   PRO   357      50.865  64.891  70.771  1.00  0.00              
ATOM    253  N   PRO   358      50.890  66.807  71.928  1.00  0.00              
ATOM    254  CA  PRO   358      51.110  66.169  73.206  1.00  0.00              
ATOM    255  C   PRO   358      49.877  65.480  73.798  1.00  0.00              
ATOM    256  O   PRO   358      50.006  64.436  74.418  1.00  0.00              
END
