
#######################################################
#                                                     #
#                        LGA                          #
#                  ---------------                    #
#                                                     #
#               Local-Global Alignment                #
#        A Method for Finding 3-D Similarities        #
#               in Protein Structures                 #
#                                                     #
#                  ------------ 10/2009               #
#                                                     #
#      Adam Zemla (adamz@llnl.gov)                    #
#      Lawrence Livermore National Laboratory, CA     #
#                                                     #
#######################################################

!!!   License for LGA program has expired  !!!
#   For updated version of the LGA program   #
# please contact Adam Zemla:  adamz@llnl.gov #

# Molecule1: number of CA atoms   61 (  460),  selected   60 , name one
# Molecule2: number of CA atoms   60 (  451),  selected   60 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:A  -ch2:A  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    60       1_A - 60_A        0.36     0.36
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    60       1_A - 60_A        0.36     0.36
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    60       1_A - 60_A        0.36     0.36
  LCS_AVERAGE:    100.00

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   60
LCS_GDT     RESIDUE       RESIDUE       SEGMENT_SIZE    GLOBAL DISTANCE TEST COLUMNS: number of residues under the threshold assigned to each residue pair
LCS_GDT   NAME NUMBER   NAME NUMBER    1.0  2.0  5.0    0.5  1.0  1.5  2.0  2.5  3.0  3.5  4.0  4.5  5.0  5.5  6.0  6.5  7.0  7.5  8.0  8.5  9.0  9.5 10.0
LCS_GDT     D     1_A     D     1_A     60   60   60     44   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D     2_A     D     2_A     60   60   60     56   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K     3_A     K     3_A     60   60   60     56   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A     4_A     A     4_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A     5_A     A     5_A     60   60   60     56   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     C     6_A     C     6_A     60   60   60     56   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A     7_A     A     7_A     60   60   60     56   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D     8_A     D     8_A     60   60   60     56   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     G     9_A     G     9_A     60   60   60     56   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     I    10_A     I    10_A     60   60   60     56   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    11_A     A    11_A     60   60   60     56   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    12_A     A    12_A     60   60   60     56   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     V    13_A     V    13_A     60   60   60     56   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    14_A     K    14_A     60   60   60     56   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    15_A     A    15_A     60   60   60     56   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     R    16_A     R    16_A     60   60   60     56   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     V    17_A     V    17_A     60   60   60     56   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    18_A     E    18_A     60   60   60     56   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    19_A     K    19_A     60   60   60     56   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    20_A     L    20_A     60   60   60     56   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    21_A     A    21_A     60   60   60     56   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     P    22_A     P    22_A     60   60   60     56   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    23_A     E    23_A     60   60   60     54   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    24_A     A    24_A     60   60   60     56   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     V    25_A     V    25_A     60   60   60     56   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     P    26_A     P    26_A     60   60   60     56   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     Q    27_A     Q    27_A     60   60   60     56   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    28_A     K    28_A     60   60   60     56   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    29_A     L    29_A     60   60   60     56   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    30_A     K    30_A     60   60   60     56   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     R    31_A     R    31_A     60   60   60     56   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    32_A     A    32_A     60   60   60     56   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    33_A     L    33_A     60   60   60     56   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    34_A     K    34_A     60   60   60     56   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     I    35_A     I    35_A     60   60   60     56   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    36_A     A    36_A     60   60   60     56   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    37_A     E    37_A     60   60   60     56   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     R    38_A     R    38_A     60   60   60     56   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    39_A     E    39_A     60   60   60     56   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     Q    40_A     Q    40_A     60   60   60     56   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     G    41_A     G    41_A     60   60   60     56   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    42_A     E    42_A     60   60   60     56   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     G    43_A     G    43_A     60   60   60     56   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    44_A     E    44_A     60   60   60     56   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     F    45_A     F    45_A     60   60   60     56   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D    46_A     D    46_A     60   60   60     56   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    47_A     E    47_A     60   60   60     56   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     C    48_A     C    48_A     60   60   60     56   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    49_A     L    49_A     60   60   60     56   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    50_A     E    50_A     60   60   60     56   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    51_A     A    51_A     60   60   60     56   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    52_A     L    52_A     60   60   60     56   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D    53_A     D    53_A     60   60   60     56   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D    54_A     D    54_A     60   60   60     56   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    55_A     A    55_A     60   60   60     56   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    56_A     K    56_A     60   60   60     56   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     R    57_A     R    57_A     60   60   60     56   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    58_A     A    58_A     60   60   60     56   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    59_A     L    59_A     60   60   60     56   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     P    60_A     P    60_A     60   60   60     16   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_AVERAGE  LCS_A: 100.00  ( 100.00  100.00  100.00 )

GLOBAL_DISTANCE_TEST (summary information about detected largest sets of residues (represented by selected AToms) that can fit under specified thresholds)
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_AT     56     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60 
GDT PERCENT_AT  93.33 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.31   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36
GDT RMS_ALL_AT   0.37   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36

# Checking swapping
#   possible swapping detected:  E    18_A      E    18_A
#   possible swapping detected:  E    37_A      E    37_A
#   possible swapping detected:  E    39_A      E    39_A
#   possible swapping detected:  E    42_A      E    42_A
#   possible swapping detected:  E    44_A      E    44_A
#   possible swapping detected:  E    47_A      E    47_A
#   possible swapping detected:  E    50_A      E    50_A
#   possible swapping detected:  D    53_A      D    53_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    D     1_A      D     1_A     0.838     0    0.186   0.792     1.695   90.476   86.071
LGA    D     2_A      D     2_A     0.369     0    0.003   0.179     1.223   97.619   95.298
LGA    K     3_A      K     3_A     0.425     0    0.013   0.585     1.635  100.000   91.746
LGA    A     4_A      A     4_A     0.561     0    0.005   0.007     0.679   95.238   94.286
LGA    A     5_A      A     5_A     0.366     0    0.051   0.056     0.515  100.000   98.095
LGA    C     6_A      C     6_A     0.139     0    0.005   0.080     0.722  100.000   98.413
LGA    A     7_A      A     7_A     0.184     0    0.012   0.012     0.226  100.000  100.000
LGA    D     8_A      D     8_A     0.250     0    0.013   0.098     0.609  100.000   97.619
LGA    G     9_A      G     9_A     0.097     0    0.029   0.029     0.196  100.000  100.000
LGA    I    10_A      I    10_A     0.259     0    0.006   0.016     0.382  100.000  100.000
LGA    A    11_A      A    11_A     0.308     0    0.003   0.004     0.332  100.000  100.000
LGA    A    12_A      A    12_A     0.080     0    0.011   0.011     0.139  100.000  100.000
LGA    V    13_A      V    13_A     0.278     0    0.007   0.017     0.369  100.000  100.000
LGA    K    14_A      K    14_A     0.357     0    0.006   0.126     0.585  100.000   98.942
LGA    A    15_A      A    15_A     0.317     0    0.020   0.023     0.473  100.000  100.000
LGA    R    16_A      R    16_A     0.248     0    0.016   1.013     4.493  100.000   87.013
LGA    V    17_A      V    17_A     0.227     0    0.012   0.058     0.236  100.000  100.000
LGA    E    18_A      E    18_A     0.269     0    0.018   0.714     3.327  100.000   83.598
LGA    K    19_A      K    19_A     0.410     0    0.028   1.064     5.318   97.619   80.423
LGA    L    20_A      L    20_A     0.442     0    0.027   0.153     0.553  100.000   97.619
LGA    A    21_A      A    21_A     0.450     0    0.028   0.032     0.470  100.000  100.000
LGA    P    22_A      P    22_A     0.476     0    0.026   0.083     0.640   95.238   97.279
LGA    E    23_A      E    23_A     0.542     0    0.021   0.929     3.128   95.238   81.323
LGA    A    24_A      A    24_A     0.465     0    0.038   0.041     0.524   97.619   96.190
LGA    V    25_A      V    25_A     0.218     0    0.018   0.056     0.346  100.000  100.000
LGA    P    26_A      P    26_A     0.255     0    0.011   0.044     0.467  100.000  100.000
LGA    Q    27_A      Q    27_A     0.304     0    0.019   1.184     3.963  100.000   77.937
LGA    K    28_A      K    28_A     0.310     0    0.011   0.834     3.070  100.000   84.603
LGA    L    29_A      L    29_A     0.240     0    0.011   1.183     2.901  100.000   89.286
LGA    K    30_A      K    30_A     0.362     0    0.009   0.045     0.421  100.000  100.000
LGA    R    31_A      R    31_A     0.440     0    0.020   1.361     6.926  100.000   68.831
LGA    A    32_A      A    32_A     0.403     0    0.004   0.005     0.449  100.000  100.000
LGA    L    33_A      L    33_A     0.327     0    0.010   0.066     0.432  100.000  100.000
LGA    K    34_A      K    34_A     0.270     0    0.017   1.003     4.468  100.000   78.889
LGA    I    35_A      I    35_A     0.320     0    0.017   0.060     0.512  100.000   98.810
LGA    A    36_A      A    36_A     0.354     0    0.003   0.007     0.362  100.000  100.000
LGA    E    37_A      E    37_A     0.204     0    0.016   0.328     0.903  100.000   97.884
LGA    R    38_A      R    38_A     0.316     0    0.017   0.460     1.469  100.000   93.983
LGA    E    39_A      E    39_A     0.400     0    0.025   1.005     3.645  100.000   85.714
LGA    Q    40_A      Q    40_A     0.295     0    0.013   0.349     1.156  100.000   96.878
LGA    G    41_A      G    41_A     0.149     0    0.026   0.026     0.268  100.000  100.000
LGA    E    42_A      E    42_A     0.430     0    0.024   0.324     1.440  100.000   93.704
LGA    G    43_A      G    43_A     0.291     0    0.029   0.029     0.409  100.000  100.000
LGA    E    44_A      E    44_A     0.133     0    0.039   0.827     4.025  100.000   82.698
LGA    F    45_A      F    45_A     0.416     0    0.020   0.074     0.550  100.000   95.671
LGA    D    46_A      D    46_A     0.446     0    0.015   1.163     4.161  100.000   83.155
LGA    E    47_A      E    47_A     0.286     0    0.012   0.445     1.521  100.000   94.868
LGA    C    48_A      C    48_A     0.110     0    0.042   0.090     0.262  100.000  100.000
LGA    L    49_A      L    49_A     0.078     0    0.006   0.058     0.300  100.000  100.000
LGA    E    50_A      E    50_A     0.057     0    0.014   0.211     0.637  100.000   97.884
LGA    A    51_A      A    51_A     0.133     0    0.006   0.006     0.242  100.000  100.000
LGA    L    52_A      L    52_A     0.249     0    0.026   0.041     0.558  100.000   98.810
LGA    D    53_A      D    53_A     0.203     0    0.006   0.082     0.680  100.000   97.619
LGA    D    54_A      D    54_A     0.168     0    0.004   0.050     0.217  100.000  100.000
LGA    A    55_A      A    55_A     0.321     0    0.020   0.028     0.407  100.000  100.000
LGA    K    56_A      K    56_A     0.498     0    0.016   0.636     1.323  100.000   91.693
LGA    R    57_A      R    57_A     0.186     0    0.009   1.284     4.960  100.000   81.602
LGA    A    58_A      A    58_A     0.496     0    0.029   0.029     0.649   97.619   96.190
LGA    L    59_A      L    59_A     0.382     0    0.029   0.166     1.100  100.000   94.167
LGA    P    60_A      P    60_A     0.982     0    0.009   0.307     1.315   90.476   87.891

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       60     240    240  100.00     451    451  100.00                60
SUMMARY(RMSD_GDC):     0.362          0.349                  1.142           99.286   94.211

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   61   60    4.0     60    0.36   100.000   100.000    12.983

LGA_LOCAL      RMSD:   0.362  Number of atoms:   60  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.362  Number of assigned atoms:   60 
Std_ASGN_ATOMS RMSD:   0.362  Standard rmsd on all 60 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.406132 * X  +  -0.043992 * Y  +   0.912755 * Z  +  13.303829
  Y_new =  -0.377807 * X  +   0.917559 * Y  +  -0.123882 * Z  +   8.523353
  Z_new =  -0.832057 * X  +  -0.395158 * Y  +  -0.389271 * Z  +   7.755391 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.392311  0.982805 -2.348690   [DEG: -137.0693   56.3106 -134.5700 ]
ZXZ:  1.435897  1.970636 -2.014177   [DEG:   82.2708  112.9091 -115.4038 ]
 
# END of job
