
#######################################################
#                                                     #
#                        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   68 (  529),  selected   67 , name one
# Molecule2: number of CA atoms   67 (  519),  selected   67 , 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:    67       2_A - 68_A        0.96     0.96
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    67       2_A - 68_A        0.96     0.96
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    67       2_A - 68_A        0.96     0.96
  LCS_AVERAGE:    100.00

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   67
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     S     2_A     S     2_A     67   67   67     10   33   58   66   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     P     3_A     P     3_A     67   67   67     31   55   63   66   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E     4_A     E     4_A     67   67   67     11   45   60   66   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E     5_A     E     5_A     67   67   67     15   45   62   66   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q     6_A     Q     6_A     67   67   67     25   55   63   66   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K     7_A     K     7_A     67   67   67     31   55   63   66   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q     8_A     Q     8_A     67   67   67     13   48   63   66   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     M     9_A     M     9_A     67   67   67     17   53   63   66   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    10_A     L    10_A     67   67   67     31   55   63   66   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     G    11_A     G    11_A     67   67   67     36   55   63   66   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    12_A     E    12_A     67   67   67     36   55   63   66   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    13_A     A    13_A     67   67   67     31   55   63   66   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     I    14_A     I    14_A     67   67   67     38   55   63   66   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Y    15_A     Y    15_A     67   67   67     38   55   63   66   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     P    16_A     P    16_A     67   67   67     38   55   63   66   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K    17_A     K    17_A     67   67   67     38   55   63   66   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    18_A     V    18_A     67   67   67     38   55   63   66   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    19_A     A    19_A     67   67   67     38   55   63   66   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    20_A     A    20_A     67   67   67     31   55   63   66   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     S    21_A     S    21_A     67   67   67      3   54   63   66   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q    22_A     Q    22_A     67   67   67     31   55   63   66   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     P    23_A     P    23_A     67   67   67     26   55   63   66   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    24_A     E    24_A     67   67   67     31   55   63   66   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    25_A     L    25_A     67   67   67     31   55   63   66   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    26_A     A    26_A     67   67   67     38   55   63   66   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     G    27_A     G    27_A     67   67   67     38   55   63   66   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K    28_A     K    28_A     67   67   67     37   55   63   66   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    29_A     L    29_A     67   67   67     38   55   63   66   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     T    30_A     T    30_A     67   67   67     38   55   63   66   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     G    31_A     G    31_A     67   67   67     38   55   63   66   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     M    32_A     M    32_A     67   67   67     38   55   63   66   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     I    33_A     I    33_A     67   67   67     31   55   63   66   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    34_A     L    34_A     67   67   67     31   55   63   66   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    35_A     E    35_A     67   67   67     28   55   63   66   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    36_A     L    36_A     67   67   67     38   55   63   66   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     P    37_A     P    37_A     67   67   67     38   55   63   66   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    38_A     V    38_A     67   67   67     38   55   63   66   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     T    39_A     T    39_A     67   67   67     38   55   63   66   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    40_A     E    40_A     67   67   67     38   55   63   66   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    41_A     L    41_A     67   67   67     38   55   63   66   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    42_A     L    42_A     67   67   67     38   55   63   66   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     H    43_A     H    43_A     67   67   67     38   55   63   66   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    44_A     L    44_A     67   67   67     38   55   63   66   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    45_A     L    45_A     67   67   67     38   55   63   66   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    46_A     E    46_A     67   67   67     38   55   63   66   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    47_A     E    47_A     67   67   67     38   55   63   66   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     S    48_A     S    48_A     67   67   67     38   55   63   66   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    49_A     E    49_A     67   67   67     35   55   63   66   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    50_A     A    50_A     67   67   67     38   55   63   66   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    51_A     L    51_A     67   67   67     38   55   63   66   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     D    52_A     D    52_A     67   67   67     38   55   63   66   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    53_A     A    53_A     67   67   67     38   55   63   66   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K    54_A     K    54_A     67   67   67     38   55   63   66   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    55_A     V    55_A     67   67   67     38   55   63   66   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     N    56_A     N    56_A     67   67   67     38   55   63   66   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    57_A     E    57_A     67   67   67     38   55   63   66   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    58_A     A    58_A     67   67   67     38   55   63   66   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    59_A     L    59_A     67   67   67     38   55   63   66   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    60_A     E    60_A     67   67   67     38   55   63   66   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    61_A     V    61_A     67   67   67     38   55   63   66   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    62_A     L    62_A     67   67   67     38   55   63   66   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K    63_A     K    63_A     67   67   67     35   55   63   66   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    64_A     E    64_A     67   67   67     33   55   63   66   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Y    65_A     Y    65_A     67   67   67     12   54   63   66   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q    66_A     Q    66_A     67   67   67      6   38   63   66   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q    67_A     Q    67_A     67   67   67     13   55   63   66   66   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     N    68_A     N    68_A     67   67   67      3    3    3    7   58   62   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
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     38     55     63     66     66     66     67     67     67     67     67     67     67     67     67     67     67     67     67     67 
GDT PERCENT_AT  56.72  82.09  94.03  98.51  98.51  98.51 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.31   0.50   0.67   0.80   0.80   0.80   0.96   0.96   0.96   0.96   0.96   0.96   0.96   0.96   0.96   0.96   0.96   0.96   0.96   0.96
GDT RMS_ALL_AT   1.13   1.07   1.00   0.98   0.98   0.98   0.96   0.96   0.96   0.96   0.96   0.96   0.96   0.96   0.96   0.96   0.96   0.96   0.96   0.96

# Checking swapping
#   possible swapping detected:  E     5_A      E     5_A
#   possible swapping detected:  Y    15_A      Y    15_A
#   possible swapping detected:  E    35_A      E    35_A
#   possible swapping detected:  E    40_A      E    40_A
#   possible swapping detected:  E    60_A      E    60_A
#   possible swapping detected:  Y    65_A      Y    65_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     2_A      S     2_A     2.292     0    0.098   0.765     4.332   68.810   61.587
LGA    P     3_A      P     3_A     0.808     0    0.066   0.075     1.436   85.952   86.599
LGA    E     4_A      E     4_A     1.880     0    0.045   0.610     4.546   72.857   56.032
LGA    E     5_A      E     5_A     1.755     0    0.050   0.784     5.820   79.405   60.159
LGA    Q     6_A      Q     6_A     0.849     0    0.044   1.032     3.312   90.595   79.259
LGA    K     7_A      K     7_A     0.803     0    0.023   0.178     2.506   90.476   80.847
LGA    Q     8_A      Q     8_A     1.325     0    0.033   0.954     5.601   81.429   62.646
LGA    M     9_A      M     9_A     1.123     0    0.034   0.676     1.679   85.952   82.619
LGA    L    10_A      L    10_A     0.341     0    0.054   0.164     0.676  100.000   98.810
LGA    G    11_A      G    11_A     0.304     0    0.029   0.029     0.460  100.000  100.000
LGA    E    12_A      E    12_A     0.322     0    0.078   0.810     3.402   97.619   83.915
LGA    A    13_A      A    13_A     0.566     0    0.060   0.059     0.871   92.857   92.381
LGA    I    14_A      I    14_A     0.380     0    0.020   1.379     4.278  100.000   82.381
LGA    Y    15_A      Y    15_A     0.416     0    0.035   0.429     2.113  100.000   87.103
LGA    P    16_A      P    16_A     0.701     0    0.025   0.082     0.879   90.476   93.197
LGA    K    17_A      K    17_A     0.641     0    0.028   0.984     2.390   92.857   83.757
LGA    V    18_A      V    18_A     0.389     0    0.049   1.098     2.360   92.857   85.850
LGA    A    19_A      A    19_A     0.704     0    0.068   0.067     1.079   88.214   90.571
LGA    A    20_A      A    20_A     1.015     0    0.113   0.116     1.663   81.548   81.524
LGA    S    21_A      S    21_A     1.145     0    0.214   0.666     1.840   90.595   86.111
LGA    Q    22_A      Q    22_A     0.810     0    0.168   0.323     1.370   90.476   88.466
LGA    P    23_A      P    23_A     1.300     0    0.071   0.349     1.417   81.429   84.014
LGA    E    24_A      E    24_A     1.272     0    0.042   0.236     2.640   81.429   74.021
LGA    L    25_A      L    25_A     1.042     0    0.083   0.194     1.307   85.952   85.952
LGA    A    26_A      A    26_A     0.754     0    0.023   0.047     0.846   90.476   90.476
LGA    G    27_A      G    27_A     0.720     0    0.019   0.019     0.808   90.476   90.476
LGA    K    28_A      K    28_A     0.723     0    0.028   0.525     2.720   90.476   79.947
LGA    L    29_A      L    29_A     0.482     0    0.044   0.106     1.099   92.857   90.536
LGA    T    30_A      T    30_A     0.528     0    0.051   0.111     0.772   92.857   91.837
LGA    G    31_A      G    31_A     0.498     0    0.034   0.034     0.526   97.619   97.619
LGA    M    32_A      M    32_A     0.391     0    0.022   1.011     2.687  100.000   88.095
LGA    I    33_A      I    33_A     0.548     0    0.018   1.214     3.934   92.857   78.393
LGA    L    34_A      L    34_A     0.507     0    0.085   0.173     0.803   97.619   94.048
LGA    E    35_A      E    35_A     0.523     0    0.025   1.071     3.784   97.619   75.714
LGA    L    36_A      L    36_A     0.428     0    0.021   0.925     2.631   97.619   89.048
LGA    P    37_A      P    37_A     0.628     0    0.038   0.368     1.631   90.476   87.959
LGA    V    38_A      V    38_A     0.702     0    0.026   0.973     3.112   90.476   82.177
LGA    T    39_A      T    39_A     0.492     0    0.037   1.100     2.740   95.238   85.034
LGA    E    40_A      E    40_A     0.258     0    0.029   0.544     1.916  100.000   90.794
LGA    L    41_A      L    41_A     0.483     0    0.029   0.074     0.636   95.238   94.048
LGA    L    42_A      L    42_A     0.546     0    0.033   1.046     3.732   92.857   83.631
LGA    H    43_A      H    43_A     0.376     0    0.038   0.500     1.633  100.000   90.810
LGA    L    44_A      L    44_A     0.302     0    0.046   1.119     2.443  100.000   91.190
LGA    L    45_A      L    45_A     0.588     0    0.081   0.219     1.541   92.857   87.202
LGA    E    46_A      E    46_A     0.651     0    0.058   0.635     3.600   90.476   75.873
LGA    E    47_A      E    47_A     0.614     0    0.064   0.778     2.981   90.476   82.328
LGA    S    48_A      S    48_A     0.370     0    0.052   0.616     2.314  100.000   94.127
LGA    E    49_A      E    49_A     0.746     0    0.127   0.767     4.239   90.476   73.386
LGA    A    50_A      A    50_A     0.281     0    0.030   0.038     0.381  100.000  100.000
LGA    L    51_A      L    51_A     0.223     0    0.062   0.156     0.469  100.000  100.000
LGA    D    52_A      D    52_A     0.294     0    0.037   0.255     0.886  100.000   97.619
LGA    A    53_A      A    53_A     0.465     0    0.034   0.036     0.530   97.619   98.095
LGA    K    54_A      K    54_A     0.416     0    0.029   0.572     2.157   97.619   87.884
LGA    V    55_A      V    55_A     0.269     0    0.028   0.109     0.340  100.000  100.000
LGA    N    56_A      N    56_A     0.356     0    0.030   0.251     0.862  100.000   98.810
LGA    E    57_A      E    57_A     0.427     0    0.038   0.512     1.482  100.000   96.878
LGA    A    58_A      A    58_A     0.443     0    0.034   0.040     0.585   97.619   98.095
LGA    L    59_A      L    59_A     0.372     0    0.037   0.879     2.761   95.238   89.940
LGA    E    60_A      E    60_A     0.743     0    0.043   0.995     4.652   90.476   71.534
LGA    V    61_A      V    61_A     0.836     0    0.025   0.896     2.038   88.214   82.993
LGA    L    62_A      L    62_A     0.863     0    0.034   1.401     3.530   85.952   74.940
LGA    K    63_A      K    63_A     1.186     0    0.040   1.130     3.835   81.429   72.593
LGA    E    64_A      E    64_A     1.117     0    0.083   1.191     5.191   81.548   64.497
LGA    Y    65_A      Y    65_A     1.306     0    0.028   1.315     8.559   79.286   50.198
LGA    Q    66_A      Q    66_A     1.371     0    0.143   0.187     3.701   85.952   69.418
LGA    Q    67_A      Q    67_A     0.828     0    0.490   0.700     4.614   83.690   69.048
LGA    N    68_A      N    68_A     4.195     0    0.365   0.507     7.258   29.643   24.524

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       67     268    268  100.00     519    519  100.00                67
SUMMARY(RMSD_GDC):     0.962          1.023                  1.809           90.823   83.576

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   68   67    4.0     67    0.96    95.149    97.846     6.310

LGA_LOCAL      RMSD:   0.962  Number of atoms:   67  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.962  Number of assigned atoms:   67 
Std_ASGN_ATOMS RMSD:   0.962  Standard rmsd on all 67 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.200644 * X  +  -0.295053 * Y  +  -0.934176 * Z  +  16.979597
  Y_new =  -0.878009 * X  +  -0.477142 * Y  +  -0.037879 * Z  +  15.184254
  Z_new =  -0.434559 * X  +   0.827816 * Y  +  -0.354796 * Z  +   2.270903 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.346132  0.449548  1.975706   [DEG:  -77.1277   25.7572  113.1996 ]
ZXZ: -1.530271  1.933492 -0.483405   [DEG:  -87.6781  110.7809  -27.6971 ]
 
# END of job
