
#######################################################
#                                                     #
#                        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   71 (  576),  selected   63 , name one
# Molecule2: number of CA atoms   72 (  603),  selected   63 , 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:    63       2_A - 72_A        2.68     2.68
  LCS_AVERAGE:     87.50

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    60       2_A - 69_A        1.72     2.91
  LCS_AVERAGE:     79.63

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    58       2_A - 67_A        0.43     3.25
  LCS_AVERAGE:     74.49

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   63
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     T     2_A     T     2_A     58   60   63     51   56   58   58   58   58   58   58   58   59   59   62   62   63   63   63   63   63   63   63 
LCS_GDT     S     3_A     S     3_A     58   60   63     24   56   58   58   58   58   58   58   58   59   59   62   62   63   63   63   63   63   63   63 
LCS_GDT     L     4_A     L     4_A     58   60   63     45   56   58   58   58   58   58   58   58   59   59   62   62   63   63   63   63   63   63   63 
LCS_GDT     I     5_A     I     5_A     58   60   63     51   56   58   58   58   58   58   58   58   59   59   62   62   63   63   63   63   63   63   63 
LCS_GDT     E     6_A     E     6_A     58   60   63     51   56   58   58   58   58   58   58   58   59   59   62   62   63   63   63   63   63   63   63 
LCS_GDT     E     7_A     E     7_A     58   60   63     51   56   58   58   58   58   58   58   58   59   59   62   62   63   63   63   63   63   63   63 
LCS_GDT     L     8_A     L     8_A     58   60   63     51   56   58   58   58   58   58   58   58   59   59   62   62   63   63   63   63   63   63   63 
LCS_GDT     I     9_A     I     9_A     58   60   63     51   56   58   58   58   58   58   58   58   59   59   62   62   63   63   63   63   63   63   63 
LCS_GDT     R    10_A     R    10_A     58   60   63     51   56   58   58   58   58   58   58   58   59   59   62   62   63   63   63   63   63   63   63 
LCS_GDT     R    11_A     R    11_A     58   60   63     51   56   58   58   58   58   58   58   58   59   59   62   62   63   63   63   63   63   63   63 
LCS_GDT     S    12_A     S    12_A     58   60   63     51   56   58   58   58   58   58   58   58   59   59   62   62   63   63   63   63   63   63   63 
LCS_GDT     E    13_A     E    13_A     58   60   63     51   56   58   58   58   58   58   58   58   59   59   62   62   63   63   63   63   63   63   63 
LCS_GDT     E    14_A     E    14_A     58   60   63     51   56   58   58   58   58   58   58   58   59   59   62   62   63   63   63   63   63   63   63 
LCS_GDT     Q    15_A     Q    15_A     58   60   63     51   56   58   58   58   58   58   58   58   59   59   62   62   63   63   63   63   63   63   63 
LCS_GDT     Q    16_A     Q    16_A     58   60   63     51   56   58   58   58   58   58   58   58   59   59   62   62   63   63   63   63   63   63   63 
LCS_GDT     R    17_A     R    17_A     58   60   63     51   56   58   58   58   58   58   58   58   59   59   62   62   63   63   63   63   63   63   63 
LCS_GDT     R    18_A     R    18_A     58   60   63     51   56   58   58   58   58   58   58   58   59   59   62   62   63   63   63   63   63   63   63 
LCS_GDT     N    19_A     N    19_A     58   60   63     51   56   58   58   58   58   58   58   58   59   59   62   62   63   63   63   63   63   63   63 
LCS_GDT     E    20_A     E    20_A     58   60   63     51   56   58   58   58   58   58   58   58   59   59   62   62   63   63   63   63   63   63   63 
LCS_GDT     E    21_A     E    21_A     58   60   63     51   56   58   58   58   58   58   58   58   59   59   62   62   63   63   63   63   63   63   63 
LCS_GDT     A    22_A     A    22_A     58   60   63     51   56   58   58   58   58   58   58   58   59   59   62   62   63   63   63   63   63   63   63 
LCS_GDT     L    23_A     L    23_A     58   60   63     51   56   58   58   58   58   58   58   58   59   59   62   62   63   63   63   63   63   63   63 
LCS_GDT     R    24_A     R    24_A     58   60   63     19   56   58   58   58   58   58   58   58   59   59   62   62   63   63   63   63   63   63   63 
LCS_GDT     Q    33_A     Q    33_A     58   60   63      9   56   58   58   58   58   58   58   58   59   59   62   62   63   63   63   63   63   63   63 
LCS_GDT     L    34_A     L    34_A     58   60   63     51   56   58   58   58   58   58   58   58   59   59   62   62   63   63   63   63   63   63   63 
LCS_GDT     L    35_A     L    35_A     58   60   63     51   56   58   58   58   58   58   58   58   59   59   62   62   63   63   63   63   63   63   63 
LCS_GDT     S    36_A     S    36_A     58   60   63     51   56   58   58   58   58   58   58   58   59   59   62   62   63   63   63   63   63   63   63 
LCS_GDT     G    37_A     G    37_A     58   60   63     51   56   58   58   58   58   58   58   58   59   59   62   62   63   63   63   63   63   63   63 
LCS_GDT     I    38_A     I    38_A     58   60   63     51   56   58   58   58   58   58   58   58   59   59   62   62   63   63   63   63   63   63   63 
LCS_GDT     V    39_A     V    39_A     58   60   63     51   56   58   58   58   58   58   58   58   59   59   62   62   63   63   63   63   63   63   63 
LCS_GDT     Q    40_A     Q    40_A     58   60   63     51   56   58   58   58   58   58   58   58   59   59   62   62   63   63   63   63   63   63   63 
LCS_GDT     Q    41_A     Q    41_A     58   60   63     51   56   58   58   58   58   58   58   58   59   59   62   62   63   63   63   63   63   63   63 
LCS_GDT     Q    42_A     Q    42_A     58   60   63     51   56   58   58   58   58   58   58   58   59   59   62   62   63   63   63   63   63   63   63 
LCS_GDT     N    43_A     N    43_A     58   60   63     51   56   58   58   58   58   58   58   58   59   59   62   62   63   63   63   63   63   63   63 
LCS_GDT     N    44_A     N    44_A     58   60   63     51   56   58   58   58   58   58   58   58   59   59   62   62   63   63   63   63   63   63   63 
LCS_GDT     L    45_A     L    45_A     58   60   63     51   56   58   58   58   58   58   58   58   59   59   62   62   63   63   63   63   63   63   63 
LCS_GDT     L    46_A     L    46_A     58   60   63     51   56   58   58   58   58   58   58   58   59   59   62   62   63   63   63   63   63   63   63 
LCS_GDT     R    47_A     R    47_A     58   60   63     51   56   58   58   58   58   58   58   58   59   59   62   62   63   63   63   63   63   63   63 
LCS_GDT     A    48_A     A    48_A     58   60   63     51   56   58   58   58   58   58   58   58   59   59   62   62   63   63   63   63   63   63   63 
LCS_GDT     I    49_A     I    49_A     58   60   63     51   56   58   58   58   58   58   58   58   59   59   62   62   63   63   63   63   63   63   63 
LCS_GDT     E    50_A     E    50_A     58   60   63     51   56   58   58   58   58   58   58   58   59   59   62   62   63   63   63   63   63   63   63 
LCS_GDT     A    51_A     A    51_A     58   60   63     51   56   58   58   58   58   58   58   58   59   59   62   62   63   63   63   63   63   63   63 
LCS_GDT     Q    52_A     Q    52_A     58   60   63     51   56   58   58   58   58   58   58   58   59   59   62   62   63   63   63   63   63   63   63 
LCS_GDT     Q    53_A     Q    53_A     58   60   63     51   56   58   58   58   58   58   58   58   59   59   62   62   63   63   63   63   63   63   63 
LCS_GDT     H    54_A     H    54_A     58   60   63     51   56   58   58   58   58   58   58   58   59   59   62   62   63   63   63   63   63   63   63 
LCS_GDT     L    55_A     L    55_A     58   60   63     51   56   58   58   58   58   58   58   58   59   59   62   62   63   63   63   63   63   63   63 
LCS_GDT     L    56_A     L    56_A     58   60   63     51   56   58   58   58   58   58   58   58   59   59   62   62   63   63   63   63   63   63   63 
LCS_GDT     Q    57_A     Q    57_A     58   60   63     51   56   58   58   58   58   58   58   58   59   59   62   62   63   63   63   63   63   63   63 
LCS_GDT     L    58_A     L    58_A     58   60   63     51   56   58   58   58   58   58   58   58   59   59   62   62   63   63   63   63   63   63   63 
LCS_GDT     T    59_A     T    59_A     58   60   63     51   56   58   58   58   58   58   58   58   59   59   62   62   63   63   63   63   63   63   63 
LCS_GDT     V    60_A     V    60_A     58   60   63     51   56   58   58   58   58   58   58   58   59   59   62   62   63   63   63   63   63   63   63 
LCS_GDT     W    61_A     W    61_A     58   60   63     32   56   58   58   58   58   58   58   58   59   59   62   62   63   63   63   63   63   63   63 
LCS_GDT     G    62_A     G    62_A     58   60   63     51   56   58   58   58   58   58   58   58   59   59   62   62   63   63   63   63   63   63   63 
LCS_GDT     I    63_A     I    63_A     58   60   63     51   56   58   58   58   58   58   58   58   59   59   62   62   63   63   63   63   63   63   63 
LCS_GDT     K    64_A     K    64_A     58   60   63     51   56   58   58   58   58   58   58   58   59   59   62   62   63   63   63   63   63   63   63 
LCS_GDT     Q    65_A     Q    65_A     58   60   63     51   56   58   58   58   58   58   58   58   59   59   62   62   63   63   63   63   63   63   63 
LCS_GDT     L    66_A     L    66_A     58   60   63      7   56   58   58   58   58   58   58   58   59   59   62   62   63   63   63   63   63   63   63 
LCS_GDT     Q    67_A     Q    67_A     58   60   63     12   53   58   58   58   58   58   58   58   59   59   62   62   63   63   63   63   63   63   63 
LCS_GDT     A    68_A     A    68_A      3   60   63      3    4    5   11   13   41   45   49   56   59   59   62   62   63   63   63   63   63   63   63 
LCS_GDT     R    69_A     R    69_A      3   60   63      3    4    5   17   32   36   43   47   50   52   54   62   62   63   63   63   63   63   63   63 
LCS_GDT     I    70_A     I    70_A      3    4   63      3    3   13   17   32   36   38   47   50   52   54   62   62   63   63   63   63   63   63   63 
LCS_GDT     L    71_A     L    71_A      3    4   63      4    6   19   28   32   38   43   47   50   59   59   62   62   63   63   63   63   63   63   63 
LCS_GDT     A    72_A     A    72_A      3    4   63      3    3    3    4    4    4    5   10   13   14   35   53   55   63   63   63   63   63   63   63 
LCS_AVERAGE  LCS_A:  80.54  (  74.49   79.63   87.50 )

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     51     56     58     58     58     58     58     58     58     59     59     62     62     63     63     63     63     63     63     63 
GDT PERCENT_AT  70.83  77.78  80.56  80.56  80.56  80.56  80.56  80.56  80.56  81.94  81.94  86.11  86.11  87.50  87.50  87.50  87.50  87.50  87.50  87.50
GDT RMS_LOCAL    0.27   0.35   0.43   0.43   0.43   0.43   0.43   0.43   0.43   1.12   1.12   2.32   2.32   2.68   2.68   2.68   2.68   2.68   2.68   2.68
GDT RMS_ALL_AT   3.27   3.28   3.25   3.25   3.25   3.25   3.25   3.25   3.25   3.12   3.12   2.70   2.70   2.68   2.68   2.68   2.68   2.68   2.68   2.68

# Checking swapping
#   possible swapping detected:  E    13_A      E    13_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    T     2_A      T     2_A     0.445     0    0.569   1.388     4.785   88.810   68.707
LGA    S     3_A      S     3_A     1.057     0    0.096   0.143     2.458   88.214   81.746
LGA    L     4_A      L     4_A     0.642     0    0.028   0.102     0.937   95.238   92.857
LGA    I     5_A      I     5_A     0.241     0    0.024   0.138     0.638  100.000   98.810
LGA    E     6_A      E     6_A     0.374     0    0.070   0.826     4.286  100.000   80.370
LGA    E     7_A      E     7_A     0.297     0    0.024   0.924     3.889  100.000   85.026
LGA    L     8_A      L     8_A     0.238     0    0.031   0.028     0.493  100.000  100.000
LGA    I     9_A      I     9_A     0.325     0    0.037   0.115     0.713   97.619   97.619
LGA    R    10_A      R    10_A     0.199     0    0.020   1.078     2.809  100.000   90.519
LGA    R    11_A      R    11_A     0.248     0    0.009   0.920     3.745  100.000   81.861
LGA    S    12_A      S    12_A     0.207     0    0.022   0.067     0.266  100.000  100.000
LGA    E    13_A      E    13_A     0.195     0    0.013   0.776     3.437  100.000   84.974
LGA    E    14_A      E    14_A     0.222     0    0.024   0.666     2.572  100.000   83.492
LGA    Q    15_A      Q    15_A     0.183     0    0.032   0.165     0.567  100.000   98.942
LGA    Q    16_A      Q    16_A     0.196     0    0.000   0.031     0.507  100.000   98.942
LGA    R    17_A      R    17_A     0.086     0    0.017   1.033     3.939  100.000   91.429
LGA    R    18_A      R    18_A     0.093     0    0.026   1.162     4.878  100.000   83.333
LGA    N    19_A      N    19_A     0.121     0    0.027   0.045     0.319  100.000  100.000
LGA    E    20_A      E    20_A     0.220     0    0.032   0.317     1.342  100.000   96.878
LGA    E    21_A      E    21_A     0.436     0    0.023   0.240     2.018  100.000   89.841
LGA    A    22_A      A    22_A     0.446     0    0.030   0.028     0.546  100.000   98.095
LGA    L    23_A      L    23_A     0.374     0    0.071   0.198     1.236   95.238   91.786
LGA    R    24_A      R    24_A     0.862     0    0.265   1.246     7.022   83.810   62.511
LGA    Q    33_A      Q    33_A     1.063     0    0.037   1.070     4.229   85.952   73.333
LGA    L    34_A      L    34_A     0.266     0    0.053   0.109     1.008  100.000   95.298
LGA    L    35_A      L    35_A     0.145     0    0.017   0.485     1.711  100.000   94.226
LGA    S    36_A      S    36_A     0.451     0    0.036   0.668     2.568  100.000   91.270
LGA    G    37_A      G    37_A     0.362     0    0.020   0.020     0.388  100.000  100.000
LGA    I    38_A      I    38_A     0.095     0    0.000   0.077     0.390  100.000  100.000
LGA    V    39_A      V    39_A     0.178     0    0.012   0.072     0.489  100.000  100.000
LGA    Q    40_A      Q    40_A     0.421     0    0.025   1.211     4.185  100.000   85.926
LGA    Q    41_A      Q    41_A     0.411     0    0.008   0.139     0.460  100.000  100.000
LGA    Q    42_A      Q    42_A     0.173     0    0.039   0.183     1.029  100.000   94.762
LGA    N    43_A      N    43_A     0.175     0    0.027   1.340     3.717  100.000   81.429
LGA    N    44_A      N    44_A     0.223     0    0.027   0.080     0.552  100.000   98.810
LGA    L    45_A      L    45_A     0.234     0    0.015   0.171     0.812  100.000   98.810
LGA    L    46_A      L    46_A     0.120     0    0.000   1.388     3.610  100.000   83.155
LGA    R    47_A      R    47_A     0.126     0    0.008   0.931     2.421  100.000   93.593
LGA    A    48_A      A    48_A     0.167     0    0.030   0.038     0.172  100.000  100.000
LGA    I    49_A      I    49_A     0.281     0    0.023   0.113     0.606  100.000   98.810
LGA    E    50_A      E    50_A     0.284     0    0.034   0.073     0.377  100.000  100.000
LGA    A    51_A      A    51_A     0.296     0    0.017   0.013     0.317  100.000  100.000
LGA    Q    52_A      Q    52_A     0.221     0    0.018   0.089     0.684  100.000   97.884
LGA    Q    53_A      Q    53_A     0.221     0    0.000   0.316     0.957  100.000   95.767
LGA    H    54_A      H    54_A     0.352     0    0.015   1.140     2.627  100.000   89.333
LGA    L    55_A      L    55_A     0.239     0    0.025   0.121     0.907  100.000   96.429
LGA    L    56_A      L    56_A     0.120     0    0.020   1.368     3.247  100.000   85.000
LGA    Q    57_A      Q    57_A     0.275     0    0.063   1.389     4.495  100.000   78.942
LGA    L    58_A      L    58_A     0.306     0    0.015   0.138     0.759  100.000   97.619
LGA    T    59_A      T    59_A     0.086     0    0.027   0.039     0.229  100.000  100.000
LGA    V    60_A      V    60_A     0.383     0    0.036   0.088     0.631   97.619   98.639
LGA    W    61_A      W    61_A     0.718     0    0.086   1.300     9.802   95.238   45.306
LGA    G    62_A      G    62_A     0.360     0    0.049   0.049     0.409  100.000  100.000
LGA    I    63_A      I    63_A     0.218     0    0.000   0.085     0.604  100.000   98.810
LGA    K    64_A      K    64_A     0.441     0    0.016   1.105     6.173   97.619   73.228
LGA    Q    65_A      Q    65_A     0.228     0    0.008   0.829     3.535   95.238   83.757
LGA    L    66_A      L    66_A     0.723     0    0.620   1.354     5.476   78.095   65.774
LGA    Q    67_A      Q    67_A     1.624     0    0.598   0.662     3.656   61.905   68.254
LGA    A    68_A      A    68_A     8.276     0    0.613   0.578    10.889    5.833    4.667
LGA    R    69_A      R    69_A    11.221     0    0.608   1.297    14.133    0.357    0.130
LGA    I    70_A      I    70_A    11.854     0    0.599   1.721    13.007    0.000    0.000
LGA    L    71_A      L    71_A    10.796     0    0.481   1.574    12.337    0.000    0.000
LGA    A    72_A      A    72_A    14.219     0    0.505   0.470    17.595    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       63     252    252  100.00     519    519  100.00                72
SUMMARY(RMSD_GDC):     2.676          2.782                  3.171           78.705   72.593

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   71   72    4.0     58    0.43    81.597    81.226    10.848

LGA_LOCAL      RMSD:   0.435  Number of atoms:   58  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   3.248  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:   2.676  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.298716 * X  +  -0.471641 * Y  +  -0.829653 * Z  + 103.839165
  Y_new =  -0.946137 * X  +   0.260112 * Y  +   0.192788 * Z  + -16.249617
  Z_new =   0.124876 * X  +   0.842554 * Y  +  -0.523936 * Z  +  36.665245 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.876613 -0.125203  2.127122   [DEG: -107.5220   -7.1736  121.8751 ]
ZXZ: -1.799116  2.122262  0.147140   [DEG: -103.0817  121.5967    8.4305 ]
 
# END of job
