
#######################################################
#                                                     #
#                        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        0.68     0.68
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    67       2_A - 68_A        0.68     0.68
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    67       2_A - 68_A        0.68     0.68
  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     14   51   63   67   67   67   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     27   58   65   67   67   67   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     19   58   65   67   67   67   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     16   58   65   67   67   67   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     28   60   65   67   67   67   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     47   60   65   67   67   67   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     27   60   65   67   67   67   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     41   60   65   67   67   67   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     56   60   65   67   67   67   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     56   60   65   67   67   67   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     56   60   65   67   67   67   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     56   60   65   67   67   67   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     56   60   65   67   67   67   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     56   60   65   67   67   67   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     56   60   65   67   67   67   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     56   60   65   67   67   67   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     56   60   65   67   67   67   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     56   60   65   67   67   67   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     56   60   65   67   67   67   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     56   60   65   67   67   67   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     56   60   65   67   67   67   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     56   60   65   67   67   67   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     56   60   65   67   67   67   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     56   60   65   67   67   67   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     56   60   65   67   67   67   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     56   60   65   67   67   67   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     56   60   65   67   67   67   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     56   60   65   67   67   67   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     56   60   65   67   67   67   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     56   60   65   67   67   67   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     56   60   65   67   67   67   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     56   60   65   67   67   67   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     56   60   65   67   67   67   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     56   60   65   67   67   67   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     56   60   65   67   67   67   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     56   60   65   67   67   67   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     56   60   65   67   67   67   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     56   60   65   67   67   67   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     56   60   65   67   67   67   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     56   60   65   67   67   67   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     56   60   65   67   67   67   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     56   60   65   67   67   67   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     56   60   65   67   67   67   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     56   60   65   67   67   67   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     56   60   65   67   67   67   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     56   60   65   67   67   67   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     56   60   65   67   67   67   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     56   60   65   67   67   67   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     56   60   65   67   67   67   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     56   60   65   67   67   67   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     56   60   65   67   67   67   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     56   60   65   67   67   67   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     56   60   65   67   67   67   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     56   60   65   67   67   67   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     56   60   65   67   67   67   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     56   60   65   67   67   67   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     56   60   65   67   67   67   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     56   60   65   67   67   67   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     56   60   65   67   67   67   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     56   60   65   67   67   67   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     56   60   65   67   67   67   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     56   60   65   67   67   67   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     56   60   65   67   67   67   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     56   60   65   67   67   67   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     38   59   65   67   67   67   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      3   59   65   67   67   67   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   41   64   67   67   67   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     56     60     65     67     67     67     67     67     67     67     67     67     67     67     67     67     67     67     67     67 
GDT PERCENT_AT  83.58  89.55  97.01 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.25   0.39   0.56   0.68   0.68   0.68   0.68   0.68   0.68   0.68   0.68   0.68   0.68   0.68   0.68   0.68   0.68   0.68   0.68   0.68
GDT RMS_ALL_AT   0.79   0.72   0.69   0.68   0.68   0.68   0.68   0.68   0.68   0.68   0.68   0.68   0.68   0.68   0.68   0.68   0.68   0.68   0.68   0.68

# Checking swapping
#   possible swapping detected:  E     4_A      E     4_A
#   possible swapping detected:  E     5_A      E     5_A
#   possible swapping detected:  E    12_A      E    12_A
#   possible swapping detected:  Y    15_A      Y    15_A
#   possible swapping detected:  E    24_A      E    24_A
#   possible swapping detected:  E    47_A      E    47_A
#   possible swapping detected:  E    49_A      E    49_A
#   possible swapping detected:  E    57_A      E    57_A
#   possible swapping detected:  E    60_A      E    60_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     2_A      S     2_A     2.053     0    0.026   0.072     2.193   68.810   68.810
LGA    P     3_A      P     3_A     1.363     0    0.012   0.039     1.588   79.286   77.755
LGA    E     4_A      E     4_A     1.427     0    0.023   0.688     4.373   81.429   65.132
LGA    E     5_A      E     5_A     1.444     0    0.050   0.496     4.180   83.690   67.725
LGA    Q     6_A      Q     6_A     1.021     0    0.019   0.293     1.401   85.952   83.439
LGA    K     7_A      K     7_A     0.481     0    0.030   0.625     2.215   97.619   87.937
LGA    Q     8_A      Q     8_A     0.812     0    0.054   0.780     4.381   92.857   76.402
LGA    M     9_A      M     9_A     0.653     0    0.029   0.823     1.735   95.238   88.393
LGA    L    10_A      L    10_A     0.363     0    0.030   0.084     0.702   97.619   97.619
LGA    G    11_A      G    11_A     0.509     0    0.050   0.050     0.561   92.857   92.857
LGA    E    12_A      E    12_A     0.490     0    0.011   0.802     3.025   97.619   87.143
LGA    A    13_A      A    13_A     0.361     0    0.028   0.043     0.544  100.000   98.095
LGA    I    14_A      I    14_A     0.285     0    0.012   0.047     0.356  100.000  100.000
LGA    Y    15_A      Y    15_A     0.289     0    0.008   0.229     0.547  100.000   97.619
LGA    P    16_A      P    16_A     0.289     0    0.013   0.311     1.254  100.000   97.347
LGA    K    17_A      K    17_A     0.264     0    0.017   0.729     2.764  100.000   90.265
LGA    V    18_A      V    18_A     0.371     0    0.007   0.089     0.469  100.000  100.000
LGA    A    19_A      A    19_A     0.406     0    0.018   0.020     0.652   97.619   98.095
LGA    A    20_A      A    20_A     0.397     0    0.058   0.078     0.602   97.619   98.095
LGA    S    21_A      S    21_A     0.215     0    0.067   0.091     0.567  100.000   98.413
LGA    Q    22_A      Q    22_A     0.153     0    0.046   0.099     0.504  100.000   98.942
LGA    P    23_A      P    23_A     0.321     0    0.061   0.062     0.622   97.619   98.639
LGA    E    24_A      E    24_A     0.370     0    0.074   0.608     1.697   95.238   91.852
LGA    L    25_A      L    25_A     0.288     0    0.036   0.063     0.516  100.000   97.619
LGA    A    26_A      A    26_A     0.276     0    0.016   0.022     0.502  100.000   98.095
LGA    G    27_A      G    27_A     0.354     0    0.016   0.016     0.370  100.000  100.000
LGA    K    28_A      K    28_A     0.377     0    0.030   1.167     5.772  100.000   76.508
LGA    L    29_A      L    29_A     0.093     0    0.025   0.088     0.609  100.000   98.810
LGA    T    30_A      T    30_A     0.272     0    0.013   0.072     0.447  100.000  100.000
LGA    G    31_A      G    31_A     0.447     0    0.035   0.035     0.447  100.000  100.000
LGA    M    32_A      M    32_A     0.250     0    0.027   0.088     0.393  100.000  100.000
LGA    I    33_A      I    33_A     0.163     0    0.036   0.081     0.320  100.000  100.000
LGA    L    34_A      L    34_A     0.179     0    0.024   0.093     0.310  100.000  100.000
LGA    E    35_A      E    35_A     0.399     0    0.046   0.755     3.215   97.619   75.661
LGA    L    36_A      L    36_A     0.390     0    0.034   0.094     0.506   97.619   98.810
LGA    P    37_A      P    37_A     0.588     0    0.073   0.320     1.421   90.476   89.184
LGA    V    38_A      V    38_A     0.688     0    0.024   0.045     0.932   90.476   90.476
LGA    T    39_A      T    39_A     0.713     0    0.024   0.978     2.892   90.476   80.952
LGA    E    40_A      E    40_A     0.373     0    0.041   1.095     3.899  100.000   77.937
LGA    L    41_A      L    41_A     0.380     0    0.024   0.054     0.511   97.619   98.810
LGA    L    42_A      L    42_A     0.535     0    0.045   0.055     0.898   95.238   92.857
LGA    H    43_A      H    43_A     0.442     0    0.016   1.153     2.632  100.000   85.714
LGA    L    44_A      L    44_A     0.346     0    0.032   0.075     0.428  100.000  100.000
LGA    L    45_A      L    45_A     0.443     0    0.026   0.046     0.542  100.000   97.619
LGA    E    46_A      E    46_A     0.441     0    0.041   0.831     3.002  100.000   80.159
LGA    E    47_A      E    47_A     0.452     0    0.050   0.728     3.370  100.000   85.767
LGA    S    48_A      S    48_A     0.333     0    0.022   0.072     0.676  100.000   98.413
LGA    E    49_A      E    49_A     0.312     0    0.081   0.214     0.748  100.000   96.825
LGA    A    50_A      A    50_A     0.151     0    0.008   0.022     0.178  100.000  100.000
LGA    L    51_A      L    51_A     0.089     0    0.025   0.075     0.490  100.000  100.000
LGA    D    52_A      D    52_A     0.071     0    0.009   0.125     0.513  100.000   98.810
LGA    A    53_A      A    53_A     0.262     0    0.050   0.066     0.426  100.000  100.000
LGA    K    54_A      K    54_A     0.103     0    0.023   0.575     1.723  100.000   92.804
LGA    V    55_A      V    55_A     0.091     0    0.018   0.043     0.201  100.000  100.000
LGA    N    56_A      N    56_A     0.194     0    0.036   0.052     0.289  100.000  100.000
LGA    E    57_A      E    57_A     0.250     0    0.014   0.268     0.952  100.000   98.942
LGA    A    58_A      A    58_A     0.243     0    0.025   0.025     0.250  100.000  100.000
LGA    L    59_A      L    59_A     0.310     0    0.022   0.219     0.849   97.619   95.238
LGA    E    60_A      E    60_A     0.513     0    0.112   1.093     4.891   95.238   76.667
LGA    V    61_A      V    61_A     0.477     0    0.025   0.061     0.746   95.238   95.918
LGA    L    62_A      L    62_A     0.762     0    0.056   0.065     1.016   88.214   88.214
LGA    K    63_A      K    63_A     0.949     0    0.013   0.212     1.307   88.214   85.450
LGA    E    64_A      E    64_A     0.622     0    0.032   0.911     3.026   90.476   75.926
LGA    Y    65_A      Y    65_A     0.904     0    0.069   1.134     5.813   85.952   65.119
LGA    Q    66_A      Q    66_A     1.504     0    0.013   0.155     3.278   77.143   66.138
LGA    Q    67_A      Q    67_A     1.306     0    0.337   0.565     3.621   81.548   69.153
LGA    N    68_A      N    68_A     2.127     0    0.097   0.996     5.707   49.762   45.119

# 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):     0.676          0.775                  1.361           95.075   90.064

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   68   67    4.0     67    0.68    97.388    98.953     8.636

LGA_LOCAL      RMSD:   0.676  Number of atoms:   67  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.676  Number of assigned atoms:   67 
Std_ASGN_ATOMS RMSD:   0.676  Standard rmsd on all 67 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.128266 * X  +   0.009283 * Y  +   0.991696 * Z  +   7.395593
  Y_new =  -0.903904 * X  +  -0.412527 * Y  +  -0.113049 * Z  +   3.912497
  Z_new =   0.408052 * X  +  -0.910898 * Y  +   0.061304 * Z  +   6.238268 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.711757 -0.420319 -1.503597   [DEG:  -98.0765  -24.0825  -86.1497 ]
ZXZ:  1.457291  1.509454  2.720431   [DEG:   83.4966   86.4853  155.8692 ]
 
# END of job
