
#######################################################
#                                                     #
#                        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        0.64     0.64
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    67       2_A - 68_A        0.64     0.64
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    67       2_A - 68_A        0.64     0.64
  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     15   52   65   66   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     29   62   65   66   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     27   62   65   66   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     19   62   65   66   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     32   62   65   66   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     54   62   65   66   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     48   62   65   66   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     48   62   65   66   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     55   62   65   66   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     55   62   65   66   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     55   62   65   66   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     55   62   65   66   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     55   62   65   66   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     55   62   65   66   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     55   62   65   66   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     55   62   65   66   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     55   62   65   66   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     55   62   65   66   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     55   62   65   66   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     55   62   65   66   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     55   62   65   66   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     55   62   65   66   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     55   62   65   66   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     55   62   65   66   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     55   62   65   66   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     55   62   65   66   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     55   62   65   66   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     55   62   65   66   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     55   62   65   66   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     55   62   65   66   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     55   62   65   66   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     55   62   65   66   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     55   62   65   66   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     55   62   65   66   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     55   62   65   66   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     55   62   65   66   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     55   62   65   66   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     55   62   65   66   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     55   62   65   66   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     55   62   65   66   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     55   62   65   66   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     55   62   65   66   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     55   62   65   66   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     55   62   65   66   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     55   62   65   66   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     55   62   65   66   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     55   62   65   66   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     55   62   65   66   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     55   62   65   66   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     55   62   65   66   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     55   62   65   66   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     55   62   65   66   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     55   62   65   66   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     55   62   65   66   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     55   62   65   66   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     55   62   65   66   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     55   62   65   66   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     55   62   65   66   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     55   62   65   66   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     55   62   65   66   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     55   62   65   66   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     55   61   65   66   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     55   62   65   66   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     55   62   65   66   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     54   61   65   66   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     50   61   65   66   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   22   47   64   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     55     62     65     66     67     67     67     67     67     67     67     67     67     67     67     67     67     67     67     67 
GDT PERCENT_AT  82.09  92.54  97.01  98.51 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.20   0.47   0.49   0.54   0.64   0.64   0.64   0.64   0.64   0.64   0.64   0.64   0.64   0.64   0.64   0.64   0.64   0.64   0.64   0.64
GDT RMS_ALL_AT   0.75   0.65   0.66   0.65   0.64   0.64   0.64   0.64   0.64   0.64   0.64   0.64   0.64   0.64   0.64   0.64   0.64   0.64   0.64   0.64

# 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    40_A      E    40_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
#   possible swapping detected:  E    64_A      E    64_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     1.837     0    0.023   0.071     1.909   72.857   72.857
LGA    P     3_A      P     3_A     1.329     0    0.010   0.039     1.513   81.429   80.204
LGA    E     4_A      E     4_A     1.174     0    0.022   0.633     3.638   83.690   67.725
LGA    E     5_A      E     5_A     1.205     0    0.055   0.517     3.649   85.952   71.005
LGA    Q     6_A      Q     6_A     0.966     0    0.014   0.277     1.338   88.214   84.444
LGA    K     7_A      K     7_A     0.294     0    0.031   0.625     1.923   97.619   88.836
LGA    Q     8_A      Q     8_A     0.566     0    0.059   0.787     4.127   97.619   79.524
LGA    M     9_A      M     9_A     0.500     0    0.031   0.827     1.707  100.000   90.774
LGA    L    10_A      L    10_A     0.440     0    0.027   0.102     0.733   97.619   97.619
LGA    G    11_A      G    11_A     0.528     0    0.047   0.047     0.615   92.857   92.857
LGA    E    12_A      E    12_A     0.565     0    0.013   0.799     2.952   95.238   86.878
LGA    A    13_A      A    13_A     0.396     0    0.020   0.035     0.556  100.000   98.095
LGA    I    14_A      I    14_A     0.308     0    0.016   0.053     0.328  100.000  100.000
LGA    Y    15_A      Y    15_A     0.327     0    0.010   0.329     1.015  100.000   93.690
LGA    P    16_A      P    16_A     0.237     0    0.018   0.296     1.177  100.000   97.347
LGA    K    17_A      K    17_A     0.203     0    0.015   0.767     3.108  100.000   90.370
LGA    V    18_A      V    18_A     0.253     0    0.008   0.082     0.366  100.000  100.000
LGA    A    19_A      A    19_A     0.224     0    0.029   0.027     0.477  100.000  100.000
LGA    A    20_A      A    20_A     0.145     0    0.068   0.088     0.397  100.000  100.000
LGA    S    21_A      S    21_A     0.130     0    0.068   0.098     0.351  100.000  100.000
LGA    Q    22_A      Q    22_A     0.169     0    0.053   0.101     0.553  100.000   98.942
LGA    P    23_A      P    23_A     0.241     0    0.067   0.068     0.648   97.619   98.639
LGA    E    24_A      E    24_A     0.378     0    0.071   0.691     2.041   95.238   91.852
LGA    L    25_A      L    25_A     0.410     0    0.044   0.070     0.724  100.000   95.238
LGA    A    26_A      A    26_A     0.221     0    0.011   0.014     0.378  100.000  100.000
LGA    G    27_A      G    27_A     0.424     0    0.014   0.014     0.431  100.000  100.000
LGA    K    28_A      K    28_A     0.466     0    0.032   1.083     5.093  100.000   76.667
LGA    L    29_A      L    29_A     0.187     0    0.034   0.087     0.664  100.000   98.810
LGA    T    30_A      T    30_A     0.184     0    0.015   0.081     0.330  100.000  100.000
LGA    G    31_A      G    31_A     0.461     0    0.029   0.029     0.461  100.000  100.000
LGA    M    32_A      M    32_A     0.263     0    0.027   0.095     0.402  100.000  100.000
LGA    I    33_A      I    33_A     0.202     0    0.039   0.086     0.333  100.000  100.000
LGA    L    34_A      L    34_A     0.216     0    0.029   0.082     0.333  100.000  100.000
LGA    E    35_A      E    35_A     0.477     0    0.010   0.737     3.122   97.619   77.249
LGA    L    36_A      L    36_A     0.392     0    0.039   0.090     0.528   97.619   98.810
LGA    P    37_A      P    37_A     0.447     0    0.076   0.314     1.305   95.238   93.265
LGA    V    38_A      V    38_A     0.682     0    0.021   0.029     0.949   90.476   90.476
LGA    T    39_A      T    39_A     0.686     0    0.028   0.968     2.999   90.476   82.041
LGA    E    40_A      E    40_A     0.402     0    0.047   0.879     3.567  100.000   85.026
LGA    L    41_A      L    41_A     0.405     0    0.025   0.045     0.562   97.619   98.810
LGA    L    42_A      L    42_A     0.577     0    0.044   0.058     0.898   92.857   91.667
LGA    H    43_A      H    43_A     0.524     0    0.017   1.154     2.748   95.238   83.810
LGA    L    44_A      L    44_A     0.395     0    0.035   0.064     0.543   97.619   98.810
LGA    L    45_A      L    45_A     0.504     0    0.022   0.064     0.578   92.857   91.667
LGA    E    46_A      E    46_A     0.457     0    0.050   0.851     3.044  100.000   80.159
LGA    E    47_A      E    47_A     0.468     0    0.048   0.718     3.176  100.000   86.614
LGA    S    48_A      S    48_A     0.297     0    0.024   0.084     0.644  100.000   98.413
LGA    E    49_A      E    49_A     0.317     0    0.082   0.200     0.654  100.000   97.884
LGA    A    50_A      A    50_A     0.181     0    0.006   0.018     0.190  100.000  100.000
LGA    L    51_A      L    51_A     0.080     0    0.022   0.081     0.423  100.000  100.000
LGA    D    52_A      D    52_A     0.049     0    0.007   0.189     0.741  100.000   97.619
LGA    A    53_A      A    53_A     0.330     0    0.059   0.075     0.549  100.000   98.095
LGA    K    54_A      K    54_A     0.070     0    0.021   0.584     1.589  100.000   93.862
LGA    V    55_A      V    55_A     0.095     0    0.019   0.050     0.274  100.000  100.000
LGA    N    56_A      N    56_A     0.242     0    0.034   0.071     0.307  100.000  100.000
LGA    E    57_A      E    57_A     0.299     0    0.012   0.233     0.861  100.000   98.942
LGA    A    58_A      A    58_A     0.216     0    0.023   0.024     0.261  100.000  100.000
LGA    L    59_A      L    59_A     0.285     0    0.019   0.191     0.815  100.000   96.429
LGA    E    60_A      E    60_A     0.399     0    0.113   1.067     4.837  100.000   78.783
LGA    V    61_A      V    61_A     0.271     0    0.019   0.070     0.389  100.000  100.000
LGA    L    62_A      L    62_A     0.598     0    0.043   0.088     0.911   92.857   91.667
LGA    K    63_A      K    63_A     0.722     0    0.015   0.192     1.359   90.476   87.460
LGA    E    64_A      E    64_A     0.323     0    0.031   0.785     3.409   97.619   84.497
LGA    Y    65_A      Y    65_A     0.680     0    0.061   0.811     3.305   92.857   77.897
LGA    Q    66_A      Q    66_A     1.227     0    0.019   0.153     3.232   83.690   70.741
LGA    Q    67_A      Q    67_A     0.913     0    0.388   0.696     4.113   88.214   73.175
LGA    N    68_A      N    68_A     2.673     0    0.666   0.927     6.488   43.333   41.786

# 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):     0.639          0.766                  1.260           95.860   91.015

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   68   67    4.0     67    0.64    97.761    99.084     9.072

LGA_LOCAL      RMSD:   0.639  Number of atoms:   67  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.639  Number of assigned atoms:   67 
Std_ASGN_ATOMS RMSD:   0.639  Standard rmsd on all 67 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.825524 * X  +   0.082897 * Y  +   0.558245 * Z  +   7.496206
  Y_new =   0.341375 * X  +  -0.714332 * Y  +   0.610895 * Z  +   3.071055
  Z_new =   0.449413 * X  +   0.694880 * Y  +   0.561400 * Z  +   5.886415 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.749481 -0.466109  0.891251   [DEG:  157.5337  -26.7061   51.0649 ]
ZXZ:  2.401197  0.974720  0.574087   [DEG:  137.5785   55.8474   32.8928 ]
 
# END of job
