
#######################################################
#                                                     #
#                        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   62 (  466),  selected   62 , name one
# Molecule2: number of CA atoms   63 (  471),  selected   62 , 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:    62       2_A - 63_A        2.22     2.22
  LCS_AVERAGE:     98.41

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    61       3_A - 63_A        1.92     2.24
  LCS_AVERAGE:     96.26

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    33       7_A - 39_A        1.00     2.70
  LCS_AVERAGE:     37.33

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   62
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     H     2_A     H     2_A      4   39   62      3    3    5    5    7   10   13   24   27   31   50   57   60   62   62   62   62   62   62   62 
LCS_GDT     I     3_A     I     3_A      4   61   62      3    3    4    6   25   41   47   55   61   61   61   61   61   62   62   62   62   62   62   62 
LCS_GDT     D     4_A     D     4_A     20   61   62      7   19   42   53   56   57   58   60   61   61   61   61   61   62   62   62   62   62   62   62 
LCS_GDT     C     5_A     C     5_A     21   61   62      7   16   38   53   56   57   58   60   61   61   61   61   61   62   62   62   62   62   62   62 
LCS_GDT     D     6_A     D     6_A     21   61   62      7   19   37   53   56   57   58   60   61   61   61   61   61   62   62   62   62   62   62   62 
LCS_GDT     K     7_A     K     7_A     33   61   62      7   20   42   53   56   57   58   60   61   61   61   61   61   62   62   62   62   62   62   62 
LCS_GDT     E     8_A     E     8_A     33   61   62      8   23   42   53   56   57   58   60   61   61   61   61   61   62   62   62   62   62   62   62 
LCS_GDT     C     9_A     C     9_A     33   61   62      7   22   42   53   56   57   58   60   61   61   61   61   61   62   62   62   62   62   62   62 
LCS_GDT     N    10_A     N    10_A     33   61   62      9   23   42   53   56   57   58   60   61   61   61   61   61   62   62   62   62   62   62   62 
LCS_GDT     R    11_A     R    11_A     33   61   62      9   23   42   53   56   57   58   60   61   61   61   61   61   62   62   62   62   62   62   62 
LCS_GDT     R    12_A     R    12_A     33   61   62      5   23   42   53   56   57   58   60   61   61   61   61   61   62   62   62   62   62   62   62 
LCS_GDT     C    13_A     C    13_A     33   61   62      5   23   42   53   56   57   58   60   61   61   61   61   61   62   62   62   62   62   62   62 
LCS_GDT     S    14_A     S    14_A     33   61   62      7   23   42   53   56   57   58   60   61   61   61   61   61   62   62   62   62   62   62   62 
LCS_GDT     K    15_A     K    15_A     33   61   62      4   14   26   49   56   57   57   60   61   61   61   61   61   62   62   62   62   62   62   62 
LCS_GDT     A    16_A     A    16_A     33   61   62      6   23   42   53   56   57   58   60   61   61   61   61   61   62   62   62   62   62   62   62 
LCS_GDT     S    17_A     S    17_A     33   61   62      7   23   42   53   56   57   57   60   61   61   61   61   61   62   62   62   62   62   62   62 
LCS_GDT     A    18_A     A    18_A     33   61   62      3   19   42   53   56   57   58   60   61   61   61   61   61   62   62   62   62   62   62   62 
LCS_GDT     H    19_A     H    19_A     33   61   62      4   23   42   53   56   57   58   60   61   61   61   61   61   62   62   62   62   62   62   62 
LCS_GDT     D    20_A     D    20_A     33   61   62      9   23   42   53   56   57   58   60   61   61   61   61   61   62   62   62   62   62   62   62 
LCS_GDT     R    21_A     R    21_A     33   61   62      7   23   42   53   56   57   58   60   61   61   61   61   61   62   62   62   62   62   62   62 
LCS_GDT     C    22_A     C    22_A     33   61   62      8   23   42   53   56   57   58   60   61   61   61   61   61   62   62   62   62   62   62   62 
LCS_GDT     L    23_A     L    23_A     33   61   62      9   23   42   53   56   57   58   60   61   61   61   61   61   62   62   62   62   62   62   62 
LCS_GDT     K    24_A     K    24_A     33   61   62      8   23   42   53   56   57   58   60   61   61   61   61   61   62   62   62   62   62   62   62 
LCS_GDT     Y    25_A     Y    25_A     33   61   62      8   23   42   53   56   57   58   60   61   61   61   61   61   62   62   62   62   62   62   62 
LCS_GDT     C    26_A     C    26_A     33   61   62      5   22   42   53   56   57   58   60   61   61   61   61   61   62   62   62   62   62   62   62 
LCS_GDT     G    27_A     G    27_A     33   61   62      5   20   42   53   56   57   58   60   61   61   61   61   61   62   62   62   62   62   62   62 
LCS_GDT     I    28_A     I    28_A     33   61   62      7   23   42   53   56   57   58   60   61   61   61   61   61   62   62   62   62   62   62   62 
LCS_GDT     C    29_A     C    29_A     33   61   62      7   23   42   53   56   57   58   60   61   61   61   61   61   62   62   62   62   62   62   62 
LCS_GDT     C    30_A     C    30_A     33   61   62      5   22   42   53   56   57   58   60   61   61   61   61   61   62   62   62   62   62   62   62 
LCS_GDT     E    31_A     E    31_A     33   61   62      4   17   42   53   56   57   58   60   61   61   61   61   61   62   62   62   62   62   62   62 
LCS_GDT     K    32_A     K    32_A     33   61   62      5   23   42   53   56   57   58   60   61   61   61   61   61   62   62   62   62   62   62   62 
LCS_GDT     C    33_A     C    33_A     33   61   62      8   23   42   53   56   57   58   60   61   61   61   61   61   62   62   62   62   62   62   62 
LCS_GDT     N    34_A     N    34_A     33   61   62      8   23   42   53   56   57   58   60   61   61   61   61   61   62   62   62   62   62   62   62 
LCS_GDT     C    35_A     C    35_A     33   61   62      8   23   42   53   56   57   58   60   61   61   61   61   61   62   62   62   62   62   62   62 
LCS_GDT     V    36_A     V    36_A     33   61   62      9   22   42   53   56   57   58   60   61   61   61   61   61   62   62   62   62   62   62   62 
LCS_GDT     P    37_A     P    37_A     33   61   62      9   22   42   53   56   57   58   60   61   61   61   61   61   62   62   62   62   62   62   62 
LCS_GDT     P    38_A     P    38_A     33   61   62      9   23   42   53   56   57   58   60   61   61   61   61   61   62   62   62   62   62   62   62 
LCS_GDT     G    39_A     G    39_A     33   61   62      8   23   42   53   56   57   58   60   61   61   61   61   61   62   62   62   62   62   62   62 
LCS_GDT     T    40_A     T    40_A      8   61   62      3    6   14   32   44   53   58   60   61   61   61   61   61   62   62   62   62   62   62   62 
LCS_GDT     Y    41_A     Y    41_A      8   61   62      3    7   15   28   42   51   58   60   61   61   61   61   61   62   62   62   62   62   62   62 
LCS_GDT     G    42_A     G    42_A     12   61   62      4    5   15   28   42   51   58   60   61   61   61   61   61   62   62   62   62   62   62   62 
LCS_GDT     N    43_A     N    43_A     13   61   62      4   19   41   53   56   57   58   60   61   61   61   61   61   62   62   62   62   62   62   62 
LCS_GDT     E    44_A     E    44_A     13   61   62      9   22   42   53   56   57   58   60   61   61   61   61   61   62   62   62   62   62   62   62 
LCS_GDT     D    45_A     D    45_A     13   61   62      8   22   42   53   56   57   58   60   61   61   61   61   61   62   62   62   62   62   62   62 
LCS_GDT     S    46_A     S    46_A     13   61   62      4   13   42   53   56   57   58   60   61   61   61   61   61   62   62   62   62   62   62   62 
LCS_GDT     C    47_A     C    47_A     13   61   62      4   22   42   53   56   57   58   60   61   61   61   61   61   62   62   62   62   62   62   62 
LCS_GDT     P    48_A     P    48_A     13   61   62      8   22   42   53   56   57   58   60   61   61   61   61   61   62   62   62   62   62   62   62 
LCS_GDT     C    49_A     C    49_A     13   61   62      4   19   34   53   56   57   58   60   61   61   61   61   61   62   62   62   62   62   62   62 
LCS_GDT     Y    50_A     Y    50_A     13   61   62      9   22   42   53   56   57   58   60   61   61   61   61   61   62   62   62   62   62   62   62 
LCS_GDT     A    51_A     A    51_A     13   61   62      9   22   42   53   56   57   58   60   61   61   61   61   61   62   62   62   62   62   62   62 
LCS_GDT     N    52_A     N    52_A     13   61   62      9   22   40   53   56   57   58   60   61   61   61   61   61   62   62   62   62   62   62   62 
LCS_GDT     L    53_A     L    53_A     13   61   62      5   20   42   53   56   57   58   60   61   61   61   61   61   62   62   62   62   62   62   62 
LCS_GDT     K    54_A     K    54_A     13   61   62      3   15   37   53   56   57   58   60   61   61   61   61   61   62   62   62   62   62   62   62 
LCS_GDT     N    55_A     N    55_A     13   61   62      5   18   32   53   56   57   58   60   61   61   61   61   61   62   62   62   62   62   62   62 
LCS_GDT     S    56_A     S    56_A     13   61   62      4   14   20   40   55   57   58   60   61   61   61   61   61   62   62   62   62   62   62   62 
LCS_GDT     K    57_A     K    57_A     13   61   62      5   15   32   47   56   57   58   60   61   61   61   61   61   62   62   62   62   62   62   62 
LCS_GDT     G    58_A     G    58_A     13   61   62      5   15   32   51   56   57   58   60   61   61   61   61   61   62   62   62   62   62   62   62 
LCS_GDT     G    59_A     G    59_A     13   61   62      5   15   33   53   56   57   58   60   61   61   61   61   61   62   62   62   62   62   62   62 
LCS_GDT     H    60_A     H    60_A     13   61   62      3   16   42   53   56   57   58   60   61   61   61   61   61   62   62   62   62   62   62   62 
LCS_GDT     K    61_A     K    61_A     13   61   62      3   17   42   53   56   57   58   60   61   61   61   61   61   62   62   62   62   62   62   62 
LCS_GDT     C    62_A     C    62_A     12   61   62      5   23   42   53   56   57   58   60   61   61   61   61   61   62   62   62   62   62   62   62 
LCS_GDT     P    63_A     P    63_A     12   61   62      3   23   42   53   56   57   58   60   61   61   61   61   61   62   62   62   62   62   62   62 
LCS_AVERAGE  LCS_A:  77.33  (  37.33   96.26   98.41 )

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      9     23     42     53     56     57     58     60     61     61     61     61     61     62     62     62     62     62     62     62 
GDT PERCENT_AT  14.29  36.51  66.67  84.13  88.89  90.48  92.06  95.24  96.83  96.83  96.83  96.83  96.83  98.41  98.41  98.41  98.41  98.41  98.41  98.41
GDT RMS_LOCAL    0.32   0.70   1.06   1.32   1.44   1.51   1.75   1.79   1.92   1.92   1.92   1.92   1.92   2.22   2.22   2.22   2.22   2.22   2.22   2.22
GDT RMS_ALL_AT   2.76   2.87   2.47   2.31   2.29   2.29   2.28   2.26   2.24   2.24   2.24   2.24   2.24   2.22   2.22   2.22   2.22   2.22   2.22   2.22

# Checking swapping
#   possible swapping detected:  Y    25_A      Y    25_A
#   possible swapping detected:  E    31_A      E    31_A
#   possible swapping detected:  Y    41_A      Y    41_A
#   possible swapping detected:  D    45_A      D    45_A
#   possible swapping detected:  Y    50_A      Y    50_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    H     2_A      H     2_A     9.551     0    0.539   0.772    15.896    7.976    3.238
LGA    I     3_A      I     3_A     5.744     0    0.149   1.278    11.986   26.548   14.405
LGA    D     4_A      D     4_A     0.898     0    0.549   0.748     2.606   86.071   75.476
LGA    C     5_A      C     5_A     1.707     0    0.149   0.240     2.378   75.000   72.937
LGA    D     6_A      D     6_A     1.566     0    0.027   0.672     3.514   77.143   69.286
LGA    K     7_A      K     7_A     0.764     0    0.077   0.973     3.838   90.476   76.561
LGA    E     8_A      E     8_A     0.874     0    0.024   0.695     4.111   85.952   72.593
LGA    C     9_A      C     9_A     1.251     0    0.073   0.093     1.546   81.429   80.000
LGA    N    10_A      N    10_A     0.576     0    0.100   0.650     2.208   90.476   87.262
LGA    R    11_A      R    11_A     1.142     0    0.048   1.176     8.037   83.690   51.385
LGA    R    12_A      R    12_A     1.346     0    0.047   1.467     6.571   81.429   63.030
LGA    C    13_A      C    13_A     1.113     0    0.197   0.241     3.101   83.690   77.698
LGA    S    14_A      S    14_A     1.062     0    0.110   0.647     3.063   75.476   73.730
LGA    K    15_A      K    15_A     2.888     0    0.055   0.995     3.809   57.262   56.720
LGA    A    16_A      A    16_A     1.759     0    0.030   0.031     2.081   68.810   71.333
LGA    S    17_A      S    17_A     2.483     0    0.031   0.673     4.639   62.857   56.667
LGA    A    18_A      A    18_A     1.944     0    0.125   0.123     2.054   70.833   71.238
LGA    H    19_A      H    19_A     1.783     0    0.168   0.805     3.802   68.929   63.000
LGA    D    20_A      D    20_A     1.409     0    0.165   0.181     1.866   81.429   77.143
LGA    R    21_A      R    21_A     1.511     0    0.064   1.252     8.714   79.286   47.229
LGA    C    22_A      C    22_A     1.080     0    0.113   0.156     1.374   83.690   85.952
LGA    L    23_A      L    23_A     0.833     0    0.085   0.159     1.616   92.857   86.071
LGA    K    24_A      K    24_A     1.949     0    0.067   0.475     5.232   72.857   57.302
LGA    Y    25_A      Y    25_A     2.003     0    0.023   0.380     3.299   68.810   61.746
LGA    C    26_A      C    26_A     1.738     0    0.074   0.183     2.024   72.857   72.937
LGA    G    27_A      G    27_A     1.730     0    0.191   0.191     2.582   68.929   68.929
LGA    I    28_A      I    28_A     1.487     0    0.088   0.695     4.272   81.429   71.667
LGA    C    29_A      C    29_A     1.512     0    0.055   0.691     1.617   77.143   77.143
LGA    C    30_A      C    30_A     1.377     0    0.040   0.098     2.129   79.286   75.794
LGA    E    31_A      E    31_A     1.288     0    0.027   0.408     3.299   81.429   71.587
LGA    K    32_A      K    32_A     1.220     0    0.055   1.013     6.459   83.690   61.693
LGA    C    33_A      C    33_A     0.850     0    0.620   0.538     3.584   74.286   72.619
LGA    N    34_A      N    34_A     0.925     0    0.194   0.316     2.925   90.595   77.857
LGA    C    35_A      C    35_A     1.150     0    0.019   0.449     1.841   83.690   80.079
LGA    V    36_A      V    36_A     0.548     0    0.202   0.237     1.754   92.857   88.027
LGA    P    37_A      P    37_A     0.189     0    0.062   0.189     0.444  100.000  100.000
LGA    P    38_A      P    38_A     1.241     0    0.063   0.093     1.566   83.690   82.789
LGA    G    39_A      G    39_A     1.801     0    0.178   0.178     2.468   68.810   68.810
LGA    T    40_A      T    40_A     4.305     0    0.558   0.517     5.332   37.619   35.034
LGA    Y    41_A      Y    41_A     4.508     0    0.108   1.225     5.195   34.286   32.937
LGA    G    42_A      G    42_A     4.285     0    0.595   0.595     5.531   34.762   34.762
LGA    N    43_A      N    43_A     1.361     0    0.234   0.286     1.916   77.143   78.214
LGA    E    44_A      E    44_A     0.539     0    0.131   0.780     3.302   90.476   82.222
LGA    D    45_A      D    45_A     1.152     0    0.168   0.721     2.741   81.548   75.298
LGA    S    46_A      S    46_A     1.623     0    0.080   0.230     1.960   77.143   75.714
LGA    C    47_A      C    47_A     0.727     0    0.037   0.376     1.638   92.857   87.619
LGA    P    48_A      P    48_A     0.465     0    0.052   0.327     1.294   92.976   93.265
LGA    C    49_A      C    49_A     1.701     0    0.093   0.229     2.973   72.976   68.968
LGA    Y    50_A      Y    50_A     0.837     0    0.078   0.267     2.700   88.214   80.357
LGA    A    51_A      A    51_A     0.908     0    0.127   0.141     1.526   83.810   85.143
LGA    N    52_A      N    52_A     1.327     0    0.094   0.312     2.651   81.429   75.179
LGA    L    53_A      L    53_A     1.095     0    0.093   0.701     2.528   79.286   78.452
LGA    K    54_A      K    54_A     1.392     0    0.071   1.214     3.727   81.429   70.265
LGA    N    55_A      N    55_A     1.846     0    0.023   0.306     2.615   69.048   67.917
LGA    S    56_A      S    56_A     3.498     0    0.148   0.658     5.824   46.905   41.032
LGA    K    57_A      K    57_A     2.646     0    0.163   0.499     4.834   57.143   52.804
LGA    G    58_A      G    58_A     2.485     0    0.081   0.081     2.485   64.762   64.762
LGA    G    59_A      G    59_A     1.667     0    0.024   0.024     1.902   79.405   79.405
LGA    H    60_A      H    60_A     1.225     0    0.139   1.335     8.127   85.952   51.714
LGA    K    61_A      K    61_A     1.378     0    0.075   0.737     1.873   79.405   80.635
LGA    C    62_A      C    62_A     2.027     0    0.094   0.137     2.246   66.786   66.111
LGA    P    63_A      P    63_A     1.915     0    0.266   0.378     2.392   68.810   70.544

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       62     248    248  100.00     466    466  100.00                63
SUMMARY(RMSD_GDC):     2.222          2.205                  3.133           73.267   67.465

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   62   63    4.0     60    1.79    78.571    87.662     3.168

LGA_LOCAL      RMSD:   1.794  Number of atoms:   60  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.262  Number of assigned atoms:   62 
Std_ASGN_ATOMS RMSD:   2.222  Standard rmsd on all 62 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.510382 * X  +   0.577134 * Y  +   0.637516 * Z  + -13.153056
  Y_new =   0.821560 * X  +  -0.546265 * Y  +  -0.163198 * Z  +   9.232553
  Z_new =   0.254065 * X  +   0.607051 * Y  +  -0.752954 * Z  + -18.918736 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.014909 -0.256881  2.463067   [DEG:   58.1500  -14.7182  141.1233 ]
ZXZ:  1.320187  2.423336  0.396372   [DEG:   75.6412  138.8469   22.7105 ]
 
# END of job
