
#######################################################
#                                                     #
#                        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   63 (  471),  selected   63 , name one
# Molecule2: number of CA atoms   63 (  471),  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       1_A - 63_A        1.81     1.81
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    63       1_A - 63_A        1.81     1.81
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    26      13_A - 38_A        0.99     2.26
  LONGEST_CONTINUOUS_SEGMENT:    26      14_A - 39_A        0.99     2.34
  LCS_AVERAGE:     31.17

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     A     1_A     A     1_A     13   63   63      4   13   23   49   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H     2_A     H     2_A     13   63   63      4   14   32   53   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     I     3_A     I     3_A     15   63   63      6   26   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D     4_A     D     4_A     21   63   63      7   22   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     5_A     C     5_A     21   63   63      7   16   38   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D     6_A     D     6_A     21   63   63      7   13   39   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K     7_A     K     7_A     21   63   63      7   25   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E     8_A     E     8_A     22   63   63     10   26   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     9_A     C     9_A     22   63   63      7   20   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    10_A     N    10_A     22   63   63     11   26   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    11_A     R    11_A     22   63   63      4   21   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    12_A     R    12_A     24   63   63      4   21   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    13_A     C    13_A     26   63   63      4   19   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    14_A     S    14_A     26   63   63      4   26   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    15_A     K    15_A     26   63   63      3    5   22   47   57   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    16_A     A    16_A     26   63   63      4   23   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    17_A     S    17_A     26   63   63      7   26   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    18_A     A    18_A     26   63   63      4   11   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H    19_A     H    19_A     26   63   63      5   26   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    20_A     D    20_A     26   63   63     11   26   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    21_A     R    21_A     26   63   63     11   26   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    22_A     C    22_A     26   63   63     11   26   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    23_A     L    23_A     26   63   63     11   26   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    24_A     K    24_A     26   63   63      6   26   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    25_A     Y    25_A     26   63   63      6   26   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    26_A     C    26_A     26   63   63      5   26   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    27_A     G    27_A     26   63   63      4   26   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     I    28_A     I    28_A     26   63   63      7   26   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    29_A     C    29_A     26   63   63      6   26   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    30_A     C    30_A     26   63   63      5   21   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    31_A     E    31_A     26   63   63      4   14   44   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    32_A     K    32_A     26   63   63      4   23   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    33_A     C    33_A     26   63   63      7   26   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    34_A     N    34_A     26   63   63      4   26   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    35_A     C    35_A     26   63   63      7   26   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    36_A     V    36_A     26   63   63     11   26   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    37_A     P    37_A     26   63   63     11   26   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    38_A     P    38_A     26   63   63      7   26   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    39_A     G    39_A     26   63   63      4   22   44   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     T    40_A     T    40_A      8   63   63      3    6   14   31   47   55   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    41_A     Y    41_A      8   63   63      3    7   16   29   43   53   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    42_A     G    42_A     12   63   63      3    6   16   29   44   53   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    43_A     N    43_A     13   63   63      6   19   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    44_A     E    44_A     13   63   63     11   22   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    45_A     D    45_A     13   63   63      7   26   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    46_A     S    46_A     13   63   63      6   14   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    47_A     C    47_A     13   63   63      6   20   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    48_A     P    48_A     13   63   63     11   26   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    49_A     C    49_A     13   63   63      4   20   39   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    50_A     Y    50_A     13   63   63     11   20   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    51_A     A    51_A     13   63   63     11   20   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    52_A     N    52_A     13   63   63      4   20   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    53_A     L    53_A     13   63   63      4   20   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    54_A     K    54_A     13   63   63      4   14   44   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    55_A     N    55_A     13   63   63      5   17   32   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    56_A     S    56_A     13   63   63      5    9   19   34   56   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    57_A     K    57_A     13   63   63      5   13   32   46   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    58_A     G    58_A     13   63   63      5   14   32   49   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    59_A     G    59_A     13   63   63      5   14   41   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H    60_A     H    60_A     13   63   63      5   18   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    61_A     K    61_A     12   63   63      5   20   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    62_A     C    62_A     12   63   63      7   26   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    63_A     P    63_A     12   63   63      7   26   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_AVERAGE  LCS_A:  77.06  (  31.17  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     11     26     46     54     58     60     61     63     63     63     63     63     63     63     63     63     63     63     63     63 
GDT PERCENT_AT  17.46  41.27  73.02  85.71  92.06  95.24  96.83 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.39   0.81   1.08   1.27   1.44   1.54   1.72   1.81   1.81   1.81   1.81   1.81   1.81   1.81   1.81   1.81   1.81   1.81   1.81   1.81
GDT RMS_ALL_AT   2.24   2.20   1.98   1.88   1.83   1.84   1.82   1.81   1.81   1.81   1.81   1.81   1.81   1.81   1.81   1.81   1.81   1.81   1.81   1.81

# Checking swapping
#   possible swapping detected:  E     8_A      E     8_A
#   possible swapping detected:  Y    41_A      Y    41_A
#   possible swapping detected:  E    44_A      E    44_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    A     1_A      A     1_A     2.699     0    0.097   0.140     3.346   64.881   61.905
LGA    H     2_A      H     2_A     1.875     0    0.013   1.076     3.667   75.119   63.857
LGA    I     3_A      I     3_A     0.351     0    0.058   0.918     2.781   90.595   85.238
LGA    D     4_A      D     4_A     1.052     0    0.068   1.067     3.660   83.690   71.786
LGA    C     5_A      C     5_A     1.912     0    0.089   0.232     2.524   72.857   68.889
LGA    D     6_A      D     6_A     1.541     0    0.016   0.539     3.501   81.667   72.560
LGA    K     7_A      K     7_A     0.437     0    0.085   0.539     3.157   92.857   80.317
LGA    E     8_A      E     8_A     1.029     0    0.055   0.432     1.619   81.548   84.497
LGA    C     9_A      C     9_A     1.377     0    0.082   0.091     1.857   81.429   78.571
LGA    N    10_A      N    10_A     0.558     0    0.121   0.385     1.417   88.214   88.214
LGA    R    11_A      R    11_A     1.401     0    0.026   1.490     5.726   79.286   62.771
LGA    R    12_A      R    12_A     1.363     0    0.022   1.453     6.614   81.429   62.424
LGA    C    13_A      C    13_A     1.127     0    0.258   0.273     3.058   81.548   76.270
LGA    S    14_A      S    14_A     1.118     0    0.066   0.667     3.347   73.452   72.381
LGA    K    15_A      K    15_A     3.143     0    0.156   1.020     4.839   57.262   51.323
LGA    A    16_A      A    16_A     1.812     0    0.061   0.070     2.219   70.833   72.952
LGA    S    17_A      S    17_A     1.976     0    0.026   0.688     3.821   70.833   65.238
LGA    A    18_A      A    18_A     1.959     0    0.056   0.062     2.131   70.833   69.619
LGA    H    19_A      H    19_A     1.697     0    0.203   1.173     3.334   68.929   66.619
LGA    D    20_A      D    20_A     1.340     0    0.198   0.227     1.981   81.429   78.214
LGA    R    21_A      R    21_A     1.491     0    0.067   0.935     4.478   83.690   64.545
LGA    C    22_A      C    22_A     1.024     0    0.081   0.128     1.321   85.952   87.460
LGA    L    23_A      L    23_A     1.011     0    0.066   0.169     1.803   85.952   82.619
LGA    K    24_A      K    24_A     2.170     0    0.092   0.430     5.031   66.786   54.339
LGA    Y    25_A      Y    25_A     2.025     0    0.019   0.738     3.173   70.833   67.024
LGA    C    26_A      C    26_A     1.540     0    0.095   0.203     1.777   72.857   74.286
LGA    G    27_A      G    27_A     1.650     0    0.189   0.189     2.644   68.929   68.929
LGA    I    28_A      I    28_A     1.681     0    0.107   0.714     4.572   75.000   65.714
LGA    C    29_A      C    29_A     1.518     0    0.050   0.666     1.530   77.143   77.143
LGA    C    30_A      C    30_A     1.314     0    0.031   0.072     1.918   81.429   78.571
LGA    E    31_A      E    31_A     1.306     0    0.044   0.711     4.185   81.429   67.831
LGA    K    32_A      K    32_A     1.021     0    0.043   1.075     6.398   85.952   63.704
LGA    C    33_A      C    33_A     0.715     0    0.602   0.525     3.433   78.095   75.159
LGA    N    34_A      N    34_A     0.952     0    0.233   0.376     3.094   90.595   76.964
LGA    C    35_A      C    35_A     0.976     0    0.016   0.386     1.607   88.214   84.524
LGA    V    36_A      V    36_A     0.776     0    0.147   0.170     1.737   90.476   85.374
LGA    P    37_A      P    37_A     0.432     0    0.075   0.330     0.711   92.857   94.558
LGA    P    38_A      P    38_A     1.466     0    0.045   0.098     1.758   79.286   78.980
LGA    G    39_A      G    39_A     2.132     0    0.144   0.144     2.842   62.976   62.976
LGA    T    40_A      T    40_A     4.408     0    0.567   0.584     5.457   37.619   33.469
LGA    Y    41_A      Y    41_A     4.420     0    0.145   1.075     5.678   35.714   34.167
LGA    G    42_A      G    42_A     4.212     0    0.601   0.601     5.412   35.952   35.952
LGA    N    43_A      N    43_A     1.171     0    0.296   0.359     1.853   77.143   78.214
LGA    E    44_A      E    44_A     0.279     0    0.101   0.657     2.404  100.000   84.339
LGA    D    45_A      D    45_A     1.166     0    0.099   1.088     5.800   83.690   64.762
LGA    S    46_A      S    46_A     1.504     0    0.155   0.163     1.971   77.143   77.143
LGA    C    47_A      C    47_A     0.835     0    0.085   0.336     1.643   92.857   87.619
LGA    P    48_A      P    48_A     0.378     0    0.070   0.333     1.270   92.976   93.265
LGA    C    49_A      C    49_A     1.845     0    0.029   0.241     3.272   72.976   67.778
LGA    Y    50_A      Y    50_A     0.945     0    0.104   0.299     2.328   85.952   82.381
LGA    A    51_A      A    51_A     0.987     0    0.108   0.109     1.495   85.952   86.857
LGA    N    52_A      N    52_A     1.261     0    0.089   0.168     2.512   83.690   75.298
LGA    L    53_A      L    53_A     1.065     0    0.083   0.917     3.249   81.429   78.750
LGA    K    54_A      K    54_A     1.398     0    0.106   1.282     5.141   81.429   68.254
LGA    N    55_A      N    55_A     1.852     0    0.051   0.115     2.689   67.143   71.071
LGA    S    56_A      S    56_A     3.810     0    0.166   0.677     6.413   42.024   37.063
LGA    K    57_A      K    57_A     2.776     0    0.174   0.555     5.241   57.143   51.534
LGA    G    58_A      G    58_A     2.507     0    0.137   0.137     2.507   62.857   62.857
LGA    G    59_A      G    59_A     1.445     0    0.036   0.036     1.753   81.548   81.548
LGA    H    60_A      H    60_A     1.254     0    0.168   1.031     5.866   83.690   59.381
LGA    K    61_A      K    61_A     1.318     0    0.038   0.733     1.797   81.548   83.545
LGA    C    62_A      C    62_A     1.707     0    0.030   0.077     2.219   77.143   73.016
LGA    P    63_A      P    63_A     1.340     0    0.326   0.474     1.942   79.286   77.755

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       63     252    252  100.00     471    471  100.00                63
SUMMARY(RMSD_GDC):     1.807          1.838                  2.327           76.572   71.276

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63   63    4.0     63    1.81    81.746    91.353     3.304

LGA_LOCAL      RMSD:   1.807  Number of atoms:   63  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.807  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:   1.807  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.406233 * X  +   0.905540 * Y  +   0.122357 * Z  +  -7.895850
  Y_new =  -0.888166 * X  +  -0.359819 * Y  +  -0.285817 * Z  +  -2.784623
  Z_new =  -0.214792 * X  +  -0.224781 * Y  +   0.950441 * Z  + -11.929157 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.999774  0.216479 -0.232235   [DEG: -114.5786   12.4033  -13.3061 ]
ZXZ:  0.404489  0.316146 -2.378915   [DEG:   23.1755   18.1138 -136.3018 ]
 
# END of job
