
#######################################################
#                                                     #
#                        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        1.87     1.87
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    63       1_A - 63_A        1.87     1.87
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    27      12_A - 38_A        1.00     2.44
  LONGEST_CONTINUOUS_SEGMENT:    27      13_A - 39_A        0.98     2.50
  LCS_AVERAGE:     32.45

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     12   63   63      5   13   23   45   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H     2_A     H     2_A     13   63   63      6   14   31   52   58   60   60   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   24   44   52   58   60   60   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   23   44   52   58   60   60   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   15   34   52   58   60   60   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   14   33   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K     7_A     K     7_A     23   63   63      7   24   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E     8_A     E     8_A     23   63   63     10   24   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     9_A     C     9_A     23   63   63      7   22   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    10_A     N    10_A     23   63   63     10   24   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    11_A     R    11_A     23   63   63      4   22   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    12_A     R    12_A     27   63   63      4   22   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    13_A     C    13_A     27   63   63      4   22   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    14_A     S    14_A     27   63   63      5   24   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    15_A     K    15_A     27   63   63      3    5   24   44   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    16_A     A    16_A     27   63   63      4   24   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    17_A     S    17_A     27   63   63      6   24   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    18_A     A    18_A     27   63   63      4   10   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H    19_A     H    19_A     27   63   63      4   23   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    20_A     D    20_A     27   63   63     10   24   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    21_A     R    21_A     27   63   63     10   24   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    22_A     C    22_A     27   63   63     10   24   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    23_A     L    23_A     27   63   63     10   24   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    24_A     K    24_A     27   63   63      5   24   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    25_A     Y    25_A     27   63   63      6   24   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    26_A     C    26_A     27   63   63      5   24   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    27_A     G    27_A     27   63   63      6   24   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     I    28_A     I    28_A     27   63   63      6   24   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    29_A     C    29_A     27   63   63      6   24   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    30_A     C    30_A     27   63   63      5   21   43   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    31_A     E    31_A     27   63   63      5   13   37   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    32_A     K    32_A     27   63   63      5   22   41   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    33_A     C    33_A     27   63   63      6   24   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    34_A     N    34_A     27   63   63      6   24   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    35_A     C    35_A     27   63   63      6   24   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    36_A     V    36_A     27   63   63     10   24   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    37_A     P    37_A     27   63   63     10   24   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    38_A     P    38_A     27   63   63     10   24   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    39_A     G    39_A     27   63   63      5   24   42   52   58   60   60   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   33   44   54   60   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   14   26   39   51   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    42_A     G    42_A     12   63   63      4    4   15   26   40   52   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    43_A     N    43_A     13   63   63      5   18   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    44_A     E    44_A     13   63   63      7   22   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    45_A     D    45_A     13   63   63      6   22   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    46_A     S    46_A     13   63   63      5   17   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    47_A     C    47_A     13   63   63      8   22   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    48_A     P    48_A     13   63   63     10   22   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    49_A     C    49_A     14   63   63      4   22   38   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    50_A     Y    50_A     14   63   63     10   22   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    51_A     A    51_A     14   63   63      9   22   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    52_A     N    52_A     14   63   63      4   22   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    53_A     L    53_A     14   63   63      4   22   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    54_A     K    54_A     14   63   63      4   13   35   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    55_A     N    55_A     14   63   63      5   14   31   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    56_A     S    56_A     14   63   63      5    9   19   31   54   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    57_A     K    57_A     14   63   63      5   11   30   43   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    58_A     G    58_A     14   63   63      5   11   29   50   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    59_A     G    59_A     14   63   63      5   13   34   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H    60_A     H    60_A     14   63   63      4   15   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    61_A     K    61_A     14   63   63      4   19   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    62_A     C    62_A     14   63   63      6   24   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    63_A     P    63_A     12   63   63      6   24   44   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_AVERAGE  LCS_A:  77.48  (  32.45  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     10     24     44     52     58     60     60     63     63     63     63     63     63     63     63     63     63     63     63     63 
GDT PERCENT_AT  15.87  38.10  69.84  82.54  92.06  95.24  95.24 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.36   0.72   1.10   1.26   1.48   1.60   1.60   1.87   1.87   1.87   1.87   1.87   1.87   1.87   1.87   1.87   1.87   1.87   1.87   1.87
GDT RMS_ALL_AT   2.38   2.61   2.09   2.02   1.91   1.90   1.90   1.87   1.87   1.87   1.87   1.87   1.87   1.87   1.87   1.87   1.87   1.87   1.87   1.87

# 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     2.498     0    0.092   0.143     3.317   72.976   68.381
LGA    H     2_A      H     2_A     1.842     0    0.014   1.166     4.274   75.119   61.095
LGA    I     3_A      I     3_A     0.170     0    0.101   0.928     2.961   90.595   85.238
LGA    D     4_A      D     4_A     1.197     0    0.079   1.054     3.921   83.690   71.786
LGA    C     5_A      C     5_A     2.035     0    0.110   0.254     2.555   70.833   67.540
LGA    D     6_A      D     6_A     1.608     0    0.018   0.560     3.398   79.405   73.333
LGA    K     7_A      K     7_A     0.428     0    0.091   0.538     2.587   92.857   84.074
LGA    E     8_A      E     8_A     1.067     0    0.060   0.414     1.558   81.548   84.497
LGA    C     9_A      C     9_A     1.461     0    0.080   0.108     1.737   81.429   78.571
LGA    N    10_A      N    10_A     0.745     0    0.104   0.319     1.518   88.214   84.881
LGA    R    11_A      R    11_A     1.502     0    0.040   1.493     5.835   75.000   60.606
LGA    R    12_A      R    12_A     1.427     0    0.033   1.420     6.530   81.429   63.030
LGA    C    13_A      C    13_A     1.129     0    0.206   0.241     3.002   83.690   77.698
LGA    S    14_A      S    14_A     1.039     0    0.071   0.645     3.189   77.381   75.000
LGA    K    15_A      K    15_A     2.940     0    0.130   1.013     4.387   59.048   55.926
LGA    A    16_A      A    16_A     1.801     0    0.059   0.076     2.150   70.833   72.952
LGA    S    17_A      S    17_A     2.149     0    0.035   0.686     4.100   66.786   61.508
LGA    A    18_A      A    18_A     2.207     0    0.066   0.062     2.319   64.762   64.762
LGA    H    19_A      H    19_A     1.887     0    0.184   1.159     3.372   68.929   65.810
LGA    D    20_A      D    20_A     1.541     0    0.171   0.217     2.408   77.143   71.964
LGA    R    21_A      R    21_A     1.719     0    0.074   0.988     4.982   77.143   56.753
LGA    C    22_A      C    22_A     1.210     0    0.115   0.157     1.532   79.286   81.508
LGA    L    23_A      L    23_A     1.087     0    0.088   0.191     1.787   85.952   81.548
LGA    K    24_A      K    24_A     2.279     0    0.084   0.438     5.313   66.786   53.016
LGA    Y    25_A      Y    25_A     2.213     0    0.017   0.723     3.334   64.762   62.976
LGA    C    26_A      C    26_A     1.662     0    0.076   0.192     1.895   72.857   74.286
LGA    G    27_A      G    27_A     1.755     0    0.197   0.197     2.744   66.905   66.905
LGA    I    28_A      I    28_A     1.708     0    0.076   0.713     4.540   72.857   64.643
LGA    C    29_A      C    29_A     1.624     0    0.052   0.689     1.697   75.000   75.714
LGA    C    30_A      C    30_A     1.466     0    0.040   0.057     2.047   79.286   75.794
LGA    E    31_A      E    31_A     1.501     0    0.045   0.708     4.059   77.143   64.974
LGA    K    32_A      K    32_A     1.207     0    0.053   1.035     6.283   81.429   60.688
LGA    C    33_A      C    33_A     0.830     0    0.593   0.528     3.582   74.286   72.619
LGA    N    34_A      N    34_A     1.031     0    0.249   0.358     3.087   88.333   75.833
LGA    C    35_A      C    35_A     1.059     0    0.042   0.370     1.703   88.214   84.524
LGA    V    36_A      V    36_A     0.610     0    0.175   0.183     1.553   90.476   87.959
LGA    P    37_A      P    37_A     0.313     0    0.047   0.323     0.797   95.238   95.918
LGA    P    38_A      P    38_A     1.321     0    0.063   0.104     1.488   81.429   84.014
LGA    G    39_A      G    39_A     2.071     0    0.130   0.130     2.882   62.976   62.976
LGA    T    40_A      T    40_A     4.404     0    0.542   0.563     5.407   36.190   32.653
LGA    Y    41_A      Y    41_A     4.582     0    0.115   1.256     5.132   34.286   31.587
LGA    G    42_A      G    42_A     4.310     0    0.592   0.592     5.419   34.524   34.524
LGA    N    43_A      N    43_A     1.130     0    0.297   0.332     1.812   77.143   80.417
LGA    E    44_A      E    44_A     0.314     0    0.144   0.717     3.017  100.000   81.005
LGA    D    45_A      D    45_A     0.981     0    0.099   1.093     5.643   88.214   67.024
LGA    S    46_A      S    46_A     1.334     0    0.122   0.158     1.674   79.286   80.000
LGA    C    47_A      C    47_A     0.709     0    0.064   0.335     1.638   92.857   87.619
LGA    P    48_A      P    48_A     0.458     0    0.065   0.373     1.320   92.976   93.265
LGA    C    49_A      C    49_A     1.832     0    0.032   0.229     3.145   72.976   67.778
LGA    Y    50_A      Y    50_A     0.950     0    0.074   0.343     2.720   85.952   81.746
LGA    A    51_A      A    51_A     0.964     0    0.152   0.164     1.529   83.810   85.143
LGA    N    52_A      N    52_A     1.190     0    0.099   0.163     2.364   85.952   78.393
LGA    L    53_A      L    53_A     1.098     0    0.080   0.606     2.273   79.286   79.405
LGA    K    54_A      K    54_A     1.411     0    0.086   1.245     4.993   79.286   67.884
LGA    N    55_A      N    55_A     1.988     0    0.040   0.133     2.819   67.143   70.060
LGA    S    56_A      S    56_A     3.932     0    0.169   0.674     6.514   40.714   34.603
LGA    K    57_A      K    57_A     2.927     0    0.155   0.567     5.292   55.357   49.101
LGA    G    58_A      G    58_A     2.654     0    0.132   0.132     2.654   60.952   60.952
LGA    G    59_A      G    59_A     1.597     0    0.020   0.020     1.901   79.405   79.405
LGA    H    60_A      H    60_A     1.366     0    0.165   1.036     5.894   83.690   59.381
LGA    K    61_A      K    61_A     1.330     0    0.061   0.740     1.809   77.143   81.587
LGA    C    62_A      C    62_A     1.823     0    0.042   0.055     2.187   72.857   70.159
LGA    P    63_A      P    63_A     1.915     0    0.190   0.314     2.212   68.810   69.388

# 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):     1.868          1.896                  2.369           75.410   70.387

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63   63    4.0     63    1.87    80.159    90.553     3.201

LGA_LOCAL      RMSD:   1.868  Number of atoms:   63  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.868  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:   1.868  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.649723 * X  +  -0.139076 * Y  +   0.747341 * Z  + -11.190528
  Y_new =  -0.192158 * X  +  -0.921145 * Y  +  -0.338478 * Z  +   0.715063
  Z_new =   0.735483 * X  +  -0.363524 * Y  +   0.571764 * Z  +  -6.279762 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.854036 -0.826380 -0.566324   [DEG: -163.5242  -47.3481  -32.4480 ]
ZXZ:  1.145525  0.962142  2.029846   [DEG:   65.6337   55.1267  116.3016 ]
 
# END of job
