
#######################################################
#                                                     #
#                        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        1.85     1.85
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    63       1_A - 63_A        1.85     1.85
  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     2.36
  LONGEST_CONTINUOUS_SEGMENT:    26      14_A - 39_A        0.99     2.45
  LCS_AVERAGE:     31.27

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     11   63   63      4    8   24   48   57   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   25   52   57   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      7   24   45   53   57   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   45   53   57   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   36   53   57   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   14   36   53   57   60   61   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   45   53   57   60   61   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   45   53   57   60   61   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   21   45   53   57   60   61   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   45   53   57   60   61   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   45   53   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    12_A     R    12_A     23   63   63      4   22   45   53   57   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   21   45   53   57   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      5   24   45   53   57   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   24   46   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      5   24   45   53   57   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      6   24   45   53   57   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   10   45   53   57   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      6   23   45   53   57   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     10   24   45   53   57   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     10   24   45   53   57   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     10   24   45   53   57   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     10   24   45   53   57   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   24   45   53   57   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   24   45   53   57   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   24   45   53   57   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      5   22   45   53   57   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      8   24   45   53   57   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   24   45   53   57   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   19   45   53   57   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   13   40   53   57   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   22   45   53   57   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      8   24   45   53   57   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      5   24   45   53   57   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   24   45   53   57   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     10   24   45   53   57   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     10   24   45   53   57   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      6   24   45   53   57   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   43   52   57   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   30   45   53   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    6   14   28   40   52   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   15   28   43   52   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   20   45   53   57   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     10   21   45   53   57   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      8   23   45   53   57   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   20   45   53   57   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   21   45   53   57   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     10   23   45   53   57   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      3   21   37   53   57   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     10   21   45   53   57   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      7   21   45   53   57   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      7   20   42   53   57   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      7   20   45   53   57   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   13   37   53   57   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   16   31   53   57   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   21   36   55   60   60   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   10   31   44   57   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   13   28   52   57   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   13   36   53   57   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   16   45   53   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    61_A     K    61_A     13   63   63      5   19   45   53   57   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      8   24   45   53   57   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      8   24   45   53   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_AVERAGE  LCS_A:  77.09  (  31.27  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     45     53     57     60     61     63     63     63     63     63     63     63     63     63     63     63     63     63 
GDT PERCENT_AT  15.87  38.10  71.43  84.13  90.48  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    0.34   0.76   1.08   1.29   1.43   1.58   1.76   1.85   1.85   1.85   1.85   1.85   1.85   1.85   1.85   1.85   1.85   1.85   1.85   1.85
GDT RMS_ALL_AT   2.27   2.35   2.04   1.92   1.90   1.88   1.86   1.85   1.85   1.85   1.85   1.85   1.85   1.85   1.85   1.85   1.85   1.85   1.85   1.85

# 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     2.812     0    0.113   0.164     3.684   69.048   63.905
LGA    H     2_A      H     2_A     2.055     0    0.032   0.703     4.658   73.095   56.857
LGA    I     3_A      I     3_A     0.247     0    0.086   0.905     2.807   90.595   86.369
LGA    D     4_A      D     4_A     1.120     0    0.065   1.065     3.762   83.690   71.786
LGA    C     5_A      C     5_A     1.906     0    0.086   0.223     2.469   72.857   70.159
LGA    D     6_A      D     6_A     1.553     0    0.019   0.528     3.500   79.405   72.500
LGA    K     7_A      K     7_A     0.315     0    0.084   0.540     2.628   92.857   82.116
LGA    E     8_A      E     8_A     0.973     0    0.055   0.447     1.547   83.810   85.503
LGA    C     9_A      C     9_A     1.375     0    0.078   0.085     1.795   81.429   78.571
LGA    N    10_A      N    10_A     0.630     0    0.123   0.305     1.372   88.214   87.083
LGA    R    11_A      R    11_A     1.358     0    0.023   1.498     5.502   81.429   63.550
LGA    R    12_A      R    12_A     1.336     0    0.023   1.450     6.715   81.429   63.030
LGA    C    13_A      C    13_A     1.102     0    0.260   0.276     3.010   81.548   76.270
LGA    S    14_A      S    14_A     1.091     0    0.070   0.668     3.317   75.476   73.730
LGA    K    15_A      K    15_A     3.075     0    0.150   1.022     4.565   57.262   53.016
LGA    A    16_A      A    16_A     1.812     0    0.058   0.068     2.210   70.833   72.952
LGA    S    17_A      S    17_A     2.064     0    0.022   0.688     3.946   66.786   62.540
LGA    A    18_A      A    18_A     2.062     0    0.064   0.069     2.237   68.810   68.000
LGA    H    19_A      H    19_A     1.778     0    0.200   1.201     3.637   68.929   65.238
LGA    D    20_A      D    20_A     1.444     0    0.197   0.217     2.132   79.286   76.131
LGA    R    21_A      R    21_A     1.610     0    0.071   0.984     4.743   77.143   58.009
LGA    C    22_A      C    22_A     1.088     0    0.081   0.125     1.390   83.690   85.952
LGA    L    23_A      L    23_A     1.024     0    0.065   0.154     1.822   85.952   82.619
LGA    K    24_A      K    24_A     2.205     0    0.095   0.425     4.971   66.786   54.921
LGA    Y    25_A      Y    25_A     2.089     0    0.019   0.721     3.152   66.786   64.325
LGA    C    26_A      C    26_A     1.621     0    0.100   0.199     1.870   72.857   74.286
LGA    G    27_A      G    27_A     1.740     0    0.184   0.184     2.709   68.929   68.929
LGA    I    28_A      I    28_A     1.697     0    0.092   0.711     4.531   75.000   65.714
LGA    C    29_A      C    29_A     1.573     0    0.044   0.678     1.590   77.143   77.143
LGA    C    30_A      C    30_A     1.422     0    0.038   0.060     1.970   79.286   77.143
LGA    E    31_A      E    31_A     1.453     0    0.034   0.693     4.018   79.286   67.460
LGA    K    32_A      K    32_A     1.155     0    0.047   1.044     6.229   81.429   60.688
LGA    C    33_A      C    33_A     0.810     0    0.601   0.526     3.617   74.286   72.619
LGA    N    34_A      N    34_A     1.074     0    0.212   0.371     3.245   86.071   72.857
LGA    C    35_A      C    35_A     1.055     0    0.023   0.364     1.522   83.690   80.079
LGA    V    36_A      V    36_A     0.705     0    0.145   0.170     1.616   90.476   85.374
LGA    P    37_A      P    37_A     0.407     0    0.077   0.315     0.778   95.238   95.918
LGA    P    38_A      P    38_A     1.551     0    0.046   0.097     1.872   77.143   77.755
LGA    G    39_A      G    39_A     2.224     0    0.168   0.168     2.804   62.976   62.976
LGA    T    40_A      T    40_A     4.528     0    0.554   0.497     5.671   34.762   31.973
LGA    Y    41_A      Y    41_A     4.471     0    0.154   1.052     5.411   34.405   34.127
LGA    G    42_A      G    42_A     4.257     0    0.598   0.598     5.419   35.952   35.952
LGA    N    43_A      N    43_A     1.153     0    0.298   0.384     1.924   81.548   79.345
LGA    E    44_A      E    44_A     0.343     0    0.098   0.623     2.521  100.000   82.434
LGA    D    45_A      D    45_A     1.172     0    0.098   1.061     5.691   83.690   64.762
LGA    S    46_A      S    46_A     1.442     0    0.123   0.215     1.785   79.286   78.571
LGA    C    47_A      C    47_A     0.799     0    0.090   0.335     1.501   92.857   87.619
LGA    P    48_A      P    48_A     0.398     0    0.069   0.321     1.335   92.976   94.626
LGA    C    49_A      C    49_A     1.859     0    0.039   0.237     3.113   72.976   67.778
LGA    Y    50_A      Y    50_A     0.832     0    0.096   0.246     2.271   90.476   83.889
LGA    A    51_A      A    51_A     0.980     0    0.172   0.175     1.518   83.810   85.143
LGA    N    52_A      N    52_A     1.289     0    0.133   0.149     2.544   83.690   74.286
LGA    L    53_A      L    53_A     1.196     0    0.063   0.222     1.626   79.286   81.488
LGA    K    54_A      K    54_A     1.538     0    0.116   1.226     4.474   79.286   69.312
LGA    N    55_A      N    55_A     1.942     0    0.062   0.095     2.787   67.143   70.060
LGA    S    56_A      S    56_A     3.821     0    0.171   0.492     6.107   42.024   37.063
LGA    K    57_A      K    57_A     2.900     0    0.162   0.562     5.375   55.357   49.101
LGA    G    58_A      G    58_A     2.658     0    0.142   0.142     2.658   59.048   59.048
LGA    G    59_A      G    59_A     1.546     0    0.036   0.036     1.872   79.405   79.405
LGA    H    60_A      H    60_A     1.230     0    0.159   1.240     6.335   83.690   60.190
LGA    K    61_A      K    61_A     1.108     0    0.030   0.702     1.577   83.690   83.492
LGA    C    62_A      C    62_A     1.650     0    0.026   0.049     2.129   79.286   75.794
LGA    P    63_A      P    63_A     1.501     0    0.322   0.460     1.931   72.857   74.082

# 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):     1.850          1.878                  2.350           75.848   70.692

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63   63    4.0     63    1.85    80.556    90.769     3.230

LGA_LOCAL      RMSD:   1.850  Number of atoms:   63  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.850  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:   1.850  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.395703 * X  +  -0.888231 * Y  +  -0.233379 * Z  + -11.534687
  Y_new =  -0.613536 * X  +   0.066584 * Y  +   0.786855 * Z  +   0.363258
  Z_new =  -0.683369 * X  +   0.454547 * Y  +  -0.571309 * Z  + -13.950462 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.143616  0.752368  2.469526   [DEG: -122.8202   43.1075  141.4934 ]
ZXZ: -2.853260  2.178896 -0.983840   [DEG: -163.4798  124.8415  -56.3699 ]
 
# END of job
