
#######################################################
#                                                     #
#                        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        1.83     1.83
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    63       1_A - 63_A        1.83     1.83
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    26      13_A - 38_A        0.98     2.33
  LONGEST_CONTINUOUS_SEGMENT:    26      14_A - 39_A        0.98     2.41
  LCS_AVERAGE:     31.19

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    7   18   36   54   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      5   13   23   51   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      6   25   45   54   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   21   45   54   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   15   37   54   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   39   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K     7_A     K     7_A     22   63   63      7   25   45   54   57   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     11   25   45   54   57   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   21   45   54   57   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   25   45   54   57   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      5   23   45   54   57   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      5   21   45   54   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   17   45   54   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   25   45   54   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   23   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   25   45   54   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      7   25   45   54   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   11   45   54   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      4   23   45   54   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     11   25   45   54   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     11   25   45   54   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     11   25   45   54   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     11   25   45   54   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   25   45   54   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      7   25   45   54   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   25   45   54   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      4   25   45   54   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   25   45   54   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   25   45   54   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   21   45   54   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   14   40   54   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   44   54   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   25   45   54   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      4   25   45   54   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   25   45   54   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     11   25   45   54   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     11   25   45   54   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      7   25   45   54   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      5   23   44   54   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   32   45   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   14   28   41   53   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    42_A     G    42_A     13   63   63      4    6   17   29   43   54   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      5   18   45   54   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      7   21   45   54   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      5   21   45   54   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      5   18   45   54   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      5   21   45   54   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     11   24   45   54   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      4   21   36   54   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     11   21   45   54   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     11   21   45   54   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   21   45   54   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   21   45   54   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      3   14   41   54   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   17   33   54   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    8   20   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   12   33   47   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   14   33   51   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   14   41   54   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   54   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   21   45   54   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   25   45   54   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   25   45   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_AVERAGE  LCS_A:  77.06  (  31.19  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     25     45     54     57     60     61     63     63     63     63     63     63     63     63     63     63     63     63     63 
GDT PERCENT_AT  17.46  39.68  71.43  85.71  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    0.37   0.78   1.09   1.28   1.40   1.57   1.74   1.83   1.83   1.83   1.83   1.83   1.83   1.83   1.83   1.83   1.83   1.83   1.83   1.83
GDT RMS_ALL_AT   2.28   2.33   2.02   1.91   1.88   1.86   1.84   1.83   1.83   1.83   1.83   1.83   1.83   1.83   1.83   1.83   1.83   1.83   1.83   1.83

# 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     3.184     0    0.117   0.171     3.839   63.095   59.143
LGA    H     2_A      H     2_A     2.246     0    0.029   0.787     5.364   66.905   52.762
LGA    I     3_A      I     3_A     0.409     0    0.073   0.935     2.696   88.333   84.107
LGA    D     4_A      D     4_A     1.146     0    0.068   1.064     3.768   83.690   71.786
LGA    C     5_A      C     5_A     1.912     0    0.088   0.232     2.475   72.857   71.508
LGA    D     6_A      D     6_A     1.515     0    0.012   0.572     3.403   79.405   73.333
LGA    K     7_A      K     7_A     0.312     0    0.080   0.534     2.378   92.857   84.762
LGA    E     8_A      E     8_A     0.993     0    0.055   0.451     1.557   83.810   85.503
LGA    C     9_A      C     9_A     1.394     0    0.079   0.088     1.807   81.429   78.571
LGA    N    10_A      N    10_A     0.652     0    0.120   0.446     1.787   85.952   84.881
LGA    R    11_A      R    11_A     1.386     0    0.025   1.492     5.666   79.286   62.771
LGA    R    12_A      R    12_A     1.428     0    0.019   1.419     6.396   81.429   63.117
LGA    C    13_A      C    13_A     1.213     0    0.256   0.264     3.010   81.548   76.270
LGA    S    14_A      S    14_A     1.118     0    0.068   0.668     3.289   73.452   72.381
LGA    K    15_A      K    15_A     3.135     0    0.151   1.016     4.603   57.262   52.169
LGA    A    16_A      A    16_A     1.870     0    0.052   0.059     2.258   70.833   72.952
LGA    S    17_A      S    17_A     2.095     0    0.024   0.687     3.944   66.786   62.540
LGA    A    18_A      A    18_A     2.053     0    0.064   0.069     2.237   68.810   68.000
LGA    H    19_A      H    19_A     1.809     0    0.195   1.172     3.516   68.929   65.238
LGA    D    20_A      D    20_A     1.439     0    0.196   0.225     2.029   79.286   75.119
LGA    R    21_A      R    21_A     1.582     0    0.067   1.012     4.810   77.143   58.009
LGA    C    22_A      C    22_A     1.085     0    0.080   0.114     1.395   83.690   85.952
LGA    L    23_A      L    23_A     1.024     0    0.069   0.174     1.744   85.952   82.619
LGA    K    24_A      K    24_A     2.143     0    0.093   0.425     4.927   66.786   54.921
LGA    Y    25_A      Y    25_A     2.017     0    0.019   0.739     3.130   70.833   67.024
LGA    C    26_A      C    26_A     1.527     0    0.095   0.210     1.772   72.857   74.286
LGA    G    27_A      G    27_A     1.624     0    0.188   0.188     2.595   68.929   68.929
LGA    I    28_A      I    28_A     1.593     0    0.099   0.701     4.441   77.143   68.512
LGA    C    29_A      C    29_A     1.480     0    0.046   0.658     1.504   81.429   80.000
LGA    C    30_A      C    30_A     1.351     0    0.029   0.061     1.970   81.429   78.571
LGA    E    31_A      E    31_A     1.398     0    0.034   0.698     4.115   79.286   66.878
LGA    K    32_A      K    32_A     1.195     0    0.040   1.056     6.363   81.429   60.688
LGA    C    33_A      C    33_A     0.773     0    0.603   0.526     3.565   74.286   72.619
LGA    N    34_A      N    34_A     1.045     0    0.227   0.353     3.036   86.071   74.702
LGA    C    35_A      C    35_A     1.093     0    0.013   0.386     1.587   83.690   80.079
LGA    V    36_A      V    36_A     0.707     0    0.146   0.172     1.538   90.476   87.959
LGA    P    37_A      P    37_A     0.487     0    0.071   0.316     0.789   92.857   94.558
LGA    P    38_A      P    38_A     1.497     0    0.038   0.094     1.776   79.286   78.980
LGA    G    39_A      G    39_A     2.080     0    0.147   0.147     2.842   62.976   62.976
LGA    T    40_A      T    40_A     4.360     0    0.565   0.554     5.458   37.619   33.469
LGA    Y    41_A      Y    41_A     4.421     0    0.157   1.069     5.647   35.714   32.698
LGA    G    42_A      G    42_A     4.207     0    0.599   0.599     5.353   35.952   35.952
LGA    N    43_A      N    43_A     1.117     0    0.286   0.290     1.797   77.143   78.214
LGA    E    44_A      E    44_A     0.401     0    0.114   0.713     2.930  100.000   81.799
LGA    D    45_A      D    45_A     0.984     0    0.105   1.111     5.681   85.952   66.667
LGA    S    46_A      S    46_A     1.401     0    0.150   0.165     1.796   79.286   78.571
LGA    C    47_A      C    47_A     0.839     0    0.077   0.341     1.541   90.476   86.032
LGA    P    48_A      P    48_A     0.463     0    0.064   0.326     1.205   92.976   93.265
LGA    C    49_A      C    49_A     1.754     0    0.035   0.232     3.080   72.976   67.778
LGA    Y    50_A      Y    50_A     0.795     0    0.101   0.302     2.299   90.476   83.889
LGA    A    51_A      A    51_A     0.858     0    0.132   0.135     1.415   85.952   86.857
LGA    N    52_A      N    52_A     1.167     0    0.103   0.224     2.414   83.690   77.262
LGA    L    53_A      L    53_A     1.234     0    0.082   0.598     2.201   79.286   79.405
LGA    K    54_A      K    54_A     1.489     0    0.103   1.306     5.356   81.429   68.254
LGA    N    55_A      N    55_A     1.864     0    0.050   0.121     2.717   67.143   70.060
LGA    S    56_A      S    56_A     3.785     0    0.172   0.677     6.514   42.024   36.429
LGA    K    57_A      K    57_A     2.674     0    0.172   0.550     5.101   57.143   52.222
LGA    G    58_A      G    58_A     2.424     0    0.138   0.138     2.424   64.762   64.762
LGA    G    59_A      G    59_A     1.391     0    0.034   0.034     1.717   81.548   81.548
LGA    H    60_A      H    60_A     1.272     0    0.179   1.053     5.969   83.690   59.381
LGA    K    61_A      K    61_A     1.348     0    0.038   0.713     1.800   77.143   82.646
LGA    C    62_A      C    62_A     1.738     0    0.029   0.064     2.161   75.000   72.937
LGA    P    63_A      P    63_A     1.498     0    0.329   0.475     2.159   72.976   74.150

# 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):     1.830          1.860                  2.354           75.760   70.784

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63   63    4.0     63    1.83    81.349    91.005     3.264

LGA_LOCAL      RMSD:   1.830  Number of atoms:   63  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.830  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:   1.830  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.048211 * X  +   0.994766 * Y  +   0.090092 * Z  +  -8.256942
  Y_new =  -0.998752 * X  +  -0.046830 * Y  +  -0.017379 * Z  +  -1.739386
  Z_new =  -0.013068 * X  +  -0.090818 * Y  +   0.995782 * Z  + -11.267594 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.619030  0.013069 -0.090951   [DEG:  -92.7636    0.7488   -5.2111 ]
ZXZ:  1.380240  0.091882 -2.998676   [DEG:   79.0819    5.2645 -171.8114 ]
 
# END of job
