
#######################################################
#                                                     #
#                        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   83 (  684),  selected   72 , name one
# Molecule2: number of CA atoms   72 (  603),  selected   72 , 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:    55      19_A - 81_A        4.73    20.06
  LCS_AVERAGE:     66.55

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    50      24_A - 81_A        1.79    21.20
  LCS_AVERAGE:     57.99

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    49      33_A - 81_A        0.80    21.82
  LCS_AVERAGE:     55.71

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   72
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     T     2_A     T     2_A      3   23   25      0    3    3    3    3    4    6   22   23   23   23   23   23   23   23   23   23   23   24   25 
LCS_GDT     S     3_A     S     3_A     22   23   25     15   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   24   24   25   25 
LCS_GDT     L     4_A     L     4_A     22   23   25     20   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   24   24   25   25 
LCS_GDT     I     5_A     I     5_A     22   23   25     20   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   24   24   25   25 
LCS_GDT     E     6_A     E     6_A     22   23   25     20   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   24   24   25   25 
LCS_GDT     E     7_A     E     7_A     22   23   25     20   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   24   24   25   25 
LCS_GDT     L     8_A     L     8_A     22   23   25     20   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   24   24   25   25 
LCS_GDT     I     9_A     I     9_A     22   23   25     20   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   24   24   25   25 
LCS_GDT     R    10_A     R    10_A     22   23   25     20   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   24   24   25   25 
LCS_GDT     R    11_A     R    11_A     22   23   25     20   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   24   24   25   25 
LCS_GDT     S    12_A     S    12_A     22   23   25     20   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   24   24   25   25 
LCS_GDT     E    13_A     E    13_A     22   23   25     20   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   24   24   25   25 
LCS_GDT     E    14_A     E    14_A     22   23   25     20   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   24   24   25   25 
LCS_GDT     Q    15_A     Q    15_A     22   23   25     20   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   24   24   25   25 
LCS_GDT     Q    16_A     Q    16_A     22   23   25     20   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   24   24   25   25 
LCS_GDT     R    17_A     R    17_A     22   23   25     20   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   24   24   25   25 
LCS_GDT     R    18_A     R    18_A     22   23   25     20   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   24   24   25   25 
LCS_GDT     N    19_A     N    19_A     22   23   55     20   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   24   24   25   25 
LCS_GDT     E    20_A     E    20_A     22   23   55     20   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   24   24   29   48 
LCS_GDT     E    21_A     E    21_A     22   23   55     20   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   24   27   44   52 
LCS_GDT     A    22_A     A    22_A     22   23   55     20   22   22   22   22   22   22   22   23   23   23   23   23   23   47   51   52   52   52   52 
LCS_GDT     L    23_A     L    23_A     22   23   55     20   22   22   22   22   22   22   22   23   23   23   28   49   51   51   51   52   52   52   52 
LCS_GDT     R    24_A     R    24_A     22   50   55     13   22   22   22   22   22   22   22   23   23   23   28   45   51   51   51   52   52   52   52 
LCS_GDT     Q    33_A     Q    33_A     49   50   55     20   45   47   48   48   49   49   49   49   49   49   49   49   51   51   51   52   52   52   52 
LCS_GDT     L    34_A     L    34_A     49   50   55     11   45   47   48   48   49   49   49   49   49   49   49   49   51   51   51   52   52   52   52 
LCS_GDT     L    35_A     L    35_A     49   50   55     39   45   47   48   48   49   49   49   49   49   49   49   49   51   51   51   52   52   52   52 
LCS_GDT     S    36_A     S    36_A     49   50   55     39   45   47   48   48   49   49   49   49   49   49   49   49   51   51   51   52   52   52   52 
LCS_GDT     G    37_A     G    37_A     49   50   55     27   45   47   48   48   49   49   49   49   49   49   49   49   51   51   51   52   52   52   52 
LCS_GDT     I    38_A     I    38_A     49   50   55     39   45   47   48   48   49   49   49   49   49   49   49   49   51   51   51   52   52   52   52 
LCS_GDT     V    39_A     V    39_A     49   50   55     39   45   47   48   48   49   49   49   49   49   49   49   49   51   51   51   52   52   52   52 
LCS_GDT     Q    40_A     Q    40_A     49   50   55     18   45   47   48   48   49   49   49   49   49   49   49   49   51   51   51   52   52   52   52 
LCS_GDT     Q    41_A     Q    41_A     49   50   55     39   45   47   48   48   49   49   49   49   49   49   49   49   51   51   51   52   52   52   52 
LCS_GDT     Q    42_A     Q    42_A     49   50   55     39   45   47   48   48   49   49   49   49   49   49   49   49   51   51   51   52   52   52   52 
LCS_GDT     N    43_A     N    43_A     49   50   55     39   45   47   48   48   49   49   49   49   49   49   49   49   51   51   51   52   52   52   52 
LCS_GDT     N    44_A     N    44_A     49   50   55     39   45   47   48   48   49   49   49   49   49   49   49   49   51   51   51   52   52   52   52 
LCS_GDT     L    45_A     L    45_A     49   50   55     39   45   47   48   48   49   49   49   49   49   49   49   49   51   51   51   52   52   52   52 
LCS_GDT     L    46_A     L    46_A     49   50   55     39   45   47   48   48   49   49   49   49   49   49   49   49   51   51   51   52   52   52   52 
LCS_GDT     R    47_A     R    47_A     49   50   55     39   45   47   48   48   49   49   49   49   49   49   49   49   51   51   51   52   52   52   52 
LCS_GDT     A    48_A     A    48_A     49   50   55     39   45   47   48   48   49   49   49   49   49   49   49   49   51   51   51   52   52   52   52 
LCS_GDT     I    49_A     I    49_A     49   50   55     39   45   47   48   48   49   49   49   49   49   49   49   49   51   51   51   52   52   52   52 
LCS_GDT     E    50_A     E    50_A     49   50   55     39   45   47   48   48   49   49   49   49   49   49   49   49   51   51   51   52   52   52   52 
LCS_GDT     A    51_A     A    51_A     49   50   55     39   45   47   48   48   49   49   49   49   49   49   49   49   51   51   51   52   52   52   52 
LCS_GDT     Q    52_A     Q    52_A     49   50   55     39   45   47   48   48   49   49   49   49   49   49   49   49   51   51   51   52   52   52   52 
LCS_GDT     Q    53_A     Q    53_A     49   50   55     39   45   47   48   48   49   49   49   49   49   49   49   49   51   51   51   52   52   52   52 
LCS_GDT     H    54_A     H    54_A     49   50   55     38   45   47   48   48   49   49   49   49   49   49   49   49   51   51   51   52   52   52   52 
LCS_GDT     L    55_A     L    55_A     49   50   55     39   45   47   48   48   49   49   49   49   49   49   49   49   51   51   51   52   52   52   52 
LCS_GDT     L    56_A     L    56_A     49   50   55     39   45   47   48   48   49   49   49   49   49   49   49   49   51   51   51   52   52   52   52 
LCS_GDT     Q    57_A     Q    57_A     49   50   55     39   45   47   48   48   49   49   49   49   49   49   49   49   51   51   51   52   52   52   52 
LCS_GDT     L    58_A     L    58_A     49   50   55     39   45   47   48   48   49   49   49   49   49   49   49   49   51   51   51   52   52   52   52 
LCS_GDT     T    59_A     T    59_A     49   50   55     39   45   47   48   48   49   49   49   49   49   49   49   49   51   51   51   52   52   52   52 
LCS_GDT     V    60_A     V    60_A     49   50   55     39   45   47   48   48   49   49   49   49   49   49   49   49   51   51   51   52   52   52   52 
LCS_GDT     W    61_A     W    61_A     49   50   55     39   45   47   48   48   49   49   49   49   49   49   49   49   51   51   51   52   52   52   52 
LCS_GDT     G    62_A     G    62_A     49   50   55     39   45   47   48   48   49   49   49   49   49   49   49   49   51   51   51   52   52   52   52 
LCS_GDT     I    63_A     I    63_A     49   50   55     39   45   47   48   48   49   49   49   49   49   49   49   49   51   51   51   52   52   52   52 
LCS_GDT     K    64_A     K    64_A     49   50   55     39   45   47   48   48   49   49   49   49   49   49   49   49   51   51   51   52   52   52   52 
LCS_GDT     Q    65_A     Q    65_A     49   50   55     39   45   47   48   48   49   49   49   49   49   49   49   49   51   51   51   52   52   52   52 
LCS_GDT     L    66_A     L    66_A     49   50   55     39   45   47   48   48   49   49   49   49   49   49   49   49   51   51   51   52   52   52   52 
LCS_GDT     Q    67_A     Q    67_A     49   50   55     39   45   47   48   48   49   49   49   49   49   49   49   49   51   51   51   52   52   52   52 
LCS_GDT     A    68_A     A    68_A     49   50   55     39   45   47   48   48   49   49   49   49   49   49   49   49   51   51   51   52   52   52   52 
LCS_GDT     R    69_A     R    69_A     49   50   55     39   45   47   48   48   49   49   49   49   49   49   49   49   51   51   51   52   52   52   52 
LCS_GDT     I    70_A     I    70_A     49   50   55     39   45   47   48   48   49   49   49   49   49   49   49   49   51   51   51   52   52   52   52 
LCS_GDT     L    71_A     L    71_A     49   50   55     39   45   47   48   48   49   49   49   49   49   49   49   49   51   51   51   52   52   52   52 
LCS_GDT     A    72_A     A    72_A     49   50   55     39   45   47   48   48   49   49   49   49   49   49   49   49   51   51   51   52   52   52   52 
LCS_GDT     V    73_A     V    73_A     49   50   55     39   45   47   48   48   49   49   49   49   49   49   49   49   51   51   51   52   52   52   52 
LCS_GDT     E    74_A     E    74_A     49   50   55     39   45   47   48   48   49   49   49   49   49   49   49   49   51   51   51   52   52   52   52 
LCS_GDT     R    75_A     R    75_A     49   50   55     39   45   47   48   48   49   49   49   49   49   49   49   49   51   51   51   52   52   52   52 
LCS_GDT     Y    76_A     Y    76_A     49   50   55     39   45   47   48   48   49   49   49   49   49   49   49   49   51   51   51   52   52   52   52 
LCS_GDT     L    77_A     L    77_A     49   50   55     20   45   47   48   48   49   49   49   49   49   49   49   49   51   51   51   52   52   52   52 
LCS_GDT     R    78_A     R    78_A     49   50   55      4   44   47   48   48   49   49   49   49   49   49   49   49   51   51   51   52   52   52   52 
LCS_GDT     D    79_A     D    79_A     49   50   55      4    4   41   48   48   49   49   49   49   49   49   49   49   51   51   51   52   52   52   52 
LCS_GDT     Q    80_A     Q    80_A     49   50   55     14   44   47   48   48   49   49   49   49   49   49   49   49   51   51   51   52   52   52   52 
LCS_GDT     Q    81_A     Q    81_A     49   50   55      0   17   23   29   48   49   49   49   49   49   49   49   49   51   51   51   52   52   52   52 
LCS_AVERAGE  LCS_A:  60.08  (  55.71   57.99   66.55 )

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     39     45     47     48     48     49     49     49     49     49     49     49     49     51     51     51     52     52     52     52 
GDT PERCENT_AT  54.17  62.50  65.28  66.67  66.67  68.06  68.06  68.06  68.06  68.06  68.06  68.06  68.06  70.83  70.83  70.83  72.22  72.22  72.22  72.22
GDT RMS_LOCAL    0.33   0.43   0.51   0.61   0.61   0.80   0.80   0.80   0.80   0.80   0.80   0.80   0.80   2.22   2.22   2.22   2.80   2.80   2.80   2.80
GDT RMS_ALL_AT  21.80  21.63  21.64  21.70  21.70  21.82  21.82  21.82  21.82  21.82  21.82  21.82  21.82  21.08  21.08  21.08  20.83  20.83  20.83  20.83

# Checking swapping
#   possible swapping detected:  E     6_A      E     6_A
#   possible swapping detected:  E    20_A      E    20_A
#   possible swapping detected:  E    21_A      E    21_A
#   possible swapping detected:  Y    76_A      Y    76_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    T     2_A      T     2_A    62.613     0    0.106   1.111    63.223    0.000    0.000
LGA    S     3_A      S     3_A    59.669     0    0.661   0.789    61.125    0.000    0.000
LGA    L     4_A      L     4_A    56.019     0    0.018   0.051    57.837    0.000    0.000
LGA    I     5_A      I     5_A    52.123     0    0.035   0.110    54.668    0.000    0.000
LGA    E     6_A      E     6_A    51.915     0    0.053   0.913    58.029    0.000    0.000
LGA    E     7_A      E     7_A    50.518     0    0.042   0.909    52.054    0.000    0.000
LGA    L     8_A      L     8_A    45.945     0    0.024   0.036    48.698    0.000    0.000
LGA    I     9_A      I     9_A    43.345     0    0.023   0.125    46.422    0.000    0.000
LGA    R    10_A      R    10_A    43.647     0    0.029   0.682    54.418    0.000    0.000
LGA    R    11_A      R    11_A    40.571     0    0.025   1.246    46.482    0.000    0.000
LGA    S    12_A      S    12_A    35.834     0    0.061   0.064    38.096    0.000    0.000
LGA    E    13_A      E    13_A    35.308     0    0.032   0.934    38.994    0.000    0.000
LGA    E    14_A      E    14_A    34.476     0    0.006   0.661    40.272    0.000    0.000
LGA    Q    15_A      Q    15_A    29.975     0    0.057   1.419    32.028    0.000    0.000
LGA    Q    16_A      Q    16_A    26.629     0    0.009   1.390    28.416    0.000    0.000
LGA    R    17_A      R    17_A    26.897     0    0.000   1.023    38.978    0.000    0.000
LGA    R    18_A      R    18_A    24.116     0    0.008   1.121    34.714    0.000    0.000
LGA    N    19_A      N    19_A    19.577     0    0.033   0.059    22.741    0.000    0.000
LGA    E    20_A      E    20_A    18.471     0    0.000   1.274    23.045    0.000    0.000
LGA    E    21_A      E    21_A    18.146     0    0.040   1.031    22.236    0.000    0.000
LGA    A    22_A      A    22_A    13.593     0    0.054   0.055    15.570    0.119    0.095
LGA    L    23_A      L    23_A    10.192     0    0.093   1.355    11.955    1.310    0.893
LGA    R    24_A      R    24_A    12.101     0    0.248   1.081    21.788    0.000    0.000
LGA    Q    33_A      Q    33_A     1.136     0    0.055   1.087     5.797   83.690   59.894
LGA    L    34_A      L    34_A     1.259     0    0.060   0.095     2.295   85.952   78.393
LGA    L    35_A      L    35_A     0.492     0    0.020   0.486     2.697   97.619   86.548
LGA    S    36_A      S    36_A     0.680     0    0.046   0.056     1.052   92.857   89.048
LGA    G    37_A      G    37_A     0.858     0    0.097   0.097     0.858   95.238   95.238
LGA    I    38_A      I    38_A     0.216     0    0.028   0.063     0.960  100.000   97.619
LGA    V    39_A      V    39_A     0.546     0    0.019   0.052     0.805   92.857   91.837
LGA    Q    40_A      Q    40_A     0.844     0    0.003   0.968     3.929   90.476   77.566
LGA    Q    41_A      Q    41_A     0.476     0    0.027   1.399     4.563   97.619   75.556
LGA    Q    42_A      Q    42_A     0.310     0    0.058   0.221     1.151  100.000   95.820
LGA    N    43_A      N    43_A     0.341     0    0.007   1.335     3.951  100.000   81.429
LGA    N    44_A      N    44_A     0.284     0    0.021   0.089     0.729  100.000   96.429
LGA    L    45_A      L    45_A     0.283     0    0.032   1.404     3.633  100.000   82.262
LGA    L    46_A      L    46_A     0.232     0    0.012   1.403     3.733  100.000   83.155
LGA    R    47_A      R    47_A     0.324     0    0.000   0.241     1.220  100.000   96.580
LGA    A    48_A      A    48_A     0.364     0    0.025   0.032     0.376  100.000  100.000
LGA    I    49_A      I    49_A     0.464     0    0.044   0.093     0.584  100.000   96.429
LGA    E    50_A      E    50_A     0.415     0    0.016   0.125     1.221  100.000   94.762
LGA    A    51_A      A    51_A     0.297     0    0.017   0.017     0.397  100.000  100.000
LGA    Q    52_A      Q    52_A     0.452     0    0.017   0.205     1.353  100.000   94.762
LGA    Q    53_A      Q    53_A     0.434     0    0.015   1.555     5.453  100.000   73.968
LGA    H    54_A      H    54_A     0.452     0    0.022   1.141     2.627  100.000   89.333
LGA    L    55_A      L    55_A     0.422     0    0.011   1.410     3.976  100.000   80.119
LGA    L    56_A      L    56_A     0.497     0    0.013   1.377     3.096   97.619   83.571
LGA    Q    57_A      Q    57_A     0.482     0    0.052   1.173     5.114  100.000   77.143
LGA    L    58_A      L    58_A     0.416     0    0.022   0.104     0.568  100.000   98.810
LGA    T    59_A      T    59_A     0.453     0    0.066   1.115     2.118   97.619   87.211
LGA    V    60_A      V    60_A     0.413     0    0.010   0.049     0.623   97.619   97.279
LGA    W    61_A      W    61_A     0.512     0    0.057   0.173     1.309   97.619   89.932
LGA    G    62_A      G    62_A     0.437     0    0.049   0.049     0.473  100.000  100.000
LGA    I    63_A      I    63_A     0.425     0    0.019   0.092     0.609  100.000   97.619
LGA    K    64_A      K    64_A     0.407     0    0.040   1.149     6.367  100.000   74.286
LGA    Q    65_A      Q    65_A     0.376     0    0.035   1.094     4.451  100.000   81.323
LGA    L    66_A      L    66_A     0.334     0    0.000   0.066     0.592  100.000   97.619
LGA    Q    67_A      Q    67_A     0.295     0    0.026   0.039     0.636  100.000   98.942
LGA    A    68_A      A    68_A     0.201     0    0.022   0.023     0.260  100.000  100.000
LGA    R    69_A      R    69_A     0.088     0    0.011   1.010     4.205  100.000   87.749
LGA    I    70_A      I    70_A     0.367     0    0.033   1.384     4.244  100.000   83.155
LGA    L    71_A      L    71_A     0.315     0    0.021   1.406     3.530  100.000   83.155
LGA    A    72_A      A    72_A     0.171     0    0.058   0.060     0.450  100.000  100.000
LGA    V    73_A      V    73_A     0.388     0    0.019   0.056     0.529   97.619   98.639
LGA    E    74_A      E    74_A     0.572     0    0.054   0.188     0.944   92.857   91.534
LGA    R    75_A      R    75_A     0.527     0    0.069   0.262     1.637   92.857   89.784
LGA    Y    76_A      Y    76_A     0.473     0    0.040   1.245     8.922   95.238   57.579
LGA    L    77_A      L    77_A     0.995     0    0.625   0.624     3.453   78.095   83.155
LGA    R    78_A      R    78_A     0.985     0    0.454   1.236     7.728   73.690   54.459
LGA    D    79_A      D    79_A     2.206     0    0.525   0.523     4.446   54.167   58.512
LGA    Q    80_A      Q    80_A     1.228     0    0.139   1.034     3.410   79.881   73.704
LGA    Q    81_A      Q    81_A     3.459     0    0.433   0.747     5.714   43.333   47.090

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       72     288    288  100.00     603    603  100.00                72
SUMMARY(RMSD_GDC):    16.693         16.366                 17.082           64.388   58.472

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   83   72    4.0     49    0.80    67.014    64.996     5.451

LGA_LOCAL      RMSD:   0.799  Number of atoms:   49  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  21.819  Number of assigned atoms:   72 
Std_ASGN_ATOMS RMSD:  16.693  Standard rmsd on all 72 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.262765 * X  +  -0.964857 * Y  +   0.002390 * Z  +  23.323740
  Y_new =   0.565408 * X  +   0.155987 * Y  +   0.809927 * Z  + -36.716324
  Z_new =  -0.781836 * X  +  -0.211470 * Y  +   0.586526 * Z  + 112.086624 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.135756  0.897605 -0.346039   [DEG:   65.0740   51.4290  -19.8266 ]
ZXZ:  3.138642  0.944033 -1.834954   [DEG:  179.8309   54.0891 -105.1351 ]
 
# END of job
