
#######################################################
#                                                     #
#                        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        4.72    18.57
  LCS_AVERAGE:     66.88

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    50      24_A - 81_A        1.85    19.80
  LCS_AVERAGE:     57.99

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    49      33_A - 81_A        0.60    20.64
  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   26      0    3    3    3    3    4    6    9   15   23   23   23   23   23   23   23   23   24   26   26 
LCS_GDT     S     3_A     S     3_A     22   23   26     16   22   22   22   22   22   22   22   22   23   23   23   23   23   23   24   25   25   26   26 
LCS_GDT     L     4_A     L     4_A     22   23   26     20   22   22   22   22   22   22   22   22   23   23   23   23   23   23   24   25   25   26   26 
LCS_GDT     I     5_A     I     5_A     22   23   26     20   22   22   22   22   22   22   22   22   23   23   23   23   23   23   24   25   25   26   26 
LCS_GDT     E     6_A     E     6_A     22   23   26     20   22   22   22   22   22   22   22   22   23   23   23   23   23   23   24   25   25   26   26 
LCS_GDT     E     7_A     E     7_A     22   23   26     20   22   22   22   22   22   22   22   22   23   23   23   23   23   23   24   25   25   26   26 
LCS_GDT     L     8_A     L     8_A     22   23   26     20   22   22   22   22   22   22   22   22   23   23   23   23   23   23   24   25   25   26   26 
LCS_GDT     I     9_A     I     9_A     22   23   26     20   22   22   22   22   22   22   22   22   23   23   23   23   23   23   24   25   25   26   26 
LCS_GDT     R    10_A     R    10_A     22   23   26     20   22   22   22   22   22   22   22   22   23   23   23   23   23   23   24   25   25   26   26 
LCS_GDT     R    11_A     R    11_A     22   23   26     20   22   22   22   22   22   22   22   22   23   23   23   23   23   23   24   25   25   26   26 
LCS_GDT     S    12_A     S    12_A     22   23   26     20   22   22   22   22   22   22   22   22   23   23   23   23   23   23   24   25   25   26   26 
LCS_GDT     E    13_A     E    13_A     22   23   26     20   22   22   22   22   22   22   22   22   23   23   23   23   23   23   24   25   25   26   26 
LCS_GDT     E    14_A     E    14_A     22   23   26     20   22   22   22   22   22   22   22   22   23   23   23   23   23   23   24   25   25   26   26 
LCS_GDT     Q    15_A     Q    15_A     22   23   26     20   22   22   22   22   22   22   22   22   23   23   23   23   23   23   24   25   25   26   26 
LCS_GDT     Q    16_A     Q    16_A     22   23   26     20   22   22   22   22   22   22   22   22   23   23   23   23   23   23   24   25   25   26   26 
LCS_GDT     R    17_A     R    17_A     22   23   26     20   22   22   22   22   22   22   22   22   23   23   23   23   23   23   24   25   25   26   26 
LCS_GDT     R    18_A     R    18_A     22   23   26     20   22   22   22   22   22   22   22   22   23   23   23   23   23   23   24   25   25   26   26 
LCS_GDT     N    19_A     N    19_A     22   23   55     20   22   22   22   22   22   22   22   22   23   23   23   23   23   23   24   25   25   26   30 
LCS_GDT     E    20_A     E    20_A     22   23   55     20   22   22   22   22   22   22   22   22   23   23   23   23   23   23   24   25   29   44   54 
LCS_GDT     E    21_A     E    21_A     22   23   55     20   22   22   22   22   22   22   22   22   23   23   23   23   23   23   24   25   30   47   54 
LCS_GDT     A    22_A     A    22_A     22   23   55     20   22   22   22   22   22   22   22   22   23   23   23   23   23   28   50   52   52   52   54 
LCS_GDT     L    23_A     L    23_A     22   23   55     20   22   22   22   22   22   22   22   22   23   23   23   39   50   51   51   52   52   52   54 
LCS_GDT     R    24_A     R    24_A     22   50   55     18   22   22   22   22   22   22   22   22   23   23   23   31   47   51   51   52   52   52   54 
LCS_GDT     Q    33_A     Q    33_A     49   50   55     18   46   48   49   49   49   49   49   49   49   49   49   49   50   51   51   52   52   52   54 
LCS_GDT     L    34_A     L    34_A     49   50   55     15   46   48   49   49   49   49   49   49   49   49   49   49   50   51   51   52   52   52   54 
LCS_GDT     L    35_A     L    35_A     49   50   55     38   46   48   49   49   49   49   49   49   49   49   49   49   50   51   51   52   52   52   54 
LCS_GDT     S    36_A     S    36_A     49   50   55     38   46   48   49   49   49   49   49   49   49   49   49   49   50   51   51   52   52   52   54 
LCS_GDT     G    37_A     G    37_A     49   50   55     38   46   48   49   49   49   49   49   49   49   49   49   49   50   51   51   52   52   52   54 
LCS_GDT     I    38_A     I    38_A     49   50   55     38   46   48   49   49   49   49   49   49   49   49   49   49   50   51   51   52   52   52   54 
LCS_GDT     V    39_A     V    39_A     49   50   55     38   46   48   49   49   49   49   49   49   49   49   49   49   50   51   51   52   52   52   54 
LCS_GDT     Q    40_A     Q    40_A     49   50   55     30   46   48   49   49   49   49   49   49   49   49   49   49   50   51   51   52   52   52   54 
LCS_GDT     Q    41_A     Q    41_A     49   50   55     38   46   48   49   49   49   49   49   49   49   49   49   49   50   51   51   52   52   52   54 
LCS_GDT     Q    42_A     Q    42_A     49   50   55     38   46   48   49   49   49   49   49   49   49   49   49   49   50   51   51   52   52   52   54 
LCS_GDT     N    43_A     N    43_A     49   50   55     38   46   48   49   49   49   49   49   49   49   49   49   49   50   51   51   52   52   52   54 
LCS_GDT     N    44_A     N    44_A     49   50   55     36   46   48   49   49   49   49   49   49   49   49   49   49   50   51   51   52   52   52   54 
LCS_GDT     L    45_A     L    45_A     49   50   55     38   46   48   49   49   49   49   49   49   49   49   49   49   50   51   51   52   52   52   54 
LCS_GDT     L    46_A     L    46_A     49   50   55     38   46   48   49   49   49   49   49   49   49   49   49   49   50   51   51   52   52   52   54 
LCS_GDT     R    47_A     R    47_A     49   50   55     38   46   48   49   49   49   49   49   49   49   49   49   49   50   51   51   52   52   52   54 
LCS_GDT     A    48_A     A    48_A     49   50   55     38   46   48   49   49   49   49   49   49   49   49   49   49   50   51   51   52   52   52   54 
LCS_GDT     I    49_A     I    49_A     49   50   55     38   46   48   49   49   49   49   49   49   49   49   49   49   50   51   51   52   52   52   54 
LCS_GDT     E    50_A     E    50_A     49   50   55     38   46   48   49   49   49   49   49   49   49   49   49   49   50   51   51   52   52   52   54 
LCS_GDT     A    51_A     A    51_A     49   50   55     38   46   48   49   49   49   49   49   49   49   49   49   49   50   51   51   52   52   52   54 
LCS_GDT     Q    52_A     Q    52_A     49   50   55     38   46   48   49   49   49   49   49   49   49   49   49   49   50   51   51   52   52   52   54 
LCS_GDT     Q    53_A     Q    53_A     49   50   55     38   46   48   49   49   49   49   49   49   49   49   49   49   50   51   51   52   52   52   54 
LCS_GDT     H    54_A     H    54_A     49   50   55     38   46   48   49   49   49   49   49   49   49   49   49   49   50   51   51   52   52   52   54 
LCS_GDT     L    55_A     L    55_A     49   50   55     38   46   48   49   49   49   49   49   49   49   49   49   49   50   51   51   52   52   52   54 
LCS_GDT     L    56_A     L    56_A     49   50   55     38   46   48   49   49   49   49   49   49   49   49   49   49   50   51   51   52   52   52   54 
LCS_GDT     Q    57_A     Q    57_A     49   50   55     38   46   48   49   49   49   49   49   49   49   49   49   49   50   51   51   52   52   52   54 
LCS_GDT     L    58_A     L    58_A     49   50   55     38   46   48   49   49   49   49   49   49   49   49   49   49   50   51   51   52   52   52   54 
LCS_GDT     T    59_A     T    59_A     49   50   55     38   46   48   49   49   49   49   49   49   49   49   49   49   50   51   51   52   52   52   54 
LCS_GDT     V    60_A     V    60_A     49   50   55     38   46   48   49   49   49   49   49   49   49   49   49   49   50   51   51   52   52   52   54 
LCS_GDT     W    61_A     W    61_A     49   50   55     38   46   48   49   49   49   49   49   49   49   49   49   49   50   51   51   52   52   52   54 
LCS_GDT     G    62_A     G    62_A     49   50   55     38   46   48   49   49   49   49   49   49   49   49   49   49   50   51   51   52   52   52   54 
LCS_GDT     I    63_A     I    63_A     49   50   55     38   46   48   49   49   49   49   49   49   49   49   49   49   50   51   51   52   52   52   54 
LCS_GDT     K    64_A     K    64_A     49   50   55     38   46   48   49   49   49   49   49   49   49   49   49   49   50   51   51   52   52   52   54 
LCS_GDT     Q    65_A     Q    65_A     49   50   55     38   46   48   49   49   49   49   49   49   49   49   49   49   50   51   51   52   52   52   54 
LCS_GDT     L    66_A     L    66_A     49   50   55     38   46   48   49   49   49   49   49   49   49   49   49   49   50   51   51   52   52   52   54 
LCS_GDT     Q    67_A     Q    67_A     49   50   55     38   46   48   49   49   49   49   49   49   49   49   49   49   50   51   51   52   52   52   54 
LCS_GDT     A    68_A     A    68_A     49   50   55     38   46   48   49   49   49   49   49   49   49   49   49   49   50   51   51   52   52   52   54 
LCS_GDT     R    69_A     R    69_A     49   50   55     38   46   48   49   49   49   49   49   49   49   49   49   49   50   51   51   52   52   52   54 
LCS_GDT     I    70_A     I    70_A     49   50   55     38   46   48   49   49   49   49   49   49   49   49   49   49   50   51   51   52   52   52   54 
LCS_GDT     L    71_A     L    71_A     49   50   55     38   46   48   49   49   49   49   49   49   49   49   49   49   50   51   51   52   52   52   54 
LCS_GDT     A    72_A     A    72_A     49   50   55     38   46   48   49   49   49   49   49   49   49   49   49   49   50   51   51   52   52   52   54 
LCS_GDT     V    73_A     V    73_A     49   50   55     38   46   48   49   49   49   49   49   49   49   49   49   49   50   51   51   52   52   52   54 
LCS_GDT     E    74_A     E    74_A     49   50   55     38   46   48   49   49   49   49   49   49   49   49   49   49   50   51   51   52   52   52   54 
LCS_GDT     R    75_A     R    75_A     49   50   55     36   46   48   49   49   49   49   49   49   49   49   49   49   50   51   51   52   52   52   54 
LCS_GDT     Y    76_A     Y    76_A     49   50   55     36   46   48   49   49   49   49   49   49   49   49   49   49   50   51   51   52   52   52   54 
LCS_GDT     L    77_A     L    77_A     49   50   55     33   46   48   49   49   49   49   49   49   49   49   49   49   50   51   51   52   52   52   54 
LCS_GDT     R    78_A     R    78_A     49   50   55     33   46   48   49   49   49   49   49   49   49   49   49   49   50   51   51   52   52   52   54 
LCS_GDT     D    79_A     D    79_A     49   50   55     12   45   48   49   49   49   49   49   49   49   49   49   49   50   51   51   52   52   52   54 
LCS_GDT     Q    80_A     Q    80_A     49   50   55     12   42   48   49   49   49   49   49   49   49   49   49   49   50   51   51   52   52   52   54 
LCS_GDT     Q    81_A     Q    81_A     49   50   55      3   11   38   49   49   49   49   49   49   49   49   49   49   50   51   51   52   52   52   54 
LCS_AVERAGE  LCS_A:  60.19  (  55.71   57.99   66.88 )

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     38     46     48     49     49     49     49     49     49     49     49     49     49     50     51     51     52     52     52     54 
GDT PERCENT_AT  52.78  63.89  66.67  68.06  68.06  68.06  68.06  68.06  68.06  68.06  68.06  68.06  68.06  69.44  70.83  70.83  72.22  72.22  72.22  75.00
GDT RMS_LOCAL    0.35   0.45   0.51   0.60   0.60   0.60   0.60   0.60   0.60   0.60   0.60   0.60   0.60   1.60   2.30   2.30   2.93   2.93   2.93   4.18
GDT RMS_ALL_AT  20.65  20.59  20.60  20.64  20.64  20.64  20.64  20.64  20.64  20.64  20.64  20.64  20.64  20.18  19.67  19.67  19.38  19.38  19.38  18.76

# Checking swapping
#   possible swapping detected:  E     6_A      E     6_A
#   possible swapping detected:  E    20_A      E    20_A
#   possible swapping detected:  E    74_A      E    74_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    T     2_A      T     2_A    59.180     0    0.111   1.100    59.784    0.000    0.000
LGA    S     3_A      S     3_A    55.815     0    0.663   0.793    57.383    0.000    0.000
LGA    L     4_A      L     4_A    52.380     0    0.019   0.052    54.046    0.000    0.000
LGA    I     5_A      I     5_A    47.900     0    0.037   0.111    50.035    0.000    0.000
LGA    E     6_A      E     6_A    48.293     0    0.056   0.914    54.813    0.000    0.000
LGA    E     7_A      E     7_A    47.884     0    0.043   0.897    49.516    0.000    0.000
LGA    L     8_A      L     8_A    43.005     0    0.033   0.041    45.131    0.000    0.000
LGA    I     9_A      I     9_A    40.089     0    0.019   0.122    42.087    0.000    0.000
LGA    R    10_A      R    10_A    41.406     0    0.027   0.678    52.043    0.000    0.000
LGA    R    11_A      R    11_A    38.786     0    0.027   1.245    45.215    0.000    0.000
LGA    S    12_A      S    12_A    33.506     0    0.066   0.694    35.860    0.000    0.000
LGA    E    13_A      E    13_A    33.370     0    0.026   0.938    36.560    0.000    0.000
LGA    E    14_A      E    14_A    33.603     0    0.008   0.657    39.785    0.000    0.000
LGA    Q    15_A      Q    15_A    28.922     0    0.055   1.421    30.950    0.000    0.000
LGA    Q    16_A      Q    16_A    25.242     0    0.009   1.525    27.046    0.000    0.000
LGA    R    17_A      R    17_A    26.353     0    0.010   1.018    37.927    0.000    0.000
LGA    R    18_A      R    18_A    24.251     0    0.002   1.122    35.329    0.000    0.000
LGA    N    19_A      N    19_A    19.149     0    0.037   0.064    21.482    0.000    0.000
LGA    E    20_A      E    20_A    18.168     0    0.008   1.263    22.604    0.000    0.000
LGA    E    21_A      E    21_A    19.091     0    0.032   0.243    24.365    0.000    0.000
LGA    A    22_A      A    22_A    14.679     0    0.053   0.053    16.532    0.000    0.000
LGA    L    23_A      L    23_A    10.827     0    0.045   1.355    12.602    0.119    0.595
LGA    R    24_A      R    24_A    13.476     0    0.248   1.090    21.800    0.000    0.000
LGA    Q    33_A      Q    33_A     1.046     0    0.059   1.103     5.238   85.952   63.545
LGA    L    34_A      L    34_A     1.051     0    0.055   0.089     1.500   85.952   83.690
LGA    L    35_A      L    35_A     0.618     0    0.020   0.481     2.457   95.238   85.298
LGA    S    36_A      S    36_A     0.696     0    0.043   0.055     1.069   90.476   88.968
LGA    G    37_A      G    37_A     0.744     0    0.089   0.089     0.744   95.238   95.238
LGA    I    38_A      I    38_A     0.406     0    0.024   0.061     0.704   95.238   96.429
LGA    V    39_A      V    39_A     0.547     0    0.011   0.050     0.674   92.857   91.837
LGA    Q    40_A      Q    40_A     0.724     0    0.006   0.970     4.093   90.476   76.878
LGA    Q    41_A      Q    41_A     0.509     0    0.032   1.399     4.301   95.238   74.868
LGA    Q    42_A      Q    42_A     0.414     0    0.058   0.226     1.231   97.619   93.704
LGA    N    43_A      N    43_A     0.269     0    0.000   1.334     4.138  100.000   80.655
LGA    N    44_A      N    44_A     0.368     0    0.021   0.089     0.930   97.619   94.048
LGA    L    45_A      L    45_A     0.350     0    0.014   0.203     0.686  100.000   96.429
LGA    L    46_A      L    46_A     0.311     0    0.014   1.391     3.866  100.000   83.155
LGA    R    47_A      R    47_A     0.353     0    0.019   0.244     1.065  100.000   96.580
LGA    A    48_A      A    48_A     0.372     0    0.053   0.064     0.372  100.000  100.000
LGA    I    49_A      I    49_A     0.551     0    0.479   1.525     2.827   84.048   79.881
LGA    E    50_A      E    50_A     0.447     0    0.029   0.168     1.369   97.619   91.640
LGA    A    51_A      A    51_A     0.188     0    0.019   0.018     0.384  100.000  100.000
LGA    Q    52_A      Q    52_A     0.569     0    0.019   0.265     1.403   92.857   88.519
LGA    Q    53_A      Q    53_A     0.618     0    0.025   1.578     5.977   92.857   70.741
LGA    H    54_A      H    54_A     0.343     0    0.015   1.139     2.316  100.000   88.381
LGA    L    55_A      L    55_A     0.347     0    0.007   1.411     4.010  100.000   81.190
LGA    L    56_A      L    56_A     0.674     0    0.011   1.376     3.161   90.476   81.071
LGA    Q    57_A      Q    57_A     0.654     0    0.045   1.446     5.124   95.238   72.646
LGA    L    58_A      L    58_A     0.306     0    0.029   0.124     0.851  100.000   97.619
LGA    T    59_A      T    59_A     0.264     0    0.069   1.114     2.437  100.000   89.728
LGA    V    60_A      V    60_A     0.416     0    0.010   0.045     0.581   97.619   98.639
LGA    W    61_A      W    61_A     0.497     0    0.060   0.090     0.938  100.000   93.197
LGA    G    62_A      G    62_A     0.321     0    0.079   0.079     0.591   97.619   97.619
LGA    I    63_A      I    63_A     0.350     0    0.021   0.092     0.591  100.000   98.810
LGA    K    64_A      K    64_A     0.370     0    0.038   1.150     6.570  100.000   74.921
LGA    Q    65_A      Q    65_A     0.388     0    0.030   1.093     4.603  100.000   80.688
LGA    L    66_A      L    66_A     0.393     0    0.013   0.066     0.658  100.000   96.429
LGA    Q    67_A      Q    67_A     0.198     0    0.024   0.032     0.438  100.000  100.000
LGA    A    68_A      A    68_A     0.299     0    0.025   0.026     0.398  100.000  100.000
LGA    R    69_A      R    69_A     0.387     0    0.011   1.011     4.594  100.000   85.801
LGA    I    70_A      I    70_A     0.513     0    0.031   1.374     4.307   97.619   81.964
LGA    L    71_A      L    71_A     0.386     0    0.011   1.416     3.224  100.000   83.095
LGA    A    72_A      A    72_A     0.286     0    0.027   0.031     0.305  100.000  100.000
LGA    V    73_A      V    73_A     0.314     0    0.015   0.058     0.487  100.000  100.000
LGA    E    74_A      E    74_A     0.307     0    0.019   0.958     3.687  100.000   79.418
LGA    R    75_A      R    75_A     0.249     0    0.038   1.220     4.857  100.000   82.424
LGA    Y    76_A      Y    76_A     0.158     0    0.030   0.112     0.941  100.000   96.825
LGA    L    77_A      L    77_A     0.384     0    0.013   0.028     0.570   97.619   96.429
LGA    R    78_A      R    78_A     0.531     0    0.006   1.234     5.185   92.857   74.892
LGA    D    79_A      D    79_A     0.904     0    0.028   0.080     1.426   85.952   84.821
LGA    Q    80_A      Q    80_A     1.221     0    0.110   0.975     4.836   81.429   66.825
LGA    Q    81_A      Q    81_A     2.187     0    0.330   0.360     3.781   61.429   63.333

# 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):    15.343         15.054                 15.750           65.101   59.437

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   83   72    4.0     49    0.60    67.708    65.362     6.953

LGA_LOCAL      RMSD:   0.605  Number of atoms:   49  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  20.639  Number of assigned atoms:   72 
Std_ASGN_ATOMS RMSD:  15.343  Standard rmsd on all 72 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.766229 * X  +  -0.637534 * Y  +   0.080270 * Z  +  24.315094
  Y_new =  -0.545242 * X  +   0.578980 * Y  +  -0.606213 * Z  + -37.179535
  Z_new =   0.340006 * X  +  -0.508265 * Y  +  -0.791241 * Z  + 103.671455 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.523130 -0.346924 -2.570604   [DEG: -144.5647  -19.8773 -147.2848 ]
ZXZ:  0.131647  2.483633  2.552007   [DEG:    7.5428  142.3017  146.2192 ]
 
# END of job
