
#######################################################
#                                                     #
#                        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        4.79    19.78
  LCS_AVERAGE:     66.55

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    50      24_A - 81_A        1.85    21.18
  LCS_AVERAGE:     57.99

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    49      33_A - 81_A        0.55    22.19
  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    9   15   23   23   23   23   23   23   23   23   23   23   24 
LCS_GDT     S     3_A     S     3_A     22   23   25     17   22   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   25   25   25 
LCS_GDT     L     4_A     L     4_A     22   23   25     20   22   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   25   25   25 
LCS_GDT     I     5_A     I     5_A     22   23   25     20   22   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   25   25   25 
LCS_GDT     E     6_A     E     6_A     22   23   25     20   22   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   25   25   25 
LCS_GDT     E     7_A     E     7_A     22   23   25     20   22   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   25   25   25 
LCS_GDT     L     8_A     L     8_A     22   23   25     20   22   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   25   25   25 
LCS_GDT     I     9_A     I     9_A     22   23   25     20   22   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   25   25   25 
LCS_GDT     R    10_A     R    10_A     22   23   25     20   22   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   25   25   25 
LCS_GDT     R    11_A     R    11_A     22   23   25     20   22   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   25   25   25 
LCS_GDT     S    12_A     S    12_A     22   23   25     20   22   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   25   25   25 
LCS_GDT     E    13_A     E    13_A     22   23   25     20   22   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   25   25   25 
LCS_GDT     E    14_A     E    14_A     22   23   25     20   22   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   25   25   25 
LCS_GDT     Q    15_A     Q    15_A     22   23   25     20   22   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   25   25   25 
LCS_GDT     Q    16_A     Q    16_A     22   23   25     20   22   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   25   25   25 
LCS_GDT     R    17_A     R    17_A     22   23   25     20   22   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   25   25   25 
LCS_GDT     R    18_A     R    18_A     22   23   25     20   22   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   25   25   25 
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   23   23   25   25   25 
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   23   23   25   36   53 
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   23   23   32   50   53 
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   35   52   52   52   52   53 
LCS_GDT     L    23_A     L    23_A     22   23   55     20   22   22   22   22   22   22   22   22   23   23   24   46   51   51   52   52   52   52   53 
LCS_GDT     R    24_A     R    24_A     22   50   55     18   22   22   22   22   22   22   22   22   23   23   28   44   51   51   52   52   52   52   53 
LCS_GDT     Q    33_A     Q    33_A     49   50   55     42   47   48   49   49   49   49   49   49   49   49   49   49   51   51   52   52   52   52   53 
LCS_GDT     L    34_A     L    34_A     49   50   55     42   47   48   49   49   49   49   49   49   49   49   49   49   51   51   52   52   52   52   53 
LCS_GDT     L    35_A     L    35_A     49   50   55     42   47   48   49   49   49   49   49   49   49   49   49   49   51   51   52   52   52   52   53 
LCS_GDT     S    36_A     S    36_A     49   50   55     42   47   48   49   49   49   49   49   49   49   49   49   49   51   51   52   52   52   52   53 
LCS_GDT     G    37_A     G    37_A     49   50   55     42   47   48   49   49   49   49   49   49   49   49   49   49   51   51   52   52   52   52   53 
LCS_GDT     I    38_A     I    38_A     49   50   55     42   47   48   49   49   49   49   49   49   49   49   49   49   51   51   52   52   52   52   53 
LCS_GDT     V    39_A     V    39_A     49   50   55     42   47   48   49   49   49   49   49   49   49   49   49   49   51   51   52   52   52   52   53 
LCS_GDT     Q    40_A     Q    40_A     49   50   55     42   47   48   49   49   49   49   49   49   49   49   49   49   51   51   52   52   52   52   53 
LCS_GDT     Q    41_A     Q    41_A     49   50   55     42   47   48   49   49   49   49   49   49   49   49   49   49   51   51   52   52   52   52   53 
LCS_GDT     Q    42_A     Q    42_A     49   50   55     42   47   48   49   49   49   49   49   49   49   49   49   49   51   51   52   52   52   52   53 
LCS_GDT     N    43_A     N    43_A     49   50   55     42   47   48   49   49   49   49   49   49   49   49   49   49   51   51   52   52   52   52   53 
LCS_GDT     N    44_A     N    44_A     49   50   55     42   47   48   49   49   49   49   49   49   49   49   49   49   51   51   52   52   52   52   53 
LCS_GDT     L    45_A     L    45_A     49   50   55     42   47   48   49   49   49   49   49   49   49   49   49   49   51   51   52   52   52   52   53 
LCS_GDT     L    46_A     L    46_A     49   50   55     42   47   48   49   49   49   49   49   49   49   49   49   49   51   51   52   52   52   52   53 
LCS_GDT     R    47_A     R    47_A     49   50   55     42   47   48   49   49   49   49   49   49   49   49   49   49   51   51   52   52   52   52   53 
LCS_GDT     A    48_A     A    48_A     49   50   55     42   47   48   49   49   49   49   49   49   49   49   49   49   51   51   52   52   52   52   53 
LCS_GDT     I    49_A     I    49_A     49   50   55     42   47   48   49   49   49   49   49   49   49   49   49   49   51   51   52   52   52   52   53 
LCS_GDT     E    50_A     E    50_A     49   50   55     42   47   48   49   49   49   49   49   49   49   49   49   49   51   51   52   52   52   52   53 
LCS_GDT     A    51_A     A    51_A     49   50   55     42   47   48   49   49   49   49   49   49   49   49   49   49   51   51   52   52   52   52   53 
LCS_GDT     Q    52_A     Q    52_A     49   50   55     42   47   48   49   49   49   49   49   49   49   49   49   49   51   51   52   52   52   52   53 
LCS_GDT     Q    53_A     Q    53_A     49   50   55     42   47   48   49   49   49   49   49   49   49   49   49   49   51   51   52   52   52   52   53 
LCS_GDT     H    54_A     H    54_A     49   50   55     42   47   48   49   49   49   49   49   49   49   49   49   49   51   51   52   52   52   52   53 
LCS_GDT     L    55_A     L    55_A     49   50   55     42   47   48   49   49   49   49   49   49   49   49   49   49   51   51   52   52   52   52   53 
LCS_GDT     L    56_A     L    56_A     49   50   55     42   47   48   49   49   49   49   49   49   49   49   49   49   51   51   52   52   52   52   53 
LCS_GDT     Q    57_A     Q    57_A     49   50   55     42   47   48   49   49   49   49   49   49   49   49   49   49   51   51   52   52   52   52   53 
LCS_GDT     L    58_A     L    58_A     49   50   55     42   47   48   49   49   49   49   49   49   49   49   49   49   51   51   52   52   52   52   53 
LCS_GDT     T    59_A     T    59_A     49   50   55     42   47   48   49   49   49   49   49   49   49   49   49   49   51   51   52   52   52   52   53 
LCS_GDT     V    60_A     V    60_A     49   50   55     42   47   48   49   49   49   49   49   49   49   49   49   49   51   51   52   52   52   52   53 
LCS_GDT     W    61_A     W    61_A     49   50   55     42   47   48   49   49   49   49   49   49   49   49   49   49   51   51   52   52   52   52   53 
LCS_GDT     G    62_A     G    62_A     49   50   55     42   47   48   49   49   49   49   49   49   49   49   49   49   51   51   52   52   52   52   53 
LCS_GDT     I    63_A     I    63_A     49   50   55     42   47   48   49   49   49   49   49   49   49   49   49   49   51   51   52   52   52   52   53 
LCS_GDT     K    64_A     K    64_A     49   50   55     42   47   48   49   49   49   49   49   49   49   49   49   49   51   51   52   52   52   52   53 
LCS_GDT     Q    65_A     Q    65_A     49   50   55     42   47   48   49   49   49   49   49   49   49   49   49   49   51   51   52   52   52   52   53 
LCS_GDT     L    66_A     L    66_A     49   50   55     42   47   48   49   49   49   49   49   49   49   49   49   49   51   51   52   52   52   52   53 
LCS_GDT     Q    67_A     Q    67_A     49   50   55     42   47   48   49   49   49   49   49   49   49   49   49   49   51   51   52   52   52   52   53 
LCS_GDT     A    68_A     A    68_A     49   50   55     42   47   48   49   49   49   49   49   49   49   49   49   49   51   51   52   52   52   52   53 
LCS_GDT     R    69_A     R    69_A     49   50   55     42   47   48   49   49   49   49   49   49   49   49   49   49   51   51   52   52   52   52   53 
LCS_GDT     I    70_A     I    70_A     49   50   55     42   47   48   49   49   49   49   49   49   49   49   49   49   51   51   52   52   52   52   53 
LCS_GDT     L    71_A     L    71_A     49   50   55     42   47   48   49   49   49   49   49   49   49   49   49   49   51   51   52   52   52   52   53 
LCS_GDT     A    72_A     A    72_A     49   50   55     42   47   48   49   49   49   49   49   49   49   49   49   49   51   51   52   52   52   52   53 
LCS_GDT     V    73_A     V    73_A     49   50   55     42   47   48   49   49   49   49   49   49   49   49   49   49   51   51   52   52   52   52   53 
LCS_GDT     E    74_A     E    74_A     49   50   55     42   47   48   49   49   49   49   49   49   49   49   49   49   51   51   52   52   52   52   53 
LCS_GDT     R    75_A     R    75_A     49   50   55     42   47   48   49   49   49   49   49   49   49   49   49   49   51   51   52   52   52   52   53 
LCS_GDT     Y    76_A     Y    76_A     49   50   55     41   47   48   49   49   49   49   49   49   49   49   49   49   51   51   52   52   52   52   53 
LCS_GDT     L    77_A     L    77_A     49   50   55     33   47   48   49   49   49   49   49   49   49   49   49   49   51   51   52   52   52   52   53 
LCS_GDT     R    78_A     R    78_A     49   50   55     33   47   48   49   49   49   49   49   49   49   49   49   49   51   51   52   52   52   52   53 
LCS_GDT     D    79_A     D    79_A     49   50   55     25   47   48   49   49   49   49   49   49   49   49   49   49   51   51   52   52   52   52   53 
LCS_GDT     Q    80_A     Q    80_A     49   50   55     14   43   48   49   49   49   49   49   49   49   49   49   49   51   51   52   52   52   52   53 
LCS_GDT     Q    81_A     Q    81_A     49   50   55      3   11   39   49   49   49   49   49   49   49   49   49   49   51   51   52   52   52   52   53 
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     42     47     48     49     49     49     49     49     49     49     49     49     49     51     51     52     52     52     52     53 
GDT PERCENT_AT  58.33  65.28  66.67  68.06  68.06  68.06  68.06  68.06  68.06  68.06  68.06  68.06  68.06  70.83  70.83  72.22  72.22  72.22  72.22  73.61
GDT RMS_LOCAL    0.31   0.40   0.45   0.55   0.55   0.55   0.55   0.55   0.55   0.55   0.55   0.55   0.55   2.28   2.28   2.90   2.90   2.90   2.90   3.65
GDT RMS_ALL_AT  22.13  22.17  22.15  22.19  22.19  22.19  22.19  22.19  22.19  22.19  22.19  22.19  22.19  20.97  20.97  20.65  20.65  20.65  20.65  20.23

# 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:  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    63.192     0    0.088   1.092    63.748    0.000    0.000
LGA    S     3_A      S     3_A    60.302     0    0.656   0.797    61.700    0.000    0.000
LGA    L     4_A      L     4_A    56.575     0    0.021   0.057    58.394    0.000    0.000
LGA    I     5_A      I     5_A    52.061     0    0.040   0.111    54.262    0.000    0.000
LGA    E     6_A      E     6_A    52.259     0    0.045   0.950    59.308    0.000    0.000
LGA    E     7_A      E     7_A    51.482     0    0.048   0.908    53.159    0.000    0.000
LGA    L     8_A      L     8_A    46.418     0    0.033   0.042    48.814    0.000    0.000
LGA    I     9_A      I     9_A    43.434     0    0.019   0.122    45.922    0.000    0.000
LGA    R    10_A      R    10_A    44.466     0    0.028   0.212    55.980    0.000    0.000
LGA    R    11_A      R    11_A    41.535     0    0.026   1.245    47.721    0.000    0.000
LGA    S    12_A      S    12_A    36.181     0    0.066   0.694    38.617    0.000    0.000
LGA    E    13_A      E    13_A    35.963     0    0.026   0.938    39.316    0.000    0.000
LGA    E    14_A      E    14_A    35.819     0    0.011   0.655    42.103    0.000    0.000
LGA    Q    15_A      Q    15_A    30.907     0    0.054   1.421    33.065    0.000    0.000
LGA    Q    16_A      Q    16_A    27.242     0    0.011   1.524    29.096    0.000    0.000
LGA    R    17_A      R    17_A    28.154     0    0.005   1.012    40.151    0.000    0.000
LGA    R    18_A      R    18_A    25.623     0    0.010   1.127    36.426    0.000    0.000
LGA    N    19_A      N    19_A    20.390     0    0.045   0.068    22.947    0.000    0.000
LGA    E    20_A      E    20_A    19.518     0    0.018   0.955    26.377    0.000    0.000
LGA    E    21_A      E    21_A    20.035     0    0.040   1.011    24.722    0.000    0.000
LGA    A    22_A      A    22_A    15.187     0    0.054   0.056    17.255    0.000    0.000
LGA    L    23_A      L    23_A    11.230     0    0.066   1.354    13.132    0.119    0.238
LGA    R    24_A      R    24_A    13.965     0    0.196   1.124    21.477    0.000    0.000
LGA    Q    33_A      Q    33_A     0.547     0    0.074   1.108     4.292   92.857   72.328
LGA    L    34_A      L    34_A     0.657     0    0.059   0.086     1.135   92.857   89.405
LGA    L    35_A      L    35_A     0.388     0    0.020   0.485     2.095  100.000   91.012
LGA    S    36_A      S    36_A     0.547     0    0.041   0.049     0.737   90.476   90.476
LGA    G    37_A      G    37_A     0.634     0    0.087   0.087     0.634   95.238   95.238
LGA    I    38_A      I    38_A     0.367     0    0.022   0.055     0.472  100.000  100.000
LGA    V    39_A      V    39_A     0.507     0    0.019   0.052     0.598   92.857   91.837
LGA    Q    40_A      Q    40_A     0.705     0    0.010   0.966     3.854   90.476   78.466
LGA    Q    41_A      Q    41_A     0.514     0    0.035   1.399     4.472   95.238   74.868
LGA    Q    42_A      Q    42_A     0.321     0    0.059   0.245     1.278  100.000   96.878
LGA    N    43_A      N    43_A     0.224     0    0.000   1.334     4.139  100.000   80.655
LGA    N    44_A      N    44_A     0.177     0    0.020   0.088     0.614  100.000   96.429
LGA    L    45_A      L    45_A     0.191     0    0.009   0.198     0.810  100.000   98.810
LGA    L    46_A      L    46_A     0.205     0    0.005   1.399     3.694  100.000   83.155
LGA    R    47_A      R    47_A     0.157     0    0.006   0.240     1.097  100.000   96.580
LGA    A    48_A      A    48_A     0.174     0    0.024   0.030     0.205  100.000  100.000
LGA    I    49_A      I    49_A     0.481     0    0.045   0.090     0.826  100.000   95.238
LGA    E    50_A      E    50_A     0.443     0    0.018   0.124     1.175  100.000   93.704
LGA    A    51_A      A    51_A     0.172     0    0.017   0.017     0.324  100.000  100.000
LGA    Q    52_A      Q    52_A     0.523     0    0.022   0.202     1.316   92.857   89.524
LGA    Q    53_A      Q    53_A     0.538     0    0.015   1.552     5.310   92.857   70.635
LGA    H    54_A      H    54_A     0.364     0    0.025   1.140     2.360  100.000   88.381
LGA    L    55_A      L    55_A     0.378     0    0.015   1.412     3.930  100.000   81.964
LGA    L    56_A      L    56_A     0.642     0    0.015   1.377     3.109   90.476   81.071
LGA    Q    57_A      Q    57_A     0.606     0    0.053   1.169     5.323   95.238   73.280
LGA    L    58_A      L    58_A     0.355     0    0.021   0.104     0.557  100.000   98.810
LGA    T    59_A      T    59_A     0.358     0    0.064   1.115     2.338  100.000   89.728
LGA    V    60_A      V    60_A     0.446     0    0.014   0.045     0.626   95.238   95.918
LGA    W    61_A      W    61_A     0.543     0    0.061   0.165     1.563   97.619   88.027
LGA    G    62_A      G    62_A     0.303     0    0.077   0.077     0.539   97.619   97.619
LGA    I    63_A      I    63_A     0.350     0    0.015   0.094     0.685  100.000   97.619
LGA    K    64_A      K    64_A     0.415     0    0.038   1.147     6.445  100.000   74.286
LGA    Q    65_A      Q    65_A     0.364     0    0.033   1.093     4.519  100.000   80.688
LGA    L    66_A      L    66_A     0.348     0    0.009   0.065     0.621  100.000   96.429
LGA    Q    67_A      Q    67_A     0.222     0    0.020   0.031     0.372  100.000  100.000
LGA    A    68_A      A    68_A     0.275     0    0.023   0.023     0.335  100.000  100.000
LGA    R    69_A      R    69_A     0.310     0    0.016   1.010     4.486  100.000   87.013
LGA    I    70_A      I    70_A     0.527     0    0.027   1.374     4.350   97.619   81.964
LGA    L    71_A      L    71_A     0.395     0    0.019   1.416     3.269  100.000   85.000
LGA    A    72_A      A    72_A     0.248     0    0.024   0.030     0.264  100.000  100.000
LGA    V    73_A      V    73_A     0.300     0    0.007   0.057     0.483  100.000  100.000
LGA    E    74_A      E    74_A     0.345     0    0.021   0.958     3.679  100.000   78.624
LGA    R    75_A      R    75_A     0.227     0    0.035   1.220     4.988  100.000   81.732
LGA    Y    76_A      Y    76_A     0.150     0    0.031   0.111     1.048  100.000   95.278
LGA    L    77_A      L    77_A     0.399     0    0.013   0.027     0.609   97.619   95.238
LGA    R    78_A      R    78_A     0.465     0    0.008   1.236     5.056   95.238   77.229
LGA    D    79_A      D    79_A     0.845     0    0.034   0.078     1.380   85.952   85.952
LGA    Q    80_A      Q    80_A     1.214     0    0.111   0.975     4.899   83.690   67.090
LGA    Q    81_A      Q    81_A     2.144     0    0.338   0.371     3.737   61.429   64.233

# 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):    16.432         16.111                 16.845           65.744   60.120

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   83   72    4.0     49    0.55    68.403    65.532     7.570

LGA_LOCAL      RMSD:   0.547  Number of atoms:   49  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  22.193  Number of assigned atoms:   72 
Std_ASGN_ATOMS RMSD:  16.432  Standard rmsd on all 72 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.354154 * X  +  -0.923810 * Y  +   0.145429 * Z  +  15.984052
  Y_new =   0.424974 * X  +   0.297504 * Y  +   0.854920 * Z  + -39.341259
  Z_new =  -0.833050 * X  +  -0.240970 * Y  +   0.497958 * Z  + 112.148720 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.876046  0.984598 -0.450698   [DEG:   50.1937   56.4133  -25.8231 ]
ZXZ:  2.973097  1.049554 -1.852373   [DEG:  170.3459   60.1350 -106.1332 ]
 
# END of job
