
#######################################################
#                                                     #
#                        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    19.83
  LCS_AVERAGE:     66.88

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    50      24_A - 81_A        1.81    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        0.58    21.88
  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    4    6    9   16   17   23   23   23   23   23   23   23   23   23   24   24 
LCS_GDT     S     3_A     S     3_A     22   23   26      8   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   26     21   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   26     21   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   26     21   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   26     21   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   26     21   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   26     21   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   26     21   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   26     21   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   26     21   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   26     21   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   26     21   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   26     21   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   26     21   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   26     21   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   26     21   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     21   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     21   22   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   25   27   41 
LCS_GDT     E    21_A     E    21_A     22   23   55     21   22   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   26   39   51 
LCS_GDT     A    22_A     A    22_A     22   23   55     21   22   22   22   22   22   22   22   22   23   23   23   23   23   36   51   52   52   52   52 
LCS_GDT     L    23_A     L    23_A     22   23   55     21   22   22   22   22   22   22   22   22   23   23   23   39   50   50   51   52   52   52   52 
LCS_GDT     R    24_A     R    24_A     22   50   55     21   22   22   22   22   22   22   22   22   23   23   23   23   39   50   51   52   52   52   52 
LCS_GDT     Q    33_A     Q    33_A     49   50   55     16   48   48   49   49   49   49   49   49   49   49   49   49   50   50   51   52   52   52   52 
LCS_GDT     L    34_A     L    34_A     49   50   55     15   48   48   49   49   49   49   49   49   49   49   49   49   50   50   51   52   52   52   52 
LCS_GDT     L    35_A     L    35_A     49   50   55     32   48   48   49   49   49   49   49   49   49   49   49   49   50   50   51   52   52   52   52 
LCS_GDT     S    36_A     S    36_A     49   50   55     39   48   48   49   49   49   49   49   49   49   49   49   49   50   50   51   52   52   52   52 
LCS_GDT     G    37_A     G    37_A     49   50   55     39   48   48   49   49   49   49   49   49   49   49   49   49   50   50   51   52   52   52   52 
LCS_GDT     I    38_A     I    38_A     49   50   55     39   48   48   49   49   49   49   49   49   49   49   49   49   50   50   51   52   52   52   52 
LCS_GDT     V    39_A     V    39_A     49   50   55     39   48   48   49   49   49   49   49   49   49   49   49   49   50   50   51   52   52   52   52 
LCS_GDT     Q    40_A     Q    40_A     49   50   55     26   48   48   49   49   49   49   49   49   49   49   49   49   50   50   51   52   52   52   52 
LCS_GDT     Q    41_A     Q    41_A     49   50   55     39   48   48   49   49   49   49   49   49   49   49   49   49   50   50   51   52   52   52   52 
LCS_GDT     Q    42_A     Q    42_A     49   50   55     39   48   48   49   49   49   49   49   49   49   49   49   49   50   50   51   52   52   52   52 
LCS_GDT     N    43_A     N    43_A     49   50   55     39   48   48   49   49   49   49   49   49   49   49   49   49   50   50   51   52   52   52   52 
LCS_GDT     N    44_A     N    44_A     49   50   55     39   48   48   49   49   49   49   49   49   49   49   49   49   50   50   51   52   52   52   52 
LCS_GDT     L    45_A     L    45_A     49   50   55     39   48   48   49   49   49   49   49   49   49   49   49   49   50   50   51   52   52   52   52 
LCS_GDT     L    46_A     L    46_A     49   50   55     39   48   48   49   49   49   49   49   49   49   49   49   49   50   50   51   52   52   52   52 
LCS_GDT     R    47_A     R    47_A     49   50   55     39   48   48   49   49   49   49   49   49   49   49   49   49   50   50   51   52   52   52   52 
LCS_GDT     A    48_A     A    48_A     49   50   55     39   48   48   49   49   49   49   49   49   49   49   49   49   50   50   51   52   52   52   52 
LCS_GDT     I    49_A     I    49_A     49   50   55     39   48   48   49   49   49   49   49   49   49   49   49   49   50   50   51   52   52   52   52 
LCS_GDT     E    50_A     E    50_A     49   50   55     39   48   48   49   49   49   49   49   49   49   49   49   49   50   50   51   52   52   52   52 
LCS_GDT     A    51_A     A    51_A     49   50   55     39   48   48   49   49   49   49   49   49   49   49   49   49   50   50   51   52   52   52   52 
LCS_GDT     Q    52_A     Q    52_A     49   50   55     39   48   48   49   49   49   49   49   49   49   49   49   49   50   50   51   52   52   52   52 
LCS_GDT     Q    53_A     Q    53_A     49   50   55     39   48   48   49   49   49   49   49   49   49   49   49   49   50   50   51   52   52   52   52 
LCS_GDT     H    54_A     H    54_A     49   50   55     39   48   48   49   49   49   49   49   49   49   49   49   49   50   50   51   52   52   52   52 
LCS_GDT     L    55_A     L    55_A     49   50   55     39   48   48   49   49   49   49   49   49   49   49   49   49   50   50   51   52   52   52   52 
LCS_GDT     L    56_A     L    56_A     49   50   55     39   48   48   49   49   49   49   49   49   49   49   49   49   50   50   51   52   52   52   52 
LCS_GDT     Q    57_A     Q    57_A     49   50   55     39   48   48   49   49   49   49   49   49   49   49   49   49   50   50   51   52   52   52   52 
LCS_GDT     L    58_A     L    58_A     49   50   55     39   48   48   49   49   49   49   49   49   49   49   49   49   50   50   51   52   52   52   52 
LCS_GDT     T    59_A     T    59_A     49   50   55     39   48   48   49   49   49   49   49   49   49   49   49   49   50   50   51   52   52   52   52 
LCS_GDT     V    60_A     V    60_A     49   50   55     39   48   48   49   49   49   49   49   49   49   49   49   49   50   50   51   52   52   52   52 
LCS_GDT     W    61_A     W    61_A     49   50   55     39   48   48   49   49   49   49   49   49   49   49   49   49   50   50   51   52   52   52   52 
LCS_GDT     G    62_A     G    62_A     49   50   55     39   48   48   49   49   49   49   49   49   49   49   49   49   50   50   51   52   52   52   52 
LCS_GDT     I    63_A     I    63_A     49   50   55     39   48   48   49   49   49   49   49   49   49   49   49   49   50   50   51   52   52   52   52 
LCS_GDT     K    64_A     K    64_A     49   50   55     39   48   48   49   49   49   49   49   49   49   49   49   49   50   50   51   52   52   52   52 
LCS_GDT     Q    65_A     Q    65_A     49   50   55     39   48   48   49   49   49   49   49   49   49   49   49   49   50   50   51   52   52   52   52 
LCS_GDT     L    66_A     L    66_A     49   50   55     39   48   48   49   49   49   49   49   49   49   49   49   49   50   50   51   52   52   52   52 
LCS_GDT     Q    67_A     Q    67_A     49   50   55     39   48   48   49   49   49   49   49   49   49   49   49   49   50   50   51   52   52   52   52 
LCS_GDT     A    68_A     A    68_A     49   50   55     39   48   48   49   49   49   49   49   49   49   49   49   49   50   50   51   52   52   52   52 
LCS_GDT     R    69_A     R    69_A     49   50   55     39   48   48   49   49   49   49   49   49   49   49   49   49   50   50   51   52   52   52   52 
LCS_GDT     I    70_A     I    70_A     49   50   55     39   48   48   49   49   49   49   49   49   49   49   49   49   50   50   51   52   52   52   52 
LCS_GDT     L    71_A     L    71_A     49   50   55     39   48   48   49   49   49   49   49   49   49   49   49   49   50   50   51   52   52   52   52 
LCS_GDT     A    72_A     A    72_A     49   50   55     39   48   48   49   49   49   49   49   49   49   49   49   49   50   50   51   52   52   52   52 
LCS_GDT     V    73_A     V    73_A     49   50   55     39   48   48   49   49   49   49   49   49   49   49   49   49   50   50   51   52   52   52   52 
LCS_GDT     E    74_A     E    74_A     49   50   55     39   48   48   49   49   49   49   49   49   49   49   49   49   50   50   51   52   52   52   52 
LCS_GDT     R    75_A     R    75_A     49   50   55     39   48   48   49   49   49   49   49   49   49   49   49   49   50   50   51   52   52   52   52 
LCS_GDT     Y    76_A     Y    76_A     49   50   55     37   48   48   49   49   49   49   49   49   49   49   49   49   50   50   51   52   52   52   52 
LCS_GDT     L    77_A     L    77_A     49   50   55     35   48   48   49   49   49   49   49   49   49   49   49   49   50   50   51   52   52   52   52 
LCS_GDT     R    78_A     R    78_A     49   50   55     35   48   48   49   49   49   49   49   49   49   49   49   49   50   50   51   52   52   52   52 
LCS_GDT     D    79_A     D    79_A     49   50   55     30   48   48   49   49   49   49   49   49   49   49   49   49   50   50   51   52   52   52   52 
LCS_GDT     Q    80_A     Q    80_A     49   50   55     27   48   48   49   49   49   49   49   49   49   49   49   49   50   50   51   52   52   52   52 
LCS_GDT     Q    81_A     Q    81_A     49   50   55      3   17   39   49   49   49   49   49   49   49   49   49   49   50   50   51   52   52   52   52 
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     39     48     48     49     49     49     49     49     49     49     49     49     49     50     50     51     52     52     52     52 
GDT PERCENT_AT  54.17  66.67  66.67  68.06  68.06  68.06  68.06  68.06  68.06  68.06  68.06  68.06  68.06  69.44  69.44  70.83  72.22  72.22  72.22  72.22
GDT RMS_LOCAL    0.32   0.48   0.48   0.58   0.58   0.58   0.58   0.58   0.58   0.58   0.58   0.58   0.58   1.58   1.58   2.26   2.84   2.84   2.84   2.84
GDT RMS_ALL_AT  21.95  21.83  21.83  21.88  21.88  21.88  21.88  21.88  21.88  21.88  21.88  21.88  21.88  21.41  21.41  21.00  20.70  20.70  20.70  20.70

# Checking swapping
#   possible swapping detected:  E     7_A      E     7_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    63.310     0    0.043   1.076    63.878    0.000    0.000
LGA    S     3_A      S     3_A    59.490     0    0.717   0.828    61.359    0.000    0.000
LGA    L     4_A      L     4_A    55.933     0    0.241   0.270    58.418    0.000    0.000
LGA    I     5_A      I     5_A    51.901     0    0.044   0.712    54.009    0.000    0.000
LGA    E     6_A      E     6_A    51.926     0    0.022   0.862    56.679    0.000    0.000
LGA    E     7_A      E     7_A    50.690     0    0.021   1.022    52.387    0.000    0.000
LGA    L     8_A      L     8_A    45.759     0    0.027   0.059    48.138    0.000    0.000
LGA    I     9_A      I     9_A    43.241     0    0.022   0.123    46.182    0.000    0.000
LGA    R    10_A      R    10_A    43.876     0    0.032   1.195    53.687    0.000    0.000
LGA    R    11_A      R    11_A    40.640     0    0.024   1.512    47.028    0.000    0.000
LGA    S    12_A      S    12_A    35.668     0    0.061   0.065    37.996    0.000    0.000
LGA    E    13_A      E    13_A    35.511     0    0.030   0.937    39.126    0.000    0.000
LGA    E    14_A      E    14_A    34.778     0    0.008   0.657    40.618    0.000    0.000
LGA    Q    15_A      Q    15_A    29.998     0    0.057   1.421    32.139    0.000    0.000
LGA    Q    16_A      Q    16_A    26.719     0    0.008   1.393    28.417    0.000    0.000
LGA    R    17_A      R    17_A    27.322     0    0.000   1.016    39.594    0.000    0.000
LGA    R    18_A      R    18_A    24.455     0    0.010   1.134    34.961    0.000    0.000
LGA    N    19_A      N    19_A    19.611     0    0.039   0.064    22.136    0.000    0.000
LGA    E    20_A      E    20_A    19.034     0    0.020   0.939    26.411    0.000    0.000
LGA    E    21_A      E    21_A    18.720     0    0.035   1.005    22.400    0.000    0.000
LGA    A    22_A      A    22_A    14.086     0    0.055   0.055    16.081    0.000    0.000
LGA    L    23_A      L    23_A    10.792     0    0.065   1.360    12.425    0.357    0.298
LGA    R    24_A      R    24_A    12.929     0    0.203   1.116    21.823    0.000    0.000
LGA    Q    33_A      Q    33_A     1.029     0    0.063   1.128     5.723   88.214   62.275
LGA    L    34_A      L    34_A     1.001     0    0.045   0.090     1.481   85.952   83.690
LGA    L    35_A      L    35_A     0.585     0    0.013   0.475     2.478   95.238   86.310
LGA    S    36_A      S    36_A     0.609     0    0.046   0.054     0.877   90.476   90.476
LGA    G    37_A      G    37_A     0.730     0    0.092   0.092     0.730   95.238   95.238
LGA    I    38_A      I    38_A     0.396     0    0.023   0.063     0.731   97.619   96.429
LGA    V    39_A      V    39_A     0.604     0    0.016   0.049     0.746   92.857   91.837
LGA    Q    40_A      Q    40_A     0.790     0    0.005   0.969     3.946   90.476   77.566
LGA    Q    41_A      Q    41_A     0.557     0    0.033   1.399     4.313   92.857   73.810
LGA    Q    42_A      Q    42_A     0.430     0    0.059   0.230     1.185   95.238   92.646
LGA    N    43_A      N    43_A     0.290     0    0.000   1.335     3.975  100.000   81.429
LGA    N    44_A      N    44_A     0.345     0    0.016   0.087     0.877  100.000   95.238
LGA    L    45_A      L    45_A     0.333     0    0.008   0.198     0.737  100.000   96.429
LGA    L    46_A      L    46_A     0.302     0    0.012   1.399     3.720  100.000   83.155
LGA    R    47_A      R    47_A     0.285     0    0.000   0.240     0.953  100.000   99.134
LGA    A    48_A      A    48_A     0.285     0    0.024   0.030     0.295  100.000  100.000
LGA    I    49_A      I    49_A     0.511     0    0.045   0.091     0.740   97.619   94.048
LGA    E    50_A      E    50_A     0.477     0    0.016   0.124     1.229   97.619   92.646
LGA    A    51_A      A    51_A     0.260     0    0.014   0.015     0.381  100.000  100.000
LGA    Q    52_A      Q    52_A     0.514     0    0.019   0.202     1.289   92.857   90.529
LGA    Q    53_A      Q    53_A     0.528     0    0.016   1.553     5.370   92.857   69.735
LGA    H    54_A      H    54_A     0.425     0    0.019   1.140     2.484   97.619   89.143
LGA    L    55_A      L    55_A     0.415     0    0.011   1.411     3.877  100.000   81.964
LGA    L    56_A      L    56_A     0.641     0    0.007   1.377     3.125   90.476   81.071
LGA    Q    57_A      Q    57_A     0.584     0    0.053   1.169     5.212   95.238   75.026
LGA    L    58_A      L    58_A     0.356     0    0.022   0.106     0.454  100.000  100.000
LGA    T    59_A      T    59_A     0.369     0    0.063   1.116     2.341  100.000   89.728
LGA    V    60_A      V    60_A     0.353     0    0.010   0.047     0.501   97.619   98.639
LGA    W    61_A      W    61_A     0.426     0    0.061   0.168     1.429  100.000   91.293
LGA    G    62_A      G    62_A     0.233     0    0.077   0.077     0.514   97.619   97.619
LGA    I    63_A      I    63_A     0.275     0    0.015   0.093     0.647  100.000   98.810
LGA    K    64_A      K    64_A     0.324     0    0.038   1.148     6.603  100.000   74.921
LGA    Q    65_A      Q    65_A     0.289     0    0.034   1.093     4.575  100.000   80.688
LGA    L    66_A      L    66_A     0.297     0    0.012   0.066     0.628  100.000   96.429
LGA    Q    67_A      Q    67_A     0.130     0    0.024   0.035     0.379  100.000  100.000
LGA    A    68_A      A    68_A     0.263     0    0.023   0.024     0.363  100.000  100.000
LGA    R    69_A      R    69_A     0.310     0    0.013   1.008     4.500  100.000   86.494
LGA    I    70_A      I    70_A     0.557     0    0.030   1.376     4.361   97.619   81.964
LGA    L    71_A      L    71_A     0.391     0    0.015   1.416     3.240  100.000   83.988
LGA    A    72_A      A    72_A     0.207     0    0.028   0.031     0.233  100.000  100.000
LGA    V    73_A      V    73_A     0.326     0    0.009   0.058     0.561  100.000   98.639
LGA    E    74_A      E    74_A     0.368     0    0.017   0.960     3.805  100.000   76.772
LGA    R    75_A      R    75_A     0.229     0    0.041   1.220     4.989  100.000   81.732
LGA    Y    76_A      Y    76_A     0.185     0    0.032   0.108     1.275  100.000   94.484
LGA    L    77_A      L    77_A     0.384     0    0.026   0.047     0.639  100.000   96.429
LGA    R    78_A      R    78_A     0.400     0    0.001   1.231     5.028   95.238   78.095
LGA    D    79_A      D    79_A     0.726     0    0.008   0.076     1.051   90.595   90.536
LGA    Q    80_A      Q    80_A     1.015     0    0.092   0.219     1.324   83.690   87.460
LGA    Q    81_A      Q    81_A     2.228     0    0.344   0.384     3.913   59.524   61.587

# 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):    16.314         16.000                 16.746           65.427   60.089

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   83   72    4.0     49    0.58    68.403    65.550     7.195

LGA_LOCAL      RMSD:   0.581  Number of atoms:   49  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  21.881  Number of assigned atoms:   72 
Std_ASGN_ATOMS RMSD:  16.314  Standard rmsd on all 72 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.905873 * X  +  -0.285320 * Y  +  -0.313030 * Z  +  17.281000
  Y_new =  -0.054935 * X  +   0.811966 * Y  +  -0.581113 * Z  + -39.474125
  Z_new =   0.419973 * X  +  -0.509218 * Y  +  -0.751212 * Z  + 108.104935 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -3.081023 -0.433415 -2.545879   [DEG: -176.5296  -24.8329 -145.8681 ]
ZXZ: -0.494105  2.420693  2.451947   [DEG:  -28.3101  138.6955  140.4862 ]
 
# END of job
