
#######################################################
#                                                     #
#                        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   73 (  570),  selected   71 , name one
# Molecule2: number of CA atoms   71 (  553),  selected   71 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:B  -ch2:B  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    71       1_B - 71_B        1.42     1.42
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    71       1_B - 71_B        1.42     1.42
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    69       1_B - 69_B        0.90     1.47
  LCS_AVERAGE:     94.60

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   71
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     G     1_B     G     1_B     69   71   71      5   13   58   67   69   69   69   69   69   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S     2_B     S     2_B     69   71   71     21   51   64   68   69   69   69   69   69   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V     3_B     V     3_B     69   71   71     26   52   64   68   69   69   69   69   69   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S     4_B     S     4_B     69   71   71     26   52   64   68   69   69   69   69   69   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K     5_B     K     5_B     69   71   71     26   52   64   68   69   69   69   69   69   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     W     6_B     W     6_B     69   71   71     26   52   64   68   69   69   69   69   69   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S     7_B     S     7_B     69   71   71     26   52   64   68   69   69   69   69   69   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     T     8_B     T     8_B     69   71   71     26   52   64   68   69   69   69   69   69   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D     9_B     D     9_B     69   71   71     25   52   64   68   69   69   69   69   69   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    10_B     E    10_B     69   71   71     21   52   64   68   69   69   69   69   69   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V    11_B     V    11_B     69   71   71     24   52   64   68   69   69   69   69   69   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    12_B     S    12_B     69   71   71     17   39   64   68   69   69   69   69   69   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    13_B     E    13_B     69   71   71     10   33   64   68   69   69   69   69   69   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    14_B     F    14_B     69   71   71     21   51   64   68   69   69   69   69   69   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    15_B     I    15_B     69   71   71     23   52   64   68   69   69   69   69   69   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     Q    16_B     Q    16_B     69   71   71     17   37   64   68   69   69   69   69   69   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    17_B     S    17_B     69   71   71     14   38   64   68   69   69   69   69   69   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    18_B     L    18_B     69   71   71     18   51   64   68   69   69   69   69   69   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     P    19_B     P    19_B     69   71   71     19   52   64   68   69   69   69   69   69   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    20_B     G    20_B     69   71   71      8   51   64   68   69   69   69   69   69   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     C    21_B     C    21_B     69   71   71     23   52   64   68   69   69   69   69   69   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    22_B     E    22_B     69   71   71     14   48   64   68   69   69   69   69   69   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    23_B     E    23_B     69   71   71     24   52   64   68   69   69   69   69   69   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     H    24_B     H    24_B     69   71   71     26   52   64   68   69   69   69   69   69   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    25_B     G    25_B     69   71   71     10   52   64   68   69   69   69   69   69   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    26_B     K    26_B     69   71   71     10   52   64   68   69   69   69   69   69   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V    27_B     V    27_B     69   71   71     24   52   64   68   69   69   69   69   69   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    28_B     F    28_B     69   71   71     23   52   64   68   69   69   69   69   69   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    29_B     K    29_B     69   71   71     10   52   64   68   69   69   69   69   69   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D    30_B     D    30_B     69   71   71     21   52   64   68   69   69   69   69   69   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    31_B     E    31_B     69   71   71     23   52   64   68   69   69   69   69   69   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     Q    32_B     Q    32_B     69   71   71     23   52   64   68   69   69   69   69   69   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    33_B     I    33_B     69   71   71     24   52   64   68   69   69   69   69   69   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D    34_B     D    34_B     69   71   71     26   52   64   68   69   69   69   69   69   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    35_B     G    35_B     69   71   71     26   52   64   68   69   69   69   69   69   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    36_B     E    36_B     69   71   71     24   52   64   68   69   69   69   69   69   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    37_B     A    37_B     69   71   71     23   52   64   68   69   69   69   69   69   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    38_B     F    38_B     69   71   71     23   52   64   68   69   69   69   69   69   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    39_B     L    39_B     69   71   71     26   52   64   68   69   69   69   69   69   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    40_B     L    40_B     69   71   71     26   52   64   68   69   69   69   69   69   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     M    41_B     M    41_B     69   71   71     26   52   64   68   69   69   69   69   69   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     T    42_B     T    42_B     69   71   71     26   52   64   68   69   69   69   69   69   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     Q    43_B     Q    43_B     69   71   71     13   52   64   68   69   69   69   69   69   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     T    44_B     T    44_B     69   71   71     13   52   64   68   69   69   69   69   69   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D    45_B     D    45_B     69   71   71     26   52   64   68   69   69   69   69   69   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    46_B     I    46_B     69   71   71     26   52   64   68   69   69   69   69   69   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V    47_B     V    47_B     69   71   71     26   52   64   68   69   69   69   69   69   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    48_B     K    48_B     69   71   71     22   52   64   68   69   69   69   69   69   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    49_B     I    49_B     69   71   71     26   52   64   68   69   69   69   69   69   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     M    50_B     M    50_B     69   71   71     26   52   64   68   69   69   69   69   69   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    51_B     S    51_B     69   71   71     26   52   64   68   69   69   69   69   69   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    52_B     I    52_B     69   71   71     26   52   64   68   69   69   69   69   69   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    53_B     K    53_B     69   71   71     26   52   64   68   69   69   69   69   69   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    54_B     E    54_B     69   71   71     26   52   64   68   69   69   69   69   69   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    55_B     G    55_B     69   71   71     26   52   64   68   69   69   69   69   69   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     P    56_B     P    56_B     69   71   71     26   52   64   68   69   69   69   69   69   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    57_B     A    57_B     69   71   71     26   52   64   68   69   69   69   69   69   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    58_B     E    58_B     69   71   71     26   52   64   68   69   69   69   69   69   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    59_B     K    59_B     69   71   71     22   52   64   68   69   69   69   69   69   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    60_B     I    60_B     69   71   71     22   52   64   68   69   69   69   69   69   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    61_B     F    61_B     69   71   71     22   52   64   68   69   69   69   69   69   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     N    62_B     N    62_B     69   71   71     22   52   64   68   69   69   69   69   69   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    63_B     S    63_B     69   71   71     18   51   64   68   69   69   69   69   69   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    64_B     I    64_B     69   71   71     18   41   64   68   69   69   69   69   69   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    65_B     L    65_B     69   71   71     19   51   64   68   69   69   69   69   69   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     M    66_B     M    66_B     69   71   71     18   44   64   68   69   69   69   69   69   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    67_B     F    67_B     69   71   71     18   36   61   68   69   69   69   69   69   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    68_B     K    68_B     69   71   71     18   38   64   68   69   69   69   69   69   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    69_B     A    69_B     69   71   71     19   51   64   68   69   69   69   69   69   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    70_B     A    70_B      4   71   71      3    4    5   26   32   44   65   69   69   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    71_B     E    71_B      4   71   71      3    4    5   17   29   38   45   59   68   71   71   71   71   71   71   71   71   71   71   71 
LCS_AVERAGE  LCS_A:  98.20  (  94.60  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     26     52     64     68     69     69     69     69     69     71     71     71     71     71     71     71     71     71     71     71 
GDT PERCENT_AT  36.62  73.24  90.14  95.77  97.18  97.18  97.18  97.18  97.18 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.36   0.60   0.79   0.87   0.90   0.90   0.90   0.90   0.90   1.42   1.42   1.42   1.42   1.42   1.42   1.42   1.42   1.42   1.42   1.42
GDT RMS_ALL_AT   1.49   1.47   1.45   1.46   1.47   1.47   1.47   1.47   1.47   1.42   1.42   1.42   1.42   1.42   1.42   1.42   1.42   1.42   1.42   1.42

# Checking swapping
#   possible swapping detected:  D     9_B      D     9_B
#   possible swapping detected:  F    61_B      F    61_B
#   possible swapping detected:  E    71_B      E    71_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    G     1_B      G     1_B     2.186     0    0.349   0.349     3.915   70.000   70.000
LGA    S     2_B      S     2_B     1.007     0    0.041   0.640     1.879   85.952   83.016
LGA    V     3_B      V     3_B     0.324     0    0.077   0.960     3.090  100.000   85.374
LGA    S     4_B      S     4_B     0.352     0    0.007   0.065     0.588  100.000   98.413
LGA    K     5_B      K     5_B     0.422     0    0.034   0.954     3.502  100.000   80.265
LGA    W     6_B      W     6_B     0.603     0    0.025   0.113     1.266   90.476   88.537
LGA    S     7_B      S     7_B     0.609     0    0.057   0.082     0.729   95.238   93.651
LGA    T     8_B      T     8_B     0.452     0    0.018   1.021     3.030  100.000   86.463
LGA    D     9_B      D     9_B     0.415     0    0.022   0.837     3.437   95.238   82.560
LGA    E    10_B      E    10_B     0.672     0    0.019   0.321     1.915   92.857   86.561
LGA    V    11_B      V    11_B     0.366     0    0.021   0.039     0.633   95.238   95.918
LGA    S    12_B      S    12_B     1.175     0    0.037   0.509     2.884   83.690   78.889
LGA    E    13_B      E    13_B     1.583     0    0.022   0.640     4.391   77.143   59.577
LGA    F    14_B      F    14_B     1.054     0    0.021   0.251     2.094   83.690   80.000
LGA    I    15_B      I    15_B     0.798     0    0.041   0.647     2.050   88.214   83.869
LGA    Q    16_B      Q    16_B     1.729     0    0.056   1.031     3.090   75.000   70.582
LGA    S    17_B      S    17_B     1.618     0    0.060   0.076     1.737   77.143   77.143
LGA    L    18_B      L    18_B     1.016     0    0.136   0.267     1.192   83.690   84.821
LGA    P    19_B      P    19_B     0.958     0    0.087   0.203     1.217   90.476   87.891
LGA    G    20_B      G    20_B     1.191     0    0.094   0.094     1.191   81.429   81.429
LGA    C    21_B      C    21_B     0.690     0    0.056   0.052     0.873   90.476   90.476
LGA    E    22_B      E    22_B     1.192     0    0.015   1.043     5.072   85.952   70.159
LGA    E    23_B      E    23_B     0.409     0    0.063   1.005     4.900   97.619   78.095
LGA    H    24_B      H    24_B     0.297     0    0.017   0.162     0.866   95.238   94.286
LGA    G    25_B      G    25_B     0.955     0    0.049   0.049     0.955   90.476   90.476
LGA    K    26_B      K    26_B     0.836     0    0.057   1.492     5.653   90.476   74.603
LGA    V    27_B      V    27_B     0.624     0    0.028   0.957     2.704   90.476   83.197
LGA    F    28_B      F    28_B     0.598     0    0.019   0.161     1.241   90.476   88.831
LGA    K    29_B      K    29_B     0.896     0    0.013   1.017     3.818   90.476   75.714
LGA    D    30_B      D    30_B     1.055     0    0.041   0.180     1.839   85.952   82.619
LGA    E    31_B      E    31_B     0.909     0    0.013   0.133     1.517   90.476   86.508
LGA    Q    32_B      Q    32_B     0.888     0    0.038   0.083     1.488   90.476   86.455
LGA    I    33_B      I    33_B     0.558     0    0.047   0.560     1.305   95.238   91.726
LGA    D    34_B      D    34_B     0.422     0    0.021   0.041     0.786  100.000   95.238
LGA    G    35_B      G    35_B     0.279     0    0.025   0.025     0.361  100.000  100.000
LGA    E    36_B      E    36_B     0.632     0    0.018   1.138     4.384   90.476   77.831
LGA    A    37_B      A    37_B     0.694     0    0.015   0.017     0.781   90.476   90.476
LGA    F    38_B      F    38_B     0.424     0    0.020   0.110     0.580  100.000   97.403
LGA    L    39_B      L    39_B     0.247     0    0.030   0.076     0.417  100.000  100.000
LGA    L    40_B      L    40_B     0.228     0    0.057   0.136     0.662  100.000   98.810
LGA    M    41_B      M    41_B     0.205     0    0.053   0.312     1.961  100.000   93.095
LGA    T    42_B      T    42_B     0.732     0    0.040   0.080     0.962   92.857   91.837
LGA    Q    43_B      Q    43_B     1.272     0    0.011   0.304     3.537   81.429   68.995
LGA    T    44_B      T    44_B     1.309     0    0.039   0.956     3.524   81.429   73.605
LGA    D    45_B      D    45_B     0.887     0    0.015   0.065     0.999   90.476   90.476
LGA    I    46_B      I    46_B     0.715     0    0.061   0.142     1.315   90.476   89.345
LGA    V    47_B      V    47_B     0.882     0    0.049   0.061     1.049   90.476   89.184
LGA    K    48_B      K    48_B     0.998     0    0.023   1.345     8.723   90.476   59.153
LGA    I    49_B      I    49_B     0.777     0    0.066   0.661     3.107   90.476   84.286
LGA    M    50_B      M    50_B     0.454     0    0.021   0.240     0.553   92.857   94.048
LGA    S    51_B      S    51_B     0.475     0    0.058   0.116     0.504   97.619   98.413
LGA    I    52_B      I    52_B     0.575     0    0.023   0.387     1.646   90.476   86.071
LGA    K    53_B      K    53_B     0.504     0    0.036   1.113     5.479   90.476   73.757
LGA    E    54_B      E    54_B     0.463     0    0.026   1.206     5.271   97.619   74.074
LGA    G    55_B      G    55_B     0.472     0    0.029   0.029     0.524   97.619   97.619
LGA    P    56_B      P    56_B     0.474     0    0.036   0.255     0.632  100.000   98.639
LGA    A    57_B      A    57_B     0.491     0    0.012   0.012     0.579   95.238   96.190
LGA    E    58_B      E    58_B     0.617     0    0.031   0.896     2.726   90.476   79.153
LGA    K    59_B      K    59_B     0.736     0    0.025   0.272     0.774   90.476   91.534
LGA    I    60_B      I    60_B     0.536     0    0.014   0.124     0.702   90.476   92.857
LGA    F    61_B      F    61_B     0.528     0    0.034   0.564     1.909   97.619   87.403
LGA    N    62_B      N    62_B     0.596     0    0.018   0.619     2.294   92.857   86.190
LGA    S    63_B      S    63_B     1.117     0    0.020   0.672     1.431   83.690   82.937
LGA    I    64_B      I    64_B     1.187     0    0.020   0.215     1.563   81.429   81.488
LGA    L    65_B      L    65_B     1.006     0    0.033   0.374     1.422   81.429   84.821
LGA    M    66_B      M    66_B     1.450     0    0.025   0.613     3.922   77.143   64.762
LGA    F    67_B      F    67_B     1.808     0    0.067   0.812     3.659   70.833   62.381
LGA    K    68_B      K    68_B     1.596     0    0.033   0.770     2.600   75.000   70.317
LGA    A    69_B      A    69_B     1.056     0    0.263   0.247     4.094   64.286   64.381
LGA    A    70_B      A    70_B     6.478     0    0.142   0.151     9.752   15.476   13.333
LGA    E    71_B      E    71_B     7.448     0    0.648   1.156    10.252    7.500   12.698

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       71     284    284  100.00     553    553  100.00                71
SUMMARY(RMSD_GDC):     1.424          1.551                  1.892           87.591   82.266

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   73   71    4.0     69    0.90    91.549    96.053     6.875

LGA_LOCAL      RMSD:   0.904  Number of atoms:   69  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.472  Number of assigned atoms:   71 
Std_ASGN_ATOMS RMSD:   1.424  Standard rmsd on all 71 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.612766 * X  +   0.777564 * Y  +  -0.141111 * Z  +   2.719377
  Y_new =  -0.025906 * X  +  -0.158701 * Y  +  -0.986987 * Z  +  56.272587
  Z_new =  -0.789840 * X  +   0.608447 * Y  +  -0.077103 * Z  +  32.786572 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.042252  0.910548  1.696845   [DEG:   -2.4209   52.1706   97.2221 ]
ZXZ: -0.142009  1.647976 -0.914403   [DEG:   -8.1365   94.4221  -52.3914 ]
 
# END of job
