
#######################################################
#                                                     #
#                        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:    72       2_A - 81_A        4.64     4.64
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    49      33_A - 81_A        0.55    11.64
  LCS_AVERAGE:     56.52

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    49      33_A - 81_A        0.55    11.64
  LCS_AVERAGE:     56.52

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     23   23   72     21   24   25   27   30   34   36   38   43   52   59   64   67   68   71   72   72   72   72   72 
LCS_GDT     S     3_A     S     3_A     23   23   72     20   24   25   27   30   34   36   38   43   52   59   64   67   68   71   72   72   72   72   72 
LCS_GDT     L     4_A     L     4_A     23   23   72     21   24   25   27   30   34   36   38   43   52   59   64   67   68   71   72   72   72   72   72 
LCS_GDT     I     5_A     I     5_A     23   23   72     21   24   25   27   30   34   36   38   43   52   59   64   67   68   71   72   72   72   72   72 
LCS_GDT     E     6_A     E     6_A     23   23   72     21   24   25   27   30   34   36   38   43   52   59   64   67   68   71   72   72   72   72   72 
LCS_GDT     E     7_A     E     7_A     23   23   72     21   24   25   27   30   34   36   38   43   52   59   64   67   68   71   72   72   72   72   72 
LCS_GDT     L     8_A     L     8_A     23   23   72     21   24   25   27   30   34   36   38   43   52   59   64   67   68   71   72   72   72   72   72 
LCS_GDT     I     9_A     I     9_A     23   23   72     21   24   25   27   30   34   36   38   43   52   59   64   67   68   71   72   72   72   72   72 
LCS_GDT     R    10_A     R    10_A     23   23   72     21   24   25   27   30   34   36   38   43   52   59   64   67   68   71   72   72   72   72   72 
LCS_GDT     R    11_A     R    11_A     23   23   72     21   24   25   27   30   34   36   38   43   52   59   64   67   68   71   72   72   72   72   72 
LCS_GDT     S    12_A     S    12_A     23   23   72     21   24   25   27   30   34   36   38   43   52   59   64   67   68   71   72   72   72   72   72 
LCS_GDT     E    13_A     E    13_A     23   23   72     21   24   25   27   30   34   36   38   43   52   59   64   67   68   71   72   72   72   72   72 
LCS_GDT     E    14_A     E    14_A     23   23   72     21   24   25   27   30   34   36   38   43   52   59   64   67   68   71   72   72   72   72   72 
LCS_GDT     Q    15_A     Q    15_A     23   23   72     21   24   25   27   30   34   36   38   43   52   59   64   67   68   71   72   72   72   72   72 
LCS_GDT     Q    16_A     Q    16_A     23   23   72     21   24   25   27   30   34   36   38   43   52   59   64   67   68   71   72   72   72   72   72 
LCS_GDT     R    17_A     R    17_A     23   23   72     21   24   25   27   30   34   36   38   43   52   59   64   67   68   71   72   72   72   72   72 
LCS_GDT     R    18_A     R    18_A     23   23   72     21   24   25   27   30   34   36   38   43   52   59   64   67   68   71   72   72   72   72   72 
LCS_GDT     N    19_A     N    19_A     23   23   72     21   24   25   27   30   34   36   38   43   52   59   64   67   68   71   72   72   72   72   72 
LCS_GDT     E    20_A     E    20_A     23   23   72     21   24   25   27   30   34   36   38   43   52   59   64   67   68   71   72   72   72   72   72 
LCS_GDT     E    21_A     E    21_A     23   23   72     21   24   25   27   30   34   36   38   43   52   59   64   67   68   71   72   72   72   72   72 
LCS_GDT     A    22_A     A    22_A     23   23   72     21   24   25   27   30   34   36   38   43   52   59   64   67   68   71   72   72   72   72   72 
LCS_GDT     L    23_A     L    23_A     23   23   72     21   24   25   27   30   34   36   38   43   52   59   64   67   68   71   72   72   72   72   72 
LCS_GDT     R    24_A     R    24_A     23   23   72     21   24   25   27   30   34   36   38   43   52   59   64   67   68   71   72   72   72   72   72 
LCS_GDT     Q    33_A     Q    33_A     49   49   72     32   48   49   49   49   49   49   49   49   52   59   64   67   68   71   72   72   72   72   72 
LCS_GDT     L    34_A     L    34_A     49   49   72     25   48   49   49   49   49   49   49   49   52   59   62   67   68   71   72   72   72   72   72 
LCS_GDT     L    35_A     L    35_A     49   49   72     32   48   49   49   49   49   49   49   49   52   59   64   67   68   71   72   72   72   72   72 
LCS_GDT     S    36_A     S    36_A     49   49   72     32   48   49   49   49   49   49   49   49   52   59   64   67   68   71   72   72   72   72   72 
LCS_GDT     G    37_A     G    37_A     49   49   72     32   48   49   49   49   49   49   49   49   52   59   64   67   68   71   72   72   72   72   72 
LCS_GDT     I    38_A     I    38_A     49   49   72     32   48   49   49   49   49   49   49   49   52   59   64   67   68   71   72   72   72   72   72 
LCS_GDT     V    39_A     V    39_A     49   49   72     32   48   49   49   49   49   49   49   49   52   59   64   67   68   71   72   72   72   72   72 
LCS_GDT     Q    40_A     Q    40_A     49   49   72     26   48   49   49   49   49   49   49   49   52   59   64   67   68   71   72   72   72   72   72 
LCS_GDT     Q    41_A     Q    41_A     49   49   72     32   48   49   49   49   49   49   49   49   52   59   64   67   68   71   72   72   72   72   72 
LCS_GDT     Q    42_A     Q    42_A     49   49   72     32   48   49   49   49   49   49   49   49   52   59   64   67   68   71   72   72   72   72   72 
LCS_GDT     N    43_A     N    43_A     49   49   72     32   48   49   49   49   49   49   49   49   52   59   64   67   68   71   72   72   72   72   72 
LCS_GDT     N    44_A     N    44_A     49   49   72     32   48   49   49   49   49   49   49   49   52   59   64   67   68   71   72   72   72   72   72 
LCS_GDT     L    45_A     L    45_A     49   49   72     32   48   49   49   49   49   49   49   49   52   59   64   67   68   71   72   72   72   72   72 
LCS_GDT     L    46_A     L    46_A     49   49   72     32   48   49   49   49   49   49   49   49   52   59   64   67   68   71   72   72   72   72   72 
LCS_GDT     R    47_A     R    47_A     49   49   72     32   48   49   49   49   49   49   49   49   52   59   64   67   68   71   72   72   72   72   72 
LCS_GDT     A    48_A     A    48_A     49   49   72     32   48   49   49   49   49   49   49   49   52   59   64   67   68   71   72   72   72   72   72 
LCS_GDT     I    49_A     I    49_A     49   49   72     32   48   49   49   49   49   49   49   49   52   59   64   67   68   71   72   72   72   72   72 
LCS_GDT     E    50_A     E    50_A     49   49   72     32   48   49   49   49   49   49   49   49   52   59   64   67   68   71   72   72   72   72   72 
LCS_GDT     A    51_A     A    51_A     49   49   72     32   48   49   49   49   49   49   49   49   52   59   63   67   68   71   72   72   72   72   72 
LCS_GDT     Q    52_A     Q    52_A     49   49   72     31   48   49   49   49   49   49   49   49   52   59   64   67   68   71   72   72   72   72   72 
LCS_GDT     Q    53_A     Q    53_A     49   49   72     31   48   49   49   49   49   49   49   49   52   59   64   67   68   71   72   72   72   72   72 
LCS_GDT     H    54_A     H    54_A     49   49   72     31   48   49   49   49   49   49   49   49   52   59   62   67   68   71   72   72   72   72   72 
LCS_GDT     L    55_A     L    55_A     49   49   72     31   48   49   49   49   49   49   49   49   52   59   64   67   68   71   72   72   72   72   72 
LCS_GDT     L    56_A     L    56_A     49   49   72     31   48   49   49   49   49   49   49   49   52   59   64   67   68   71   72   72   72   72   72 
LCS_GDT     Q    57_A     Q    57_A     49   49   72     32   48   49   49   49   49   49   49   49   52   59   64   67   68   71   72   72   72   72   72 
LCS_GDT     L    58_A     L    58_A     49   49   72     32   48   49   49   49   49   49   49   49   52   59   64   67   68   71   72   72   72   72   72 
LCS_GDT     T    59_A     T    59_A     49   49   72     32   48   49   49   49   49   49   49   49   52   59   64   67   68   71   72   72   72   72   72 
LCS_GDT     V    60_A     V    60_A     49   49   72     32   48   49   49   49   49   49   49   49   52   59   64   67   68   71   72   72   72   72   72 
LCS_GDT     W    61_A     W    61_A     49   49   72     32   48   49   49   49   49   49   49   49   52   59   64   67   68   71   72   72   72   72   72 
LCS_GDT     G    62_A     G    62_A     49   49   72     32   48   49   49   49   49   49   49   49   52   59   64   67   68   71   72   72   72   72   72 
LCS_GDT     I    63_A     I    63_A     49   49   72     32   48   49   49   49   49   49   49   49   52   58   64   67   68   71   72   72   72   72   72 
LCS_GDT     K    64_A     K    64_A     49   49   72     32   48   49   49   49   49   49   49   49   52   59   64   67   68   71   72   72   72   72   72 
LCS_GDT     Q    65_A     Q    65_A     49   49   72     32   48   49   49   49   49   49   49   49   52   59   64   67   68   71   72   72   72   72   72 
LCS_GDT     L    66_A     L    66_A     49   49   72     32   48   49   49   49   49   49   49   49   52   58   64   67   68   71   72   72   72   72   72 
LCS_GDT     Q    67_A     Q    67_A     49   49   72     32   48   49   49   49   49   49   49   49   52   58   64   67   68   71   72   72   72   72   72 
LCS_GDT     A    68_A     A    68_A     49   49   72     32   48   49   49   49   49   49   49   49   52   59   64   67   68   71   72   72   72   72   72 
LCS_GDT     R    69_A     R    69_A     49   49   72     32   48   49   49   49   49   49   49   49   52   59   64   67   68   71   72   72   72   72   72 
LCS_GDT     I    70_A     I    70_A     49   49   72     32   48   49   49   49   49   49   49   49   52   58   64   67   68   71   72   72   72   72   72 
LCS_GDT     L    71_A     L    71_A     49   49   72     32   48   49   49   49   49   49   49   49   52   58   64   67   68   71   72   72   72   72   72 
LCS_GDT     A    72_A     A    72_A     49   49   72     32   48   49   49   49   49   49   49   49   52   59   64   67   68   71   72   72   72   72   72 
LCS_GDT     V    73_A     V    73_A     49   49   72     31   48   49   49   49   49   49   49   49   52   58   64   67   68   71   72   72   72   72   72 
LCS_GDT     E    74_A     E    74_A     49   49   72     31   48   49   49   49   49   49   49   49   49   52   59   67   68   71   72   72   72   72   72 
LCS_GDT     R    75_A     R    75_A     49   49   72     31   48   49   49   49   49   49   49   49   52   58   64   67   68   71   72   72   72   72   72 
LCS_GDT     Y    76_A     Y    76_A     49   49   72     31   48   49   49   49   49   49   49   49   52   59   64   67   68   71   72   72   72   72   72 
LCS_GDT     L    77_A     L    77_A     49   49   72     31   48   49   49   49   49   49   49   49   49   49   56   65   68   71   72   72   72   72   72 
LCS_GDT     R    78_A     R    78_A     49   49   72     31   48   49   49   49   49   49   49   49   49   51   56   60   67   71   72   72   72   72   72 
LCS_GDT     D    79_A     D    79_A     49   49   72     31   48   49   49   49   49   49   49   49   52   58   64   67   68   71   72   72   72   72   72 
LCS_GDT     Q    80_A     Q    80_A     49   49   72     31   48   49   49   49   49   49   49   49   52   58   64   67   68   71   72   72   72   72   72 
LCS_GDT     Q    81_A     Q    81_A     49   49   72      3   24   49   49   49   49   49   49   49   49   49   50   59   62   68   72   72   72   72   72 
LCS_AVERAGE  LCS_A:  71.01  (  56.52   56.52  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     32     48     49     49     49     49     49     49     49     52     59     64     67     68     71     72     72     72     72     72 
GDT PERCENT_AT  44.44  66.67  68.06  68.06  68.06  68.06  68.06  68.06  68.06  72.22  81.94  88.89  93.06  94.44  98.61 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.32   0.52   0.55   0.55   0.55   0.55   0.55   0.55   0.55   3.61   3.93   4.13   4.27   4.32   4.55   4.64   4.64   4.64   4.64   4.64
GDT RMS_ALL_AT  11.66  11.63  11.64  11.64  11.64  11.64  11.64  11.64  11.64   4.78   5.54   4.75   4.74   4.75   4.64   4.64   4.64   4.64   4.64   4.64

# Checking swapping
#   possible swapping detected:  E     7_A      E     7_A
#   possible swapping detected:  E    13_A      E    13_A
#   possible swapping detected:  E    50_A      E    50_A
#   possible swapping detected:  E    74_A      E    74_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    20.052     0    0.561   1.202    21.832    0.000    0.000
LGA    S     3_A      S     3_A    26.075     0    0.038   0.677    30.039    0.000    0.000
LGA    L     4_A      L     4_A    23.227     0    0.024   0.093    24.402    0.000    0.000
LGA    I     5_A      I     5_A    16.739     0    0.047   0.125    18.915    0.000    0.000
LGA    E     6_A      E     6_A    21.781     0    0.081   1.044    26.806    0.000    0.000
LGA    E     7_A      E     7_A    24.725     0    0.016   0.262    30.399    0.000    0.000
LGA    L     8_A      L     8_A    18.431     0    0.049   0.077    20.500    0.000    0.000
LGA    I     9_A      I     9_A    16.971     0    0.074   0.122    19.128    0.000    0.000
LGA    R    10_A      R    10_A    23.647     0    0.054   1.418    35.266    0.000    0.000
LGA    R    11_A      R    11_A    21.968     0    0.012   1.459    28.231    0.000    0.000
LGA    S    12_A      S    12_A    15.555     0    0.058   0.690    17.659    0.000    0.000
LGA    E    13_A      E    13_A    20.298     0    0.035   1.237    23.948    0.000    0.000
LGA    E    14_A      E    14_A    23.961     0    0.019   0.429    30.050    0.000    0.000
LGA    Q    15_A      Q    15_A    18.205     0    0.040   0.070    20.010    0.000    0.000
LGA    Q    16_A      Q    16_A    16.282     0    0.037   0.798    18.447    0.000    0.000
LGA    R    17_A      R    17_A    22.958     0    0.019   1.104    32.564    0.000    0.000
LGA    R    18_A      R    18_A    21.458     0    0.016   1.122    27.455    0.000    0.000
LGA    N    19_A      N    19_A    14.850     0    0.035   0.097    17.048    0.000    0.000
LGA    E    20_A      E    20_A    19.373     0    0.013   1.008    22.901    0.000    0.000
LGA    E    21_A      E    21_A    23.688     0    0.018   0.877    30.659    0.000    0.000
LGA    A    22_A      A    22_A    18.114     0    0.064   0.072    19.861    0.000    0.000
LGA    L    23_A      L    23_A    16.128     0    0.074   0.179    18.377    0.000    0.000
LGA    R    24_A      R    24_A    22.799     0    0.298   1.119    29.327    0.000    0.000
LGA    Q    33_A      Q    33_A     0.424     0    0.098   1.107     4.159   97.619   77.725
LGA    L    34_A      L    34_A     0.586     0    0.048   0.096     1.443   97.619   90.655
LGA    L    35_A      L    35_A     0.542     0    0.011   0.529     2.579   92.857   85.238
LGA    S    36_A      S    36_A     0.645     0    0.018   0.668     2.625   92.857   86.508
LGA    G    37_A      G    37_A     0.577     0    0.055   0.055     0.577   95.238   95.238
LGA    I    38_A      I    38_A     0.375     0    0.033   0.056     0.573   97.619   97.619
LGA    V    39_A      V    39_A     0.746     0    0.012   0.037     0.969   90.476   90.476
LGA    Q    40_A      Q    40_A     0.898     0    0.014   0.941     2.715   90.476   81.111
LGA    Q    41_A      Q    41_A     0.530     0    0.029   0.249     0.891   95.238   92.593
LGA    Q    42_A      Q    42_A     0.475     0    0.089   0.394     1.716   92.857   90.635
LGA    N    43_A      N    43_A     0.557     0    0.041   1.152     3.727   95.238   80.595
LGA    N    44_A      N    44_A     0.297     0    0.016   0.030     0.583  100.000   98.810
LGA    L    45_A      L    45_A     0.072     0    0.020   0.171     0.556  100.000   98.810
LGA    L    46_A      L    46_A     0.315     0    0.068   1.368     3.848  100.000   83.929
LGA    R    47_A      R    47_A     0.126     0    0.040   1.106     4.077  100.000   85.281
LGA    A    48_A      A    48_A     0.194     0    0.047   0.050     0.492  100.000  100.000
LGA    I    49_A      I    49_A     0.348     0    0.048   0.093     0.537  100.000   98.810
LGA    E    50_A      E    50_A     0.222     0    0.054   0.073     0.597  100.000   98.942
LGA    A    51_A      A    51_A     0.485     0    0.013   0.019     0.696   95.238   94.286
LGA    Q    52_A      Q    52_A     0.856     0    0.019   0.324     1.333   90.476   88.466
LGA    Q    53_A      Q    53_A     0.776     0    0.029   1.018     4.157   90.476   75.608
LGA    H    54_A      H    54_A     0.688     0    0.014   1.095     5.527   90.476   65.810
LGA    L    55_A      L    55_A     0.992     0    0.047   1.391     4.042   90.476   78.274
LGA    L    56_A      L    56_A     0.975     0    0.016   1.362     3.314   90.476   80.952
LGA    Q    57_A      Q    57_A     0.527     0    0.035   1.468     5.103   95.238   74.815
LGA    L    58_A      L    58_A     0.432     0    0.039   0.183     0.947  100.000   96.429
LGA    T    59_A      T    59_A     0.664     0    0.054   1.053     2.895   92.857   85.782
LGA    V    60_A      V    60_A     0.448     0    0.011   0.039     0.702   97.619   94.558
LGA    W    61_A      W    61_A     0.194     0    0.075   1.237     8.683  100.000   53.163
LGA    G    62_A      G    62_A     0.309     0    0.052   0.052     0.309  100.000  100.000
LGA    I    63_A      I    63_A     0.344     0    0.018   0.062     0.518  100.000   98.810
LGA    K    64_A      K    64_A     0.172     0    0.042   1.131     6.356  100.000   75.344
LGA    Q    65_A      Q    65_A     0.151     0    0.037   1.376     5.123  100.000   78.360
LGA    L    66_A      L    66_A     0.260     0    0.028   0.070     0.566  100.000   98.810
LGA    Q    67_A      Q    67_A     0.239     0    0.011   0.056     0.659  100.000   96.825
LGA    A    68_A      A    68_A     0.208     0    0.015   0.025     0.273  100.000  100.000
LGA    R    69_A      R    69_A     0.200     0    0.014   0.135     0.692  100.000   99.134
LGA    I    70_A      I    70_A     0.409     0    0.067   1.353     3.840  100.000   84.940
LGA    L    71_A      L    71_A     0.436     0    0.021   0.049     0.594   97.619   97.619
LGA    A    72_A      A    72_A     0.250     0    0.022   0.038     0.297  100.000  100.000
LGA    V    73_A      V    73_A     0.200     0    0.018   0.051     0.312  100.000  100.000
LGA    E    74_A      E    74_A     0.456     0    0.020   0.100     0.766  100.000   94.709
LGA    R    75_A      R    75_A     0.644     0    0.081   0.240     1.831   92.857   88.095
LGA    Y    76_A      Y    76_A     0.485     0    0.016   0.064     0.565   95.238   96.825
LGA    L    77_A      L    77_A     0.427     0    0.032   0.087     0.525   97.619   98.810
LGA    R    78_A      R    78_A     0.661     0    0.051   1.147     4.303   90.476   73.290
LGA    D    79_A      D    79_A     0.816     0    0.012   0.094     0.956   90.476   90.476
LGA    Q    80_A      Q    80_A     0.731     0    0.026   0.179     1.480   88.214   86.455
LGA    Q    81_A      Q    81_A     1.366     0    0.458   0.525     2.979   75.476   77.831

# 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):     4.636          4.144                  7.042           65.270   60.520

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   83   72    4.0     49    0.55    75.694    70.057     7.521

LGA_LOCAL      RMSD:   0.552  Number of atoms:   49  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  11.636  Number of assigned atoms:   72 
Std_ASGN_ATOMS RMSD:   4.636  Standard rmsd on all 72 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.143756 * X  +   0.900084 * Y  +   0.411318 * Z  +  -0.978966
  Y_new =  -0.806403 * X  +   0.347467 * Y  +  -0.478519 * Z  +   2.145244
  Z_new =  -0.573627 * X  +  -0.262898 * Y  +   0.775781 * Z  +  68.790421 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.394381  0.610927 -0.326736   [DEG:  -79.8921   35.0035  -18.7206 ]
ZXZ:  0.710021  0.682844 -2.000538   [DEG:   40.6812   39.1241 -114.6224 ]
 
# END of job
