
#######################################################
#                                                     #
#                        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        4.69     4.69
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    49      33_A - 81_A        0.69    11.74
  LCS_AVERAGE:     56.52

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    49      33_A - 81_A        0.69    11.74
  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     13   24   25   27   33   35   37   38   43   51   57   63   67   68   71   72   72   72   72   72 
LCS_GDT     S     3_A     S     3_A     23   23   72     19   24   25   27   33   35   37   38   43   50   57   63   67   68   71   72   72   72   72   72 
LCS_GDT     L     4_A     L     4_A     23   23   72     21   24   25   27   31   35   37   38   43   50   57   63   67   68   71   72   72   72   72   72 
LCS_GDT     I     5_A     I     5_A     23   23   72     21   24   25   27   33   35   37   38   43   51   57   63   67   68   71   72   72   72   72   72 
LCS_GDT     E     6_A     E     6_A     23   23   72     21   24   25   27   33   35   37   38   43   51   57   63   67   68   71   72   72   72   72   72 
LCS_GDT     E     7_A     E     7_A     23   23   72     21   24   25   27   33   35   37   38   43   50   57   63   67   68   71   72   72   72   72   72 
LCS_GDT     L     8_A     L     8_A     23   23   72     21   24   25   27   33   35   37   38   43   51   57   63   67   68   71   72   72   72   72   72 
LCS_GDT     I     9_A     I     9_A     23   23   72     21   24   25   27   33   35   37   38   43   51   57   63   67   68   71   72   72   72   72   72 
LCS_GDT     R    10_A     R    10_A     23   23   72     21   24   25   27   33   35   37   38   43   51   57   63   67   68   71   72   72   72   72   72 
LCS_GDT     R    11_A     R    11_A     23   23   72     21   24   25   27   33   35   37   38   43   51   57   63   67   68   71   72   72   72   72   72 
LCS_GDT     S    12_A     S    12_A     23   23   72     21   24   25   27   33   35   37   38   43   51   57   63   67   68   71   72   72   72   72   72 
LCS_GDT     E    13_A     E    13_A     23   23   72     21   24   25   27   33   35   37   38   43   51   57   63   67   68   71   72   72   72   72   72 
LCS_GDT     E    14_A     E    14_A     23   23   72     21   24   25   27   33   35   37   38   43   51   57   63   67   68   71   72   72   72   72   72 
LCS_GDT     Q    15_A     Q    15_A     23   23   72     21   24   25   27   33   35   37   38   43   51   57   63   67   68   71   72   72   72   72   72 
LCS_GDT     Q    16_A     Q    16_A     23   23   72     21   24   25   27   33   35   37   38   43   51   57   63   67   68   71   72   72   72   72   72 
LCS_GDT     R    17_A     R    17_A     23   23   72     21   24   25   27   33   35   37   38   43   51   57   63   67   68   71   72   72   72   72   72 
LCS_GDT     R    18_A     R    18_A     23   23   72     21   24   25   27   33   35   37   38   43   51   57   63   67   68   71   72   72   72   72   72 
LCS_GDT     N    19_A     N    19_A     23   23   72     21   24   25   27   33   35   37   38   43   51   57   63   67   68   71   72   72   72   72   72 
LCS_GDT     E    20_A     E    20_A     23   23   72     21   24   25   27   33   35   37   38   43   51   57   63   67   68   71   72   72   72   72   72 
LCS_GDT     E    21_A     E    21_A     23   23   72     21   24   25   27   33   35   37   38   43   51   57   63   67   68   71   72   72   72   72   72 
LCS_GDT     A    22_A     A    22_A     23   23   72     21   24   25   27   33   35   37   38   43   51   57   63   67   68   71   72   72   72   72   72 
LCS_GDT     L    23_A     L    23_A     23   23   72     21   24   25   27   31   35   37   38   43   51   57   63   67   68   71   72   72   72   72   72 
LCS_GDT     R    24_A     R    24_A     23   23   72     21   24   25   27   33   35   37   38   43   51   57   63   67   68   71   72   72   72   72   72 
LCS_GDT     Q    33_A     Q    33_A     49   49   72     25   43   49   49   49   49   49   49   49   51   57   63   67   68   71   72   72   72   72   72 
LCS_GDT     L    34_A     L    34_A     49   49   72     13   43   49   49   49   49   49   49   49   49   56   61   67   68   71   72   72   72   72   72 
LCS_GDT     L    35_A     L    35_A     49   49   72     25   43   49   49   49   49   49   49   49   51   57   63   67   68   71   72   72   72   72   72 
LCS_GDT     S    36_A     S    36_A     49   49   72     25   43   49   49   49   49   49   49   49   51   57   63   67   68   71   72   72   72   72   72 
LCS_GDT     G    37_A     G    37_A     49   49   72     25   43   49   49   49   49   49   49   49   51   57   63   67   68   71   72   72   72   72   72 
LCS_GDT     I    38_A     I    38_A     49   49   72     25   43   49   49   49   49   49   49   49   51   57   63   67   68   71   72   72   72   72   72 
LCS_GDT     V    39_A     V    39_A     49   49   72     25   43   49   49   49   49   49   49   49   51   57   63   67   68   71   72   72   72   72   72 
LCS_GDT     Q    40_A     Q    40_A     49   49   72     24   43   49   49   49   49   49   49   49   51   57   63   67   68   71   72   72   72   72   72 
LCS_GDT     Q    41_A     Q    41_A     49   49   72     25   43   49   49   49   49   49   49   49   51   57   63   67   68   71   72   72   72   72   72 
LCS_GDT     Q    42_A     Q    42_A     49   49   72     25   43   49   49   49   49   49   49   49   51   57   63   67   68   71   72   72   72   72   72 
LCS_GDT     N    43_A     N    43_A     49   49   72     25   43   49   49   49   49   49   49   49   51   57   63   67   68   71   72   72   72   72   72 
LCS_GDT     N    44_A     N    44_A     49   49   72     25   43   49   49   49   49   49   49   49   50   57   63   67   68   71   72   72   72   72   72 
LCS_GDT     L    45_A     L    45_A     49   49   72     26   43   49   49   49   49   49   49   49   51   57   63   67   68   71   72   72   72   72   72 
LCS_GDT     L    46_A     L    46_A     49   49   72     25   43   49   49   49   49   49   49   49   51   57   63   67   68   71   72   72   72   72   72 
LCS_GDT     R    47_A     R    47_A     49   49   72     25   43   49   49   49   49   49   49   49   49   56   62   67   68   71   72   72   72   72   72 
LCS_GDT     A    48_A     A    48_A     49   49   72     27   43   49   49   49   49   49   49   49   51   57   63   67   68   71   72   72   72   72   72 
LCS_GDT     I    49_A     I    49_A     49   49   72     27   43   49   49   49   49   49   49   49   51   57   63   67   68   71   72   72   72   72   72 
LCS_GDT     E    50_A     E    50_A     49   49   72     27   43   49   49   49   49   49   49   49   50   56   63   67   68   71   72   72   72   72   72 
LCS_GDT     A    51_A     A    51_A     49   49   72     27   43   49   49   49   49   49   49   49   50   56   62   67   68   71   72   72   72   72   72 
LCS_GDT     Q    52_A     Q    52_A     49   49   72     27   43   49   49   49   49   49   49   49   51   57   63   67   68   71   72   72   72   72   72 
LCS_GDT     Q    53_A     Q    53_A     49   49   72     27   43   49   49   49   49   49   49   49   51   57   63   67   68   71   72   72   72   72   72 
LCS_GDT     H    54_A     H    54_A     49   49   72     27   43   49   49   49   49   49   49   49   50   56   61   67   68   71   72   72   72   72   72 
LCS_GDT     L    55_A     L    55_A     49   49   72     25   43   49   49   49   49   49   49   49   51   57   63   67   68   71   72   72   72   72   72 
LCS_GDT     L    56_A     L    56_A     49   49   72     25   43   49   49   49   49   49   49   49   51   57   63   67   68   71   72   72   72   72   72 
LCS_GDT     Q    57_A     Q    57_A     49   49   72     27   43   49   49   49   49   49   49   49   51   56   63   67   68   71   72   72   72   72   72 
LCS_GDT     L    58_A     L    58_A     49   49   72     27   43   49   49   49   49   49   49   49   51   56   63   67   68   71   72   72   72   72   72 
LCS_GDT     T    59_A     T    59_A     49   49   72     25   43   49   49   49   49   49   49   49   51   57   63   67   68   71   72   72   72   72   72 
LCS_GDT     V    60_A     V    60_A     49   49   72     27   43   49   49   49   49   49   49   49   51   57   63   67   68   71   72   72   72   72   72 
LCS_GDT     W    61_A     W    61_A     49   49   72     27   43   49   49   49   49   49   49   49   51   56   63   67   68   71   72   72   72   72   72 
LCS_GDT     G    62_A     G    62_A     49   49   72     27   43   49   49   49   49   49   49   49   51   57   63   67   68   71   72   72   72   72   72 
LCS_GDT     I    63_A     I    63_A     49   49   72     27   43   49   49   49   49   49   49   49   50   57   63   67   68   71   72   72   72   72   72 
LCS_GDT     K    64_A     K    64_A     49   49   72     27   43   49   49   49   49   49   49   49   51   57   63   67   68   71   72   72   72   72   72 
LCS_GDT     Q    65_A     Q    65_A     49   49   72     27   43   49   49   49   49   49   49   49   51   57   63   67   68   71   72   72   72   72   72 
LCS_GDT     L    66_A     L    66_A     49   49   72     27   43   49   49   49   49   49   49   49   50   57   63   67   68   71   72   72   72   72   72 
LCS_GDT     Q    67_A     Q    67_A     49   49   72     27   43   49   49   49   49   49   49   49   50   57   63   67   68   71   72   72   72   72   72 
LCS_GDT     A    68_A     A    68_A     49   49   72     27   43   49   49   49   49   49   49   49   51   57   63   67   68   71   72   72   72   72   72 
LCS_GDT     R    69_A     R    69_A     49   49   72     27   43   49   49   49   49   49   49   49   51   57   63   67   68   71   72   72   72   72   72 
LCS_GDT     I    70_A     I    70_A     49   49   72     27   43   49   49   49   49   49   49   49   49   57   62   66   68   71   72   72   72   72   72 
LCS_GDT     L    71_A     L    71_A     49   49   72     27   43   49   49   49   49   49   49   49   50   57   63   67   68   71   72   72   72   72   72 
LCS_GDT     A    72_A     A    72_A     49   49   72     27   43   49   49   49   49   49   49   49   51   57   63   67   68   71   72   72   72   72   72 
LCS_GDT     V    73_A     V    73_A     49   49   72     27   43   49   49   49   49   49   49   49   49   57   63   67   68   71   72   72   72   72   72 
LCS_GDT     E    74_A     E    74_A     49   49   72     27   43   49   49   49   49   49   49   49   49   50   58   66   68   71   72   72   72   72   72 
LCS_GDT     R    75_A     R    75_A     49   49   72     27   43   49   49   49   49   49   49   49   50   57   63   67   68   71   72   72   72   72   72 
LCS_GDT     Y    76_A     Y    76_A     49   49   72     27   42   49   49   49   49   49   49   49   51   57   63   67   68   71   72   72   72   72   72 
LCS_GDT     L    77_A     L    77_A     49   49   72     27   42   49   49   49   49   49   49   49   49   49   53   64   68   71   72   72   72   72   72 
LCS_GDT     R    78_A     R    78_A     49   49   72     19   42   49   49   49   49   49   49   49   49   49   54   61   67   71   72   72   72   72   72 
LCS_GDT     D    79_A     D    79_A     49   49   72     25   42   49   49   49   49   49   49   49   51   57   63   67   68   71   72   72   72   72   72 
LCS_GDT     Q    80_A     Q    80_A     49   49   72     19   42   49   49   49   49   49   49   49   50   57   63   67   68   71   72   72   72   72   72 
LCS_GDT     Q    81_A     Q    81_A     49   49   72      3   18   49   49   49   49   49   49   49   49   49   50   55   64   71   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     27     43     49     49     49     49     49     49     49     51     57     63     67     68     71     72     72     72     72     72 
GDT PERCENT_AT  37.50  59.72  68.06  68.06  68.06  68.06  68.06  68.06  68.06  70.83  79.17  87.50  93.06  94.44  98.61 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.32   0.57   0.69   0.69   0.69   0.69   0.69   0.69   0.69   3.84   3.87   4.18   4.37   4.41   4.62   4.69   4.69   4.69   4.69   4.69
GDT RMS_ALL_AT  11.50  11.73  11.74  11.74  11.74  11.74  11.74  11.74  11.74   5.12   4.79   4.80   4.84   4.80   4.70   4.69   4.69   4.69   4.69   4.69

# 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    21.133     0    0.347   1.227    22.427    0.000    0.000
LGA    S     3_A      S     3_A    26.464     0    0.036   0.684    30.725    0.000    0.000
LGA    L     4_A      L     4_A    23.716     0    0.031   0.104    25.054    0.000    0.000
LGA    I     5_A      I     5_A    17.238     0    0.033   0.100    19.431    0.000    0.000
LGA    E     6_A      E     6_A    21.912     0    0.072   1.042    26.788    0.000    0.000
LGA    E     7_A      E     7_A    24.920     0    0.013   0.136    30.844    0.000    0.000
LGA    L     8_A      L     8_A    18.829     0    0.044   0.094    20.824    0.000    0.000
LGA    I     9_A      I     9_A    17.108     0    0.068   0.118    19.192    0.000    0.000
LGA    R    10_A      R    10_A    23.602     0    0.047   1.384    35.234    0.000    0.000
LGA    R    11_A      R    11_A    22.097     0    0.017   1.489    28.539    0.000    0.000
LGA    S    12_A      S    12_A    15.742     0    0.054   0.673    17.838    0.000    0.000
LGA    E    13_A      E    13_A    20.175     0    0.037   1.258    23.836    0.000    0.000
LGA    E    14_A      E    14_A    23.898     0    0.024   0.370    29.597    0.000    0.000
LGA    Q    15_A      Q    15_A    18.346     0    0.041   0.133    20.085    0.000    0.000
LGA    Q    16_A      Q    16_A    16.259     0    0.039   0.886    18.387    0.000    0.000
LGA    R    17_A      R    17_A    22.837     0    0.019   1.150    32.374    0.000    0.000
LGA    R    18_A      R    18_A    21.525     0    0.015   1.062    27.408    0.000    0.000
LGA    N    19_A      N    19_A    15.045     0    0.016   0.079    17.190    0.000    0.000
LGA    E    20_A      E    20_A    19.347     0    0.007   1.013    22.637    0.000    0.000
LGA    E    21_A      E    21_A    23.712     0    0.020   0.895    30.738    0.000    0.000
LGA    A    22_A      A    22_A    18.216     0    0.067   0.074    19.934    0.000    0.000
LGA    L    23_A      L    23_A    16.375     0    0.038   0.238    18.684    0.000    0.000
LGA    R    24_A      R    24_A    23.038     0    0.314   1.100    29.134    0.000    0.000
LGA    Q    33_A      Q    33_A     0.522     0    0.079   1.142     4.530   92.976   73.492
LGA    L    34_A      L    34_A     0.829     0    0.036   0.136     2.100   90.476   81.726
LGA    L    35_A      L    35_A     1.017     0    0.030   0.501     2.792   85.952   78.512
LGA    S    36_A      S    36_A     1.063     0    0.019   0.672     3.213   85.952   79.206
LGA    G    37_A      G    37_A     0.671     0    0.057   0.057     0.722   95.238   95.238
LGA    I    38_A      I    38_A     0.478     0    0.032   0.060     1.027   95.238   91.726
LGA    V    39_A      V    39_A     1.101     0    0.032   0.054     1.659   83.690   80.272
LGA    Q    40_A      Q    40_A     1.165     0    0.026   0.918     2.513   81.429   76.878
LGA    Q    41_A      Q    41_A     0.500     0    0.023   0.337     0.822   97.619   96.825
LGA    Q    42_A      Q    42_A     0.539     0    0.079   0.391     1.793   92.857   88.571
LGA    N    43_A      N    43_A     0.830     0    0.051   1.361     3.701   90.476   74.345
LGA    N    44_A      N    44_A     0.453     0    0.018   0.034     0.816   97.619   94.048
LGA    L    45_A      L    45_A     0.141     0    0.021   0.214     0.879  100.000   97.619
LGA    L    46_A      L    46_A     0.415     0    0.057   0.141     1.100  100.000   94.107
LGA    R    47_A      R    47_A     0.237     0    0.043   1.131     4.562  100.000   82.597
LGA    A    48_A      A    48_A     0.374     0    0.049   0.051     0.687   97.619   98.095
LGA    I    49_A      I    49_A     0.495     0    0.048   0.098     0.783  100.000   95.238
LGA    E    50_A      E    50_A     0.220     0    0.052   0.067     0.837  100.000   96.825
LGA    A    51_A      A    51_A     0.584     0    0.014   0.018     0.802   92.857   92.381
LGA    Q    52_A      Q    52_A     0.982     0    0.022   0.288     1.263   85.952   83.439
LGA    Q    53_A      Q    53_A     0.869     0    0.029   1.125     4.435   90.476   75.608
LGA    H    54_A      H    54_A     0.787     0    0.015   0.609     1.678   90.476   86.000
LGA    L    55_A      L    55_A     1.128     0    0.020   1.386     4.006   83.690   74.881
LGA    L    56_A      L    56_A     1.139     0    0.019   1.361     3.374   85.952   78.690
LGA    Q    57_A      Q    57_A     0.679     0    0.049   1.479     5.177   90.476   71.640
LGA    L    58_A      L    58_A     0.582     0    0.033   0.176     0.934   90.476   90.476
LGA    T    59_A      T    59_A     0.859     0    0.056   1.074     3.035   90.476   82.109
LGA    V    60_A      V    60_A     0.673     0    0.020   0.043     0.928   92.857   91.837
LGA    W    61_A      W    61_A     0.331     0    0.069   1.291     8.697   97.619   53.673
LGA    G    62_A      G    62_A     0.475     0    0.055   0.055     0.475  100.000  100.000
LGA    I    63_A      I    63_A     0.523     0    0.019   0.061     0.655   97.619   94.048
LGA    K    64_A      K    64_A     0.312     0    0.045   1.134     6.734  100.000   72.646
LGA    Q    65_A      Q    65_A     0.233     0    0.034   1.354     5.380  100.000   78.360
LGA    L    66_A      L    66_A     0.318     0    0.029   0.056     0.502  100.000   98.810
LGA    Q    67_A      Q    67_A     0.360     0    0.013   0.781     3.756  100.000   82.857
LGA    A    68_A      A    68_A     0.357     0    0.014   0.022     0.450  100.000  100.000
LGA    R    69_A      R    69_A     0.271     0    0.014   0.114     0.502  100.000   99.134
LGA    I    70_A      I    70_A     0.364     0    0.067   1.365     3.812  100.000   83.929
LGA    L    71_A      L    71_A     0.367     0    0.031   0.064     0.466  100.000  100.000
LGA    A    72_A      A    72_A     0.193     0    0.021   0.035     0.313  100.000  100.000
LGA    V    73_A      V    73_A     0.253     0    0.016   0.052     0.406  100.000  100.000
LGA    E    74_A      E    74_A     0.419     0    0.023   0.103     0.770  100.000   96.825
LGA    R    75_A      R    75_A     0.590     0    0.079   0.230     1.416   92.857   90.519
LGA    Y    76_A      Y    76_A     0.590     0    0.020   0.141     1.077   90.476   89.722
LGA    L    77_A      L    77_A     0.693     0    0.047   0.111     0.796   90.476   91.667
LGA    R    78_A      R    78_A     0.885     0    0.043   1.127     4.258   88.214   71.126
LGA    D    79_A      D    79_A     0.953     0    0.022   0.091     1.106   85.952   88.214
LGA    Q    80_A      Q    80_A     0.997     0    0.041   0.156     1.471   85.952   83.439
LGA    Q    81_A      Q    81_A     1.501     0    0.454   0.521     2.760   71.071   75.873

# 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):     4.691          4.190                  7.121           63.626   59.073

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   83   72    4.0     49    0.69    73.958    69.290     6.173

LGA_LOCAL      RMSD:   0.694  Number of atoms:   49  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  11.743  Number of assigned atoms:   72 
Std_ASGN_ATOMS RMSD:   4.691  Standard rmsd on all 72 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.256206 * X  +  -0.958402 * Y  +   0.125791 * Z  +  -2.598664
  Y_new =   0.621830 * X  +   0.263049 * Y  +   0.737653 * Z  +   6.155284
  Z_new =  -0.740058 * X  +  -0.110771 * Y  +   0.663358 * Z  +  66.639977 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.179971  0.833157 -0.165458   [DEG:   67.6073   47.7364   -9.4801 ]
ZXZ:  2.972688  0.845499 -1.719372   [DEG:  170.3225   48.4435  -98.5127 ]
 
# END of job
