
#######################################################
#                                                     #
#                        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:    52      22_A - 81_A        4.22    27.16
  LCS_AVERAGE:     61.42

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    49      33_A - 81_A        0.53    27.93
  LCS_AVERAGE:     56.52

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    49      33_A - 81_A        0.53    27.93
  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   24     11   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   24 
LCS_GDT     S     3_A     S     3_A     23   23   24     15   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   24 
LCS_GDT     L     4_A     L     4_A     23   23   24     20   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   24 
LCS_GDT     I     5_A     I     5_A     23   23   24     20   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   24 
LCS_GDT     E     6_A     E     6_A     23   23   24     20   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   24 
LCS_GDT     E     7_A     E     7_A     23   23   24     20   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   24 
LCS_GDT     L     8_A     L     8_A     23   23   24     20   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   24 
LCS_GDT     I     9_A     I     9_A     23   23   24     20   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   24 
LCS_GDT     R    10_A     R    10_A     23   23   24     20   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   24 
LCS_GDT     R    11_A     R    11_A     23   23   24     20   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   24 
LCS_GDT     S    12_A     S    12_A     23   23   24     20   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   24 
LCS_GDT     E    13_A     E    13_A     23   23   24     20   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   24 
LCS_GDT     E    14_A     E    14_A     23   23   24     20   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   24 
LCS_GDT     Q    15_A     Q    15_A     23   23   24     20   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   24 
LCS_GDT     Q    16_A     Q    16_A     23   23   24     20   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   24 
LCS_GDT     R    17_A     R    17_A     23   23   24     20   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   24 
LCS_GDT     R    18_A     R    18_A     23   23   24     20   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   24 
LCS_GDT     N    19_A     N    19_A     23   23   24     20   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   24 
LCS_GDT     E    20_A     E    20_A     23   23   24     20   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   24 
LCS_GDT     E    21_A     E    21_A     23   23   24     20   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   24 
LCS_GDT     A    22_A     A    22_A     23   23   52     20   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   24   35   47 
LCS_GDT     L    23_A     L    23_A     23   23   52     20   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   34   44   51 
LCS_GDT     R    24_A     R    24_A     23   23   52     20   23   23   23   23   23   23   23   23   23   23   23   23   28   35   46   50   50   50   51 
LCS_GDT     Q    33_A     Q    33_A     49   49   52     29   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     L    34_A     L    34_A     49   49   52     24   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     L    35_A     L    35_A     49   49   52     29   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     S    36_A     S    36_A     49   49   52     29   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     G    37_A     G    37_A     49   49   52     33   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     I    38_A     I    38_A     49   49   52     29   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     V    39_A     V    39_A     49   49   52     29   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     Q    40_A     Q    40_A     49   49   52     25   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     Q    41_A     Q    41_A     49   49   52     33   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     Q    42_A     Q    42_A     49   49   52     33   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     N    43_A     N    43_A     49   49   52     33   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     N    44_A     N    44_A     49   49   52     33   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     L    45_A     L    45_A     49   49   52     33   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     L    46_A     L    46_A     49   49   52     33   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     R    47_A     R    47_A     49   49   52     33   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     A    48_A     A    48_A     49   49   52     33   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     I    49_A     I    49_A     49   49   52     33   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     E    50_A     E    50_A     49   49   52     33   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     A    51_A     A    51_A     49   49   52     33   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     Q    52_A     Q    52_A     49   49   52     30   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     Q    53_A     Q    53_A     49   49   52     32   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     H    54_A     H    54_A     49   49   52     33   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     L    55_A     L    55_A     49   49   52     30   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     L    56_A     L    56_A     49   49   52     30   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     Q    57_A     Q    57_A     49   49   52     33   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     L    58_A     L    58_A     49   49   52     33   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     T    59_A     T    59_A     49   49   52     33   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     V    60_A     V    60_A     49   49   52     33   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     W    61_A     W    61_A     49   49   52     33   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     G    62_A     G    62_A     49   49   52     33   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     I    63_A     I    63_A     49   49   52     33   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     K    64_A     K    64_A     49   49   52     33   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     Q    65_A     Q    65_A     49   49   52     33   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     L    66_A     L    66_A     49   49   52     33   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     Q    67_A     Q    67_A     49   49   52     33   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     A    68_A     A    68_A     49   49   52     33   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     R    69_A     R    69_A     49   49   52     33   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     I    70_A     I    70_A     49   49   52     33   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     L    71_A     L    71_A     49   49   52     33   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     A    72_A     A    72_A     49   49   52     33   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     V    73_A     V    73_A     49   49   52     33   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     E    74_A     E    74_A     49   49   52     33   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     R    75_A     R    75_A     49   49   52     33   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     Y    76_A     Y    76_A     49   49   52     33   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     L    77_A     L    77_A     49   49   52     33   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     R    78_A     R    78_A     49   49   52     33   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     D    79_A     D    79_A     49   49   52     30   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     Q    80_A     Q    80_A     49   49   52     32   48   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     Q    81_A     Q    81_A     49   49   52      3   11   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_AVERAGE  LCS_A:  58.15  (  56.52   56.52   61.42 )

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     33     48     49     49     49     49     49     49     49     49     49     49     49     49     49     49     50     50     50     51 
GDT PERCENT_AT  45.83  66.67  68.06  68.06  68.06  68.06  68.06  68.06  68.06  68.06  68.06  68.06  68.06  68.06  68.06  68.06  69.44  69.44  69.44  70.83
GDT RMS_LOCAL    0.34   0.50   0.53   0.53   0.53   0.53   0.53   0.53   0.53   0.53   0.53   0.53   0.53   0.53   0.53   0.53   2.57   2.57   2.57   3.43
GDT RMS_ALL_AT  27.99  27.94  27.93  27.93  27.93  27.93  27.93  27.93  27.93  27.93  27.93  27.93  27.93  27.93  27.93  27.93  27.56  27.56  27.56  27.37

# Checking swapping
#   possible swapping detected:  E     7_A      E     7_A
#   possible swapping detected:  E    13_A      E    13_A
#   possible swapping detected:  E    14_A      E    14_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    78.038     0    0.590   1.403    79.078    0.000    0.000
LGA    S     3_A      S     3_A    74.365     0    0.033   0.597    76.310    0.000    0.000
LGA    L     4_A      L     4_A    69.916     0    0.028   0.066    72.152    0.000    0.000
LGA    I     5_A      I     5_A    68.099     0    0.051   0.120    73.947    0.000    0.000
LGA    E     6_A      E     6_A    66.370     0    0.072   0.871    72.486    0.000    0.000
LGA    E     7_A      E     7_A    62.191     0    0.040   1.299    64.346    0.000    0.000
LGA    L     8_A      L     8_A    58.519     0    0.026   0.048    63.181    0.000    0.000
LGA    I     9_A      I     9_A    57.083     0    0.024   0.127    62.939    0.000    0.000
LGA    R    10_A      R    10_A    54.846     0    0.024   0.705    65.890    0.000    0.000
LGA    R    11_A      R    11_A    50.048     0    0.023   1.241    52.955    0.000    0.000
LGA    S    12_A      S    12_A    47.499     0    0.058   0.062    50.610    0.000    0.000
LGA    E    13_A      E    13_A    46.497     0    0.030   1.162    50.768    0.000    0.000
LGA    E    14_A      E    14_A    42.992     0    0.006   1.183    46.048    0.000    0.000
LGA    Q    15_A      Q    15_A    38.284     0    0.058   1.419    40.540    0.000    0.000
LGA    Q    16_A      Q    16_A    36.978     0    0.010   1.395    40.318    0.000    0.000
LGA    R    17_A      R    17_A    35.749     0    0.001   1.019    46.855    0.000    0.000
LGA    R    18_A      R    18_A    30.932     0    0.008   1.136    36.747    0.000    0.000
LGA    N    19_A      N    19_A    27.466     0    0.041   0.065    31.861    0.000    0.000
LGA    E    20_A      E    20_A    27.014     0    0.024   0.953    33.588    0.000    0.000
LGA    E    21_A      E    21_A    25.599     0    0.031   1.013    29.379    0.000    0.000
LGA    A    22_A      A    22_A    19.852     0    0.058   0.059    22.306    0.000    0.000
LGA    L    23_A      L    23_A    17.767     0    0.081   1.360    20.359    0.000    0.000
LGA    R    24_A      R    24_A    18.699     0    0.223   1.138    26.945    0.000    0.000
LGA    Q    33_A      Q    33_A     0.587     0    0.075   1.129     4.462   90.595   74.603
LGA    L    34_A      L    34_A     0.761     0    0.019   1.427     4.494   90.476   74.345
LGA    L    35_A      L    35_A     0.896     0    0.016   0.480     2.594   90.476   82.917
LGA    S    36_A      S    36_A     0.754     0    0.041   0.050     0.860   90.476   90.476
LGA    G    37_A      G    37_A     0.433     0    0.096   0.096     0.480  100.000  100.000
LGA    I    38_A      I    38_A     0.476     0    0.023   0.057     1.121   95.238   91.726
LGA    V    39_A      V    39_A     0.763     0    0.018   0.051     1.074   90.476   87.891
LGA    Q    40_A      Q    40_A     0.754     0    0.004   0.965     3.635   90.476   80.317
LGA    Q    41_A      Q    41_A     0.318     0    0.038   1.402     4.799  100.000   75.926
LGA    Q    42_A      Q    42_A     0.323     0    0.060   0.237     1.692  100.000   90.741
LGA    N    43_A      N    43_A     0.266     0    0.000   1.332     3.793  100.000   82.262
LGA    N    44_A      N    44_A     0.141     0    0.016   0.089     0.698  100.000   96.429
LGA    L    45_A      L    45_A     0.118     0    0.007   0.201     0.634  100.000   97.619
LGA    L    46_A      L    46_A     0.126     0    0.000   1.399     3.732  100.000   83.155
LGA    R    47_A      R    47_A     0.170     0    0.000   0.241     0.834  100.000   98.268
LGA    A    48_A      A    48_A     0.327     0    0.025   0.031     0.480  100.000  100.000
LGA    I    49_A      I    49_A     0.282     0    0.046   0.091     0.734  100.000   97.619
LGA    E    50_A      E    50_A     0.201     0    0.017   0.124     1.066  100.000   95.820
LGA    A    51_A      A    51_A     0.558     0    0.016   0.017     0.737   92.857   92.381
LGA    Q    52_A      Q    52_A     0.746     0    0.025   0.208     1.498   90.476   87.460
LGA    Q    53_A      Q    53_A     0.684     0    0.015   1.556     5.535   90.476   67.937
LGA    H    54_A      H    54_A     0.670     0    0.017   1.140     2.316   90.476   82.667
LGA    L    55_A      L    55_A     0.842     0    0.008   1.412     4.120   90.476   76.250
LGA    L    56_A      L    56_A     0.717     0    0.008   1.377     3.036   92.857   82.262
LGA    Q    57_A      Q    57_A     0.369     0    0.056   1.173     4.627   97.619   80.265
LGA    L    58_A      L    58_A     0.391     0    0.023   0.105     0.896  100.000   95.238
LGA    T    59_A      T    59_A     0.522     0    0.068   1.117     2.698   97.619   87.279
LGA    V    60_A      V    60_A     0.480     0    0.011   0.049     0.827  100.000   95.918
LGA    W    61_A      W    61_A     0.334     0    0.059   0.178     0.916  100.000   93.197
LGA    G    62_A      G    62_A     0.353     0    0.076   0.076     0.353  100.000  100.000
LGA    I    63_A      I    63_A     0.301     0    0.023   0.094     0.348  100.000  100.000
LGA    K    64_A      K    64_A     0.291     0    0.040   1.144     6.941  100.000   72.646
LGA    Q    65_A      Q    65_A     0.194     0    0.030   1.090     4.602  100.000   79.788
LGA    L    66_A      L    66_A     0.065     0    0.008   0.070     0.331  100.000  100.000
LGA    Q    67_A      Q    67_A     0.297     0    0.021   0.038     0.999  100.000   94.709
LGA    A    68_A      A    68_A     0.277     0    0.021   0.021     0.342  100.000  100.000
LGA    R    69_A      R    69_A     0.256     0    0.007   1.006     4.551  100.000   86.494
LGA    I    70_A      I    70_A     0.393     0    0.025   1.376     3.831  100.000   82.917
LGA    L    71_A      L    71_A     0.380     0    0.016   1.417     3.140  100.000   83.095
LGA    A    72_A      A    72_A     0.417     0    0.023   0.028     0.542   97.619   98.095
LGA    V    73_A      V    73_A     0.480     0    0.009   0.056     0.600   95.238   95.918
LGA    E    74_A      E    74_A     0.616     0    0.015   0.966     3.982   90.476   72.540
LGA    R    75_A      R    75_A     0.633     0    0.045   1.219     4.928   92.857   78.268
LGA    Y    76_A      Y    76_A     0.537     0    0.032   0.094     0.561   90.476   94.444
LGA    L    77_A      L    77_A     0.634     0    0.017   0.043     0.771   90.476   90.476
LGA    R    78_A      R    78_A     0.599     0    0.000   1.232     5.019   90.476   74.502
LGA    D    79_A      D    79_A     0.654     0    0.029   0.072     1.191   90.476   87.083
LGA    Q    80_A      Q    80_A     0.547     0    0.104   0.199     0.923   92.857   91.534
LGA    Q    81_A      Q    81_A     1.329     0    0.336   0.371     2.642   75.476   76.931

# 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):    23.161         22.715                 23.295           65.104   59.728

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   83   72    4.0     49    0.53    67.708    65.099     7.733

LGA_LOCAL      RMSD:   0.534  Number of atoms:   49  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  27.929  Number of assigned atoms:   72 
Std_ASGN_ATOMS RMSD:  23.161  Standard rmsd on all 72 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.186377 * X  +  -0.978844 * Y  +   0.084431 * Z  +  14.626284
  Y_new =  -0.593798 * X  +  -0.043763 * Y  +   0.803423 * Z  +   4.144285
  Z_new =  -0.782731 * X  +  -0.199875 * Y  +  -0.589391 * Z  + 142.879425 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.266661  0.899042 -2.814643   [DEG:  -72.5743   51.5113 -161.2672 ]
ZXZ:  3.036888  2.201102 -1.820809   [DEG:  174.0009  126.1138 -104.3247 ]
 
# END of job
