
#######################################################
#                                                     #
#                        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        4.34    27.43
  LCS_AVERAGE:     61.42

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    49      33_A - 81_A        0.66    28.33
  LCS_AVERAGE:     56.52

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    49      33_A - 81_A        0.66    28.33
  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   24      0    3    3    3    3    4    6    9   14   16   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     S     3_A     S     3_A     22   23   24     21   22   22   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     L     4_A     L     4_A     22   23   24     21   22   22   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     I     5_A     I     5_A     22   23   24     21   22   22   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     E     6_A     E     6_A     22   23   24     21   22   22   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     E     7_A     E     7_A     22   23   24     21   22   22   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     L     8_A     L     8_A     22   23   24     21   22   22   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     I     9_A     I     9_A     22   23   24     21   22   22   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     R    10_A     R    10_A     22   23   24     21   22   22   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     R    11_A     R    11_A     22   23   24     21   22   22   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     S    12_A     S    12_A     22   23   24     21   22   22   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     E    13_A     E    13_A     22   23   24     21   22   22   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     E    14_A     E    14_A     22   23   24     21   22   22   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     Q    15_A     Q    15_A     22   23   24     21   22   22   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     Q    16_A     Q    16_A     22   23   24     21   22   22   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     R    17_A     R    17_A     22   23   24     21   22   22   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     R    18_A     R    18_A     22   23   24     21   22   22   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     N    19_A     N    19_A     22   23   24     21   22   22   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     E    20_A     E    20_A     22   23   24     21   22   22   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     E    21_A     E    21_A     22   23   24     21   22   22   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     A    22_A     A    22_A     22   23   52     21   22   22   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   35   44 
LCS_GDT     L    23_A     L    23_A     22   23   52     21   22   22   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   36   45 
LCS_GDT     R    24_A     R    24_A     22   23   52     20   22   22   22   22   22   22   22   22   22   23   23   23   29   37   48   50   50   50   50 
LCS_GDT     Q    33_A     Q    33_A     49   49   52     13   41   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   50 
LCS_GDT     L    34_A     L    34_A     49   49   52     15   41   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   50 
LCS_GDT     L    35_A     L    35_A     49   49   52     22   41   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   50 
LCS_GDT     S    36_A     S    36_A     49   49   52     22   42   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   50 
LCS_GDT     G    37_A     G    37_A     49   49   52     32   42   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   50 
LCS_GDT     I    38_A     I    38_A     49   49   52     32   42   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   50 
LCS_GDT     V    39_A     V    39_A     49   49   52     32   42   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   50 
LCS_GDT     Q    40_A     Q    40_A     49   49   52     19   42   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   50 
LCS_GDT     Q    41_A     Q    41_A     49   49   52     33   42   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   50 
LCS_GDT     Q    42_A     Q    42_A     49   49   52     33   42   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   50 
LCS_GDT     N    43_A     N    43_A     49   49   52     33   42   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   50 
LCS_GDT     N    44_A     N    44_A     49   49   52     33   42   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   50 
LCS_GDT     L    45_A     L    45_A     49   49   52     33   42   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   50 
LCS_GDT     L    46_A     L    46_A     49   49   52     33   42   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   50 
LCS_GDT     R    47_A     R    47_A     49   49   52     33   42   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   50 
LCS_GDT     A    48_A     A    48_A     49   49   52     33   42   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   50 
LCS_GDT     I    49_A     I    49_A     49   49   52     33   42   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   50 
LCS_GDT     E    50_A     E    50_A     49   49   52     33   42   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   50 
LCS_GDT     A    51_A     A    51_A     49   49   52     33   42   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   50 
LCS_GDT     Q    52_A     Q    52_A     49   49   52     33   42   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   50 
LCS_GDT     Q    53_A     Q    53_A     49   49   52     33   42   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   50 
LCS_GDT     H    54_A     H    54_A     49   49   52     28   42   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   50 
LCS_GDT     L    55_A     L    55_A     49   49   52     33   42   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   50 
LCS_GDT     L    56_A     L    56_A     49   49   52     33   42   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   50 
LCS_GDT     Q    57_A     Q    57_A     49   49   52     33   42   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   50 
LCS_GDT     L    58_A     L    58_A     49   49   52     33   42   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   50 
LCS_GDT     T    59_A     T    59_A     49   49   52     33   42   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   50 
LCS_GDT     V    60_A     V    60_A     49   49   52     33   42   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   50 
LCS_GDT     W    61_A     W    61_A     49   49   52     33   42   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   50 
LCS_GDT     G    62_A     G    62_A     49   49   52     33   42   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   50 
LCS_GDT     I    63_A     I    63_A     49   49   52     33   42   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   50 
LCS_GDT     K    64_A     K    64_A     49   49   52     33   42   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   50 
LCS_GDT     Q    65_A     Q    65_A     49   49   52     33   42   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   50 
LCS_GDT     L    66_A     L    66_A     49   49   52     33   42   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   50 
LCS_GDT     Q    67_A     Q    67_A     49   49   52     33   42   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   50 
LCS_GDT     A    68_A     A    68_A     49   49   52     33   42   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   50 
LCS_GDT     R    69_A     R    69_A     49   49   52     33   42   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   50 
LCS_GDT     I    70_A     I    70_A     49   49   52     33   42   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   50 
LCS_GDT     L    71_A     L    71_A     49   49   52     33   42   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   50 
LCS_GDT     A    72_A     A    72_A     49   49   52     33   42   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   50 
LCS_GDT     V    73_A     V    73_A     49   49   52     33   42   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   50 
LCS_GDT     E    74_A     E    74_A     49   49   52      4   40   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   50 
LCS_GDT     R    75_A     R    75_A     49   49   52     33   42   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   50 
LCS_GDT     Y    76_A     Y    76_A     49   49   52     28   42   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   50 
LCS_GDT     L    77_A     L    77_A     49   49   52      6   40   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   50 
LCS_GDT     R    78_A     R    78_A     49   49   52     12   42   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   50 
LCS_GDT     D    79_A     D    79_A     49   49   52     10   42   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   50 
LCS_GDT     Q    80_A     Q    80_A     49   49   52     26   42   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   50 
LCS_GDT     Q    81_A     Q    81_A     49   49   52      3    8   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   50 
LCS_AVERAGE  LCS_A:  57.88  (  55.71   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     42     49     49     49     49     49     49     49     49     49     49     49     49     49     49     50     50     50     50 
GDT PERCENT_AT  45.83  58.33  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  69.44
GDT RMS_LOCAL    0.30   0.48   0.66   0.66   0.66   0.66   0.66   0.66   0.66   0.66   0.66   0.66   0.66   0.66   0.66   0.66   2.67   2.67   2.67   2.67
GDT RMS_ALL_AT  28.28  28.32  28.33  28.33  28.33  28.33  28.33  28.33  28.33  28.33  28.33  28.33  28.33  28.33  28.33  28.33  27.88  27.88  27.88  27.88

# 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

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    T     2_A      T     2_A    76.769     0    0.113   1.100    78.017    0.000    0.000
LGA    S     3_A      S     3_A    75.355     0    0.662   0.795    76.341    0.000    0.000
LGA    L     4_A      L     4_A    70.879     0    0.016   0.047    73.162    0.000    0.000
LGA    I     5_A      I     5_A    68.917     0    0.036   0.110    74.447    0.000    0.000
LGA    E     6_A      E     6_A    67.303     0    0.055   0.885    73.523    0.000    0.000
LGA    E     7_A      E     7_A    63.219     0    0.039   1.299    65.330    0.000    0.000
LGA    L     8_A      L     8_A    59.392     0    0.025   0.040    63.908    0.000    0.000
LGA    I     9_A      I     9_A    57.929     0    0.022   0.125    63.668    0.000    0.000
LGA    R    10_A      R    10_A    55.885     0    0.026   0.690    67.141    0.000    0.000
LGA    R    11_A      R    11_A    51.041     0    0.025   1.247    53.993    0.000    0.000
LGA    S    12_A      S    12_A    48.365     0    0.057   0.060    51.386    0.000    0.000
LGA    E    13_A      E    13_A    47.501     0    0.031   1.162    51.819    0.000    0.000
LGA    E    14_A      E    14_A    43.980     0    0.007   1.186    46.866    0.000    0.000
LGA    Q    15_A      Q    15_A    39.183     0    0.058   1.421    41.473    0.000    0.000
LGA    Q    16_A      Q    16_A    37.937     0    0.010   1.390    41.259    0.000    0.000
LGA    R    17_A      R    17_A    36.766     0    0.000   1.020    48.025    0.000    0.000
LGA    R    18_A      R    18_A    31.766     0    0.007   1.130    37.404    0.000    0.000
LGA    N    19_A      N    19_A    28.287     0    0.037   0.064    32.657    0.000    0.000
LGA    E    20_A      E    20_A    28.039     0    0.023   0.968    34.919    0.000    0.000
LGA    E    21_A      E    21_A    26.343     0    0.032   1.006    29.816    0.000    0.000
LGA    A    22_A      A    22_A    20.308     0    0.047   0.049    22.901    0.000    0.000
LGA    L    23_A      L    23_A    18.457     0    0.046   1.359    20.909    0.000    0.000
LGA    R    24_A      R    24_A    19.541     0    0.239   1.146    28.480    0.000    0.000
LGA    Q    33_A      Q    33_A     1.312     0    0.043   1.281     3.505   83.810   73.651
LGA    L    34_A      L    34_A     1.175     0    0.043   0.087     2.664   83.690   76.310
LGA    L    35_A      L    35_A     1.222     0    0.028   0.511     2.844   83.690   77.381
LGA    S    36_A      S    36_A     0.975     0    0.055   0.655     3.210   88.214   80.714
LGA    G    37_A      G    37_A     0.444     0    0.098   0.098     0.601   97.619   97.619
LGA    I    38_A      I    38_A     0.552     0    0.020   0.054     1.307   95.238   90.595
LGA    V    39_A      V    39_A     0.689     0    0.025   0.057     1.033   90.476   89.184
LGA    Q    40_A      Q    40_A     0.751     0    0.013   1.207     3.827   90.476   80.317
LGA    Q    41_A      Q    41_A     0.405     0    0.030   1.400     5.034  100.000   74.603
LGA    Q    42_A      Q    42_A     0.311     0    0.063   0.261     1.953  100.000   90.741
LGA    N    43_A      N    43_A     0.236     0    0.000   1.331     3.906  100.000   82.262
LGA    N    44_A      N    44_A     0.291     0    0.023   0.088     0.544  100.000   98.810
LGA    L    45_A      L    45_A     0.417     0    0.039   1.402     4.304  100.000   80.238
LGA    L    46_A      L    46_A     0.231     0    0.011   1.403     3.680  100.000   83.155
LGA    R    47_A      R    47_A     0.333     0    0.000   0.246     1.137  100.000   95.714
LGA    A    48_A      A    48_A     0.540     0    0.038   0.048     0.740   92.857   92.381
LGA    I    49_A      I    49_A     0.368     0    0.044   0.092     0.790  100.000   97.619
LGA    E    50_A      E    50_A     0.264     0    0.024   0.137     1.031  100.000   95.820
LGA    A    51_A      A    51_A     0.592     0    0.029   0.029     1.013   95.238   92.476
LGA    Q    52_A      Q    52_A     0.765     0    0.079   0.271     1.475   90.476   89.471
LGA    Q    53_A      Q    53_A     0.680     0    0.040   1.557     5.578   90.476   68.783
LGA    H    54_A      H    54_A     0.694     0    0.023   1.136     2.604   90.476   81.905
LGA    L    55_A      L    55_A     0.822     0    0.008   1.404     4.248   90.476   76.250
LGA    L    56_A      L    56_A     0.647     0    0.005   1.375     2.923   95.238   83.393
LGA    Q    57_A      Q    57_A     0.293     0    0.044   1.455     4.974  100.000   76.825
LGA    L    58_A      L    58_A     0.399     0    0.031   0.137     1.067  100.000   94.107
LGA    T    59_A      T    59_A     0.507     0    0.073   1.116     2.671   97.619   87.279
LGA    V    60_A      V    60_A     0.411     0    0.015   0.053     0.746  100.000   95.918
LGA    W    61_A      W    61_A     0.286     0    0.061   0.094     0.943  100.000   93.197
LGA    G    62_A      G    62_A     0.193     0    0.072   0.072     0.194  100.000  100.000
LGA    I    63_A      I    63_A     0.151     0    0.018   0.087     0.211  100.000  100.000
LGA    K    64_A      K    64_A     0.212     0    0.038   1.150     6.906  100.000   72.646
LGA    Q    65_A      Q    65_A     0.150     0    0.033   1.092     4.582  100.000   79.788
LGA    L    66_A      L    66_A     0.087     0    0.015   0.069     0.426  100.000  100.000
LGA    Q    67_A      Q    67_A     0.213     0    0.027   0.034     0.759  100.000   96.825
LGA    A    68_A      A    68_A     0.285     0    0.028   0.030     0.408  100.000  100.000
LGA    R    69_A      R    69_A     0.284     0    0.014   1.010     4.287  100.000   87.749
LGA    I    70_A      I    70_A     0.596     0    0.014   1.372     4.093   92.857   79.583
LGA    L    71_A      L    71_A     0.569     0    0.121   1.393     3.658   88.214   75.179
LGA    A    72_A      A    72_A     0.387     0    0.179   0.181     0.420  100.000  100.000
LGA    V    73_A      V    73_A     0.767     0    0.106   0.114     2.101   88.214   81.701
LGA    E    74_A      E    74_A     1.113     0    0.525   0.556     5.890   67.738   53.122
LGA    R    75_A      R    75_A     0.322     0    0.110   1.202     8.395   97.619   57.446
LGA    Y    76_A      Y    76_A     0.631     0    0.060   0.137     0.997   92.857   91.270
LGA    L    77_A      L    77_A     1.171     0    0.059   0.100     1.460   83.690   82.560
LGA    R    78_A      R    78_A     1.008     0    0.024   1.250     8.747   83.690   53.160
LGA    D    79_A      D    79_A     0.895     0    0.023   0.089     1.412   90.476   85.952
LGA    Q    80_A      Q    80_A     0.897     0    0.108   0.198     1.165   90.476   86.455
LGA    Q    81_A      Q    81_A     1.389     0    0.334   0.363     2.426   75.119   75.820

# 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):    23.343         22.909                 23.561           63.986   57.722

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   83   72    4.0     49    0.66    65.625    64.441     6.430

LGA_LOCAL      RMSD:   0.662  Number of atoms:   49  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  28.330  Number of assigned atoms:   72 
Std_ASGN_ATOMS RMSD:  23.343  Standard rmsd on all 72 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.535666 * X  +  -0.485199 * Y  +   0.691118 * Z  +   8.437994
  Y_new =  -0.546312 * X  +   0.823209 * Y  +   0.154503 * Z  +   7.850664
  Z_new =  -0.643899 * X  +  -0.294804 * Y  +  -0.706034 * Z  + 144.435669 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.346355  0.699583 -2.746050   [DEG: -134.4363   40.0832 -157.3371 ]
ZXZ:  1.790734  2.354679 -2.000153   [DEG:  102.6015  134.9132 -114.6003 ]
 
# END of job
