
#######################################################
#                                                     #
#                        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        0.64     0.64
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    71       1_B - 71_B        0.64     0.64
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    71       1_B - 71_B        0.64     0.64
  LCS_AVERAGE:    100.00

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     71   71   71      4   45   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S     2_B     S     2_B     71   71   71     49   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V     3_B     V     3_B     71   71   71     49   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S     4_B     S     4_B     71   71   71     49   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K     5_B     K     5_B     71   71   71     49   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     W     6_B     W     6_B     71   71   71     45   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S     7_B     S     7_B     71   71   71     49   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     T     8_B     T     8_B     71   71   71     49   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D     9_B     D     9_B     71   71   71     49   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    10_B     E    10_B     71   71   71     49   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V    11_B     V    11_B     71   71   71     49   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    12_B     S    12_B     71   71   71     49   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    13_B     E    13_B     71   71   71     49   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    14_B     F    14_B     71   71   71     49   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    15_B     I    15_B     71   71   71     49   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     Q    16_B     Q    16_B     71   71   71     49   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    17_B     S    17_B     71   71   71     49   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    18_B     L    18_B     71   71   71     49   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     P    19_B     P    19_B     71   71   71     43   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    20_B     G    20_B     71   71   71     49   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     C    21_B     C    21_B     71   71   71     49   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    22_B     E    22_B     71   71   71     49   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    23_B     E    23_B     71   71   71     49   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     H    24_B     H    24_B     71   71   71     49   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    25_B     G    25_B     71   71   71     49   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    26_B     K    26_B     71   71   71     49   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V    27_B     V    27_B     71   71   71     40   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    28_B     F    28_B     71   71   71     49   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    29_B     K    29_B     71   71   71     49   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D    30_B     D    30_B     71   71   71     43   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    31_B     E    31_B     71   71   71     40   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     Q    32_B     Q    32_B     71   71   71     44   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    33_B     I    33_B     71   71   71     49   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D    34_B     D    34_B     71   71   71     49   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    35_B     G    35_B     71   71   71     49   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    36_B     E    36_B     71   71   71     12   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    37_B     A    37_B     71   71   71     49   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    38_B     F    38_B     71   71   71     49   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    39_B     L    39_B     71   71   71     49   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    40_B     L    40_B     71   71   71     49   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     M    41_B     M    41_B     71   71   71     49   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     T    42_B     T    42_B     71   71   71     49   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     Q    43_B     Q    43_B     71   71   71     31   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     T    44_B     T    44_B     71   71   71     49   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D    45_B     D    45_B     71   71   71     49   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    46_B     I    46_B     71   71   71     42   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V    47_B     V    47_B     71   71   71     49   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    48_B     K    48_B     71   71   71     33   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    49_B     I    49_B     71   71   71     26   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     M    50_B     M    50_B     71   71   71     26   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    51_B     S    51_B     71   71   71     33   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    52_B     I    52_B     71   71   71     49   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    53_B     K    53_B     71   71   71     49   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    54_B     E    54_B     71   71   71     49   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    55_B     G    55_B     71   71   71     49   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     P    56_B     P    56_B     71   71   71     49   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    57_B     A    57_B     71   71   71     49   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    58_B     E    58_B     71   71   71     49   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    59_B     K    59_B     71   71   71     49   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    60_B     I    60_B     71   71   71     49   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    61_B     F    61_B     71   71   71     49   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     N    62_B     N    62_B     71   71   71     49   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    63_B     S    63_B     71   71   71     42   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    64_B     I    64_B     71   71   71     49   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    65_B     L    65_B     71   71   71     42   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     M    66_B     M    66_B     71   71   71     33   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    67_B     F    67_B     71   71   71     33   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    68_B     K    68_B     71   71   71     29   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    69_B     A    69_B     71   71   71     29   59   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    70_B     A    70_B     71   71   71     18   55   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    71_B     E    71_B     71   71   71     18   55   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_AVERAGE  LCS_A: 100.00  ( 100.00  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     49     67     70     71     71     71     71     71     71     71     71     71     71     71     71     71     71     71     71     71 
GDT PERCENT_AT  69.01  94.37  98.59 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.37   0.52   0.61   0.64   0.64   0.64   0.64   0.64   0.64   0.64   0.64   0.64   0.64   0.64   0.64   0.64   0.64   0.64   0.64   0.64
GDT RMS_ALL_AT   0.68   0.66   0.65   0.64   0.64   0.64   0.64   0.64   0.64   0.64   0.64   0.64   0.64   0.64   0.64   0.64   0.64   0.64   0.64   0.64

# Checking swapping
#   possible swapping detected:  D     9_B      D     9_B
#   possible swapping detected:  E    10_B      E    10_B
#   possible swapping detected:  F    14_B      F    14_B
#   possible swapping detected:  E    22_B      E    22_B
#   possible swapping detected:  F    28_B      F    28_B
#   possible swapping detected:  E    31_B      E    31_B
#   possible swapping detected:  F    38_B      F    38_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     1.751     0    0.333   0.333     2.855   80.119   80.119
LGA    S     2_B      S     2_B     0.671     0    0.040   0.724     2.842   90.476   84.921
LGA    V     3_B      V     3_B     0.306     0    0.066   0.063     0.438  100.000  100.000
LGA    S     4_B      S     4_B     0.609     0    0.018   0.143     0.880   90.476   90.476
LGA    K     5_B      K     5_B     0.503     0    0.048   0.840     4.766   92.857   73.757
LGA    W     6_B      W     6_B     0.686     0    0.040   0.103     0.729   90.476   91.156
LGA    S     7_B      S     7_B     0.570     0    0.018   0.047     0.606   90.476   93.651
LGA    T     8_B      T     8_B     0.574     0    0.049   1.080     2.582   90.476   82.041
LGA    D     9_B      D     9_B     0.341     0    0.067   0.780     3.409  100.000   84.940
LGA    E    10_B      E    10_B     0.291     0    0.025   0.303     1.605  100.000   91.799
LGA    V    11_B      V    11_B     0.406     0    0.016   0.031     0.515  100.000   97.279
LGA    S    12_B      S    12_B     0.388     0    0.028   0.068     0.639  100.000   98.413
LGA    E    13_B      E    13_B     0.288     0    0.038   0.785     3.732  100.000   82.646
LGA    F    14_B      F    14_B     0.376     0    0.023   0.204     1.465  100.000   90.649
LGA    I    15_B      I    15_B     0.408     0    0.010   0.617     1.619  100.000   94.226
LGA    Q    16_B      Q    16_B     0.358     0    0.016   0.142     0.605  100.000   98.942
LGA    S    17_B      S    17_B     0.571     0    0.034   0.041     0.717   92.857   92.063
LGA    L    18_B      L    18_B     0.520     0    0.091   0.135     0.520   95.238   96.429
LGA    P    19_B      P    19_B     0.728     0    0.064   0.381     2.207   90.476   85.510
LGA    G    20_B      G    20_B     0.608     0    0.071   0.071     0.816   90.476   90.476
LGA    C    21_B      C    21_B     0.297     0    0.018   0.112     0.505  100.000   98.413
LGA    E    22_B      E    22_B     0.505     0    0.015   0.119     1.049   92.857   91.587
LGA    E    23_B      E    23_B     0.534     0    0.045   1.032     5.017   95.238   72.857
LGA    H    24_B      H    24_B     0.264     0    0.103   0.159     0.898  100.000   96.190
LGA    G    25_B      G    25_B     0.384     0    0.013   0.013     0.451  100.000  100.000
LGA    K    26_B      K    26_B     0.466     0    0.014   0.616     2.166   97.619   92.910
LGA    V    27_B      V    27_B     0.747     0    0.060   1.106     3.350   90.476   82.109
LGA    F    28_B      F    28_B     0.250     0    0.017   0.076     0.513  100.000   99.134
LGA    K    29_B      K    29_B     0.325     0    0.017   0.796     2.604   95.238   85.291
LGA    D    30_B      D    30_B     0.812     0    0.076   0.100     1.094   90.476   88.214
LGA    E    31_B      E    31_B     0.846     0    0.022   0.107     1.336   90.476   87.460
LGA    Q    32_B      Q    32_B     0.796     0    0.045   0.176     1.229   90.476   86.455
LGA    I    33_B      I    33_B     0.448     0    0.041   0.618     1.602   97.619   94.226
LGA    D    34_B      D    34_B     0.563     0    0.032   0.072     0.973   97.619   94.048
LGA    G    35_B      G    35_B     0.414     0    0.029   0.029     0.506   97.619   97.619
LGA    E    36_B      E    36_B     0.622     0    0.041   0.911     2.529   90.476   84.762
LGA    A    37_B      A    37_B     0.524     0    0.053   0.063     0.561   95.238   96.190
LGA    F    38_B      F    38_B     0.265     0    0.032   0.214     0.612  100.000   98.268
LGA    L    39_B      L    39_B     0.363     0    0.073   0.180     0.550   97.619   98.810
LGA    L    40_B      L    40_B     0.242     0    0.108   0.197     0.659   97.619   95.238
LGA    M    41_B      M    41_B     0.193     0    0.077   0.092     0.630  100.000   98.810
LGA    T    42_B      T    42_B     0.563     0    0.042   0.051     0.740   95.238   93.197
LGA    Q    43_B      Q    43_B     0.604     0    0.012   0.559     2.527   95.238   87.884
LGA    T    44_B      T    44_B     0.491     0    0.015   0.143     0.883   97.619   95.918
LGA    D    45_B      D    45_B     0.351     0    0.027   0.158     0.715  100.000   97.619
LGA    I    46_B      I    46_B     0.529     0    0.035   0.078     0.908   92.857   91.667
LGA    V    47_B      V    47_B     0.437     0    0.030   0.046     0.504   97.619   98.639
LGA    K    48_B      K    48_B     0.861     0    0.018   0.943     5.009   88.214   74.921
LGA    I    49_B      I    49_B     1.000     0    0.084   0.126     1.026   88.214   88.214
LGA    M    50_B      M    50_B     1.010     0    0.017   0.685     1.699   88.214   86.012
LGA    S    51_B      S    51_B     0.811     0    0.029   0.030     1.153   92.857   90.556
LGA    I    52_B      I    52_B     0.448     0    0.018   0.040     0.689   97.619   96.429
LGA    K    53_B      K    53_B     0.332     0    0.036   0.682     2.996  100.000   89.418
LGA    E    54_B      E    54_B     0.306     0    0.035   0.740     3.173  100.000   85.767
LGA    G    55_B      G    55_B     0.288     0    0.016   0.016     0.302  100.000  100.000
LGA    P    56_B      P    56_B     0.210     0    0.024   0.281     0.781  100.000   98.639
LGA    A    57_B      A    57_B     0.219     0    0.020   0.025     0.311  100.000  100.000
LGA    E    58_B      E    58_B     0.401     0    0.020   0.106     0.700  100.000   94.709
LGA    K    59_B      K    59_B     0.348     0    0.019   0.096     0.371  100.000  100.000
LGA    I    60_B      I    60_B     0.195     0    0.031   0.041     0.253  100.000  100.000
LGA    F    61_B      F    61_B     0.279     0    0.046   0.045     0.491  100.000  100.000
LGA    N    62_B      N    62_B     0.457     0    0.026   0.095     0.715  100.000   95.238
LGA    S    63_B      S    63_B     0.441     0    0.026   0.023     0.516  100.000   98.413
LGA    I    64_B      I    64_B     0.357     0    0.014   0.048     0.449  100.000  100.000
LGA    L    65_B      L    65_B     0.439     0    0.017   0.134     0.762   95.238   96.429
LGA    M    66_B      M    66_B     0.709     0    0.018   0.622     3.709   90.476   75.357
LGA    F    67_B      F    67_B     0.840     0    0.042   0.285     1.245   88.214   88.831
LGA    K    68_B      K    68_B     1.003     0    0.045   0.955     2.866   83.690   82.751
LGA    A    69_B      A    69_B     1.209     0    0.068   0.078     1.370   81.429   81.429
LGA    A    70_B      A    70_B     1.651     0    0.123   0.140     2.131   70.833   71.238
LGA    E    71_B      E    71_B     1.770     0    0.128   0.645     1.970   72.857   76.772

# 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):     0.645          0.646                  1.037           94.754   91.185

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   73   71    4.0     71    0.64    98.592    99.450     9.535

LGA_LOCAL      RMSD:   0.645  Number of atoms:   71  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.645  Number of assigned atoms:   71 
Std_ASGN_ATOMS RMSD:   0.645  Standard rmsd on all 71 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.227349 * X  +  -0.280474 * Y  +  -0.932549 * Z  +  20.535738
  Y_new =   0.494735 * X  +  -0.858102 * Y  +   0.137470 * Z  +  38.680557
  Z_new =  -0.838778 * X  +  -0.430111 * Y  +   0.333849 * Z  +   3.645419 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.001553  0.995036 -0.910741   [DEG:  114.6806   57.0113  -52.1816 ]
ZXZ: -1.717155  1.230412 -2.044618   [DEG:  -98.3857   70.4974 -117.1480 ]
 
# END of job
