
#######################################################
#                                                     #
#                        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   67 (  521),  selected   66 , name one
# Molecule2: number of CA atoms   67 (  519),  selected   66 , 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:    66       2_A - 67_A        0.71     0.71
  LCS_AVERAGE:     98.51

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    66       2_A - 67_A        0.71     0.71
  LCS_AVERAGE:     98.51

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    66       2_A - 67_A        0.71     0.71
  LCS_AVERAGE:     98.51

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   66
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     S     2_A     S     2_A     66   66   66     11   30   60   65   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     P     3_A     P     3_A     66   66   66     26   59   64   65   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     E     4_A     E     4_A     66   66   66     23   59   64   65   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     E     5_A     E     5_A     66   66   66     23   59   64   65   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     Q     6_A     Q     6_A     66   66   66     36   59   64   65   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     K     7_A     K     7_A     66   66   66     20   59   64   65   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     Q     8_A     Q     8_A     66   66   66     23   59   64   65   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     M     9_A     M     9_A     66   66   66     26   59   64   65   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     L    10_A     L    10_A     66   66   66     44   59   64   65   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     G    11_A     G    11_A     66   66   66     20   59   64   65   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     E    12_A     E    12_A     66   66   66     44   59   64   65   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     A    13_A     A    13_A     66   66   66     44   59   64   65   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     I    14_A     I    14_A     66   66   66     44   59   64   65   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     Y    15_A     Y    15_A     66   66   66     44   59   64   65   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     P    16_A     P    16_A     66   66   66     44   59   64   65   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     K    17_A     K    17_A     66   66   66     44   59   64   65   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     V    18_A     V    18_A     66   66   66     44   59   64   65   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     A    19_A     A    19_A     66   66   66     44   59   64   65   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     A    20_A     A    20_A     66   66   66     44   59   64   65   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     S    21_A     S    21_A     66   66   66     44   59   64   65   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     Q    22_A     Q    22_A     66   66   66     44   59   64   65   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     P    23_A     P    23_A     66   66   66     44   59   64   65   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     E    24_A     E    24_A     66   66   66     44   59   64   65   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     L    25_A     L    25_A     66   66   66     44   59   64   65   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     A    26_A     A    26_A     66   66   66     44   59   64   65   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     G    27_A     G    27_A     66   66   66     44   59   64   65   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     K    28_A     K    28_A     66   66   66     44   59   64   65   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     L    29_A     L    29_A     66   66   66     44   59   64   65   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     T    30_A     T    30_A     66   66   66     35   59   64   65   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     G    31_A     G    31_A     66   66   66     44   59   64   65   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     M    32_A     M    32_A     66   66   66     44   59   64   65   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     I    33_A     I    33_A     66   66   66     44   59   64   65   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     L    34_A     L    34_A     66   66   66     44   59   64   65   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     E    35_A     E    35_A     66   66   66     26   59   64   65   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     L    36_A     L    36_A     66   66   66      5   59   64   65   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     P    37_A     P    37_A     66   66   66     44   59   64   65   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     V    38_A     V    38_A     66   66   66     44   59   64   65   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     T    39_A     T    39_A     66   66   66     44   59   64   65   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     E    40_A     E    40_A     66   66   66     44   59   64   65   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     L    41_A     L    41_A     66   66   66     44   59   64   65   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     L    42_A     L    42_A     66   66   66     44   59   64   65   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     H    43_A     H    43_A     66   66   66     44   59   64   65   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     L    44_A     L    44_A     66   66   66     44   59   64   65   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     L    45_A     L    45_A     66   66   66     44   59   64   65   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     E    46_A     E    46_A     66   66   66     44   59   64   65   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     E    47_A     E    47_A     66   66   66     44   59   64   65   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     S    48_A     S    48_A     66   66   66     37   59   64   65   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     E    49_A     E    49_A     66   66   66     32   59   64   65   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     A    50_A     A    50_A     66   66   66     44   59   64   65   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     L    51_A     L    51_A     66   66   66     44   59   64   65   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     D    52_A     D    52_A     66   66   66     44   59   64   65   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     A    53_A     A    53_A     66   66   66     44   59   64   65   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     K    54_A     K    54_A     66   66   66     44   59   64   65   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     V    55_A     V    55_A     66   66   66     44   59   64   65   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     N    56_A     N    56_A     66   66   66     44   59   64   65   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     E    57_A     E    57_A     66   66   66     44   59   64   65   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     A    58_A     A    58_A     66   66   66     44   59   64   65   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     L    59_A     L    59_A     66   66   66     44   59   64   65   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     E    60_A     E    60_A     66   66   66     44   59   64   65   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     V    61_A     V    61_A     66   66   66     44   59   64   65   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     L    62_A     L    62_A     66   66   66     30   59   64   65   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     K    63_A     K    63_A     66   66   66     10   59   64   65   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     E    64_A     E    64_A     66   66   66     38   59   64   65   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     Y    65_A     Y    65_A     66   66   66     44   59   64   65   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     Q    66_A     Q    66_A     66   66   66     10   47   64   65   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     Q    67_A     Q    67_A     66   66   66      4   20   49   65   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66   66 
LCS_AVERAGE  LCS_A:  98.51  (  98.51   98.51   98.51 )

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     44     59     64     65     66     66     66     66     66     66     66     66     66     66     66     66     66     66     66     66 
GDT PERCENT_AT  65.67  88.06  95.52  97.01  98.51  98.51  98.51  98.51  98.51  98.51  98.51  98.51  98.51  98.51  98.51  98.51  98.51  98.51  98.51  98.51
GDT RMS_LOCAL    0.36   0.50   0.61   0.66   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71
GDT RMS_ALL_AT   0.79   0.74   0.72   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71

# Checking swapping
#   possible swapping detected:  E     5_A      E     5_A
#   possible swapping detected:  Y    15_A      Y    15_A
#   possible swapping detected:  E    24_A      E    24_A
#   possible swapping detected:  E    35_A      E    35_A
#   possible swapping detected:  E    40_A      E    40_A
#   possible swapping detected:  E    49_A      E    49_A
#   possible swapping detected:  E    57_A      E    57_A
#   possible swapping detected:  E    64_A      E    64_A
#   possible swapping detected:  Y    65_A      Y    65_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     2_A      S     2_A     2.130     0    0.019   0.059     2.673   73.095   67.778
LGA    P     3_A      P     3_A     0.947     0    0.018   0.039     1.297   88.214   85.306
LGA    E     4_A      E     4_A     1.300     0    0.012   0.690     3.650   81.429   68.995
LGA    E     5_A      E     5_A     1.259     0    0.066   0.918     5.196   85.952   61.640
LGA    Q     6_A      Q     6_A     0.530     0    0.047   0.412     1.222   95.238   94.762
LGA    K     7_A      K     7_A     0.672     0    0.032   0.534     1.532   92.857   86.561
LGA    Q     8_A      Q     8_A     1.089     0    0.063   0.144     1.602   88.214   81.587
LGA    M     9_A      M     9_A     0.831     0    0.027   0.818     1.840   90.476   86.012
LGA    L    10_A      L    10_A     0.386     0    0.055   0.140     1.492  100.000   92.976
LGA    G    11_A      G    11_A     0.582     0    0.046   0.046     0.582   97.619   97.619
LGA    E    12_A      E    12_A     0.298     0    0.018   0.826     3.561  100.000   86.614
LGA    A    13_A      A    13_A     0.090     0    0.023   0.028     0.198  100.000  100.000
LGA    I    14_A      I    14_A     0.287     0    0.035   0.104     0.741  100.000   97.619
LGA    Y    15_A      Y    15_A     0.352     0    0.024   0.194     0.607   97.619   97.619
LGA    P    16_A      P    16_A     0.461     0    0.033   0.242     0.934   97.619   97.279
LGA    K    17_A      K    17_A     0.441     0    0.012   0.950     3.469   97.619   90.370
LGA    V    18_A      V    18_A     0.440     0    0.021   0.035     0.712   95.238   97.279
LGA    A    19_A      A    19_A     0.619     0    0.043   0.047     0.751   90.476   90.476
LGA    A    20_A      A    20_A     0.601     0    0.084   0.102     0.801   90.476   90.476
LGA    S    21_A      S    21_A     0.577     0    0.121   0.636     1.313   95.238   90.635
LGA    Q    22_A      Q    22_A     0.416     0    0.069   0.083     1.342  100.000   91.693
LGA    P    23_A      P    23_A     0.545     0    0.065   0.142     0.802   90.476   90.476
LGA    E    24_A      E    24_A     0.587     0    0.033   0.730     2.053   92.857   86.667
LGA    L    25_A      L    25_A     0.139     0    0.047   0.078     0.742  100.000   97.619
LGA    A    26_A      A    26_A     0.420     0    0.023   0.021     0.486  100.000  100.000
LGA    G    27_A      G    27_A     0.395     0    0.040   0.040     0.497  100.000  100.000
LGA    K    28_A      K    28_A     0.188     0    0.024   0.081     0.662  100.000   97.884
LGA    L    29_A      L    29_A     0.363     0    0.012   0.056     0.565  100.000   98.810
LGA    T    30_A      T    30_A     0.613     0    0.051   0.096     1.009   90.595   90.544
LGA    G    31_A      G    31_A     0.550     0    0.030   0.030     0.569   92.857   92.857
LGA    M    32_A      M    32_A     0.170     0    0.041   0.101     0.466  100.000  100.000
LGA    I    33_A      I    33_A     0.411     0    0.031   0.799     2.361   97.619   86.607
LGA    L    34_A      L    34_A     0.493     0    0.077   0.106     0.649   97.619   97.619
LGA    E    35_A      E    35_A     0.829     0    0.030   1.038     4.158   90.476   69.312
LGA    L    36_A      L    36_A     1.041     0    0.033   0.176     2.211   88.214   79.583
LGA    P    37_A      P    37_A     0.868     0    0.109   0.333     1.479   90.476   86.599
LGA    V    38_A      V    38_A     0.810     0    0.016   0.051     1.125   90.476   89.184
LGA    T    39_A      T    39_A     0.716     0    0.025   0.035     0.904   90.476   90.476
LGA    E    40_A      E    40_A     0.573     0    0.057   1.068     4.087   95.238   76.508
LGA    L    41_A      L    41_A     0.393     0    0.036   0.089     0.835   97.619   96.429
LGA    L    42_A      L    42_A     0.389     0    0.049   0.048     0.713  100.000   95.238
LGA    H    43_A      H    43_A     0.297     0    0.013   1.155     2.581  100.000   88.524
LGA    L    44_A      L    44_A     0.309     0    0.024   0.097     0.723  100.000   96.429
LGA    L    45_A      L    45_A     0.249     0    0.029   0.070     0.373  100.000  100.000
LGA    E    46_A      E    46_A     0.298     0    0.012   0.286     1.408   97.619   93.704
LGA    E    47_A      E    47_A     0.467     0    0.034   0.614     2.401  100.000   84.180
LGA    S    48_A      S    48_A     0.521     0    0.075   0.658     2.015   90.476   86.190
LGA    E    49_A      E    49_A     0.631     0    0.092   0.773     3.209   95.238   75.397
LGA    A    50_A      A    50_A     0.412     0    0.009   0.012     0.483  100.000  100.000
LGA    L    51_A      L    51_A     0.346     0    0.016   0.068     0.398  100.000  100.000
LGA    D    52_A      D    52_A     0.305     0    0.022   0.056     0.386  100.000  100.000
LGA    A    53_A      A    53_A     0.352     0    0.028   0.030     0.439  100.000  100.000
LGA    K    54_A      K    54_A     0.297     0    0.024   0.553     1.710  100.000   93.968
LGA    V    55_A      V    55_A     0.158     0    0.025   0.045     0.297  100.000  100.000
LGA    N    56_A      N    56_A     0.256     0    0.042   0.128     0.788  100.000   97.619
LGA    E    57_A      E    57_A     0.052     0    0.016   0.182     1.115  100.000   94.762
LGA    A    58_A      A    58_A     0.441     0    0.030   0.037     0.505  100.000   98.095
LGA    L    59_A      L    59_A     0.470     0    0.023   1.306     2.973   95.238   83.512
LGA    E    60_A      E    60_A     0.417     0    0.097   1.089     4.826   95.238   76.667
LGA    V    61_A      V    61_A     0.462     0    0.027   0.042     0.712   95.238   94.558
LGA    L    62_A      L    62_A     0.961     0    0.032   1.389     3.238   88.214   78.810
LGA    K    63_A      K    63_A     1.075     0    0.021   0.217     1.641   83.690   80.529
LGA    E    64_A      E    64_A     0.631     0    0.024   0.923     3.256   90.476   74.868
LGA    Y    65_A      Y    65_A     0.732     0    0.045   0.211     2.450   90.476   81.071
LGA    Q    66_A      Q    66_A     1.667     0    0.065   0.879     3.410   72.976   62.593
LGA    Q    67_A      Q    67_A     2.035     0    0.399   0.565     5.311   68.810   54.339

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       66     264    264  100.00     511    511  100.00                67
SUMMARY(RMSD_GDC):     0.709          0.677                  1.288           92.926   87.635

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   67   67    4.0     66    0.71    95.522    97.355     8.154

LGA_LOCAL      RMSD:   0.709  Number of atoms:   66  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.709  Number of assigned atoms:   66 
Std_ASGN_ATOMS RMSD:   0.709  Standard rmsd on all 66 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.826029 * X  +  -0.454213 * Y  +   0.333715 * Z  + -16.033031
  Y_new =  -0.510878 * X  +   0.353285 * Y  +  -0.783705 * Z  +  11.210477
  Z_new =   0.238073 * X  +  -0.817851 * Y  +  -0.523872 * Z  + -23.355589 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.587699 -0.240381 -2.140497   [DEG: -148.2643  -13.7728 -122.6415 ]
ZXZ:  0.402562  2.122186  2.858325   [DEG:   23.0651  121.5923  163.7700 ]
 
# END of job
