
#######################################################
#                                                     #
#                        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   63 (  513),  selected   63 , name one
# Molecule2: number of CA atoms   83 (  673),  selected   63 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:B  -ch2:A  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    63      12_A - 74_A        3.39     3.39
  LCS_AVERAGE:     75.90

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    32      12_A - 43_A        1.96     3.77
  LCS_AVERAGE:     32.78

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    25      15_A - 39_A        1.00     4.07
  LCS_AVERAGE:     23.60

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   63
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     R    12_B     R    12_A      3   32   63      2    3    3    5   30   42   50   51   54   56   56   57   60   61   63   63   63   63   63   63 
LCS_GDT     T    13_B     T    13_A     20   32   63     12   25   41   47   50   51   53   53   54   56   58   62   62   62   63   63   63   63   63   63 
LCS_GDT     W    14_B     W    14_A     23   32   63     14   32   41   47   50   51   53   53   54   56   58   62   62   62   63   63   63   63   63   63 
LCS_GDT     S    15_B     S    15_A     25   32   63     14   28   38   47   50   51   53   53   54   56   58   62   62   62   63   63   63   63   63   63 
LCS_GDT     K    16_B     K    16_A     25   32   63     14   25   36   47   50   51   53   53   54   56   58   62   62   62   63   63   63   63   63   63 
LCS_GDT     E    17_B     E    17_A     25   32   63     14   22   36   46   50   51   53   53   54   56   58   62   62   62   63   63   63   63   63   63 
LCS_GDT     E    18_B     E    18_A     25   32   63     14   27   38   47   50   51   53   53   54   56   58   62   62   62   63   63   63   63   63   63 
LCS_GDT     E    19_B     E    19_A     25   32   63     14   32   41   47   50   51   53   53   54   56   58   62   62   62   63   63   63   63   63   63 
LCS_GDT     E    20_B     E    20_A     25   32   63     14   28   38   47   50   51   53   53   54   56   58   62   62   62   63   63   63   63   63   63 
LCS_GDT     A    21_B     A    21_A     25   32   63     14   28   40   47   50   51   53   53   54   56   58   62   62   62   63   63   63   63   63   63 
LCS_GDT     L    22_B     L    22_A     25   32   63     15   32   41   47   50   51   53   53   54   56   58   62   62   62   63   63   63   63   63   63 
LCS_GDT     V    23_B     V    23_A     25   32   63     14   32   41   47   50   51   53   53   54   56   58   62   62   62   63   63   63   63   63   63 
LCS_GDT     E    24_B     E    24_A     25   32   63     14   32   41   47   50   51   53   53   54   56   58   62   62   62   63   63   63   63   63   63 
LCS_GDT     G    25_B     G    25_A     25   32   63     14   32   41   47   50   51   53   53   54   56   58   62   62   62   63   63   63   63   63   63 
LCS_GDT     L    26_B     L    26_A     25   32   63     15   32   41   47   50   51   53   53   54   56   58   62   62   62   63   63   63   63   63   63 
LCS_GDT     K    27_B     K    27_A     25   32   63     15   32   41   47   50   51   53   53   54   56   58   62   62   62   63   63   63   63   63   63 
LCS_GDT     E    28_B     E    28_A     25   32   63     15   32   41   47   50   51   53   53   54   56   58   62   62   62   63   63   63   63   63   63 
LCS_GDT     V    29_B     V    29_A     25   32   63     14   32   41   47   50   51   53   53   54   56   58   62   62   62   63   63   63   63   63   63 
LCS_GDT     G    30_B     G    30_A     25   32   63      4   13   26   45   50   51   53   53   54   56   58   62   62   62   63   63   63   63   63   63 
LCS_GDT     P    31_B     P    31_A     25   32   63     10   16   33   47   50   51   53   53   54   56   58   62   62   62   63   63   63   63   63   63 
LCS_GDT     S    32_B     S    32_A     25   32   63     10   32   41   47   50   51   53   53   54   56   58   62   62   62   63   63   63   63   63   63 
LCS_GDT     W    33_B     W    33_A     25   32   63     10   32   41   47   50   51   53   53   54   56   58   62   62   62   63   63   63   63   63   63 
LCS_GDT     S    34_B     S    34_A     25   32   63     10   32   41   47   50   51   53   53   54   56   58   62   62   62   63   63   63   63   63   63 
LCS_GDT     K    35_B     K    35_A     25   32   63     15   32   41   47   50   51   53   53   54   56   58   62   62   62   63   63   63   63   63   63 
LCS_GDT     I    36_B     I    36_A     25   32   63     15   32   41   47   50   51   53   53   54   56   58   62   62   62   63   63   63   63   63   63 
LCS_GDT     L    37_B     L    37_A     25   32   63     10   16   41   47   50   51   53   53   54   56   58   62   62   62   63   63   63   63   63   63 
LCS_GDT     D    38_B     D    38_A     25   32   63     10   16   41   47   50   51   53   53   54   56   58   62   62   62   63   63   63   63   63   63 
LCS_GDT     L    39_B     L    39_A     25   32   63     10   29   41   47   50   51   53   53   54   56   58   62   62   62   63   63   63   63   63   63 
LCS_GDT     Y    40_B     Y    40_A     23   32   63     10   16   41   47   50   51   53   53   54   56   58   62   62   62   63   63   63   63   63   63 
LCS_GDT     G    41_B     G    41_A      3   32   63      3   18   22   34   41   51   53   53   54   56   58   62   62   62   63   63   63   63   63   63 
LCS_GDT     P    42_B     P    42_A      3   32   63      3    3   24   34   47   51   53   53   54   56   58   62   62   62   63   63   63   63   63   63 
LCS_GDT     G    43_B     G    43_A      3   32   63      3    3    8   13   20   33   46   53   54   56   58   62   62   62   63   63   63   63   63   63 
LCS_GDT     G    44_B     G    44_A      6    8   63      4    6    6    8   10   19   28   30   33   39   49   62   62   62   63   63   63   63   63   63 
LCS_GDT     K    45_B     K    45_A      6    8   63      5    6    8   12   18   22   28   30   36   45   56   62   62   62   63   63   63   63   63   63 
LCS_GDT     I    46_B     I    46_A      6    8   63      5    6    6    7    8   12   24   32   45   53   58   62   62   62   63   63   63   63   63   63 
LCS_GDT     T    47_B     T    47_A      6    8   63      5    6    6    7   14   22   28   33   45   54   58   62   62   62   63   63   63   63   63   63 
LCS_GDT     E    48_B     E    48_A      6    8   63      5    6    6    7    8   12   28   30   36   49   57   62   62   62   63   63   63   63   63   63 
LCS_GDT     N    49_B     N    49_A      6   25   63      5    6    6    8   10   15   28   30   36   45   57   62   62   62   63   63   63   63   63   63 
LCS_GDT     L    50_B     L    50_A      4   25   63      3    3    5    8   10   15   28   30   36   52   58   62   62   62   63   63   63   63   63   63 
LCS_GDT     K    51_B     K    51_A      4   25   63      3    3    5   20   26   48   53   53   54   56   58   62   62   62   63   63   63   63   63   63 
LCS_GDT     N    52_B     N    52_A     22   25   63      8   25   41   47   50   51   53   53   54   56   58   62   62   62   63   63   63   63   63   63 
LCS_GDT     R    53_B     R    53_A     22   25   63     15   32   41   47   50   51   53   53   54   56   58   62   62   62   63   63   63   63   63   63 
LCS_GDT     T    54_B     T    54_A     22   25   63     15   32   41   47   50   51   53   53   54   56   58   62   62   62   63   63   63   63   63   63 
LCS_GDT     Q    55_B     Q    55_A     22   25   63     15   32   41   47   50   51   53   53   54   56   58   62   62   62   63   63   63   63   63   63 
LCS_GDT     V    56_B     V    56_A     22   25   63     15   32   41   47   50   51   53   53   54   56   58   62   62   62   63   63   63   63   63   63 
LCS_GDT     Q    57_B     Q    57_A     22   25   63     15   32   41   47   50   51   53   53   54   56   58   62   62   62   63   63   63   63   63   63 
LCS_GDT     L    58_B     L    58_A     22   25   63     15   32   41   47   50   51   53   53   54   56   58   62   62   62   63   63   63   63   63   63 
LCS_GDT     K    59_B     K    59_A     22   25   63     15   32   41   47   50   51   53   53   54   56   58   62   62   62   63   63   63   63   63   63 
LCS_GDT     D    60_B     D    60_A     22   25   63     15   32   41   47   50   51   53   53   54   56   58   62   62   62   63   63   63   63   63   63 
LCS_GDT     K    61_B     K    61_A     22   25   63     15   32   41   47   50   51   53   53   54   56   58   62   62   62   63   63   63   63   63   63 
LCS_GDT     A    62_B     A    62_A     22   25   63     15   32   41   47   50   51   53   53   54   56   58   62   62   62   63   63   63   63   63   63 
LCS_GDT     R    63_B     R    63_A     22   25   63     15   32   41   47   50   51   53   53   54   56   58   62   62   62   63   63   63   63   63   63 
LCS_GDT     N    64_B     N    64_A     22   25   63     14   32   41   47   50   51   53   53   54   56   58   62   62   62   63   63   63   63   63   63 
LCS_GDT     W    65_B     W    65_A     22   25   63     14   32   41   47   50   51   53   53   54   56   58   62   62   62   63   63   63   63   63   63 
LCS_GDT     K    66_B     K    66_A     22   25   63     15   32   41   47   50   51   53   53   54   56   58   62   62   62   63   63   63   63   63   63 
LCS_GDT     L    67_B     L    67_A     22   25   63     14   32   41   47   50   51   53   53   54   56   58   62   62   62   63   63   63   63   63   63 
LCS_GDT     Q    68_B     Q    68_A     22   25   63     14   32   41   47   50   51   53   53   54   56   58   62   62   62   63   63   63   63   63   63 
LCS_GDT     Y    69_B     Y    69_A     22   25   63     14   32   41   47   50   51   53   53   54   56   58   62   62   62   63   63   63   63   63   63 
LCS_GDT     L    70_B     L    70_A     22   25   63     14   31   41   47   50   51   53   53   54   56   58   62   62   62   63   63   63   63   63   63 
LCS_GDT     K    71_B     K    71_A     22   25   63     14   32   41   47   50   51   53   53   54   56   58   62   62   62   63   63   63   63   63   63 
LCS_GDT     S    72_B     S    72_A     22   25   63     15   32   41   47   50   51   53   53   54   56   58   62   62   62   63   63   63   63   63   63 
LCS_GDT     G    73_B     G    73_A     22   25   63     12   20   40   46   50   51   53   53   54   56   58   62   62   62   63   63   63   63   63   63 
LCS_GDT     K    74_B     K    74_A      3   25   63      3    3    3    3    3    4   27   38   52   56   58   62   62   62   63   63   63   63   63   63 
LCS_AVERAGE  LCS_A:  44.09  (  23.60   32.78   75.90 )

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     15     32     41     47     50     51     53     53     54     56     58     62     62     62     63     63     63     63     63     63 
GDT PERCENT_AT  18.07  38.55  49.40  56.63  60.24  61.45  63.86  63.86  65.06  67.47  69.88  74.70  74.70  74.70  75.90  75.90  75.90  75.90  75.90  75.90
GDT RMS_LOCAL    0.33   0.67   0.85   1.07   1.19   1.30   1.51   1.51   1.68   2.00   2.64   3.34   3.34   3.34   3.39   3.39   3.39   3.39   3.39   3.39
GDT RMS_ALL_AT   4.17   4.04   4.09   3.98   3.99   3.92   3.84   3.84   3.82   3.73   3.51   3.40   3.40   3.40   3.39   3.39   3.39   3.39   3.39   3.39

# Checking swapping
#   possible swapping detected:  E    28_B      E    28_A
#   possible swapping detected:  Y    40_B      Y    40_A
#   possible swapping detected:  E    48_B      E    48_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    R    12_B      R    12_A     5.725     0    0.579   1.554     9.472   26.071   13.420
LGA    T    13_B      T    13_A     1.856     0    0.617   0.909     5.612   79.286   59.864
LGA    W    14_B      W    14_A     0.598     0    0.140   0.257     1.062   88.333   89.864
LGA    S    15_B      S    15_A     1.427     0    0.039   0.055     1.795   81.429   78.571
LGA    K    16_B      K    16_A     1.879     0    0.021   1.284     5.759   72.857   58.995
LGA    E    17_B      E    17_A     2.256     0    0.049   0.760     3.091   68.810   61.534
LGA    E    18_B      E    18_A     1.300     0    0.000   0.610     1.955   83.810   80.582
LGA    E    19_B      E    19_A     0.745     0    0.034   0.309     1.470   90.476   86.455
LGA    E    20_B      E    20_A     1.446     0    0.124   0.807     3.740   81.429   66.561
LGA    A    21_B      A    21_A     1.081     0    0.035   0.037     1.381   88.333   86.952
LGA    L    22_B      L    22_A     0.301     0    0.063   0.062     0.999   97.619   95.238
LGA    V    23_B      V    23_A     0.978     0    0.000   0.047     1.799   90.476   84.150
LGA    E    24_B      E    24_A     0.752     0    0.082   0.964     3.123   92.857   83.069
LGA    G    25_B      G    25_A     0.512     0    0.000   0.000     0.688   92.857   92.857
LGA    L    26_B      L    26_A     0.782     0    0.037   0.922     2.335   88.214   81.726
LGA    K    27_B      K    27_A     0.728     0    0.089   0.917     4.422   92.857   79.101
LGA    E    28_B      E    28_A     0.425     0    0.000   0.793     3.263   95.238   76.984
LGA    V    29_B      V    29_A     0.845     0    0.032   0.081     1.643   83.810   85.374
LGA    G    30_B      G    30_A     2.359     0    0.462   0.462     4.107   57.976   57.976
LGA    P    31_B      P    31_A     1.961     0    0.031   0.453     2.836   72.857   68.299
LGA    S    32_B      S    32_A     1.097     0    0.043   0.193     1.251   83.690   85.952
LGA    W    33_B      W    33_A     1.102     0    0.019   1.236     4.824   81.429   67.789
LGA    S    34_B      S    34_A     1.418     0    0.046   0.699     3.963   81.429   73.651
LGA    K    35_B      K    35_A     0.514     0    0.049   0.655     2.700   90.476   84.868
LGA    I    36_B      I    36_A     0.699     0    0.047   0.094     1.189   85.952   89.405
LGA    L    37_B      L    37_A     1.766     0    0.070   1.409     4.631   75.000   68.929
LGA    D    38_B      D    38_A     1.889     0    0.082   0.854     2.337   70.833   75.119
LGA    L    39_B      L    39_A     1.649     0    0.194   0.229     2.614   77.143   70.060
LGA    Y    40_B      Y    40_A     1.746     0    0.700   0.886    10.118   77.619   38.611
LGA    G    41_B      G    41_A     3.732     0    0.351   0.351     3.810   50.357   50.357
LGA    P    42_B      P    42_A     3.582     0    0.619   0.533     7.406   32.381   37.143
LGA    G    43_B      G    43_A     7.014     0    0.581   0.581    10.222    9.762    9.762
LGA    G    44_B      G    44_A    10.973     0    0.662   0.662    11.810    0.357    0.357
LGA    K    45_B      K    45_A    11.508     0    0.057   0.595    13.413    0.000    0.000
LGA    I    46_B      I    46_A     9.722     0    0.111   0.703    10.946    0.357    1.369
LGA    T    47_B      T    47_A     9.644     0    0.180   1.197    11.913    0.714    1.293
LGA    E    48_B      E    48_A     9.912     0    0.376   0.991    16.236    1.786    0.794
LGA    N    49_B      N    49_A     9.727     0    0.187   0.384    13.282    1.667    0.833
LGA    L    50_B      L    50_A     7.753     0    0.506   0.797    11.902   11.071    6.488
LGA    K    51_B      K    51_A     4.393     0    0.114   0.922     5.572   47.024   36.085
LGA    N    52_B      N    52_A     1.839     0    0.597   1.117     7.523   77.143   49.464
LGA    R    53_B      R    53_A     1.112     0    0.090   0.934     4.066   83.690   76.667
LGA    T    54_B      T    54_A     0.629     0    0.035   0.070     0.711   90.476   90.476
LGA    Q    55_B      Q    55_A     0.497     0    0.004   1.239     4.735   95.238   78.677
LGA    V    56_B      V    56_A     0.617     0    0.096   0.092     0.621   90.476   90.476
LGA    Q    57_B      Q    57_A     0.668     0    0.033   0.180     1.236   90.476   89.471
LGA    L    58_B      L    58_A     0.478     0    0.036   0.090     0.925  100.000   96.429
LGA    K    59_B      K    59_A     0.444     0    0.061   1.233     7.321  100.000   68.677
LGA    D    60_B      D    60_A     0.475     0    0.105   0.204     0.914  100.000   97.619
LGA    K    61_B      K    61_A     0.608     0    0.000   0.530     1.791   90.476   85.556
LGA    A    62_B      A    62_A     0.463     0    0.000   0.022     0.520  100.000   98.095
LGA    R    63_B      R    63_A     0.487     0    0.040   1.163     7.498   95.238   61.039
LGA    N    64_B      N    64_A     0.911     0    0.030   0.211     1.969   90.476   83.810
LGA    W    65_B      W    65_A     0.994     0    0.043   1.249     6.585   90.476   62.619
LGA    K    66_B      K    66_A     0.701     0    0.000   0.824     6.116   92.857   66.720
LGA    L    67_B      L    67_A     0.545     0    0.014   0.030     1.508   92.857   87.202
LGA    Q    68_B      Q    68_A     1.103     0    0.056   0.093     3.337   83.690   70.741
LGA    Y    69_B      Y    69_A     1.538     0    0.035   1.486     4.774   77.143   68.690
LGA    L    70_B      L    70_A     1.332     0    0.057   0.133     1.822   81.429   78.214
LGA    K    71_B      K    71_A     0.752     0    0.032   1.005     4.124   90.476   79.048
LGA    S    72_B      S    72_A     1.443     0    0.070   0.583     2.058   75.119   74.365
LGA    G    73_B      G    73_A     2.488     0    0.162   0.162     2.488   68.810   68.810
LGA    K    74_B      K    74_A     5.625     0    0.024   1.246    12.141   20.833   10.688

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       63     252    252  100.00     513    513  100.00                83
SUMMARY(RMSD_GDC):     3.394          3.407                  3.984           54.000   48.434

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63   83    4.0     53    1.51    58.735    54.364     3.286

LGA_LOCAL      RMSD:   1.513  Number of atoms:   53  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   3.839  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:   3.394  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.393425 * X  +  -0.490822 * Y  +  -0.777374 * Z  + 453.517853
  Y_new =   0.918710 * X  +  -0.178169 * Y  +  -0.352460 * Z  + -116.276627
  Z_new =   0.034491 * X  +  -0.852848 * Y  +   0.521019 * Z  +  29.086779 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.975405 -0.034498 -1.022388   [DEG:  113.1824   -1.9766  -58.5785 ]
ZXZ: -1.145120  1.022751  3.101172   [DEG:  -65.6105   58.5993  177.6841 ]
 
# END of job
