
#######################################################
#                                                     #
#                        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   97 (  681),  selected   64 , name one
# Molecule2: number of CA atoms   64 (  433),  selected   64 , 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:    64      22_A - 85_A        4.03     4.03
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    24      44_A - 67_A        1.95     6.21
  LCS_AVERAGE:     30.52

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17      47_A - 63_A        0.92     7.51
  LONGEST_CONTINUOUS_SEGMENT:    17      48_A - 64_A        0.98     8.01
  LONGEST_CONTINUOUS_SEGMENT:    17      69_A - 85_A        0.83     4.80
  LCS_AVERAGE:     21.39

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   64
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     A    22_A     A    22_A      3    3   64      3    3    7    8   10   10   15   21   25   34   39   58   60   61   63   63   63   63   64   64 
LCS_GDT     D    23_A     D    23_A      3    4   64      3    3    5    8   10   23   25   36   48   58   59   60   60   61   63   63   63   63   64   64 
LCS_GDT     G    24_A     G    24_A      3   16   64      3    5   14   23   33   43   50   53   57   58   59   60   60   61   63   63   63   63   64   64 
LCS_GDT     D    25_A     D    25_A     14   16   64      4    4   13   22   39   41   46   53   55   57   59   60   60   61   63   63   63   63   64   64 
LCS_GDT     G    26_A     G    26_A     14   16   64     10   26   29   31   39   43   50   53   57   58   59   60   60   61   63   63   63   63   64   64 
LCS_GDT     Q    27_A     Q    27_A     14   16   64     14   26   29   31   39   43   50   53   57   58   59   60   60   61   63   63   63   63   64   64 
LCS_GDT     G    28_A     G    28_A     14   16   64     10   26   29   31   39   43   50   53   57   58   59   60   60   61   63   63   63   63   64   64 
LCS_GDT     L    29_A     L    29_A     14   16   64     13   26   29   31   39   43   50   53   57   58   59   60   60   61   63   63   63   63   64   64 
LCS_GDT     Y    30_A     Y    30_A     14   16   64     14   26   29   31   39   43   50   53   57   58   59   60   60   61   63   63   63   63   64   64 
LCS_GDT     A    31_A     A    31_A     14   16   64     14   26   29   31   39   43   50   53   57   58   59   60   60   61   63   63   63   63   64   64 
LCS_GDT     A    32_A     A    32_A     14   16   64     14   26   29   31   39   43   50   53   57   58   59   60   60   61   63   63   63   63   64   64 
LCS_GDT     N    33_A     N    33_A     14   16   64     14   26   29   31   39   43   50   53   57   58   59   60   60   61   63   63   63   63   64   64 
LCS_GDT     C    34_A     C    34_A     14   16   64     13   26   29   31   39   43   50   53   57   58   59   60   60   61   63   63   63   63   64   64 
LCS_GDT     A    35_A     A    35_A     14   16   64      4   26   29   31   39   43   50   53   56   58   59   60   60   61   63   63   63   63   64   64 
LCS_GDT     A    36_A     A    36_A     14   16   64      4   26   29   31   39   43   50   53   57   58   59   60   60   61   63   63   63   63   64   64 
LCS_GDT     C    37_A     C    37_A     14   16   64     14   26   29   31   39   43   50   53   57   58   59   60   60   61   63   63   63   63   64   64 
LCS_GDT     H    38_A     H    38_A     14   16   64      3   26   29   31   39   43   50   53   57   58   59   60   60   61   63   63   63   63   64   64 
LCS_GDT     G    39_A     G    39_A     14   16   64      1   16   27   31   39   43   50   53   57   58   59   60   60   61   63   63   63   63   64   64 
LCS_GDT     A    40_A     A    40_A      4    5   64      3    4    4   11   14   20   36   44   57   58   59   60   60   61   63   63   63   63   64   64 
LCS_GDT     L    41_A     L    41_A      4    5   64      3    4    4    5    5    7    7    9   21   25   31   44   56   61   63   63   63   63   64   64 
LCS_GDT     A    42_A     A    42_A      4    5   64      3    4    4    5    6    7    7    9   11   19   30   31   37   46   51   56   61   62   64   64 
LCS_GDT     T    43_A     T    43_A      4    6   64      3    4    4    5    8   12   17   21   25   31   36   49   57   61   63   63   63   63   64   64 
LCS_GDT     S    44_A     S    44_A      4   24   64      3    4    7   14   20   22   29   42   57   58   59   60   60   61   63   63   63   63   64   64 
LCS_GDT     E    45_A     E    45_A      9   24   64      3   16   27   31   39   43   50   53   57   58   59   60   60   61   63   63   63   63   64   64 
LCS_GDT     K    46_A     K    46_A     16   24   64      3    8   13   19   33   43   50   53   57   58   59   60   60   61   63   63   63   63   64   64 
LCS_GDT     K    47_A     K    47_A     17   24   64      3   12   18   19   21   23   38   51   57   58   59   60   60   61   63   63   63   63   64   64 
LCS_GDT     G    48_A     G    48_A     17   24   64      3   12   18   19   21   23   27   49   57   58   59   60   60   61   63   63   63   63   64   64 
LCS_GDT     T    49_A     T    49_A     17   24   64      7   14   18   19   21   28   46   53   57   58   59   60   60   61   63   63   63   63   64   64 
LCS_GDT     T    50_A     T    50_A     17   24   64      9   14   18   19   21   41   50   53   57   58   59   60   60   61   63   63   63   63   64   64 
LCS_GDT     L    51_A     L    51_A     17   24   64      7   14   18   19   21   40   50   53   57   58   59   60   60   61   63   63   63   63   64   64 
LCS_GDT     A    52_A     A    52_A     17   24   64      7   14   18   28   39   43   50   53   57   58   59   60   60   61   63   63   63   63   64   64 
LCS_GDT     R    53_A     R    53_A     17   24   64      9   14   18   28   39   43   50   53   57   58   59   60   60   61   63   63   63   63   64   64 
LCS_GDT     L    54_A     L    54_A     17   24   64      9   14   18   22   38   43   50   53   57   58   59   60   60   61   63   63   63   63   64   64 
LCS_GDT     Q    55_A     Q    55_A     17   24   64      9   14   18   19   38   43   50   53   57   58   59   60   60   61   63   63   63   63   64   64 
LCS_GDT     S    56_A     S    56_A     17   24   64      9   14   18   28   39   43   50   53   57   58   59   60   60   61   63   63   63   63   64   64 
LCS_GDT     A    57_A     A    57_A     17   24   64      9   14   18   28   39   43   50   53   57   58   59   60   60   61   63   63   63   63   64   64 
LCS_GDT     V    58_A     V    58_A     17   24   64      9   14   18   19   34   41   50   53   57   58   59   60   60   61   63   63   63   63   64   64 
LCS_GDT     S    59_A     S    59_A     17   24   64      9   14   18   19   21   31   45   53   57   58   59   60   60   61   63   63   63   63   64   64 
LCS_GDT     A    60_A     A    60_A     17   24   64      9   14   18   19   24   39   50   53   57   58   59   60   60   61   63   63   63   63   64   64 
LCS_GDT     N    61_A     N    61_A     17   24   64      4   14   18   28   38   43   50   53   57   58   59   60   60   61   63   63   63   63   64   64 
LCS_GDT     A    62_A     A    62_A     17   24   64      6   15   24   30   39   43   50   53   57   58   59   60   60   61   63   63   63   63   64   64 
LCS_GDT     G    63_A     G    63_A     17   24   64      3    6   20   29   39   43   50   53   57   58   59   60   60   61   63   63   63   63   64   64 
LCS_GDT     G    64_A     G    64_A     17   24   64      3    4   16   29   39   43   50   53   57   58   59   60   60   61   63   63   63   63   64   64 
LCS_GDT     M    65_A     M    65_A      6   24   64      3    4   17   29   39   43   50   53   57   58   59   60   60   61   63   63   63   63   64   64 
LCS_GDT     G    66_A     G    66_A      3   24   64      0   14   18   19   34   41   50   53   57   58   59   60   60   61   63   63   63   63   64   64 
LCS_GDT     F    67_A     F    67_A      4   24   64      3    3    4   15   20   25   45   53   57   58   59   60   60   61   63   63   63   63   64   64 
LCS_GDT     L    68_A     L    68_A      4   22   64      3    4    4    6   25   35   46   53   57   58   59   60   60   61   63   63   63   63   64   64 
LCS_GDT     S    69_A     S    69_A     17   22   64     10   26   29   31   35   41   50   53   57   58   59   60   60   61   63   63   63   63   64   64 
LCS_GDT     S    70_A     S    70_A     17   22   64      3    6   16   30   35   41   50   53   57   58   59   60   60   61   63   63   63   63   64   64 
LCS_GDT     L    71_A     L    71_A     17   22   64      9   26   29   31   39   43   50   53   57   58   59   60   60   61   63   63   63   63   64   64 
LCS_GDT     T    72_A     T    72_A     17   22   64     13   26   29   31   39   43   50   53   57   58   59   60   60   61   63   63   63   63   64   64 
LCS_GDT     S    73_A     S    73_A     17   22   64     14   26   29   31   39   43   50   53   57   58   59   60   60   61   63   63   63   63   64   64 
LCS_GDT     A    74_A     A    74_A     17   22   64     14   26   29   31   39   43   50   53   57   58   59   60   60   61   63   63   63   63   64   64 
LCS_GDT     Q    75_A     Q    75_A     17   22   64     14   26   29   31   39   43   50   53   57   58   59   60   60   61   63   63   63   63   64   64 
LCS_GDT     L    76_A     L    76_A     17   22   64     11   26   29   31   39   43   50   53   57   58   59   60   60   61   63   63   63   63   64   64 
LCS_GDT     Q    77_A     Q    77_A     17   22   64     10   26   29   31   39   43   50   53   57   58   59   60   60   61   63   63   63   63   64   64 
LCS_GDT     A    78_A     A    78_A     17   22   64     14   26   29   31   39   43   50   53   57   58   59   60   60   61   63   63   63   63   64   64 
LCS_GDT     I    79_A     I    79_A     17   22   64     14   26   29   31   39   43   50   53   57   58   59   60   60   61   63   63   63   63   64   64 
LCS_GDT     V    80_A     V    80_A     17   22   64     14   26   29   31   39   43   50   53   57   58   59   60   60   61   63   63   63   63   64   64 
LCS_GDT     D    81_A     D    81_A     17   22   64     14   26   29   31   39   43   50   53   57   58   59   60   60   61   63   63   63   63   64   64 
LCS_GDT     V    82_A     V    82_A     17   22   64     14   26   29   31   39   43   50   53   57   58   59   60   60   61   63   63   63   63   64   64 
LCS_GDT     L    83_A     L    83_A     17   22   64     14   26   29   31   39   43   50   53   57   58   59   60   60   61   63   63   63   63   64   64 
LCS_GDT     A    84_A     A    84_A     17   19   64      8   26   29   31   39   43   50   53   57   58   59   60   60   61   63   63   63   63   64   64 
LCS_GDT     V    85_A     V    85_A     17   19   64     14   26   29   31   39   43   50   53   57   58   59   60   60   61   63   63   63   63   64   64 
LCS_AVERAGE  LCS_A:  50.63  (  21.39   30.52  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     14     26     29     31     39     43     50     53     57     58     59     60     60     61     63     63     63     63     64     64 
GDT PERCENT_AT  21.88  40.62  45.31  48.44  60.94  67.19  78.12  82.81  89.06  90.62  92.19  93.75  93.75  95.31  98.44  98.44  98.44  98.44 100.00 100.00
GDT RMS_LOCAL    0.36   0.53   0.63   0.83   1.60   1.90   2.22   2.33   2.93   2.94   2.96   3.09   3.09   3.26   3.71   3.71   3.71   3.71   4.03   4.03
GDT RMS_ALL_AT   4.84   4.85   4.85   4.76   4.60   4.46   4.45   4.47   4.17   4.17   4.19   4.16   4.16   4.14   4.05   4.05   4.05   4.05   4.03   4.03

# Checking swapping
#   possible swapping detected:  D    23_A      D    23_A
#   possible swapping detected:  D    25_A      D    25_A
#   possible swapping detected:  Y    30_A      Y    30_A
#   possible swapping detected:  F    67_A      F    67_A
#   possible swapping detected:  D    81_A      D    81_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A    22_A      A    22_A    10.093     0    0.610   0.564    10.350    1.071    1.143
LGA    D    23_A      D    23_A     8.653     0    0.124   1.060    13.214    9.762    4.940
LGA    G    24_A      G    24_A     3.921     0    0.490   0.490     5.887   43.214   43.214
LGA    D    25_A      D    25_A     3.124     0    0.281   1.072     8.864   51.905   30.476
LGA    G    26_A      G    26_A     1.253     0    0.091   0.091     1.440   83.690   83.690
LGA    Q    27_A      Q    27_A     0.901     0    0.032   1.327     4.880   88.214   71.217
LGA    G    28_A      G    28_A     0.971     0    0.040   0.040     0.992   90.476   90.476
LGA    L    29_A      L    29_A     0.431     0    0.043   0.996     4.928   95.238   78.095
LGA    Y    30_A      Y    30_A     0.751     0    0.055   0.191     1.213   88.214   86.706
LGA    A    31_A      A    31_A     1.154     0    0.050   0.051     1.382   83.690   83.238
LGA    A    32_A      A    32_A     1.257     0    0.117   0.115     1.476   81.429   81.429
LGA    N    33_A      N    33_A     1.449     0    0.181   1.134     3.332   73.214   73.393
LGA    C    34_A      C    34_A     1.433     0    0.021   0.136     1.870   77.143   78.651
LGA    A    35_A      A    35_A     2.454     0    0.042   0.042     2.828   64.881   63.333
LGA    A    36_A      A    36_A     2.333     0    0.092   0.089     2.333   64.762   64.762
LGA    C    37_A      C    37_A     2.095     0    0.263   0.260     2.512   64.762   63.492
LGA    H    38_A      H    38_A     2.237     0    0.701   1.175     4.816   61.429   57.476
LGA    G    39_A      G    39_A     1.261     0    0.523   0.523     4.517   61.071   61.071
LGA    A    40_A      A    40_A     8.039     0    0.507   0.524     9.208    7.976    6.667
LGA    L    41_A      L    41_A    11.338     0    0.069   1.442    14.106    0.119    0.060
LGA    A    42_A      A    42_A    15.708     0    0.571   0.568    17.180    0.000    0.000
LGA    T    43_A      T    43_A    12.862     0    0.630   0.979    15.446    1.190    0.680
LGA    S    44_A      S    44_A     8.394     0    0.102   0.700    10.598    7.976    5.397
LGA    E    45_A      E    45_A     2.230     0    0.705   1.308     5.858   57.857   51.111
LGA    K    46_A      K    46_A     3.394     0    0.604   0.816     5.072   41.190   48.677
LGA    K    47_A      K    47_A     6.708     0    0.318   1.556     9.861   24.881   12.011
LGA    G    48_A      G    48_A     6.880     0    0.483   0.483     7.593   14.762   14.762
LGA    T    49_A      T    49_A     4.955     0    0.072   1.103     6.745   28.929   29.116
LGA    T    50_A      T    50_A     3.830     0    0.046   1.051     4.204   45.119   46.259
LGA    L    51_A      L    51_A     3.611     0    0.046   1.017     6.045   48.452   40.357
LGA    A    52_A      A    52_A     2.062     0    0.034   0.049     2.334   66.786   68.000
LGA    R    53_A      R    53_A     2.094     0    0.043   1.661     8.901   66.786   43.247
LGA    L    54_A      L    54_A     2.721     0    0.031   0.221     3.998   59.048   52.024
LGA    Q    55_A      Q    55_A     2.976     0    0.039   0.626     3.133   55.357   60.847
LGA    S    56_A      S    56_A     2.171     0    0.061   0.055     2.646   62.857   66.190
LGA    A    57_A      A    57_A     1.646     0    0.029   0.042     2.288   68.810   69.619
LGA    V    58_A      V    58_A     3.552     0    0.028   0.096     4.737   45.238   40.952
LGA    S    59_A      S    59_A     4.362     0    0.124   0.600     4.962   37.262   36.270
LGA    A    60_A      A    60_A     3.644     0    0.240   0.239     3.936   45.000   46.000
LGA    N    61_A      N    61_A     2.322     0    0.592   1.585     4.929   55.952   54.286
LGA    A    62_A      A    62_A     0.625     0    0.072   0.070     1.375   85.952   86.857
LGA    G    63_A      G    63_A     2.024     0    0.675   0.675     3.561   63.571   63.571
LGA    G    64_A      G    64_A     2.550     0    0.401   0.401     4.321   54.048   54.048
LGA    M    65_A      M    65_A     2.276     0    0.722   0.815     3.497   61.071   62.143
LGA    G    66_A      G    66_A     3.573     0    0.682   0.682     3.807   46.667   46.667
LGA    F    67_A      F    67_A     4.148     0    0.357   1.103     5.835   40.357   38.398
LGA    L    68_A      L    68_A     3.684     0    0.283   0.261     9.906   53.810   30.714
LGA    S    69_A      S    69_A     3.352     0    0.248   0.241     4.463   52.500   47.381
LGA    S    70_A      S    70_A     3.480     0    0.105   0.116     4.052   53.571   50.238
LGA    L    71_A      L    71_A     1.486     0    0.033   0.978     2.527   72.976   73.214
LGA    T    72_A      T    72_A     1.888     0    0.068   0.068     1.931   72.857   72.857
LGA    S    73_A      S    73_A     2.042     0    0.031   0.648     2.213   70.833   68.810
LGA    A    74_A      A    74_A     1.416     0    0.063   0.063     1.671   79.286   79.714
LGA    Q    75_A      Q    75_A     0.713     0    0.053   0.264     1.862   90.476   86.508
LGA    L    76_A      L    76_A     1.133     0    0.031   1.443     3.198   83.690   76.548
LGA    Q    77_A      Q    77_A     1.338     0    0.048   1.173     5.832   81.429   58.307
LGA    A    78_A      A    78_A     0.935     0    0.024   0.033     1.129   83.690   85.048
LGA    I    79_A      I    79_A     1.059     0    0.035   0.193     1.551   81.429   81.488
LGA    V    80_A      V    80_A     1.423     0    0.043   0.096     1.649   79.286   77.755
LGA    D    81_A      D    81_A     1.436     0    0.036   1.056     3.662   77.143   73.452
LGA    V    82_A      V    82_A     1.497     0    0.115   1.260     4.151   81.429   71.497
LGA    L    83_A      L    83_A     1.665     0    0.132   0.180     1.910   72.857   72.857
LGA    A    84_A      A    84_A     2.522     0    0.122   0.119     2.971   59.048   58.667
LGA    V    85_A      V    85_A     2.272     0    0.368   1.113     4.799   61.071   56.803

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       64     256    256  100.00     433    433  100.00                64
SUMMARY(RMSD_GDC):     4.033          3.937                  4.386           57.574   54.420

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   97   64    4.0     53    2.33    67.578    61.632     2.181

LGA_LOCAL      RMSD:   2.330  Number of atoms:   53  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   4.466  Number of assigned atoms:   64 
Std_ASGN_ATOMS RMSD:   4.033  Standard rmsd on all 64 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.615810 * X  +   0.445510 * Y  +   0.649845 * Z  +  41.814075
  Y_new =   0.631775 * X  +   0.213619 * Y  +  -0.745136 * Z  +   8.150751
  Z_new =  -0.470785 * X  +   0.869418 * Y  +  -0.149914 * Z  + -33.401241 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.798194  0.490180  1.741547   [DEG:   45.7331   28.0852   99.7833 ]
ZXZ:  0.717194  1.721277 -0.496289   [DEG:   41.0922   98.6219  -28.4353 ]
 
# END of job
