
#######################################################
#                                                     #
#                        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        3.54     3.54
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    25      61_A - 85_A        1.99     4.01
  LCS_AVERAGE:     35.72

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    18      68_A - 85_A        0.81     4.00
  LCS_AVERAGE:     23.73

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    4   64      0    2    3    4    4    6    6   11   12   13   29   38   47   56   63   63   64   64   64   64 
LCS_GDT     D    23_A     D    23_A      3    4   64      1    5   14   18   20   27   35   41   57   60   62   62   63   63   63   63   64   64   64   64 
LCS_GDT     G    24_A     G    24_A      3   22   64      3    4   11   19   36   43   50   57   58   60   62   62   63   63   63   63   64   64   64   64 
LCS_GDT     D    25_A     D    25_A     15   22   64      3    4   12   32   40   42   45   53   58   59   60   62   63   63   63   63   64   64   64   64 
LCS_GDT     G    26_A     G    26_A     16   22   64     23   28   30   33   40   43   50   57   58   60   62   62   63   63   63   63   64   64   64   64 
LCS_GDT     Q    27_A     Q    27_A     16   22   64     23   28   30   33   40   43   50   57   58   60   62   62   63   63   63   63   64   64   64   64 
LCS_GDT     G    28_A     G    28_A     16   22   64     23   28   30   33   40   43   50   57   58   60   62   62   63   63   63   63   64   64   64   64 
LCS_GDT     L    29_A     L    29_A     16   22   64     23   28   30   33   40   43   50   57   58   60   62   62   63   63   63   63   64   64   64   64 
LCS_GDT     Y    30_A     Y    30_A     16   22   64     23   28   30   33   40   43   50   57   58   60   62   62   63   63   63   63   64   64   64   64 
LCS_GDT     A    31_A     A    31_A     16   22   64     23   28   30   33   40   43   50   57   58   60   62   62   63   63   63   63   64   64   64   64 
LCS_GDT     A    32_A     A    32_A     16   22   64     23   28   30   33   40   43   50   57   58   60   62   62   63   63   63   63   64   64   64   64 
LCS_GDT     N    33_A     N    33_A     16   22   64     23   28   30   33   40   43   50   57   58   60   62   62   63   63   63   63   64   64   64   64 
LCS_GDT     C    34_A     C    34_A     16   22   64     17   28   30   33   40   43   50   57   58   60   62   62   63   63   63   63   64   64   64   64 
LCS_GDT     A    35_A     A    35_A     16   22   64     23   28   30   33   40   43   50   57   58   60   62   62   63   63   63   63   64   64   64   64 
LCS_GDT     A    36_A     A    36_A     16   22   64      5   24   30   33   40   43   50   57   58   60   62   62   63   63   63   63   64   64   64   64 
LCS_GDT     C    37_A     C    37_A     16   22   64      5   28   30   33   40   43   50   57   58   60   62   62   63   63   63   63   64   64   64   64 
LCS_GDT     H    38_A     H    38_A     16   22   64      5   28   30   33   40   43   50   57   58   60   62   62   63   63   63   63   64   64   64   64 
LCS_GDT     G    39_A     G    39_A     16   22   64      5   28   30   33   40   43   50   57   58   60   62   62   63   63   63   63   64   64   64   64 
LCS_GDT     A    40_A     A    40_A     16   22   64      5   22   28   33   40   43   50   57   58   60   62   62   63   63   63   63   64   64   64   64 
LCS_GDT     L    41_A     L    41_A     16   22   64      5    9   27   32   38   43   50   57   58   60   62   62   63   63   63   63   64   64   64   64 
LCS_GDT     A    42_A     A    42_A      6   22   64      5    6   10   27   35   39   44   57   58   60   62   62   63   63   63   63   64   64   64   64 
LCS_GDT     T    43_A     T    43_A      6   22   64      5    7   23   31   35   41   50   57   58   60   62   62   63   63   63   63   64   64   64   64 
LCS_GDT     S    44_A     S    44_A      5   22   64      4    4    7   13   35   39   47   57   58   60   62   62   63   63   63   63   64   64   64   64 
LCS_GDT     E    45_A     E    45_A      8   23   64      4    6   13   18   29   43   50   57   58   60   62   62   63   63   63   63   64   64   64   64 
LCS_GDT     K    46_A     K    46_A     10   23   64      4    7   15   18   20   30   50   57   58   60   62   62   63   63   63   63   64   64   64   64 
LCS_GDT     K    47_A     K    47_A     10   23   64      3    6   11   18   19   20   23   30   34   51   62   62   63   63   63   63   64   64   64   64 
LCS_GDT     G    48_A     G    48_A     16   23   64      3    8   15   18   19   24   30   38   53   60   62   62   63   63   63   63   64   64   64   64 
LCS_GDT     T    49_A     T    49_A     17   23   64      3   15   15   18   20   33   50   57   58   60   62   62   63   63   63   63   64   64   64   64 
LCS_GDT     T    50_A     T    50_A     17   23   64     10   15   15   18   27   34   50   57   58   60   62   62   63   63   63   63   64   64   64   64 
LCS_GDT     L    51_A     L    51_A     17   23   64     10   15   15   18   27   34   50   57   58   60   62   62   63   63   63   63   64   64   64   64 
LCS_GDT     A    52_A     A    52_A     17   23   64     10   15   15   24   38   43   50   57   58   60   62   62   63   63   63   63   64   64   64   64 
LCS_GDT     R    53_A     R    53_A     17   23   64     10   15   15   29   40   43   50   57   58   60   62   62   63   63   63   63   64   64   64   64 
LCS_GDT     L    54_A     L    54_A     17   23   64     10   15   15   18   27   40   50   57   58   60   62   62   63   63   63   63   64   64   64   64 
LCS_GDT     Q    55_A     Q    55_A     17   23   64      9   15   15   20   27   40   50   57   58   60   62   62   63   63   63   63   64   64   64   64 
LCS_GDT     S    56_A     S    56_A     17   23   64      9   15   17   30   40   43   50   57   58   60   62   62   63   63   63   63   64   64   64   64 
LCS_GDT     A    57_A     A    57_A     17   23   64     10   15   18   30   40   43   50   57   58   60   62   62   63   63   63   63   64   64   64   64 
LCS_GDT     V    58_A     V    58_A     17   23   64     10   15   15   18   20   36   44   57   58   60   62   62   63   63   63   63   64   64   64   64 
LCS_GDT     S    59_A     S    59_A     17   23   64     10   15   15   18   20   33   40   57   58   60   62   62   63   63   63   63   64   64   64   64 
LCS_GDT     A    60_A     A    60_A     17   23   64     10   15   15   18   22   33   49   57   58   60   62   62   63   63   63   63   64   64   64   64 
LCS_GDT     N    61_A     N    61_A     17   25   64     10   15   15   18   23   36   47   57   58   60   62   62   63   63   63   63   64   64   64   64 
LCS_GDT     A    62_A     A    62_A     17   25   64      9   15   18   33   40   43   50   57   58   60   62   62   63   63   63   63   64   64   64   64 
LCS_GDT     G    63_A     G    63_A     17   25   64      5   15   19   33   40   43   50   57   58   60   62   62   63   63   63   63   64   64   64   64 
LCS_GDT     G    64_A     G    64_A     17   25   64      4    4    7   22   32   39   44   54   58   60   62   62   63   63   63   63   64   64   64   64 
LCS_GDT     M    65_A     M    65_A     17   25   64      4    4   12   25   32   41   49   57   58   60   62   62   63   63   63   63   64   64   64   64 
LCS_GDT     G    66_A     G    66_A      5   25   64      4    4    7    8    9   16   38   44   52   59   62   62   63   63   63   63   64   64   64   64 
LCS_GDT     F    67_A     F    67_A     13   25   64      5    8   18   28   40   43   50   57   58   60   62   62   63   63   63   63   64   64   64   64 
LCS_GDT     L    68_A     L    68_A     18   25   64      5    9   22   33   40   43   50   57   58   60   62   62   63   63   63   63   64   64   64   64 
LCS_GDT     S    69_A     S    69_A     18   25   64      5   22   30   33   40   43   50   57   58   60   62   62   63   63   63   63   64   64   64   64 
LCS_GDT     S    70_A     S    70_A     18   25   64      5   22   28   33   40   43   50   57   58   60   62   62   63   63   63   63   64   64   64   64 
LCS_GDT     L    71_A     L    71_A     18   25   64     23   28   30   33   40   43   50   57   58   60   62   62   63   63   63   63   64   64   64   64 
LCS_GDT     T    72_A     T    72_A     18   25   64     23   28   30   33   40   43   50   57   58   60   62   62   63   63   63   63   64   64   64   64 
LCS_GDT     S    73_A     S    73_A     18   25   64     23   28   30   33   40   43   50   57   58   60   62   62   63   63   63   63   64   64   64   64 
LCS_GDT     A    74_A     A    74_A     18   25   64     23   28   30   33   40   43   50   57   58   60   62   62   63   63   63   63   64   64   64   64 
LCS_GDT     Q    75_A     Q    75_A     18   25   64     23   28   30   33   40   43   50   57   58   60   62   62   63   63   63   63   64   64   64   64 
LCS_GDT     L    76_A     L    76_A     18   25   64     23   28   30   33   40   43   50   57   58   60   62   62   63   63   63   63   64   64   64   64 
LCS_GDT     Q    77_A     Q    77_A     18   25   64     23   28   30   33   40   43   50   57   58   60   62   62   63   63   63   63   64   64   64   64 
LCS_GDT     A    78_A     A    78_A     18   25   64     23   28   30   33   40   43   50   57   58   60   62   62   63   63   63   63   64   64   64   64 
LCS_GDT     I    79_A     I    79_A     18   25   64     23   28   30   33   40   43   50   57   58   60   62   62   63   63   63   63   64   64   64   64 
LCS_GDT     V    80_A     V    80_A     18   25   64     23   28   30   33   40   43   50   57   58   60   62   62   63   63   63   63   64   64   64   64 
LCS_GDT     D    81_A     D    81_A     18   25   64     18   28   30   33   40   43   50   57   58   60   62   62   63   63   63   63   64   64   64   64 
LCS_GDT     V    82_A     V    82_A     18   25   64     23   28   30   33   40   43   50   57   58   60   62   62   63   63   63   63   64   64   64   64 
LCS_GDT     L    83_A     L    83_A     18   25   64     23   28   30   33   40   43   50   57   58   60   62   62   63   63   63   63   64   64   64   64 
LCS_GDT     A    84_A     A    84_A     18   25   64     23   28   30   33   40   43   50   57   58   60   62   62   63   63   63   63   64   64   64   64 
LCS_GDT     V    85_A     V    85_A     18   25   64     23   28   30   33   40   43   50   57   58   60   62   62   63   63   63   63   64   64   64   64 
LCS_AVERAGE  LCS_A:  53.15  (  23.73   35.72  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     23     28     30     33     40     43     50     57     58     60     62     62     63     63     63     63     64     64     64     64 
GDT PERCENT_AT  35.94  43.75  46.88  51.56  62.50  67.19  78.12  89.06  90.62  93.75  96.88  96.88  98.44  98.44  98.44  98.44 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.31   0.44   0.57   1.00   1.56   1.87   2.35   2.67   2.70   2.99   3.19   3.10   3.21   3.21   3.21   3.21   3.54   3.54   3.54   3.54
GDT RMS_ALL_AT   4.26   4.27   4.23   4.08   3.99   3.80   3.68   3.63   3.66   3.57   3.55   3.58   3.56   3.56   3.56   3.56   3.54   3.54   3.54   3.54

# Checking swapping
#   possible swapping detected:  D    25_A      D    25_A
#   possible swapping detected:  Y    30_A      Y    30_A
#   possible swapping detected:  E    45_A      E    45_A
#   possible swapping detected:  F    67_A      F    67_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A    22_A      A    22_A    13.359     0    0.661   0.637    14.870    0.000    0.000
LGA    D    23_A      D    23_A     7.841     0    0.679   0.700    10.512   15.357    9.881
LGA    G    24_A      G    24_A     3.041     0    0.548   0.548     4.902   47.857   47.857
LGA    D    25_A      D    25_A     3.844     0    0.260   1.089     8.056   46.310   28.571
LGA    G    26_A      G    26_A     1.751     0    0.094   0.094     1.847   72.857   72.857
LGA    Q    27_A      Q    27_A     1.412     0    0.027   0.811     3.231   79.286   73.228
LGA    G    28_A      G    28_A     1.443     0    0.082   0.082     1.443   81.429   81.429
LGA    L    29_A      L    29_A     1.277     0    0.014   0.101     1.645   81.429   80.357
LGA    Y    30_A      Y    30_A     1.204     0    0.075   0.122     1.443   81.429   81.429
LGA    A    31_A      A    31_A     1.268     0    0.006   0.012     1.464   81.429   81.429
LGA    A    32_A      A    32_A     1.419     0    0.035   0.037     1.534   79.286   79.714
LGA    N    33_A      N    33_A     1.488     0    0.017   0.076     1.729   79.286   76.071
LGA    C    34_A      C    34_A     1.441     0    0.035   0.111     1.555   79.286   80.000
LGA    A    35_A      A    35_A     1.657     0    0.024   0.023     2.213   70.952   71.333
LGA    A    36_A      A    36_A     2.534     0    0.024   0.023     2.882   59.048   58.667
LGA    C    37_A      C    37_A     2.160     0    0.024   0.076     2.346   64.762   64.762
LGA    H    38_A      H    38_A     2.102     0    0.099   0.213     2.280   64.762   67.190
LGA    G    39_A      G    39_A     2.488     0    0.233   0.233     2.488   70.952   70.952
LGA    A    40_A      A    40_A     1.159     0    0.019   0.021     2.112   83.929   80.095
LGA    L    41_A      L    41_A     2.301     0    0.041   1.386     3.667   57.738   60.714
LGA    A    42_A      A    42_A     4.608     0    0.150   0.159     5.100   35.833   33.905
LGA    T    43_A      T    43_A     3.669     0    0.215   0.194     3.771   43.333   43.333
LGA    S    44_A      S    44_A     4.206     0    0.124   0.724     4.617   41.905   41.508
LGA    E    45_A      E    45_A     3.385     0    0.326   0.804     6.868   52.024   35.185
LGA    K    46_A      K    46_A     4.262     0    0.116   0.569     5.582   29.048   43.386
LGA    K    47_A      K    47_A     7.921     0    0.092   0.771    10.816    6.667    3.810
LGA    G    48_A      G    48_A     7.145     0    0.599   0.599     9.038   13.571   13.571
LGA    T    49_A      T    49_A     4.173     0    0.212   0.878     5.278   34.405   35.646
LGA    T    50_A      T    50_A     3.981     0    0.049   0.077     4.045   41.786   43.401
LGA    L    51_A      L    51_A     4.127     0    0.019   0.858     5.576   40.238   37.500
LGA    A    52_A      A    52_A     2.657     0    0.013   0.014     3.123   59.167   60.286
LGA    R    53_A      R    53_A     2.322     0    0.019   0.581     3.979   60.952   56.667
LGA    L    54_A      L    54_A     3.519     0    0.018   1.388     7.683   45.000   33.095
LGA    Q    55_A      Q    55_A     3.489     0    0.027   0.308     4.182   50.000   49.365
LGA    S    56_A      S    56_A     2.504     0    0.060   0.068     2.787   57.143   59.683
LGA    A    57_A      A    57_A     2.611     0    0.009   0.017     3.313   53.571   54.286
LGA    V    58_A      V    58_A     4.396     0    0.043   0.123     5.789   35.833   32.517
LGA    S    59_A      S    59_A     4.515     0    0.018   0.742     6.624   34.286   31.270
LGA    A    60_A      A    60_A     3.770     0    0.022   0.026     3.855   43.333   44.667
LGA    N    61_A      N    61_A     4.021     0    0.094   0.923     6.591   45.357   33.631
LGA    A    62_A      A    62_A     1.792     0    0.017   0.020     2.662   66.905   69.810
LGA    G    63_A      G    63_A     1.760     0    0.690   0.690     2.095   72.976   72.976
LGA    G    64_A      G    64_A     4.932     0    0.193   0.193     6.422   27.976   27.976
LGA    M    65_A      M    65_A     4.059     0    0.038   0.251     5.165   32.976   51.012
LGA    G    66_A      G    66_A     6.583     0    0.622   0.622     6.583   20.595   20.595
LGA    F    67_A      F    67_A     2.409     0    0.580   1.343     6.542   57.500   48.615
LGA    L    68_A      L    68_A     1.204     0    0.055   0.110     2.182   85.952   79.464
LGA    S    69_A      S    69_A     1.596     0    0.044   0.626     2.430   70.952   68.889
LGA    S    70_A      S    70_A     2.459     0    0.041   0.086     2.799   62.857   62.222
LGA    L    71_A      L    71_A     1.829     0    0.042   0.098     2.084   70.833   71.845
LGA    T    72_A      T    72_A     2.109     0    0.026   0.092     2.167   66.786   68.231
LGA    S    73_A      S    73_A     2.387     0    0.023   0.631     4.056   64.762   58.889
LGA    A    74_A      A    74_A     1.873     0    0.040   0.044     2.030   70.833   71.238
LGA    Q    75_A      Q    75_A     1.591     0    0.019   0.109     1.741   72.857   75.714
LGA    L    76_A      L    76_A     2.034     0    0.021   0.133     2.708   66.786   64.821
LGA    Q    77_A      Q    77_A     2.059     0    0.043   0.191     2.514   66.786   65.714
LGA    A    78_A      A    78_A     1.741     0    0.016   0.023     1.834   72.857   72.857
LGA    I    79_A      I    79_A     1.778     0    0.012   0.054     1.778   72.857   72.857
LGA    V    80_A      V    80_A     1.849     0    0.017   0.036     2.162   72.857   70.544
LGA    D    81_A      D    81_A     1.925     0    0.064   0.111     2.652   72.857   68.869
LGA    V    82_A      V    82_A     1.708     0    0.095   0.885     3.113   72.857   72.109
LGA    L    83_A      L    83_A     1.864     0    0.161   0.177     2.142   72.857   69.821
LGA    A    84_A      A    84_A     2.261     0    0.111   0.115     2.276   64.762   64.762
LGA    V    85_A      V    85_A     2.347     0    0.285   1.334     4.122   64.762   64.490

# 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):     3.544          3.505                  3.717           57.279   56.056

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   97   64    4.0     57    2.67    70.703    64.713     2.054

LGA_LOCAL      RMSD:   2.675  Number of atoms:   57  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   3.631  Number of assigned atoms:   64 
Std_ASGN_ATOMS RMSD:   3.544  Standard rmsd on all 64 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.043304 * X  +   0.429264 * Y  +  -0.902140 * Z  +  21.451500
  Y_new =   0.833384 * X  +  -0.513529 * Y  +  -0.204348 * Z  + -22.898739
  Z_new =  -0.550995 * X  +  -0.742981 * Y  +  -0.379980 * Z  + -13.386573 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.518881  0.583556 -2.043543   [DEG:   87.0255   33.4353 -117.0864 ]
ZXZ: -1.348041  1.960571 -2.503489   [DEG:  -77.2370  112.3324 -143.4394 ]
 
# END of job
