
#######################################################
#                                                     #
#                        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 (  546),  selected   63 , name one
# Molecule2: number of CA atoms  124 ( 1059),  selected   63 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:D  -ch2:D  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    36      88_D - 123_D       4.98    17.05
  LCS_AVERAGE:     23.35

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    29      95_D - 123_D       1.26    18.03
  LCS_AVERAGE:     12.94

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    27      97_D - 123_D       0.76    18.59
  LCS_AVERAGE:     11.19

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     K    61_D     K    61_D      4    4   13      3    4    4    4    4    6    7   11   12   12   12   13   13   14   14   16   20   21   23   25 
LCS_GDT     C    62_D     C    62_D      4    4   14      3    4    4    4    4    6    6    7   12   12   12   14   15   16   20   21   22   24   32   36 
LCS_GDT     E    63_D     E    63_D      4    5   14      3    4    4    4    4    6    6    7    8   10   11   14   15   16   20   21   22   24   28   29 
LCS_GDT     N    64_D     N    64_D      4    5   14      3    4    4    4    4    5    6    7    9   10   11   14   15   18   20   22   23   27   34   38 
LCS_GDT     P    65_D     P    65_D      4    5   14      3    4    4    4    4    6    6    7    9   10   11   14   16   19   21   26   27   32   39   42 
LCS_GDT     K    66_D     K    66_D      4    5   14      3    4    4    4    4    6    6    7    9   10   11   13   16   19   20   26   27   32   39   42 
LCS_GDT     E    67_D     E    67_D      3    5   14      3    3    3    4    4    6    6    7    9   10   11   14   16   19   21   26   27   31   33   38 
LCS_GDT     Q    68_D     Q    68_D      3    4   14      0    3    3    4    4    5    6    7    9   10   11   14   18   19   21   26   27   32   39   42 
LCS_GDT     W    69_D     W    69_D      3    3   14      3    3    3    3    4    6    7    8   11   14   16   17   18   20   23   26   34   39   41   43 
LCS_GDT     V    70_D     V    70_D      3    3   14      3    3    3    3    6    6    7    8   11   14   16   17   18   20   21   26   34   36   41   43 
LCS_GDT     A    71_D     A    71_D      3    4   14      3    3    3    4    4    6    7    8   11   14   16   17   18   20   21   26   27   31   39   42 
LCS_GDT     N    72_D     N    72_D      3    6   14      3    3    3    4    6    6    7   10   11   13   16   17   18   20   21   22   24   29   31   31 
LCS_GDT     Y    73_D     Y    73_D      4    6   14      4    4    4    4    6    6    7    9   11   14   16   17   18   20   25   31   37   43   46   47 
LCS_GDT     Q    74_D     Q    74_D      4    6   14      4    4    4    4    6    6    7   10   11   14   16   17   18   20   21   26   27   31   35   42 
LCS_GDT     N    75_D     N    75_D      4    6   14      4    4    4    4    6    6    8   10   11   13   14   15   17   19   21   21   23   25   26   27 
LCS_GDT     L    76_D     L    76_D      4    6   16      4    4    4    4    6    6    8   10   11   13   14   16   18   20   21   23   24   28   31   37 
LCS_GDT     N    77_D     N    77_D      4    6   18      3    3    4    4    5    6    8   10   11   13   16   17   18   23   26   31   41   44   46   47 
LCS_GDT     N    78_D     N    78_D      4    5   18      3    3    4    5    5    6    8   10   11   14   16   17   18   23   32   40   43   44   46   47 
LCS_GDT     V    79_D     V    79_D      4    5   18      3    3    4    5    5    6    8   10   11   14   16   17   18   20   26   31   39   44   46   47 
LCS_GDT     V    80_D     V    80_D      3    5   18      3    3    4    5    5    6    8   10   11   14   20   24   34   38   38   42   43   44   46   47 
LCS_GDT     F    81_D     F    81_D      4    5   33      3    4    4    5    5   10   12   19   28   33   34   34   36   38   38   42   43   44   46   47 
LCS_GDT     T    82_D     T    82_D      4    5   33      3    4    6    6   11   14   21   29   32   33   34   34   36   38   38   42   43   44   46   47 
LCS_GDT     N    83_D     N    83_D      4    4   33      3    4    6    6   11   13   20   29   32   33   34   34   36   38   38   42   43   44   46   47 
LCS_GDT     K    84_D     K    84_D      4    4   33      3    4    6    6   11   14   21   29   32   33   34   34   36   38   38   42   43   44   46   47 
LCS_GDT     E    85_D     E    85_D      3    4   33      3    3    4    4    4    5   10   14   19   26   29   34   36   38   38   42   43   44   46   47 
LCS_GDT     L    86_D     L    86_D      4    6   33      3    3    4    4    7   10   12   15   19   23   26   30   33   38   38   42   43   44   46   47 
LCS_GDT     E    87_D     E    87_D      4    6   33      3    3    5    5    8   10   13   15   18   20   23   26   29   32   36   39   43   44   46   47 
LCS_GDT     D    88_D     D    88_D      4    6   36      3    3    5    5    7   10   13   15   18   21   25   26   29   34   38   42   43   44   46   47 
LCS_GDT     I    89_D     I    89_D      4    6   36      3    3    5    5    7   10   13   15   18   23   26   33   36   38   38   42   43   44   46   47 
LCS_GDT     Y    90_D     Y    90_D      3    6   36      3    3    3    4    5    7   12   14   17   18   22   25   29   34   38   42   43   44   46   47 
LCS_GDT     D    91_D     D    91_D      4    6   36      4    4    4    4    5    7   12   14   17   18   20   24   29   34   38   42   43   44   46   47 
LCS_GDT     L    92_D     L    92_D      4    4   36      4    4    4    4    4    5    7   11   13   15   19   22   27   34   38   42   43   44   46   47 
LCS_GDT     S    93_D     S    93_D      4    4   36      4    4    4    4    4    6    7   11   13   15   19   21   28   34   38   42   43   44   46   47 
LCS_GDT     N    94_D     N    94_D      4    6   36      4    4    4    4    5    9   13   15   23   32   34   34   36   38   38   42   43   44   46   47 
LCS_GDT     K    95_D     K    95_D      9   29   36      5    6   12   18   28   29   29   29   32   33   34   34   36   38   38   42   43   44   46   47 
LCS_GDT     E    96_D     E    96_D      9   29   36      5    6   10   19   28   29   29   29   32   33   34   34   36   38   38   42   43   44   46   47 
LCS_GDT     E    97_D     E    97_D     27   29   36      5    5    9   20   28   29   29   29   32   33   34   34   36   38   38   42   43   44   46   47 
LCS_GDT     T    98_D     T    98_D     27   29   36     18   26   26   26   28   29   29   29   32   33   34   34   36   38   38   42   43   44   46   47 
LCS_GDT     K    99_D     K    99_D     27   29   36     20   26   26   26   28   29   29   29   32   33   34   34   36   38   38   42   43   44   46   47 
LCS_GDT     E   100_D     E   100_D     27   29   36      7   26   26   26   28   29   29   29   32   33   34   34   36   38   38   42   43   44   46   47 
LCS_GDT     V   101_D     V   101_D     27   29   36     22   26   26   26   28   29   29   29   32   33   34   34   36   38   38   42   43   44   46   47 
LCS_GDT     L   102_D     L   102_D     27   29   36     22   26   26   26   28   29   29   29   32   33   34   34   36   38   38   42   43   44   46   47 
LCS_GDT     K   103_D     K   103_D     27   29   36     22   26   26   26   28   29   29   29   32   33   34   34   36   38   38   42   43   44   46   47 
LCS_GDT     K   104_D     K   104_D     27   29   36     22   26   26   26   28   29   29   29   32   33   34   34   36   38   38   42   43   44   46   47 
LCS_GDT     F   105_D     F   105_D     27   29   36     22   26   26   26   28   29   29   29   32   33   34   34   36   38   38   42   43   44   46   47 
LCS_GDT     K   106_D     K   106_D     27   29   36     22   26   26   26   28   29   29   29   32   33   34   34   36   38   38   42   43   44   46   47 
LCS_GDT     E   107_D     E   107_D     27   29   36     22   26   26   26   28   29   29   29   32   33   34   34   36   38   38   42   43   44   46   47 
LCS_GDT     K   108_D     K   108_D     27   29   36     22   26   26   26   28   29   29   29   32   33   34   34   36   38   38   42   43   44   46   47 
LCS_GDT     V   109_D     V   109_D     27   29   36     22   26   26   26   28   29   29   29   32   33   34   34   36   38   38   42   43   44   46   47 
LCS_GDT     N   110_D     N   110_D     27   29   36     22   26   26   26   28   29   29   29   32   33   34   34   36   38   38   42   43   44   46   47 
LCS_GDT     Q   111_D     Q   111_D     27   29   36     22   26   26   26   28   29   29   29   32   33   34   34   36   38   38   42   43   44   46   47 
LCS_GDT     F   112_D     F   112_D     27   29   36     22   26   26   26   28   29   29   29   32   33   34   34   36   38   38   42   43   44   46   47 
LCS_GDT     Y   113_D     Y   113_D     27   29   36     22   26   26   26   28   29   29   29   32   33   34   34   36   38   38   42   43   44   46   47 
LCS_GDT     R   114_D     R   114_D     27   29   36     22   26   26   26   28   29   29   29   32   33   34   34   36   38   38   42   43   44   46   47 
LCS_GDT     H   115_D     H   115_D     27   29   36     22   26   26   26   28   29   29   29   32   33   34   34   36   38   38   42   43   44   46   47 
LCS_GDT     A   116_D     A   116_D     27   29   36     22   26   26   26   28   29   29   29   32   33   34   34   36   38   38   42   43   44   46   47 
LCS_GDT     F   117_D     F   117_D     27   29   36     22   26   26   26   28   29   29   29   32   33   34   34   36   38   38   42   43   44   46   47 
LCS_GDT     D   118_D     D   118_D     27   29   36     22   26   26   26   28   29   29   29   32   33   34   34   36   38   38   42   43   44   46   47 
LCS_GDT     I   119_D     I   119_D     27   29   36     22   26   26   26   28   29   29   29   32   33   34   34   36   38   38   42   43   44   46   47 
LCS_GDT     I   120_D     I   120_D     27   29   36     22   26   26   26   28   29   29   29   32   33   34   34   36   38   38   42   43   44   46   47 
LCS_GDT     N   121_D     N   121_D     27   29   36     22   26   26   26   28   29   29   29   32   33   34   34   36   38   38   42   43   44   46   47 
LCS_GDT     K   122_D     K   122_D     27   29   36     22   26   26   26   28   29   29   29   32   33   34   34   36   38   38   42   43   44   46   47 
LCS_GDT     Y   123_D     Y   123_D     27   29   36     20   26   26   26   28   29   29   29   32   33   34   34   36   38   38   42   43   44   46   47 
LCS_AVERAGE  LCS_A:  15.83  (  11.19   12.94   23.35 )

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     22     26     26     26     28     29     29     29     32     33     34     34     36     38     38     42     43     44     46     47 
GDT PERCENT_AT  17.74  20.97  20.97  20.97  22.58  23.39  23.39  23.39  25.81  26.61  27.42  27.42  29.03  30.65  30.65  33.87  34.68  35.48  37.10  37.90
GDT RMS_LOCAL    0.22   0.40   0.40   0.40   1.05   1.26   1.26   1.26   2.53   2.72   3.02   3.02   3.69   4.18   4.18   5.06   5.20   5.39   5.82   6.01
GDT RMS_ALL_AT  18.58  18.45  18.45  18.45  18.30  18.03  18.03  18.03  16.53  16.20  16.19  16.19  15.76  15.47  15.47  15.25  15.29  15.13  14.71  14.54

# Checking swapping
#   possible swapping detected:  E    63_D      E    63_D
#   possible swapping detected:  Y    73_D      Y    73_D
#   possible swapping detected:  Y    90_D      Y    90_D
#   possible swapping detected:  E    96_D      E    96_D
#   possible swapping detected:  E    97_D      E    97_D
#   possible swapping detected:  E   107_D      E   107_D
#   possible swapping detected:  F   112_D      F   112_D

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    K    61_D      K    61_D    45.333     0    0.384   1.103    46.516    0.000    0.000
LGA    C    62_D      C    62_D    41.006     0    0.175   0.645    42.705    0.000    0.000
LGA    E    63_D      E    63_D    43.743     0    0.607   0.912    47.018    0.000    0.000
LGA    N    64_D      N    64_D    41.397     0    0.204   0.817    45.722    0.000    0.000
LGA    P    65_D      P    65_D    35.331     0    0.615   0.515    37.380    0.000    0.000
LGA    K    66_D      K    66_D    34.792     0    0.631   1.289    39.989    0.000    0.000
LGA    E    67_D      E    67_D    36.479     0    0.623   1.300    39.951    0.000    0.000
LGA    Q    68_D      Q    68_D    31.387     0    0.619   0.736    34.077    0.000    0.000
LGA    W    69_D      W    69_D    26.467     0    0.607   0.925    27.837    0.000    0.000
LGA    V    70_D      V    70_D    28.167     0    0.613   0.611    30.630    0.000    0.000
LGA    A    71_D      A    71_D    27.413     0    0.196   0.196    27.432    0.000    0.000
LGA    N    72_D      N    72_D    26.275     0    0.401   0.385    30.438    0.000    0.000
LGA    Y    73_D      Y    73_D    20.865     0    0.306   1.215    22.628    0.000    0.000
LGA    Q    74_D      Q    74_D    25.614     0    0.164   0.919    34.062    0.000    0.000
LGA    N    75_D      N    75_D    27.239     0    0.170   0.244    32.038    0.000    0.000
LGA    L    76_D      L    76_D    21.031     0    0.602   0.983    22.906    0.000    0.000
LGA    N    77_D      N    77_D    17.947     0    0.636   1.261    20.880    0.000    0.000
LGA    N    78_D      N    78_D    18.018     0    0.421   0.909    18.983    0.000    0.000
LGA    V    79_D      V    79_D    17.885     0    0.135   1.227    20.572    0.000    0.000
LGA    V    80_D      V    80_D    12.521     0    0.612   0.603    14.377    0.000    0.204
LGA    F    81_D      F    81_D     9.014     0    0.536   1.270    10.095    0.833    4.372
LGA    T    82_D      T    82_D     8.869     0    0.656   0.555     9.772    2.262    2.517
LGA    N    83_D      N    83_D     8.500     0    0.249   0.836    11.420    3.810    2.262
LGA    K    84_D      K    84_D     8.419     0    0.561   0.488     9.199    4.524    5.185
LGA    E    85_D      E    85_D    12.770     0    0.580   0.966    21.708    0.000    0.000
LGA    L    86_D      L    86_D    11.727     0    0.644   0.950    11.991    0.000    0.000
LGA    E    87_D      E    87_D    12.511     0    0.624   0.795    15.107    0.000    0.000
LGA    D    88_D      D    88_D    13.433     0    0.351   0.373    16.031    0.000    0.000
LGA    I    89_D      I    89_D    11.389     0    0.213   1.381    12.639    0.119    0.060
LGA    Y    90_D      Y    90_D    12.623     0    0.592   1.317    16.136    0.000    0.000
LGA    D    91_D      D    91_D    14.288     0    0.707   1.232    19.115    0.000    0.000
LGA    L    92_D      L    92_D    15.832     0    0.062   0.131    22.508    0.000    0.000
LGA    S    93_D      S    93_D    13.974     0    0.428   0.704    15.167    0.000    0.000
LGA    N    94_D      N    94_D     9.490     0    0.232   1.245    11.102    7.024    3.929
LGA    K    95_D      K    95_D     3.643     0    0.618   0.510    11.818   46.667   26.720
LGA    E    96_D      E    96_D     3.199     0    0.016   1.080     4.237   55.476   49.630
LGA    E    97_D      E    97_D     2.531     0    0.079   0.985     5.503   62.976   45.450
LGA    T    98_D      T    98_D     0.485     0    0.039   0.082     2.324   88.452   81.837
LGA    K    99_D      K    99_D     0.629     0    0.043   0.843     3.099   90.595   76.667
LGA    E   100_D      E   100_D     1.017     0    0.074   0.387     2.477   83.690   81.640
LGA    V   101_D      V   101_D     1.455     0    0.024   0.136     1.553   79.286   80.204
LGA    L   102_D      L   102_D     1.335     0    0.041   1.330     3.514   81.429   71.548
LGA    K   103_D      K   103_D     1.231     0    0.037   0.870     3.380   81.429   72.540
LGA    K   104_D      K   104_D     0.959     0    0.025   0.509     2.471   90.476   87.619
LGA    F   105_D      F   105_D     0.877     0    0.021   0.066     0.978   90.476   90.476
LGA    K   106_D      K   106_D     0.986     0    0.011   0.625     1.791   90.476   85.503
LGA    E   107_D      E   107_D     0.964     0    0.031   1.244     4.907   90.476   67.937
LGA    K   108_D      K   108_D     0.629     0    0.021   1.195     4.804   90.476   74.550
LGA    V   109_D      V   109_D     0.535     0    0.048   0.044     0.758   90.476   90.476
LGA    N   110_D      N   110_D     0.782     0    0.062   0.060     1.151   90.476   87.083
LGA    Q   111_D      Q   111_D     0.664     0    0.042   0.984     3.834   95.238   83.439
LGA    F   112_D      F   112_D     0.292     0    0.024   0.266     1.123  100.000   94.026
LGA    Y   113_D      Y   113_D     0.291     0    0.018   1.009     7.167  100.000   64.325
LGA    R   114_D      R   114_D     0.168     0    0.056   1.025     2.334  100.000   92.727
LGA    H   115_D      H   115_D     0.422     0    0.055   1.074     2.785   97.619   87.476
LGA    A   116_D      A   116_D     0.634     0    0.028   0.028     0.831   92.857   92.381
LGA    F   117_D      F   117_D     0.369     0    0.021   1.308     6.950  100.000   65.195
LGA    D   118_D      D   118_D     0.304     0    0.023   0.811     3.549  100.000   81.964
LGA    I   119_D      I   119_D     0.475     0    0.036   0.118     0.690   95.238   96.429
LGA    I   120_D      I   120_D     0.608     0    0.011   0.706     3.166   90.476   85.417
LGA    N   121_D      N   121_D     0.857     0    0.032   0.837     3.012   88.214   79.881
LGA    K   122_D      K   122_D     0.908     0    0.101   0.594     3.990   90.476   74.286
LGA    Y   123_D      Y   123_D     0.859     0    0.140   0.146     1.389   88.214   88.968

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       63     252    252  100.00     546    546  100.00               124
SUMMARY(RMSD_GDC):    10.583         10.497                 11.353           20.647   18.346

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63  124    4.0     29    1.26    24.798    21.763     2.129

LGA_LOCAL      RMSD:   1.262  Number of atoms:   29  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  18.034  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:  10.583  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.244142 * X  +   0.958378 * Y  +  -0.148009 * Z  + -23.779108
  Y_new =  -0.848979 * X  +   0.137475 * Y  +  -0.510230 * Z  + -38.006905
  Z_new =  -0.468645 * X  +   0.250225 * Y  +   0.847207 * Z  +  60.249664 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.290780  0.487757  0.287188   [DEG:  -73.9563   27.9464   16.4547 ]
ZXZ: -0.282334  0.560091 -1.080372   [DEG:  -16.1765   32.0909  -61.9008 ]
 
# END of job
