
#######################################################
#                                                     #
#                        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   73 (  570),  selected   71 , name one
# Molecule2: number of CA atoms   71 (  553),  selected   71 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:B  -ch2:B  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    71       1_B - 71_B        1.21     1.21
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    71       1_B - 71_B        1.21     1.21
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    60       6_B - 65_B        1.00     1.28
  LCS_AVERAGE:     81.57

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   71
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     G     1_B     G     1_B     48   71   71      4   14   49   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S     2_B     S     2_B     48   71   71     19   46   63   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V     3_B     V     3_B     48   71   71     12   46   63   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S     4_B     S     4_B     48   71   71      3   46   63   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K     5_B     K     5_B     48   71   71      8   27   55   65   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     W     6_B     W     6_B     60   71   71     13   46   63   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S     7_B     S     7_B     60   71   71     11   46   63   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     T     8_B     T     8_B     60   71   71     11   46   63   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D     9_B     D     9_B     60   71   71     11   46   63   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    10_B     E    10_B     60   71   71     11   46   63   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V    11_B     V    11_B     60   71   71      8   46   63   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    12_B     S    12_B     60   71   71      8   29   63   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    13_B     E    13_B     60   71   71      8   32   63   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    14_B     F    14_B     60   71   71     12   46   63   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    15_B     I    15_B     60   71   71     11   46   63   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     Q    16_B     Q    16_B     60   71   71     11   42   63   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    17_B     S    17_B     60   71   71     11   42   63   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    18_B     L    18_B     60   71   71      8   42   63   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     P    19_B     P    19_B     60   71   71      6   42   63   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    20_B     G    20_B     60   71   71     11   42   63   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     C    21_B     C    21_B     60   71   71     14   46   63   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    22_B     E    22_B     60   71   71      6   29   63   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    23_B     E    23_B     60   71   71     17   46   63   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     H    24_B     H    24_B     60   71   71     17   46   63   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    25_B     G    25_B     60   71   71     19   46   63   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    26_B     K    26_B     60   71   71     17   46   63   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V    27_B     V    27_B     60   71   71     15   46   63   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    28_B     F    28_B     60   71   71     19   46   63   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    29_B     K    29_B     60   71   71     19   46   63   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D    30_B     D    30_B     60   71   71     12   46   63   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    31_B     E    31_B     60   71   71     12   46   63   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     Q    32_B     Q    32_B     60   71   71     12   46   63   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    33_B     I    33_B     60   71   71     12   46   63   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D    34_B     D    34_B     60   71   71     12   46   63   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    35_B     G    35_B     60   71   71     18   46   63   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    36_B     E    36_B     60   71   71      7   38   63   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    37_B     A    37_B     60   71   71      8   46   63   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    38_B     F    38_B     60   71   71      4   38   63   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    39_B     L    39_B     60   71   71     17   46   63   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    40_B     L    40_B     60   71   71     17   46   63   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     M    41_B     M    41_B     60   71   71     19   46   63   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     T    42_B     T    42_B     60   71   71     19   46   63   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     Q    43_B     Q    43_B     60   71   71     19   46   63   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     T    44_B     T    44_B     60   71   71     19   46   63   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D    45_B     D    45_B     60   71   71     19   46   63   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    46_B     I    46_B     60   71   71      5   32   63   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V    47_B     V    47_B     60   71   71      5   32   63   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    48_B     K    48_B     60   71   71      5   10   37   65   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    49_B     I    49_B     60   71   71      5    7   14   50   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     M    50_B     M    50_B     60   71   71     11   32   63   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    51_B     S    51_B     60   71   71     19   46   63   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    52_B     I    52_B     60   71   71      5   35   63   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    53_B     K    53_B     60   71   71     19   46   63   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    54_B     E    54_B     60   71   71     19   46   63   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    55_B     G    55_B     60   71   71     19   46   63   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     P    56_B     P    56_B     60   71   71     19   46   63   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    57_B     A    57_B     60   71   71     19   46   63   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    58_B     E    58_B     60   71   71     19   46   63   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    59_B     K    59_B     60   71   71     19   46   63   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    60_B     I    60_B     60   71   71     19   46   63   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    61_B     F    61_B     60   71   71     19   46   63   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     N    62_B     N    62_B     60   71   71     19   46   63   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    63_B     S    63_B     60   71   71     19   46   63   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    64_B     I    64_B     60   71   71     19   46   63   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    65_B     L    65_B     60   71   71     19   46   63   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     M    66_B     M    66_B     53   71   71     19   41   63   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    67_B     F    67_B     49   71   71     17   36   63   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    68_B     K    68_B     49   71   71     10   32   61   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    69_B     A    69_B     49   71   71     10   23   53   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    70_B     A    70_B     36   71   71     10   23   45   64   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    71_B     E    71_B     36   71   71     10   23   45   64   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_AVERAGE  LCS_A:  93.86  (  81.57  100.00  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     19     46     63     66     69     71     71     71     71     71     71     71     71     71     71     71     71     71     71     71 
GDT PERCENT_AT  26.76  64.79  88.73  92.96  97.18 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.30   0.69   0.93   1.02   1.15   1.21   1.21   1.21   1.21   1.21   1.21   1.21   1.21   1.21   1.21   1.21   1.21   1.21   1.21   1.21
GDT RMS_ALL_AT   1.35   1.27   1.25   1.22   1.21   1.21   1.21   1.21   1.21   1.21   1.21   1.21   1.21   1.21   1.21   1.21   1.21   1.21   1.21   1.21

# Checking swapping
#   possible swapping detected:  D     9_B      D     9_B
#   possible swapping detected:  E    13_B      E    13_B
#   possible swapping detected:  F    14_B      F    14_B
#   possible swapping detected:  E    36_B      E    36_B
#   possible swapping detected:  F    38_B      F    38_B
#   possible swapping detected:  E    54_B      E    54_B
#   possible swapping detected:  E    58_B      E    58_B
#   possible swapping detected:  F    67_B      F    67_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    G     1_B      G     1_B     2.235     0    0.568   0.568     3.083   59.405   59.405
LGA    S     2_B      S     2_B     0.494     0    0.233   0.647     2.308   86.429   81.984
LGA    V     3_B      V     3_B     0.941     0    0.071   0.152     2.196   90.476   81.769
LGA    S     4_B      S     4_B     0.877     0    0.681   0.845     2.795   84.048   79.127
LGA    K     5_B      K     5_B     2.449     0    0.075   0.778     7.708   68.810   44.339
LGA    W     6_B      W     6_B     1.243     0    0.051   0.283     3.052   79.286   71.497
LGA    S     7_B      S     7_B     0.721     0    0.040   0.038     0.842   90.476   90.476
LGA    T     8_B      T     8_B     0.921     0    0.028   0.122     1.217   90.476   87.891
LGA    D     9_B      D     9_B     0.850     0    0.019   0.739     2.965   90.476   81.905
LGA    E    10_B      E    10_B     0.718     0    0.030   0.250     1.800   90.476   85.503
LGA    V    11_B      V    11_B     0.935     0    0.024   0.101     1.567   90.476   85.374
LGA    S    12_B      S    12_B     1.369     0    0.023   0.726     1.765   81.429   78.571
LGA    E    13_B      E    13_B     1.469     0    0.014   0.771     5.442   79.286   60.476
LGA    F    14_B      F    14_B     0.988     0    0.027   1.381     6.876   88.214   59.567
LGA    I    15_B      I    15_B     0.610     0    0.014   0.660     1.579   90.476   87.143
LGA    Q    16_B      Q    16_B     1.340     0    0.089   0.712     3.227   79.286   73.175
LGA    S    17_B      S    17_B     1.715     0    0.151   0.716     2.182   79.286   75.794
LGA    L    18_B      L    18_B     1.504     0    0.133   1.385     3.308   75.000   72.202
LGA    P    19_B      P    19_B     1.580     0    0.030   0.397     2.586   77.143   73.061
LGA    G    20_B      G    20_B     1.332     0    0.046   0.046     1.463   83.690   83.690
LGA    C    21_B      C    21_B     0.719     0    0.021   0.028     0.959   90.476   90.476
LGA    E    22_B      E    22_B     1.269     0    0.033   0.789     3.998   81.429   67.566
LGA    E    23_B      E    23_B     0.718     0    0.077   0.824     4.345   90.476   76.349
LGA    H    24_B      H    24_B     0.606     0    0.053   0.143     1.354   95.238   87.857
LGA    G    25_B      G    25_B     0.343     0    0.101   0.101     0.459  100.000  100.000
LGA    K    26_B      K    26_B     0.660     0    0.013   0.759     1.843   90.476   85.556
LGA    V    27_B      V    27_B     0.989     0    0.048   1.042     3.631   90.476   79.932
LGA    F    28_B      F    28_B     0.593     0    0.022   0.383     1.117   90.476   92.251
LGA    K    29_B      K    29_B     0.614     0    0.016   0.792     2.260   90.476   85.820
LGA    D    30_B      D    30_B     1.120     0    0.051   0.078     1.241   83.690   82.560
LGA    E    31_B      E    31_B     1.239     0    0.019   0.115     1.549   81.429   80.476
LGA    Q    32_B      Q    32_B     1.186     0    0.025   0.806     4.267   81.429   69.577
LGA    I    33_B      I    33_B     0.991     0    0.083   0.622     1.732   88.214   84.881
LGA    D    34_B      D    34_B     1.076     0    0.031   0.150     1.767   85.952   82.619
LGA    G    35_B      G    35_B     0.619     0    0.053   0.053     0.828   90.476   90.476
LGA    E    36_B      E    36_B     1.168     0    0.033   0.915     3.363   83.690   75.185
LGA    A    37_B      A    37_B     0.991     0    0.044   0.040     1.066   85.952   85.048
LGA    F    38_B      F    38_B     1.183     0    0.019   1.094     4.126   81.429   73.983
LGA    L    39_B      L    39_B     0.773     0    0.110   0.156     1.335   90.476   89.345
LGA    L    40_B      L    40_B     0.600     0    0.017   0.043     0.890   95.238   92.857
LGA    M    41_B      M    41_B     0.446     0    0.057   0.164     0.835   97.619   96.429
LGA    T    42_B      T    42_B     0.701     0    0.016   0.026     0.701   90.476   90.476
LGA    Q    43_B      Q    43_B     0.669     0    0.010   0.210     1.963   90.476   83.598
LGA    T    44_B      T    44_B     0.760     0    0.021   0.092     1.014   90.476   89.184
LGA    D    45_B      D    45_B     0.684     0    0.018   0.220     1.215   88.214   88.214
LGA    I    46_B      I    46_B     1.111     0    0.069   0.075     1.523   81.548   82.619
LGA    V    47_B      V    47_B     1.331     0    0.023   0.073     1.866   77.143   77.755
LGA    K    48_B      K    48_B     2.355     0    0.019   0.958     7.785   64.881   47.354
LGA    I    49_B      I    49_B     2.694     0    0.015   0.108     4.270   62.857   53.155
LGA    M    50_B      M    50_B     1.446     0    0.022   0.868     4.100   81.548   67.917
LGA    S    51_B      S    51_B     0.724     0    0.092   0.089     1.074   88.214   87.460
LGA    I    52_B      I    52_B     1.447     0    0.111   1.218     3.148   79.286   69.286
LGA    K    53_B      K    53_B     1.012     0    0.035   0.647     1.528   85.952   84.497
LGA    E    54_B      E    54_B     0.886     0    0.019   0.747     3.081   90.476   79.259
LGA    G    55_B      G    55_B     0.863     0    0.066   0.066     1.004   88.214   88.214
LGA    P    56_B      P    56_B     0.705     0    0.040   0.054     0.783   90.476   90.476
LGA    A    57_B      A    57_B     0.687     0    0.020   0.019     0.743   90.476   90.476
LGA    E    58_B      E    58_B     0.629     0    0.010   0.800     3.294   92.857   80.476
LGA    K    59_B      K    59_B     0.639     0    0.007   0.137     0.743   90.476   91.534
LGA    I    60_B      I    60_B     0.474     0    0.028   0.045     0.587   97.619   94.048
LGA    F    61_B      F    61_B     0.439     0    0.059   0.110     1.078  100.000   93.983
LGA    N    62_B      N    62_B     0.535     0    0.012   0.041     0.989   97.619   94.048
LGA    S    63_B      S    63_B     0.658     0    0.014   0.043     0.833   90.476   90.476
LGA    I    64_B      I    64_B     0.402     0    0.011   0.103     0.671   97.619   96.429
LGA    L    65_B      L    65_B     0.406     0    0.025   0.130     0.898   95.238   97.619
LGA    M    66_B      M    66_B     1.072     0    0.015   0.838     3.075   83.690   79.762
LGA    F    67_B      F    67_B     1.166     0    0.020   0.509     1.683   79.286   83.939
LGA    K    68_B      K    68_B     1.595     0    0.022   0.968     2.427   72.976   72.963
LGA    A    69_B      A    69_B     2.110     0    0.062   0.063     2.478   66.786   66.381
LGA    A    70_B      A    70_B     2.666     0    0.142   0.154     2.973   59.048   60.190
LGA    E    71_B      E    71_B     2.800     0    0.030   0.143     3.615   57.143   53.280

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       71     284    284  100.00     553    553  100.00                71
SUMMARY(RMSD_GDC):     1.211          1.220                  1.772           85.089   80.384

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   73   71    4.0     71    1.21    89.437    95.701     5.414

LGA_LOCAL      RMSD:   1.211  Number of atoms:   71  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.211  Number of assigned atoms:   71 
Std_ASGN_ATOMS RMSD:   1.211  Standard rmsd on all 71 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.563288 * X  +  -0.793252 * Y  +  -0.231210 * Z  +  24.966311
  Y_new =  -0.810203 * X  +  -0.475375 * Y  +  -0.342914 * Z  +  40.118004
  Z_new =   0.162106 * X  +   0.380486 * Y  +  -0.910468 * Z  + -10.844402 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.963270 -0.162825  2.745749   [DEG:  -55.1913   -9.3292  157.3199 ]
ZXZ: -0.593234  2.715210  0.402759   [DEG:  -33.9898  155.5701   23.0764 ]
 
# END of job
