
#######################################################
#                                                     #
#                        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        1.23     1.23
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    71       1_B - 71_B        1.23     1.23
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    67       1_B - 67_B        0.99     1.29
  LONGEST_CONTINUOUS_SEGMENT:    67       2_B - 68_B        0.99     1.26
  LCS_AVERAGE:     93.10

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     67   71   71      6   26   49   63   69   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S     2_B     S     2_B     67   71   71      9   35   65   68   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V     3_B     V     3_B     67   71   71     27   49   65   68   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S     4_B     S     4_B     67   71   71     27   49   65   68   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K     5_B     K     5_B     67   71   71     28   49   65   68   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     W     6_B     W     6_B     67   71   71     28   49   65   68   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S     7_B     S     7_B     67   71   71     28   49   65   68   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     T     8_B     T     8_B     67   71   71     28   49   65   68   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D     9_B     D     9_B     67   71   71     28   49   65   68   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    10_B     E    10_B     67   71   71     28   49   65   68   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V    11_B     V    11_B     67   71   71     28   49   65   68   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    12_B     S    12_B     67   71   71     28   49   65   68   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    13_B     E    13_B     67   71   71     28   49   65   68   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    14_B     F    14_B     67   71   71     28   49   65   68   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    15_B     I    15_B     67   71   71     28   49   65   68   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     Q    16_B     Q    16_B     67   71   71     28   49   65   68   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    17_B     S    17_B     67   71   71     28   49   65   68   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    18_B     L    18_B     67   71   71     28   49   65   68   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     P    19_B     P    19_B     67   71   71     27   49   65   68   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    20_B     G    20_B     67   71   71     15   49   65   68   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     C    21_B     C    21_B     67   71   71     27   49   65   68   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    22_B     E    22_B     67   71   71      6   49   65   68   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    23_B     E    23_B     67   71   71     17   49   65   68   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     H    24_B     H    24_B     67   71   71     26   49   65   68   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    25_B     G    25_B     67   71   71     28   49   65   68   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    26_B     K    26_B     67   71   71     28   49   65   68   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V    27_B     V    27_B     67   71   71     28   49   65   68   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    28_B     F    28_B     67   71   71     28   49   65   68   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    29_B     K    29_B     67   71   71     28   49   65   68   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D    30_B     D    30_B     67   71   71     22   48   65   68   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    31_B     E    31_B     67   71   71     28   49   65   68   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     Q    32_B     Q    32_B     67   71   71     28   49   65   68   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    33_B     I    33_B     67   71   71     28   49   65   68   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D    34_B     D    34_B     67   71   71     28   49   65   68   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    35_B     G    35_B     67   71   71     28   49   65   68   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    36_B     E    36_B     67   71   71     15   49   65   68   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    37_B     A    37_B     67   71   71     28   49   65   68   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    38_B     F    38_B     67   71   71     28   49   65   68   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    39_B     L    39_B     67   71   71     27   49   65   68   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    40_B     L    40_B     67   71   71     24   49   65   68   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     M    41_B     M    41_B     67   71   71     28   49   65   68   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     T    42_B     T    42_B     67   71   71     28   49   65   68   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     Q    43_B     Q    43_B     67   71   71     25   49   65   68   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     T    44_B     T    44_B     67   71   71     19   49   65   68   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D    45_B     D    45_B     67   71   71     19   49   65   68   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    46_B     I    46_B     67   71   71     20   49   65   68   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V    47_B     V    47_B     67   71   71     20   49   65   68   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    48_B     K    48_B     67   71   71     20   39   65   68   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    49_B     I    49_B     67   71   71     20   37   65   68   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     M    50_B     M    50_B     67   71   71     20   49   65   68   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    51_B     S    51_B     67   71   71     20   49   65   68   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    52_B     I    52_B     67   71   71     20   49   65   68   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    53_B     K    53_B     67   71   71     20   45   65   68   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    54_B     E    54_B     67   71   71     20   40   65   68   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    55_B     G    55_B     67   71   71     20   37   65   68   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     P    56_B     P    56_B     67   71   71     20   49   65   68   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    57_B     A    57_B     67   71   71     20   49   65   68   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    58_B     E    58_B     67   71   71     20   49   65   68   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    59_B     K    59_B     67   71   71     20   43   65   68   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    60_B     I    60_B     67   71   71     20   49   65   68   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    61_B     F    61_B     67   71   71     27   49   65   68   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     N    62_B     N    62_B     67   71   71     17   49   65   68   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    63_B     S    63_B     67   71   71     20   38   65   68   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    64_B     I    64_B     67   71   71     17   38   65   68   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    65_B     L    65_B     67   71   71     17   45   65   68   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     M    66_B     M    66_B     67   71   71     20   38   65   68   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    67_B     F    67_B     67   71   71     11   29   50   68   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    68_B     K    68_B     67   71   71     11   28   48   68   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    69_B     A    69_B     50   71   71     11   32   56   68   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    70_B     A    70_B     48   71   71     11   18   35   57   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    71_B     E    71_B     39   71   71     11   17   27   43   66   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_AVERAGE  LCS_A:  97.70  (  93.10  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     28     49     65     68     69     70     71     71     71     71     71     71     71     71     71     71     71     71     71     71 
GDT PERCENT_AT  39.44  69.01  91.55  95.77  97.18  98.59 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.32   0.62   0.89   1.03   1.07   1.19   1.23   1.23   1.23   1.23   1.23   1.23   1.23   1.23   1.23   1.23   1.23   1.23   1.23   1.23
GDT RMS_ALL_AT   1.72   1.45   1.31   1.25   1.25   1.23   1.23   1.23   1.23   1.23   1.23   1.23   1.23   1.23   1.23   1.23   1.23   1.23   1.23   1.23

# Checking swapping
#   possible swapping detected:  D     9_B      D     9_B
#   possible swapping detected:  E    13_B      E    13_B
#   possible swapping detected:  E    54_B      E    54_B
#   possible swapping detected:  E    58_B      E    58_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    G     1_B      G     1_B     2.834     0    0.452   0.452     4.126   57.976   57.976
LGA    S     2_B      S     2_B     1.485     0    0.045   0.082     2.077   77.262   75.873
LGA    V     3_B      V     3_B     0.811     0    0.053   1.065     2.981   90.476   80.952
LGA    S     4_B      S     4_B     0.924     0    0.043   0.181     1.449   85.952   85.952
LGA    K     5_B      K     5_B     1.326     0    0.046   0.831     5.661   81.429   61.640
LGA    W     6_B      W     6_B     1.229     0    0.040   0.134     1.516   81.429   80.816
LGA    S     7_B      S     7_B     0.962     0    0.037   0.040     1.064   88.214   88.968
LGA    T     8_B      T     8_B     0.585     0    0.070   1.139     2.600   95.238   85.918
LGA    D     9_B      D     9_B     0.157     0    0.028   0.784     3.190  100.000   84.940
LGA    E    10_B      E    10_B     0.747     0    0.016   0.366     2.393   90.476   82.698
LGA    V    11_B      V    11_B     0.505     0    0.013   0.062     0.680   92.857   94.558
LGA    S    12_B      S    12_B     0.596     0    0.027   0.100     1.019   90.595   90.556
LGA    E    13_B      E    13_B     1.216     0    0.018   0.786     4.590   83.690   67.090
LGA    F    14_B      F    14_B     1.213     0    0.063   0.142     2.322   81.429   76.840
LGA    I    15_B      I    15_B     0.699     0    0.015   0.677     2.357   90.476   88.452
LGA    Q    16_B      Q    16_B     1.268     0    0.017   0.149     2.216   79.286   77.672
LGA    S    17_B      S    17_B     1.534     0    0.019   0.019     1.632   77.143   77.143
LGA    L    18_B      L    18_B     1.165     0    0.041   0.097     1.211   81.429   84.821
LGA    P    19_B      P    19_B     1.330     0    0.012   0.389     2.184   81.429   77.823
LGA    G    20_B      G    20_B     1.402     0    0.033   0.033     1.406   81.429   81.429
LGA    C    21_B      C    21_B     0.920     0    0.046   0.049     1.129   88.214   88.968
LGA    E    22_B      E    22_B     1.116     0    0.039   0.779     4.498   81.429   67.831
LGA    E    23_B      E    23_B     0.749     0    0.100   0.831     3.488   90.476   81.164
LGA    H    24_B      H    24_B     0.713     0    0.144   0.140     1.386   92.857   86.905
LGA    G    25_B      G    25_B     0.857     0    0.023   0.023     0.952   90.476   90.476
LGA    K    26_B      K    26_B     1.095     0    0.009   0.775     1.736   81.429   80.476
LGA    V    27_B      V    27_B     1.255     0    0.042   1.060     3.742   83.690   77.347
LGA    F    28_B      F    28_B     0.604     0    0.009   0.137     1.432   90.476   88.874
LGA    K    29_B      K    29_B     0.735     0    0.005   1.052     3.478   85.952   76.296
LGA    D    30_B      D    30_B     1.483     0    0.051   0.075     1.855   79.286   76.071
LGA    E    31_B      E    31_B     1.303     0    0.014   0.132     1.830   81.429   78.571
LGA    Q    32_B      Q    32_B     1.269     0    0.020   0.833     4.362   81.429   67.831
LGA    I    33_B      I    33_B     0.703     0    0.059   0.073     0.839   92.857   91.667
LGA    D    34_B      D    34_B     0.828     0    0.015   0.129     1.611   90.476   86.012
LGA    G    35_B      G    35_B     0.929     0    0.082   0.082     0.929   90.476   90.476
LGA    E    36_B      E    36_B     1.144     0    0.011   0.071     2.361   81.429   74.921
LGA    A    37_B      A    37_B     0.920     0    0.006   0.007     0.967   90.476   90.476
LGA    F    38_B      F    38_B     0.476     0    0.049   0.203     0.884   97.619   93.939
LGA    L    39_B      L    39_B     0.243     0    0.100   0.185     0.931   97.619   94.048
LGA    L    40_B      L    40_B     0.257     0    0.006   0.043     0.914  100.000   96.429
LGA    M    41_B      M    41_B     0.420     0    0.086   0.868     2.028   97.619   87.500
LGA    T    42_B      T    42_B     0.564     0    0.034   0.054     0.669   90.476   90.476
LGA    Q    43_B      Q    43_B     0.559     0    0.010   0.194     1.472   92.857   90.529
LGA    T    44_B      T    44_B     0.533     0    0.044   0.108     0.819   95.238   93.197
LGA    D    45_B      D    45_B     0.521     0    0.015   0.102     0.971   92.857   91.667
LGA    I    46_B      I    46_B     0.561     0    0.033   0.075     0.745   90.476   94.048
LGA    V    47_B      V    47_B     0.861     0    0.045   0.057     1.198   90.476   89.184
LGA    K    48_B      K    48_B     1.368     0    0.061   0.819     5.259   79.286   66.243
LGA    I    49_B      I    49_B     1.320     0    0.039   0.089     1.798   81.429   78.214
LGA    M    50_B      M    50_B     0.939     0    0.025   0.267     1.406   88.214   88.214
LGA    S    51_B      S    51_B     0.926     0    0.020   0.040     1.377   90.476   87.460
LGA    I    52_B      I    52_B     0.525     0    0.037   0.036     0.719   90.476   94.048
LGA    K    53_B      K    53_B     0.933     0    0.024   0.654     2.662   88.214   82.063
LGA    E    54_B      E    54_B     1.301     0    0.012   0.752     3.671   81.429   69.101
LGA    G    55_B      G    55_B     1.450     0    0.067   0.067     1.533   79.286   79.286
LGA    P    56_B      P    56_B     0.986     0    0.044   0.053     1.062   88.214   87.891
LGA    A    57_B      A    57_B     0.767     0    0.028   0.027     0.896   90.476   90.476
LGA    E    58_B      E    58_B     0.999     0    0.031   0.145     1.406   90.476   86.455
LGA    K    59_B      K    59_B     1.149     0    0.014   0.094     1.808   85.952   79.630
LGA    I    60_B      I    60_B     0.667     0    0.015   0.079     0.787   92.857   92.857
LGA    F    61_B      F    61_B     0.322     0    0.069   0.122     0.655  100.000   96.537
LGA    N    62_B      N    62_B     0.674     0    0.015   0.023     1.650   90.476   84.881
LGA    S    63_B      S    63_B     1.216     0    0.012   0.044     1.654   83.690   80.079
LGA    I    64_B      I    64_B     1.076     0    0.018   0.080     1.444   83.690   85.952
LGA    L    65_B      L    65_B     0.528     0    0.022   0.134     1.157   90.476   90.536
LGA    M    66_B      M    66_B     1.343     0    0.030   0.798     4.750   77.381   62.560
LGA    F    67_B      F    67_B     2.182     0    0.041   1.138     4.715   64.881   58.701
LGA    K    68_B      K    68_B     2.071     0    0.032   0.756     2.466   66.786   68.360
LGA    A    69_B      A    69_B     1.889     0    0.075   0.078     2.348   68.810   69.619
LGA    A    70_B      A    70_B     3.257     0    0.149   0.159     3.818   48.452   48.762
LGA    E    71_B      E    71_B     3.788     0    0.022   0.623     4.527   45.000   44.286

# 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):     1.230          1.233                  1.581           85.250   81.545

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   73   71    4.0     71    1.23    91.197    96.355     5.336

LGA_LOCAL      RMSD:   1.230  Number of atoms:   71  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.230  Number of assigned atoms:   71 
Std_ASGN_ATOMS RMSD:   1.230  Standard rmsd on all 71 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.099886 * X  +  -0.742846 * Y  +  -0.661968 * Z  +  24.344812
  Y_new =  -0.192934 * X  +  -0.638209 * Y  +   0.745296 * Z  +  40.259537
  Z_new =  -0.976114 * X  +   0.202161 * Y  +  -0.079572 * Z  +  -7.487733 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.048521  1.351792  1.945780   [DEG: -117.3716   77.4520  111.4850 ]
ZXZ: -2.415338  1.650453 -1.366575   [DEG: -138.3887   94.5640  -78.2990 ]
 
# END of job
