
#######################################################
#                                                     #
#                        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   68 (  529),  selected   67 , name one
# Molecule2: number of CA atoms   67 (  519),  selected   67 , 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:    67       2_A - 68_A        0.80     0.80
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    67       2_A - 68_A        0.80     0.80
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    67       2_A - 68_A        0.80     0.80
  LCS_AVERAGE:    100.00

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   67
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     S     2_A     S     2_A     67   67   67     13   43   57   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     P     3_A     P     3_A     67   67   67     20   43   60   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E     4_A     E     4_A     67   67   67     16   43   60   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E     5_A     E     5_A     67   67   67     16   44   63   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q     6_A     Q     6_A     67   67   67     21   44   63   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K     7_A     K     7_A     67   67   67     26   60   63   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q     8_A     Q     8_A     67   67   67     21   60   63   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     M     9_A     M     9_A     67   67   67     21   60   63   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    10_A     L    10_A     67   67   67     37   60   63   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     G    11_A     G    11_A     67   67   67     54   60   63   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    12_A     E    12_A     67   67   67     54   60   63   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    13_A     A    13_A     67   67   67     54   60   63   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     I    14_A     I    14_A     67   67   67     54   60   63   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Y    15_A     Y    15_A     67   67   67     54   60   63   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     P    16_A     P    16_A     67   67   67     54   60   63   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K    17_A     K    17_A     67   67   67     54   60   63   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    18_A     V    18_A     67   67   67     54   60   63   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    19_A     A    19_A     67   67   67     54   60   63   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    20_A     A    20_A     67   67   67     36   60   63   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     S    21_A     S    21_A     67   67   67     54   60   63   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q    22_A     Q    22_A     67   67   67     54   60   63   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     P    23_A     P    23_A     67   67   67     45   60   63   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    24_A     E    24_A     67   67   67     54   60   63   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    25_A     L    25_A     67   67   67     54   60   63   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    26_A     A    26_A     67   67   67     54   60   63   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     G    27_A     G    27_A     67   67   67     54   60   63   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K    28_A     K    28_A     67   67   67     54   60   63   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    29_A     L    29_A     67   67   67     54   60   63   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     T    30_A     T    30_A     67   67   67     54   60   63   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     G    31_A     G    31_A     67   67   67     54   60   63   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     M    32_A     M    32_A     67   67   67     54   60   63   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     I    33_A     I    33_A     67   67   67     54   60   63   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    34_A     L    34_A     67   67   67     54   60   63   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    35_A     E    35_A     67   67   67     54   60   63   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    36_A     L    36_A     67   67   67     54   60   63   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     P    37_A     P    37_A     67   67   67     54   60   63   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    38_A     V    38_A     67   67   67     54   60   63   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     T    39_A     T    39_A     67   67   67     54   60   63   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    40_A     E    40_A     67   67   67     54   60   63   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    41_A     L    41_A     67   67   67     54   60   63   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    42_A     L    42_A     67   67   67     54   60   63   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     H    43_A     H    43_A     67   67   67     54   60   63   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    44_A     L    44_A     67   67   67     54   60   63   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    45_A     L    45_A     67   67   67     54   60   63   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    46_A     E    46_A     67   67   67     54   60   63   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    47_A     E    47_A     67   67   67     54   60   63   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     S    48_A     S    48_A     67   67   67     54   60   63   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    49_A     E    49_A     67   67   67     54   60   63   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    50_A     A    50_A     67   67   67     54   60   63   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    51_A     L    51_A     67   67   67     54   60   63   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     D    52_A     D    52_A     67   67   67     54   60   63   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    53_A     A    53_A     67   67   67     54   60   63   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K    54_A     K    54_A     67   67   67     54   60   63   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    55_A     V    55_A     67   67   67     54   60   63   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     N    56_A     N    56_A     67   67   67     54   60   63   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    57_A     E    57_A     67   67   67     54   60   63   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    58_A     A    58_A     67   67   67     54   60   63   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    59_A     L    59_A     67   67   67     54   60   63   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    60_A     E    60_A     67   67   67     54   60   63   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    61_A     V    61_A     67   67   67     54   60   63   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    62_A     L    62_A     67   67   67     54   60   63   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K    63_A     K    63_A     67   67   67     54   60   63   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    64_A     E    64_A     67   67   67     54   60   63   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Y    65_A     Y    65_A     67   67   67     54   60   63   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q    66_A     Q    66_A     67   67   67     49   58   62   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q    67_A     Q    67_A     67   67   67     54   60   63   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     N    68_A     N    68_A     67   67   67      4   46   63   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_AVERAGE  LCS_A: 100.00  ( 100.00  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     54     60     63     66     67     67     67     67     67     67     67     67     67     67     67     67     67     67     67     67 
GDT PERCENT_AT  80.60  89.55  94.03  98.51 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.29   0.45   0.64   0.74   0.80   0.80   0.80   0.80   0.80   0.80   0.80   0.80   0.80   0.80   0.80   0.80   0.80   0.80   0.80   0.80
GDT RMS_ALL_AT   0.98   0.89   0.82   0.80   0.80   0.80   0.80   0.80   0.80   0.80   0.80   0.80   0.80   0.80   0.80   0.80   0.80   0.80   0.80   0.80

# Checking swapping
#   possible swapping detected:  E     4_A      E     4_A
#   possible swapping detected:  E     5_A      E     5_A
#   possible swapping detected:  E    12_A      E    12_A
#   possible swapping detected:  E    40_A      E    40_A
#   possible swapping detected:  E    46_A      E    46_A
#   possible swapping detected:  E    47_A      E    47_A
#   possible swapping detected:  E    49_A      E    49_A
#   possible swapping detected:  D    52_A      D    52_A
#   possible swapping detected:  E    57_A      E    57_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     2_A      S     2_A     2.494     0    0.018   0.047     2.671   62.857   60.952
LGA    P     3_A      P     3_A     1.902     0    0.010   0.039     2.248   72.976   70.612
LGA    E     4_A      E     4_A     1.804     0    0.021   0.687     4.367   75.000   60.582
LGA    E     5_A      E     5_A     1.630     0    0.047   0.812     5.015   79.405   64.497
LGA    Q     6_A      Q     6_A     1.367     0    0.040   0.304     1.800   83.690   77.672
LGA    K     7_A      K     7_A     0.688     0    0.037   0.624     2.033   92.857   84.762
LGA    Q     8_A      Q     8_A     0.830     0    0.015   0.792     4.341   92.857   76.402
LGA    M     9_A      M     9_A     0.808     0    0.016   0.815     2.152   90.476   87.321
LGA    L    10_A      L    10_A     0.491     0    0.026   0.053     0.762   97.619   96.429
LGA    G    11_A      G    11_A     0.343     0    0.019   0.019     0.586   97.619   97.619
LGA    E    12_A      E    12_A     0.496     0    0.022   0.910     3.236  100.000   88.201
LGA    A    13_A      A    13_A     0.455     0    0.023   0.025     0.544   97.619   98.095
LGA    I    14_A      I    14_A     0.454     0    0.012   0.076     0.546   97.619   97.619
LGA    Y    15_A      Y    15_A     0.410     0    0.033   0.230     0.764  100.000   95.238
LGA    P    16_A      P    16_A     0.422     0    0.007   0.272     1.260  100.000   95.986
LGA    K    17_A      K    17_A     0.482     0    0.032   0.681     2.351   97.619   88.836
LGA    V    18_A      V    18_A     0.466     0    0.012   0.027     0.538   92.857   95.918
LGA    A    19_A      A    19_A     0.484     0    0.013   0.012     0.604   95.238   96.190
LGA    A    20_A      A    20_A     0.562     0    0.067   0.078     0.868   90.476   90.476
LGA    S    21_A      S    21_A     0.222     0    0.077   0.085     0.746  100.000   98.413
LGA    Q    22_A      Q    22_A     0.195     0    0.029   0.071     0.694  100.000   95.767
LGA    P    23_A      P    23_A     0.576     0    0.042   0.065     0.941   92.857   91.837
LGA    E    24_A      E    24_A     0.501     0    0.047   0.155     0.974   92.857   94.709
LGA    L    25_A      L    25_A     0.308     0    0.057   0.054     0.462  100.000  100.000
LGA    A    26_A      A    26_A     0.352     0    0.012   0.012     0.461  100.000  100.000
LGA    G    27_A      G    27_A     0.457     0    0.013   0.013     0.459  100.000  100.000
LGA    K    28_A      K    28_A     0.425     0    0.013   1.166     5.910  100.000   75.714
LGA    L    29_A      L    29_A     0.113     0    0.011   0.051     0.491  100.000  100.000
LGA    T    30_A      T    30_A     0.408     0    0.027   0.044     0.585  100.000   95.918
LGA    G    31_A      G    31_A     0.555     0    0.006   0.006     0.555   97.619   97.619
LGA    M    32_A      M    32_A     0.326     0    0.030   0.106     0.524  100.000   96.429
LGA    I    33_A      I    33_A     0.138     0    0.014   0.132     0.548  100.000   98.810
LGA    L    34_A      L    34_A     0.245     0    0.032   0.067     0.370  100.000  100.000
LGA    E    35_A      E    35_A     0.537     0    0.080   0.658     3.313   90.595   72.540
LGA    L    36_A      L    36_A     0.527     0    0.006   0.064     0.620   90.476   95.238
LGA    P    37_A      P    37_A     0.795     0    0.036   0.276     1.543   90.476   87.959
LGA    V    38_A      V    38_A     1.026     0    0.010   0.085     1.240   85.952   84.014
LGA    T    39_A      T    39_A     1.082     0    0.011   1.017     3.377   85.952   76.054
LGA    E    40_A      E    40_A     0.738     0    0.011   1.100     4.038   90.476   74.286
LGA    L    41_A      L    41_A     0.594     0    0.005   0.027     0.640   90.476   91.667
LGA    L    42_A      L    42_A     0.787     0    0.010   0.052     1.086   90.476   89.345
LGA    H    43_A      H    43_A     0.735     0    0.014   1.133     2.674   90.476   81.905
LGA    L    44_A      L    44_A     0.606     0    0.010   0.155     0.634   90.476   92.857
LGA    L    45_A      L    45_A     0.544     0    0.007   0.053     0.582   90.476   91.667
LGA    E    46_A      E    46_A     0.669     0    0.013   0.782     3.951   90.476   74.180
LGA    E    47_A      E    47_A     0.748     0    0.054   0.097     0.950   90.476   90.476
LGA    S    48_A      S    48_A     0.656     0    0.009   0.038     0.957   92.857   92.063
LGA    E    49_A      E    49_A     0.580     0    0.070   0.539     1.591   95.238   89.630
LGA    A    50_A      A    50_A     0.210     0    0.008   0.010     0.325  100.000  100.000
LGA    L    51_A      L    51_A     0.158     0    0.026   0.093     0.552  100.000   98.810
LGA    D    52_A      D    52_A     0.220     0    0.011   0.132     0.502  100.000   98.810
LGA    A    53_A      A    53_A     0.289     0    0.026   0.033     0.450  100.000  100.000
LGA    K    54_A      K    54_A     0.116     0    0.006   0.595     2.480  100.000   91.111
LGA    V    55_A      V    55_A     0.106     0    0.017   0.024     0.178  100.000  100.000
LGA    N    56_A      N    56_A     0.294     0    0.013   0.069     0.361  100.000  100.000
LGA    E    57_A      E    57_A     0.350     0    0.034   0.099     0.754  100.000   96.825
LGA    A    58_A      A    58_A     0.339     0    0.016   0.016     0.383  100.000  100.000
LGA    L    59_A      L    59_A     0.276     0    0.003   0.226     1.060  100.000   95.298
LGA    E    60_A      E    60_A     0.522     0    0.033   1.157     5.108   95.238   76.085
LGA    V    61_A      V    61_A     0.539     0    0.008   0.064     0.709   92.857   94.558
LGA    L    62_A      L    62_A     0.754     0    0.022   0.049     0.989   90.476   90.476
LGA    K    63_A      K    63_A     0.958     0    0.026   0.228     1.261   88.214   85.450
LGA    E    64_A      E    64_A     0.801     0    0.004   0.985     3.192   88.214   72.275
LGA    Y    65_A      Y    65_A     1.002     0    0.016   0.241     1.863   83.690   80.833
LGA    Q    66_A      Q    66_A     1.355     0    0.072   0.108     3.265   81.429   69.735
LGA    Q    67_A      Q    67_A     0.937     0    0.254   0.561     3.944   90.595   74.921
LGA    N    68_A      N    68_A     1.994     0    0.116   1.054     5.498   52.976   45.893

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       67     268    268  100.00     519    519  100.00                67
SUMMARY(RMSD_GDC):     0.798          0.867                  1.373           92.823   88.412

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   68   67    4.0     67    0.80    97.015    98.625     7.461

LGA_LOCAL      RMSD:   0.798  Number of atoms:   67  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.798  Number of assigned atoms:   67 
Std_ASGN_ATOMS RMSD:   0.798  Standard rmsd on all 67 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.787042 * X  +  -0.138937 * Y  +   0.601050 * Z  +   9.738993
  Y_new =   0.604413 * X  +   0.021369 * Y  +   0.796385 * Z  +   3.889834
  Z_new =  -0.123491 * X  +   0.990071 * Y  +   0.067157 * Z  +   6.882637 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.486699  0.123807  1.503070   [DEG:  142.4774    7.0936   86.1195 ]
ZXZ:  2.495075  1.503589 -0.124089   [DEG:  142.9573   86.1493   -7.1098 ]
 
# END of job
