
#######################################################
#                                                     #
#                        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        1.40     1.40
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    71       1_B - 71_B        1.40     1.40
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    47       1_B - 47_B        0.93     1.64
  LONGEST_CONTINUOUS_SEGMENT:    47       2_B - 48_B        0.98     1.62
  LCS_AVERAGE:     60.27

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     47   71   71      5    7   48   62   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S     2_B     S     2_B     47   71   71     15   38   59   65   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V     3_B     V     3_B     47   71   71     16   39   59   65   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S     4_B     S     4_B     47   71   71     15   39   59   65   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K     5_B     K     5_B     47   71   71     16   39   59   65   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     W     6_B     W     6_B     47   71   71     16   39   59   65   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S     7_B     S     7_B     47   71   71     16   39   59   65   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     T     8_B     T     8_B     47   71   71     16   39   59   65   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D     9_B     D     9_B     47   71   71     15   39   59   65   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    10_B     E    10_B     47   71   71     15   39   59   65   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V    11_B     V    11_B     47   71   71     16   39   59   65   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    12_B     S    12_B     47   71   71     10   36   59   65   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    13_B     E    13_B     47   71   71     10   33   59   65   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    14_B     F    14_B     47   71   71     13   39   59   65   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    15_B     I    15_B     47   71   71     16   39   59   65   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     Q    16_B     Q    16_B     47   71   71     10   33   59   65   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    17_B     S    17_B     47   71   71     10   36   59   63   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    18_B     L    18_B     47   71   71     16   39   59   65   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     P    19_B     P    19_B     47   71   71     15   39   59   65   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    20_B     G    20_B     47   71   71     16   39   59   65   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     C    21_B     C    21_B     47   71   71     14   39   59   65   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    22_B     E    22_B     47   71   71      4   27   59   65   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    23_B     E    23_B     47   71   71     15   39   59   65   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     H    24_B     H    24_B     47   71   71     15   39   59   65   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    25_B     G    25_B     47   71   71     16   39   59   65   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    26_B     K    26_B     47   71   71     16   39   59   65   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V    27_B     V    27_B     47   71   71     16   39   59   65   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    28_B     F    28_B     47   71   71     16   39   59   65   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    29_B     K    29_B     47   71   71     16   39   59   65   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D    30_B     D    30_B     47   71   71     16   39   59   65   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    31_B     E    31_B     47   71   71     16   39   59   65   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     Q    32_B     Q    32_B     47   71   71     12   39   59   65   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    33_B     I    33_B     47   71   71     13   39   59   65   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D    34_B     D    34_B     47   71   71     13   39   59   65   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    35_B     G    35_B     47   71   71     13   39   59   65   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    36_B     E    36_B     47   71   71      4   33   59   65   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    37_B     A    37_B     47   71   71      6   35   59   65   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    38_B     F    38_B     47   71   71     15   38   59   65   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    39_B     L    39_B     47   71   71     15   36   59   65   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    40_B     L    40_B     47   71   71      8   34   55   65   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     M    41_B     M    41_B     47   71   71     15   39   59   65   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     T    42_B     T    42_B     47   71   71     15   39   59   65   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     Q    43_B     Q    43_B     47   71   71     15   39   59   65   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     T    44_B     T    44_B     47   71   71     15   39   59   65   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D    45_B     D    45_B     47   71   71     15   39   59   65   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    46_B     I    46_B     47   71   71      6   36   59   65   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V    47_B     V    47_B     47   71   71      6   31   59   65   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    48_B     K    48_B     47   71   71      4   10   29   57   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    49_B     I    49_B     34   71   71      4    6   14   40   65   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     M    50_B     M    50_B     34   71   71      4   33   59   65   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    51_B     S    51_B     34   71   71     15   39   59   65   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    52_B     I    52_B     34   71   71      4   25   51   65   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    53_B     K    53_B     34   71   71     11   32   59   65   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    54_B     E    54_B     34   71   71     15   39   59   65   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    55_B     G    55_B     34   71   71     15   36   59   65   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     P    56_B     P    56_B     34   71   71     15   39   59   65   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    57_B     A    57_B     34   71   71     15   39   59   65   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    58_B     E    58_B     34   71   71     15   39   59   65   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    59_B     K    59_B     34   71   71     15   39   59   65   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    60_B     I    60_B     34   71   71     15   39   59   65   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    61_B     F    61_B     34   71   71     15   39   59   65   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     N    62_B     N    62_B     34   71   71     15   39   59   65   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    63_B     S    63_B     34   71   71     15   36   59   65   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    64_B     I    64_B     34   71   71     15   36   59   65   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    65_B     L    65_B     34   71   71     15   36   59   65   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     M    66_B     M    66_B     34   71   71     15   34   54   65   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    67_B     F    67_B     34   71   71     12   32   49   65   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    68_B     K    68_B     34   71   71     12   31   49   65   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    69_B     A    69_B     34   71   71     12   32   49   65   67   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    70_B     A    70_B     34   71   71     11   21   37   53   66   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    71_B     E    71_B     34   71   71     11   21   35   50   63   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_AVERAGE  LCS_A:  86.76  (  60.27  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     16     39     59     65     67     70     71     71     71     71     71     71     71     71     71     71     71     71     71     71 
GDT PERCENT_AT  22.54  54.93  83.10  91.55  94.37  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    0.31   0.67   0.97   1.15   1.19   1.34   1.40   1.40   1.40   1.40   1.40   1.40   1.40   1.40   1.40   1.40   1.40   1.40   1.40   1.40
GDT RMS_ALL_AT   1.78   1.69   1.53   1.42   1.42   1.40   1.40   1.40   1.40   1.40   1.40   1.40   1.40   1.40   1.40   1.40   1.40   1.40   1.40   1.40

# Checking swapping
#   possible swapping detected:  D     9_B      D     9_B
#   possible swapping detected:  E    13_B      E    13_B
#   possible swapping detected:  F    28_B      F    28_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     2.482     0    0.211   0.211     3.154   65.119   65.119
LGA    S     2_B      S     2_B     1.803     0    0.023   0.714     3.380   72.857   69.048
LGA    V     3_B      V     3_B     1.715     0    0.017   0.955     3.897   72.857   65.374
LGA    S     4_B      S     4_B     1.739     0    0.028   0.134     2.151   72.857   71.508
LGA    K     5_B      K     5_B     1.625     0    0.053   0.818     5.586   77.143   58.042
LGA    W     6_B      W     6_B     1.350     0    0.076   0.135     2.097   81.429   75.986
LGA    S     7_B      S     7_B     0.944     0    0.034   0.037     1.085   88.214   88.968
LGA    T     8_B      T     8_B     0.728     0    0.017   0.097     1.108   90.476   89.184
LGA    D     9_B      D     9_B     0.528     0    0.017   0.735     2.883   90.476   81.905
LGA    E    10_B      E    10_B     0.861     0    0.015   0.356     2.500   90.476   81.693
LGA    V    11_B      V    11_B     0.756     0    0.034   0.098     1.001   90.476   89.184
LGA    S    12_B      S    12_B     1.024     0    0.030   0.085     1.371   83.690   82.937
LGA    E    13_B      E    13_B     1.627     0    0.014   0.776     5.414   75.000   58.571
LGA    F    14_B      F    14_B     1.493     0    0.047   0.283     4.039   81.429   63.766
LGA    I    15_B      I    15_B     0.633     0    0.020   0.695     1.985   90.476   88.274
LGA    Q    16_B      Q    16_B     1.735     0    0.055   0.191     3.605   72.976   65.185
LGA    S    17_B      S    17_B     2.025     0    0.013   0.017     2.242   68.810   67.460
LGA    L    18_B      L    18_B     1.329     0    0.127   1.381     3.408   81.429   74.345
LGA    P    19_B      P    19_B     1.275     0    0.026   0.395     2.251   81.429   77.823
LGA    G    20_B      G    20_B     1.019     0    0.062   0.062     1.155   85.952   85.952
LGA    C    21_B      C    21_B     0.911     0    0.044   0.059     1.150   85.952   85.952
LGA    E    22_B      E    22_B     1.694     0    0.054   1.063     5.420   77.143   61.270
LGA    E    23_B      E    23_B     0.988     0    0.084   0.830     3.698   88.214   75.661
LGA    H    24_B      H    24_B     0.430     0    0.054   0.064     1.217   97.619   90.619
LGA    G    25_B      G    25_B     0.337     0    0.027   0.027     0.489  100.000  100.000
LGA    K    26_B      K    26_B     0.706     0    0.024   0.768     1.727   90.476   86.508
LGA    V    27_B      V    27_B     0.915     0    0.044   1.047     3.486   90.476   80.884
LGA    F    28_B      F    28_B     0.607     0    0.013   0.406     1.270   90.476   88.874
LGA    K    29_B      K    29_B     0.578     0    0.022   0.805     2.352   90.476   84.921
LGA    D    30_B      D    30_B     1.118     0    0.052   0.079     1.299   83.690   82.560
LGA    E    31_B      E    31_B     1.276     0    0.021   0.136     1.600   81.429   80.476
LGA    Q    32_B      Q    32_B     1.208     0    0.024   0.764     4.095   81.429   68.783
LGA    I    33_B      I    33_B     1.129     0    0.075   0.633     1.885   81.429   80.357
LGA    D    34_B      D    34_B     1.245     0    0.019   0.141     2.027   85.952   79.464
LGA    G    35_B      G    35_B     0.707     0    0.070   0.070     0.962   90.476   90.476
LGA    E    36_B      E    36_B     1.144     0    0.014   0.087     3.004   83.690   70.741
LGA    A    37_B      A    37_B     1.095     0    0.058   0.055     1.154   83.690   83.238
LGA    F    38_B      F    38_B     0.804     0    0.028   0.927     3.196   90.476   75.325
LGA    L    39_B      L    39_B     0.686     0    0.114   1.413     3.522   85.952   76.131
LGA    L    40_B      L    40_B     1.236     0    0.045   0.051     2.135   85.952   78.452
LGA    M    41_B      M    41_B     0.523     0    0.059   0.146     1.168   92.857   90.536
LGA    T    42_B      T    42_B     0.636     0    0.011   0.028     0.684   90.476   90.476
LGA    Q    43_B      Q    43_B     0.945     0    0.015   1.016     3.760   90.476   73.968
LGA    T    44_B      T    44_B     1.093     0    0.023   0.095     1.540   85.952   82.789
LGA    D    45_B      D    45_B     0.815     0    0.014   0.208     1.209   85.952   87.083
LGA    I    46_B      I    46_B     1.065     0    0.074   0.082     1.490   83.690   83.690
LGA    V    47_B      V    47_B     1.412     0    0.028   0.086     2.111   77.143   75.374
LGA    K    48_B      K    48_B     2.687     0    0.017   0.966     8.352   57.262   41.111
LGA    I    49_B      I    49_B     3.102     0    0.012   0.104     4.948   55.357   45.595
LGA    M    50_B      M    50_B     1.734     0    0.024   0.909     4.424   77.143   62.976
LGA    S    51_B      S    51_B     0.772     0    0.090   0.087     1.259   85.952   85.952
LGA    I    52_B      I    52_B     1.703     0    0.113   1.204     3.333   75.000   67.143
LGA    K    53_B      K    53_B     1.324     0    0.037   0.637     1.673   81.429   78.571
LGA    E    54_B      E    54_B     1.083     0    0.017   0.753     3.230   83.690   74.392
LGA    G    55_B      G    55_B     1.143     0    0.073   0.073     1.270   81.429   81.429
LGA    P    56_B      P    56_B     0.943     0    0.039   0.051     1.024   90.476   89.184
LGA    A    57_B      A    57_B     0.852     0    0.022   0.021     0.953   90.476   90.476
LGA    E    58_B      E    58_B     0.854     0    0.013   0.796     3.706   90.476   75.820
LGA    K    59_B      K    59_B     0.942     0    0.003   0.134     1.113   90.476   85.450
LGA    I    60_B      I    60_B     0.635     0    0.028   0.064     0.745   92.857   91.667
LGA    F    61_B      F    61_B     0.447     0    0.086   0.168     1.275  100.000   92.338
LGA    N    62_B      N    62_B     0.566     0    0.032   0.051     1.029   90.476   89.345
LGA    S    63_B      S    63_B     1.019     0    0.010   0.707     1.189   85.952   84.444
LGA    I    64_B      I    64_B     0.806     0    0.006   0.074     1.035   88.214   90.536
LGA    L    65_B      L    65_B     0.507     0    0.023   1.010     2.886   88.214   85.238
LGA    M    66_B      M    66_B     1.511     0    0.017   0.812     4.670   72.976   60.357
LGA    F    67_B      F    67_B     2.103     0    0.054   1.252     4.680   64.881   60.476
LGA    K    68_B      K    68_B     2.000     0    0.030   0.906     3.145   64.881   60.741
LGA    A    69_B      A    69_B     2.057     0    0.072   0.075     2.488   66.786   68.000
LGA    A    70_B      A    70_B     3.220     0    0.154   0.165     3.646   50.119   50.095
LGA    E    71_B      E    71_B     3.626     0    0.016   0.721     3.990   46.667   50.265

# 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):     1.400          1.392                  1.908           82.202   76.993

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   73   71    4.0     71    1.40    86.620    94.131     4.732

LGA_LOCAL      RMSD:   1.400  Number of atoms:   71  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.400  Number of assigned atoms:   71 
Std_ASGN_ATOMS RMSD:   1.400  Standard rmsd on all 71 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.023101 * X  +  -0.942466 * Y  +  -0.333503 * Z  +  24.906469
  Y_new =  -0.999424 * X  +   0.030062 * Y  +  -0.015723 * Z  +  41.556171
  Z_new =   0.024844 * X  +   0.332948 * Y  +  -0.942618 * Z  +  -9.979763 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.593907 -0.024847  2.802055   [DEG:  -91.3241   -1.4236  160.5459 ]
ZXZ: -1.523685  2.801183  0.074482   [DEG:  -87.3007  160.4959    4.2675 ]
 
# END of job
