
#######################################################
#                                                     #
#                        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        1.12     1.12
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    71       1_B - 71_B        1.12     1.12
  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     1.15
  LONGEST_CONTINUOUS_SEGMENT:    67       2_B - 68_B        0.99     1.14
  LCS_AVERAGE:     93.00

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      3    7   14   70   71   71   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      3   34   63   70   71   71   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   48   63   70   71   71   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   48   63   70   71   71   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     27   48   63   70   71   71   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     27   48   63   70   71   71   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     27   48   63   70   71   71   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     27   48   63   70   71   71   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     27   48   63   70   71   71   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     27   48   63   70   71   71   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     27   48   63   70   71   71   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     18   48   63   70   71   71   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     19   48   63   70   71   71   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     15   48   63   70   71   71   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     27   48   63   70   71   71   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     27   48   63   70   71   71   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     27   48   63   70   71   71   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     27   48   63   70   71   71   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   48   63   70   71   71   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     27   48   63   70   71   71   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   48   63   70   71   71   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     27   48   63   70   71   71   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     27   48   63   70   71   71   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     15   48   63   70   71   71   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     15   48   63   70   71   71   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     14   48   63   70   71   71   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     11   46   63   70   71   71   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     20   48   63   70   71   71   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     12   48   63   70   71   71   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     11   45   63   70   71   71   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     11   46   63   70   71   71   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     12   46   63   70   71   71   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     27   48   63   70   71   71   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     27   48   63   70   71   71   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     27   48   63   70   71   71   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     25   48   63   70   71   71   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     20   48   63   70   71   71   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     21   48   63   70   71   71   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   48   63   70   71   71   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     27   48   63   70   71   71   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     27   48   63   70   71   71   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     27   48   63   70   71   71   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     15   48   63   70   71   71   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     15   48   63   70   71   71   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     15   48   63   70   71   71   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     18   48   63   70   71   71   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     15   48   63   70   71   71   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      9   39   60   70   71   71   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     14   39   63   70   71   71   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     27   48   63   70   71   71   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     27   48   63   70   71   71   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     15   48   63   70   71   71   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     15   48   63   70   71   71   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     15   46   63   70   71   71   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     14   39   63   70   71   71   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     14   39   63   70   71   71   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     15   48   63   70   71   71   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     15   39   63   70   71   71   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     11   39   62   70   71   71   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     11   33   63   70   71   71   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     20   48   63   70   71   71   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     14   48   63   70   71   71   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     11   33   63   70   71   71   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     11   42   63   70   71   71   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     11   45   63   70   71   71   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     11   42   63   70   71   71   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   33   63   70   71   71   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      5   33   63   70   71   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     11   22   51   70   71   71   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      3    3    4   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    71_B     E    71_B     35   71   71      9   22   32   54   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_AVERAGE  LCS_A:  97.67  (  93.00  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     27     48     63     70     71     71     71     71     71     71     71     71     71     71     71     71     71     71     71     71 
GDT PERCENT_AT  38.03  67.61  88.73  98.59 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.37   0.66   0.90   1.06   1.12   1.12   1.12   1.12   1.12   1.12   1.12   1.12   1.12   1.12   1.12   1.12   1.12   1.12   1.12   1.12
GDT RMS_ALL_AT   1.27   1.23   1.16   1.12   1.12   1.12   1.12   1.12   1.12   1.12   1.12   1.12   1.12   1.12   1.12   1.12   1.12   1.12   1.12   1.12

# Checking swapping
#   possible swapping detected:  D     9_B      D     9_B
#   possible swapping detected:  E    10_B      E    10_B
#   possible swapping detected:  E    22_B      E    22_B
#   possible swapping detected:  E    23_B      E    23_B
#   possible swapping detected:  E    36_B      E    36_B
#   possible swapping detected:  E    54_B      E    54_B
#   possible swapping detected:  E    71_B      E    71_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    G     1_B      G     1_B     1.964     0    0.112   0.112     2.323   79.643   79.643
LGA    S     2_B      S     2_B     1.439     0    0.154   0.257     3.727   81.429   71.032
LGA    V     3_B      V     3_B     0.825     0    0.082   0.994     3.331   90.476   77.619
LGA    S     4_B      S     4_B     0.801     0    0.084   0.546     1.991   90.476   87.540
LGA    K     5_B      K     5_B     0.455     0    0.157   0.714     2.671   90.595   81.111
LGA    W     6_B      W     6_B     0.859     0    0.020   0.097     1.669   90.476   85.374
LGA    S     7_B      S     7_B     0.966     0    0.081   0.090     1.252   90.476   87.460
LGA    T     8_B      T     8_B     0.392     0    0.032   0.990     2.595   97.619   87.483
LGA    D     9_B      D     9_B     0.773     0    0.029   0.756     3.378   90.476   78.036
LGA    E    10_B      E    10_B     0.985     0    0.033   0.401     2.717   90.476   78.995
LGA    V    11_B      V    11_B     0.597     0    0.047   0.868     2.470   90.476   85.646
LGA    S    12_B      S    12_B     0.972     0    0.028   0.521     3.007   85.952   79.206
LGA    E    13_B      E    13_B     1.247     0    0.036   1.254     7.121   81.429   57.354
LGA    F    14_B      F    14_B     1.060     0    0.039   0.215     2.611   85.952   75.498
LGA    I    15_B      I    15_B     0.779     0    0.025   0.119     0.971   90.476   90.476
LGA    Q    16_B      Q    16_B     1.137     0    0.070   0.705     2.696   81.429   76.825
LGA    S    17_B      S    17_B     1.180     0    0.078   0.095     1.249   85.952   84.444
LGA    L    18_B      L    18_B     0.898     0    0.026   0.102     1.130   85.952   88.214
LGA    P    19_B      P    19_B     1.040     0    0.031   0.446     2.125   83.690   80.340
LGA    G    20_B      G    20_B     1.081     0    0.048   0.048     1.137   81.429   81.429
LGA    C    21_B      C    21_B     0.914     0    0.063   0.077     1.058   88.214   88.968
LGA    E    22_B      E    22_B     0.909     0    0.073   0.849     2.217   90.476   80.741
LGA    E    23_B      E    23_B     0.715     0    0.175   0.673     2.628   88.214   77.196
LGA    H    24_B      H    24_B     0.526     0    0.144   0.906     2.853   97.619   85.762
LGA    G    25_B      G    25_B     0.672     0    0.031   0.031     0.672   90.476   90.476
LGA    K    26_B      K    26_B     0.766     0    0.034   0.865     2.204   90.476   81.905
LGA    V    27_B      V    27_B     1.097     0    0.036   1.075     3.476   88.214   80.816
LGA    F    28_B      F    28_B     0.609     0    0.029   0.081     0.750   90.476   93.074
LGA    K    29_B      K    29_B     0.766     0    0.024   0.457     2.128   88.214   86.614
LGA    D    30_B      D    30_B     1.284     0    0.077   0.921     3.532   81.429   69.702
LGA    E    31_B      E    31_B     1.155     0    0.109   0.396     3.024   83.690   77.037
LGA    Q    32_B      Q    32_B     1.165     0    0.056   0.738     2.633   83.690   77.937
LGA    I    33_B      I    33_B     0.487     0    0.130   0.143     0.844   97.619   96.429
LGA    D    34_B      D    34_B     0.625     0    0.034   0.109     1.166   92.857   88.274
LGA    G    35_B      G    35_B     0.653     0    0.028   0.028     0.682   90.476   90.476
LGA    E    36_B      E    36_B     1.006     0    0.048   0.913     3.538   88.214   73.915
LGA    A    37_B      A    37_B     0.852     0    0.037   0.042     1.045   90.476   88.667
LGA    F    38_B      F    38_B     0.251     0    0.031   0.387     2.532  100.000   83.983
LGA    L    39_B      L    39_B     0.200     0    0.119   0.126     1.089   97.619   92.917
LGA    L    40_B      L    40_B     0.461     0    0.180   0.954     3.037   92.976   83.333
LGA    M    41_B      M    41_B     0.471     0    0.029   1.187     2.590  100.000   85.774
LGA    T    42_B      T    42_B     0.597     0    0.040   0.044     0.862   92.857   93.197
LGA    Q    43_B      Q    43_B     1.125     0    0.032   0.416     3.721   81.429   69.894
LGA    T    44_B      T    44_B     1.255     0    0.043   0.911     3.622   81.429   73.605
LGA    D    45_B      D    45_B     0.913     0    0.037   0.204     1.276   88.214   88.214
LGA    I    46_B      I    46_B     0.582     0    0.048   0.679     2.258   90.476   87.262
LGA    V    47_B      V    47_B     1.171     0    0.024   1.150     3.841   83.690   76.054
LGA    K    48_B      K    48_B     1.686     0    0.102   0.849     6.371   75.000   57.884
LGA    I    49_B      I    49_B     1.581     0    0.020   0.095     2.361   77.143   71.964
LGA    M    50_B      M    50_B     0.678     0    0.065   0.922     2.689   90.476   85.179
LGA    S    51_B      S    51_B     0.301     0    0.028   0.722     3.080  100.000   90.079
LGA    I    52_B      I    52_B     0.368     0    0.038   0.123     1.209   97.619   92.917
LGA    K    53_B      K    53_B     0.624     0    0.041   0.969     5.003   90.476   75.926
LGA    E    54_B      E    54_B     1.171     0    0.034   1.313     4.927   83.690   67.090
LGA    G    55_B      G    55_B     1.648     0    0.046   0.046     1.648   75.000   75.000
LGA    P    56_B      P    56_B     1.407     0    0.045   0.101     1.495   81.429   81.429
LGA    A    57_B      A    57_B     0.903     0    0.044   0.042     1.125   88.214   88.667
LGA    E    58_B      E    58_B     1.419     0    0.034   0.997     5.453   81.429   63.122
LGA    K    59_B      K    59_B     1.779     0    0.029   1.148     7.743   72.857   53.968
LGA    I    60_B      I    60_B     1.128     0    0.037   0.086     1.361   85.952   83.690
LGA    F    61_B      F    61_B     0.463     0    0.034   1.185     5.682   97.619   68.745
LGA    N    62_B      N    62_B     0.708     0    0.052   0.775     2.716   90.476   80.893
LGA    S    63_B      S    63_B     1.377     0    0.041   0.752     1.571   79.286   78.571
LGA    I    64_B      I    64_B     1.290     0    0.026   0.141     1.556   81.429   80.357
LGA    L    65_B      L    65_B     0.945     0    0.042   0.228     1.149   83.690   85.952
LGA    M    66_B      M    66_B     1.140     0    0.035   0.965     3.323   83.690   78.631
LGA    F    67_B      F    67_B     1.510     0    0.050   1.142     5.230   75.000   61.645
LGA    K    68_B      K    68_B     1.711     0    0.049   0.662     2.683   72.857   69.312
LGA    A    69_B      A    69_B     2.311     0    0.661   0.599     3.823   59.405   58.952
LGA    A    70_B      A    70_B     1.682     0    0.512   0.471     3.698   68.929   63.810
LGA    E    71_B      E    71_B     3.021     0    0.689   1.106     4.076   52.500   63.386

# 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):     1.119          1.123                  1.780           86.177   79.621

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   73   71    4.0     71    1.12    91.549    96.504     5.823

LGA_LOCAL      RMSD:   1.119  Number of atoms:   71  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.119  Number of assigned atoms:   71 
Std_ASGN_ATOMS RMSD:   1.119  Standard rmsd on all 71 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.753103 * X  +  -0.588436 * Y  +  -0.294241 * Z  +  22.810631
  Y_new =   0.084457 * X  +   0.530011 * Y  +  -0.843774 * Z  +  72.904091
  Z_new =   0.652459 * X  +   0.610599 * Y  +   0.448851 * Z  +   6.452607 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.111678 -0.710824  0.936900   [DEG:    6.3987  -40.7272   53.6804 ]
ZXZ: -0.335534  1.105317  0.818528   [DEG:  -19.2247   63.3300   46.8982 ]
 
# END of job
