
#######################################################
#                                                     #
#                        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        0.69     0.69
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    71       1_B - 71_B        0.69     0.69
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    71       1_B - 71_B        0.69     0.69
  LCS_AVERAGE:    100.00

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     71   71   71      4   42   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S     2_B     S     2_B     71   71   71     45   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V     3_B     V     3_B     71   71   71     45   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S     4_B     S     4_B     71   71   71     44   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K     5_B     K     5_B     71   71   71     45   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     W     6_B     W     6_B     71   71   71     45   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S     7_B     S     7_B     71   71   71     45   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     T     8_B     T     8_B     71   71   71     45   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D     9_B     D     9_B     71   71   71     45   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    10_B     E    10_B     71   71   71     45   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V    11_B     V    11_B     71   71   71     45   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    12_B     S    12_B     71   71   71     45   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    13_B     E    13_B     71   71   71     45   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    14_B     F    14_B     71   71   71     45   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    15_B     I    15_B     71   71   71     45   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     Q    16_B     Q    16_B     71   71   71     45   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    17_B     S    17_B     71   71   71     45   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    18_B     L    18_B     71   71   71     45   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     P    19_B     P    19_B     71   71   71     39   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    20_B     G    20_B     71   71   71     39   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     C    21_B     C    21_B     71   71   71     45   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    22_B     E    22_B     71   71   71     45   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    23_B     E    23_B     71   71   71     45   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     H    24_B     H    24_B     71   71   71     45   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    25_B     G    25_B     71   71   71     45   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    26_B     K    26_B     71   71   71     45   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V    27_B     V    27_B     71   71   71     39   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    28_B     F    28_B     71   71   71     45   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    29_B     K    29_B     71   71   71     45   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D    30_B     D    30_B     71   71   71     39   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    31_B     E    31_B     71   71   71     39   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     Q    32_B     Q    32_B     71   71   71     39   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    33_B     I    33_B     71   71   71     45   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D    34_B     D    34_B     71   71   71     45   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    35_B     G    35_B     71   71   71     45   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    36_B     E    36_B     71   71   71     32   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    37_B     A    37_B     71   71   71     45   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    38_B     F    38_B     71   71   71     45   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    39_B     L    39_B     71   71   71     44   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    40_B     L    40_B     71   71   71     45   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     M    41_B     M    41_B     71   71   71     45   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     T    42_B     T    42_B     71   71   71     13   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     Q    43_B     Q    43_B     71   71   71     21   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     T    44_B     T    44_B     71   71   71     43   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D    45_B     D    45_B     71   71   71     45   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    46_B     I    46_B     71   71   71     27   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V    47_B     V    47_B     71   71   71     44   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    48_B     K    48_B     71   71   71     18   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    49_B     I    49_B     71   71   71     13   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     M    50_B     M    50_B     71   71   71     16   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    51_B     S    51_B     71   71   71     27   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    52_B     I    52_B     71   71   71     45   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    53_B     K    53_B     71   71   71     45   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    54_B     E    54_B     71   71   71     45   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    55_B     G    55_B     71   71   71     45   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     P    56_B     P    56_B     71   71   71     45   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    57_B     A    57_B     71   71   71     45   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    58_B     E    58_B     71   71   71     45   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    59_B     K    59_B     71   71   71     45   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    60_B     I    60_B     71   71   71     45   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    61_B     F    61_B     71   71   71     45   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     N    62_B     N    62_B     71   71   71     45   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    63_B     S    63_B     71   71   71     45   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    64_B     I    64_B     71   71   71     45   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    65_B     L    65_B     71   71   71     37   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     M    66_B     M    66_B     71   71   71     29   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    67_B     F    67_B     71   71   71     21   66   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    68_B     K    68_B     71   71   71     21   59   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    69_B     A    69_B     71   71   71     21   46   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    70_B     A    70_B     71   71   71      8   46   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    71_B     E    71_B     71   71   71      8   46   67   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
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     45     66     69     71     71     71     71     71     71     71     71     71     71     71     71     71     71     71     71     71 
GDT PERCENT_AT  63.38  92.96  97.18 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.37   0.53   0.62   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69
GDT RMS_ALL_AT   0.73   0.71   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69   0.69

# Checking swapping
#   possible swapping detected:  D     9_B      D     9_B
#   possible swapping detected:  E    10_B      E    10_B
#   possible swapping detected:  F    14_B      F    14_B
#   possible swapping detected:  E    22_B      E    22_B
#   possible swapping detected:  F    28_B      F    28_B
#   possible swapping detected:  E    31_B      E    31_B
#   possible swapping detected:  E    36_B      E    36_B
#   possible swapping detected:  F    38_B      F    38_B
#   possible swapping detected:  F    61_B      F    61_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     1.771     0    0.331   0.331     2.898   80.119   80.119
LGA    S     2_B      S     2_B     0.685     0    0.035   0.726     2.832   92.857   86.508
LGA    V     3_B      V     3_B     0.217     0    0.063   0.057     0.392  100.000  100.000
LGA    S     4_B      S     4_B     0.646     0    0.041   0.165     0.949   90.476   90.476
LGA    K     5_B      K     5_B     0.547     0    0.040   0.827     4.847   92.857   72.698
LGA    W     6_B      W     6_B     0.639     0    0.047   0.102     0.666   90.476   93.878
LGA    S     7_B      S     7_B     0.573     0    0.018   0.035     0.613   90.476   92.063
LGA    T     8_B      T     8_B     0.547     0    0.042   0.138     0.729   90.476   90.476
LGA    D     9_B      D     9_B     0.410     0    0.059   0.776     3.472  100.000   84.940
LGA    E    10_B      E    10_B     0.369     0    0.022   0.305     1.727  100.000   91.799
LGA    V    11_B      V    11_B     0.452     0    0.017   0.031     0.549  100.000   97.279
LGA    S    12_B      S    12_B     0.476     0    0.022   0.036     0.594  100.000   96.825
LGA    E    13_B      E    13_B     0.378     0    0.036   0.801     3.850  100.000   81.587
LGA    F    14_B      F    14_B     0.370     0    0.019   0.196     1.465  100.000   90.649
LGA    I    15_B      I    15_B     0.388     0    0.013   0.625     1.715  100.000   95.417
LGA    Q    16_B      Q    16_B     0.403     0    0.021   0.362     1.045  100.000   96.878
LGA    S    17_B      S    17_B     0.594     0    0.027   0.037     0.725   92.857   92.063
LGA    L    18_B      L    18_B     0.577     0    0.084   0.125     0.577   92.857   92.857
LGA    P    19_B      P    19_B     0.830     0    0.070   0.381     2.163   90.476   84.218
LGA    G    20_B      G    20_B     0.724     0    0.100   0.100     0.991   90.476   90.476
LGA    C    21_B      C    21_B     0.331     0    0.027   0.089     0.502  100.000   98.413
LGA    E    22_B      E    22_B     0.417     0    0.042   0.137     1.007   97.619   93.704
LGA    E    23_B      E    23_B     0.470     0    0.058   1.102     5.205   97.619   73.175
LGA    H    24_B      H    24_B     0.310     0    0.111   0.100     0.750  100.000   97.143
LGA    G    25_B      G    25_B     0.409     0    0.013   0.013     0.486  100.000  100.000
LGA    K    26_B      K    26_B     0.533     0    0.014   0.604     2.333   90.476   89.735
LGA    V    27_B      V    27_B     0.832     0    0.055   1.112     3.446   90.476   82.109
LGA    F    28_B      F    28_B     0.320     0    0.028   0.054     0.511  100.000   99.134
LGA    K    29_B      K    29_B     0.503     0    0.020   0.787     2.624   92.857   84.233
LGA    D    30_B      D    30_B     0.995     0    0.067   0.097     1.304   85.952   83.690
LGA    E    31_B      E    31_B     0.938     0    0.025   0.176     1.558   90.476   86.508
LGA    Q    32_B      Q    32_B     0.887     0    0.061   0.153     1.392   90.476   85.450
LGA    I    33_B      I    33_B     0.513     0    0.048   0.619     1.633   92.857   91.845
LGA    D    34_B      D    34_B     0.554     0    0.034   0.125     1.027   95.238   91.726
LGA    G    35_B      G    35_B     0.380     0    0.045   0.045     0.494  100.000  100.000
LGA    E    36_B      E    36_B     0.612     0    0.044   0.125     1.653   90.476   86.508
LGA    A    37_B      A    37_B     0.544     0    0.058   0.068     0.568   95.238   96.190
LGA    F    38_B      F    38_B     0.335     0    0.027   0.219     0.789  100.000   97.403
LGA    L    39_B      L    39_B     0.388     0    0.079   0.199     0.622   97.619   95.238
LGA    L    40_B      L    40_B     0.204     0    0.106   0.186     0.692   97.619   95.238
LGA    M    41_B      M    41_B     0.177     0    0.083   0.103     0.536  100.000   98.810
LGA    T    42_B      T    42_B     0.671     0    0.041   0.048     0.824   90.476   90.476
LGA    Q    43_B      Q    43_B     0.694     0    0.019   0.596     2.616   90.476   84.762
LGA    T    44_B      T    44_B     0.586     0    0.014   0.095     0.805   92.857   93.197
LGA    D    45_B      D    45_B     0.438     0    0.023   0.170     0.875  100.000   95.238
LGA    I    46_B      I    46_B     0.565     0    0.031   0.061     0.939   90.476   90.476
LGA    V    47_B      V    47_B     0.478     0    0.027   0.043     0.517   97.619   97.279
LGA    K    48_B      K    48_B     0.859     0    0.020   0.949     5.190   88.214   74.921
LGA    I    49_B      I    49_B     0.995     0    0.081   0.124     1.014   88.214   88.214
LGA    M    50_B      M    50_B     1.004     0    0.019   0.688     1.724   88.214   86.012
LGA    S    51_B      S    51_B     0.850     0    0.028   0.034     1.250   90.476   88.968
LGA    I    52_B      I    52_B     0.458     0    0.026   0.044     0.721   97.619   96.429
LGA    K    53_B      K    53_B     0.376     0    0.027   0.678     3.160  100.000   86.772
LGA    E    54_B      E    54_B     0.347     0    0.039   0.750     3.775  100.000   82.328
LGA    G    55_B      G    55_B     0.266     0    0.021   0.021     0.291  100.000  100.000
LGA    P    56_B      P    56_B     0.251     0    0.022   0.285     0.783  100.000   98.639
LGA    A    57_B      A    57_B     0.253     0    0.020   0.025     0.345  100.000  100.000
LGA    E    58_B      E    58_B     0.401     0    0.034   0.152     0.581  100.000   97.884
LGA    K    59_B      K    59_B     0.345     0    0.026   0.070     0.392  100.000  100.000
LGA    I    60_B      I    60_B     0.205     0    0.017   0.035     0.232  100.000  100.000
LGA    F    61_B      F    61_B     0.284     0    0.034   0.044     0.584  100.000   96.537
LGA    N    62_B      N    62_B     0.327     0    0.035   0.058     0.472  100.000  100.000
LGA    S    63_B      S    63_B     0.290     0    0.024   0.075     0.334  100.000  100.000
LGA    I    64_B      I    64_B     0.359     0    0.011   0.044     0.471  100.000  100.000
LGA    L    65_B      L    65_B     0.477     0    0.020   0.138     0.810   95.238   96.429
LGA    M    66_B      M    66_B     0.676     0    0.021   0.833     2.964   90.476   78.929
LGA    F    67_B      F    67_B     0.843     0    0.040   0.291     1.301   88.214   88.831
LGA    K    68_B      K    68_B     1.111     0    0.055   0.955     2.717   81.548   79.788
LGA    A    69_B      A    69_B     1.356     0    0.060   0.069     1.549   77.143   78.000
LGA    A    70_B      A    70_B     1.765     0    0.116   0.131     2.275   70.833   71.238
LGA    E    71_B      E    71_B     1.971     0    0.130   0.643     2.148   72.857   74.868

# 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):     0.686          0.691                  1.066           94.230   90.756

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   73   71    4.0     71    0.69    98.239    99.234     9.030

LGA_LOCAL      RMSD:   0.686  Number of atoms:   71  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.686  Number of assigned atoms:   71 
Std_ASGN_ATOMS RMSD:   0.686  Standard rmsd on all 71 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.706807 * X  +   0.459513 * Y  +   0.537839 * Z  +  18.523031
  Y_new =  -0.632339 * X  +   0.751243 * Y  +   0.189157 * Z  +  38.035995
  Z_new =  -0.317128 * X  +  -0.473794 * Y  +   0.821553 * Z  +   3.374701 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.729847  0.322700 -0.523115   [DEG:  -41.8172   18.4893  -29.9723 ]
ZXZ:  1.908983  0.606667 -2.551744   [DEG:  109.3766   34.7595 -146.2041 ]
 
# END of job
