
#######################################################
#                                                     #
#                        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        0.95     0.95
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    71       1_B - 71_B        0.95     0.95
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    71       1_B - 71_B        0.95     0.95
  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   19   63   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     71   71   71     15   56   68   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     71   71   71     27   56   68   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     71   71   71     27   56   68   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     71   71   71     27   56   68   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     71   71   71     27   56   68   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     71   71   71     27   56   68   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     71   71   71     27   56   68   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     71   71   71     15   56   68   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     71   71   71     15   56   68   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     71   71   71     22   56   68   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     71   71   71     15   53   68   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     71   71   71     12   52   68   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     71   71   71     27   56   68   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     71   71   71     13   56   68   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     71   71   71     15   53   68   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     71   71   71     15   56   68   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     71   71   71     26   56   68   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     71   71   71     15   56   68   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     71   71   71     12   56   68   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     71   71   71     27   56   68   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     71   71   71     27   56   68   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     71   71   71     27   56   68   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     71   71   71     27   56   68   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     71   71   71      9   51   68   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     71   71   71     10   56   68   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     71   71   71     22   56   68   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     71   71   71     13   56   68   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     71   71   71      9   56   68   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     71   71   71     15   56   68   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     71   71   71     15   56   68   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     71   71   71     15   56   68   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     71   71   71     15   56   68   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     71   71   71     15   56   68   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     71   71   71     27   56   68   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     71   71   71     15   56   68   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     71   71   71     15   56   68   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     71   71   71     13   56   68   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     71   71   71     14   56   68   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     71   71   71     15   56   68   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     71   71   71     15   56   68   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     71   71   71     27   56   68   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     71   71   71     27   56   68   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     71   71   71     27   56   68   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     71   71   71     27   56   68   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     71   71   71     27   56   68   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     71   71   71     27   56   68   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     71   71   71     27   56   68   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     71   71   71     27   56   68   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     71   71   71     27   56   68   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     71   71   71     27   56   68   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     71   71   71     27   56   68   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     71   71   71     27   56   68   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     71   71   71     27   56   68   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     71   71   71     27   56   68   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     71   71   71     27   56   68   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     71   71   71     27   56   68   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     71   71   71     27   56   68   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     71   71   71     11   56   68   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     71   71   71     11   56   68   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     71   71   71     12   56   68   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     71   71   71     11   56   68   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     71   71   71      8   24   68   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     71   71   71      8   31   68   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     71   71   71     12   53   68   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     71   71   71     10   43   68   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     71   71   71     10   24   68   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     71   71   71      7   43   68   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     71   71   71      4   31   68   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     71   71   71      4   15   68   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     71   71   71      3   23   48   70   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     27     56     68     70     71     71     71     71     71     71     71     71     71     71     71     71     71     71     71     71 
GDT PERCENT_AT  38.03  78.87  95.77  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    0.32   0.64   0.86   0.91   0.95   0.95   0.95   0.95   0.95   0.95   0.95   0.95   0.95   0.95   0.95   0.95   0.95   0.95   0.95   0.95
GDT RMS_ALL_AT   1.15   1.05   0.96   0.95   0.95   0.95   0.95   0.95   0.95   0.95   0.95   0.95   0.95   0.95   0.95   0.95   0.95   0.95   0.95   0.95

# Checking swapping
#   possible swapping detected:  D     9_B      D     9_B
#   possible swapping detected:  E    10_B      E    10_B
#   possible swapping detected:  E    23_B      E    23_B
#   possible swapping detected:  E    54_B      E    54_B
#   possible swapping detected:  E    58_B      E    58_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     2.229     0    0.344   0.344     3.223   67.262   67.262
LGA    S     2_B      S     2_B     1.277     0    0.103   0.628     2.734   83.810   78.968
LGA    V     3_B      V     3_B     0.921     0    0.077   1.225     4.217   88.214   75.510
LGA    S     4_B      S     4_B     0.869     0    0.058   0.137     1.509   90.476   86.032
LGA    K     5_B      K     5_B     0.221     0    0.163   1.019     6.047   92.857   71.164
LGA    W     6_B      W     6_B     0.678     0    0.045   0.112     2.050   92.857   81.701
LGA    S     7_B      S     7_B     0.618     0    0.075   0.089     0.898   95.238   93.651
LGA    T     8_B      T     8_B     0.309     0    0.043   0.126     0.706  100.000   98.639
LGA    D     9_B      D     9_B     0.774     0    0.035   0.883     4.055   90.476   76.250
LGA    E    10_B      E    10_B     0.632     0    0.036   0.586     2.242   90.476   82.698
LGA    V    11_B      V    11_B     0.456     0    0.044   0.126     0.646   95.238   94.558
LGA    S    12_B      S    12_B     1.113     0    0.029   0.048     1.665   83.690   80.079
LGA    E    13_B      E    13_B     1.343     0    0.042   0.628     3.769   83.690   65.291
LGA    F    14_B      F    14_B     0.684     0    0.027   0.133     1.570   90.476   85.584
LGA    I    15_B      I    15_B     0.583     0    0.031   0.646     1.559   92.857   87.202
LGA    Q    16_B      Q    16_B     1.255     0    0.114   0.801     2.369   85.952   79.683
LGA    S    17_B      S    17_B     0.966     0    0.107   0.131     1.175   92.857   90.556
LGA    L    18_B      L    18_B     0.724     0    0.052   0.131     0.810   90.476   90.476
LGA    P    19_B      P    19_B     0.919     0    0.549   0.659     3.160   78.095   83.401
LGA    G    20_B      G    20_B     1.131     0    0.103   0.103     1.536   83.810   83.810
LGA    C    21_B      C    21_B     0.759     0    0.126   0.119     1.044   90.476   88.968
LGA    E    22_B      E    22_B     0.733     0    0.016   0.842     3.362   90.476   78.413
LGA    E    23_B      E    23_B     0.585     0    0.136   0.598     2.000   95.238   87.672
LGA    H    24_B      H    24_B     0.298     0    0.037   0.079     1.952   92.976   86.190
LGA    G    25_B      G    25_B     1.059     0    0.029   0.029     1.120   83.690   83.690
LGA    K    26_B      K    26_B     0.898     0    0.027   1.300     5.265   90.476   71.693
LGA    V    27_B      V    27_B     0.663     0    0.030   1.140     2.983   90.476   80.952
LGA    F    28_B      F    28_B     0.775     0    0.028   0.104     1.501   90.476   84.762
LGA    K    29_B      K    29_B     0.996     0    0.027   0.683     3.542   90.476   78.519
LGA    D    30_B      D    30_B     0.856     0    0.098   0.922     3.947   92.857   76.548
LGA    E    31_B      E    31_B     0.761     0    0.141   0.133     1.582   90.476   84.550
LGA    Q    32_B      Q    32_B     1.059     0    0.031   0.284     1.366   85.952   83.439
LGA    I    33_B      I    33_B     0.563     0    0.118   0.570     2.176   95.238   89.702
LGA    D    34_B      D    34_B     0.663     0    0.034   0.180     1.874   90.476   84.881
LGA    G    35_B      G    35_B     0.453     0    0.027   0.027     0.582   95.238   95.238
LGA    E    36_B      E    36_B     0.893     0    0.036   1.104     4.316   90.476   77.831
LGA    A    37_B      A    37_B     0.954     0    0.041   0.046     1.171   90.476   88.667
LGA    F    38_B      F    38_B     0.651     0    0.028   0.490     1.761   90.476   86.450
LGA    L    39_B      L    39_B     0.562     0    0.123   1.016     2.645   88.214   82.976
LGA    L    40_B      L    40_B     0.634     0    0.186   0.175     1.324   88.214   89.345
LGA    M    41_B      M    41_B     0.567     0    0.073   1.451     5.095   95.238   73.274
LGA    T    42_B      T    42_B     0.603     0    0.032   0.040     0.864   92.857   91.837
LGA    Q    43_B      Q    43_B     1.129     0    0.036   1.251     5.932   81.429   60.899
LGA    T    44_B      T    44_B     1.176     0    0.030   0.939     3.532   85.952   76.190
LGA    D    45_B      D    45_B     0.809     0    0.018   0.163     1.202   90.476   87.083
LGA    I    46_B      I    46_B     0.658     0    0.043   0.653     2.797   90.476   86.310
LGA    V    47_B      V    47_B     0.747     0    0.034   0.070     1.117   90.476   89.184
LGA    K    48_B      K    48_B     0.923     0    0.127   0.951     6.044   90.476   64.339
LGA    I    49_B      I    49_B     0.792     0    0.033   0.639     2.740   92.857   85.238
LGA    M    50_B      M    50_B     0.211     0    0.099   1.069     2.879  100.000   89.048
LGA    S    51_B      S    51_B     0.485     0    0.051   0.070     0.596   95.238   96.825
LGA    I    52_B      I    52_B     0.509     0    0.114   1.335     3.468   92.857   79.464
LGA    K    53_B      K    53_B     0.449     0    0.057   1.341     3.764   95.238   81.640
LGA    E    54_B      E    54_B     0.656     0    0.026   0.808     4.278   90.476   76.984
LGA    G    55_B      G    55_B     0.589     0    0.048   0.048     0.657   90.476   90.476
LGA    P    56_B      P    56_B     0.567     0    0.033   0.301     0.789   92.857   93.197
LGA    A    57_B      A    57_B     0.523     0    0.033   0.037     0.606   92.857   92.381
LGA    E    58_B      E    58_B     0.731     0    0.031   1.133     3.111   90.476   78.413
LGA    K    59_B      K    59_B     0.789     0    0.026   1.064     2.838   90.476   80.899
LGA    I    60_B      I    60_B     0.634     0    0.031   0.088     0.963   90.476   90.476
LGA    F    61_B      F    61_B     0.603     0    0.040   0.330     1.441   90.476   90.563
LGA    N    62_B      N    62_B     0.735     0    0.064   1.019     3.358   90.476   80.000
LGA    S    63_B      S    63_B     1.473     0    0.025   0.735     1.834   77.143   75.714
LGA    I    64_B      I    64_B     1.603     0    0.048   1.324     5.261   77.143   66.190
LGA    L    65_B      L    65_B     0.829     0    0.042   1.429     3.985   85.952   73.095
LGA    M    66_B      M    66_B     1.274     0    0.040   1.188     4.734   79.286   67.143
LGA    F    67_B      F    67_B     1.560     0    0.029   0.619     3.143   75.000   70.173
LGA    K    68_B      K    68_B     1.395     0    0.054   0.815     2.535   79.286   73.122
LGA    A    69_B      A    69_B     1.526     0    0.094   0.093     1.654   75.000   74.571
LGA    A    70_B      A    70_B     1.816     0    0.176   0.180     1.817   72.857   72.857
LGA    E    71_B      E    71_B     2.116     0    0.094   1.367     4.444   64.762   61.852

# 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):     0.947          0.949                  1.628           88.461   81.725

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   73   71    4.0     71    0.95    94.366    97.918     6.778

LGA_LOCAL      RMSD:   0.947  Number of atoms:   71  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.947  Number of assigned atoms:   71 
Std_ASGN_ATOMS RMSD:   0.947  Standard rmsd on all 71 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.450090 * X  +  -0.560154 * Y  +  -0.695447 * Z  +  28.543961
  Y_new =  -0.525488 * X  +  -0.795814 * Y  +   0.300902 * Z  +  80.720070
  Z_new =  -0.721998 * X  +   0.230017 * Y  +  -0.652542 * Z  +  14.766902 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.862531  0.806685  2.802699   [DEG:  -49.4194   46.2197  160.5828 ]
ZXZ: -1.979149  2.281731 -1.262379   [DEG: -113.3969  130.7336  -72.3290 ]
 
# END of job
