
#######################################################
#                                                     #
#                        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        1.10     1.10
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    71       1_B - 71_B        1.10     1.10
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    69       1_B - 69_B        0.97     1.12
  LCS_AVERAGE:     96.49

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     69   71   71      5   17   53   68   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S     2_B     S     2_B     69   71   71     22   52   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V     3_B     V     3_B     69   71   71     31   52   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S     4_B     S     4_B     69   71   71     31   52   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K     5_B     K     5_B     69   71   71     31   52   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     W     6_B     W     6_B     69   71   71     31   52   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S     7_B     S     7_B     69   71   71     31   52   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     T     8_B     T     8_B     69   71   71     31   52   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D     9_B     D     9_B     69   71   71     31   52   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    10_B     E    10_B     69   71   71     31   52   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V    11_B     V    11_B     69   71   71     31   52   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    12_B     S    12_B     69   71   71     31   52   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    13_B     E    13_B     69   71   71     31   52   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    14_B     F    14_B     69   71   71     31   52   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    15_B     I    15_B     69   71   71     31   52   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     Q    16_B     Q    16_B     69   71   71     31   52   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    17_B     S    17_B     69   71   71     31   52   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    18_B     L    18_B     69   71   71     31   52   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     P    19_B     P    19_B     69   71   71     31   52   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    20_B     G    20_B     69   71   71     27   51   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     C    21_B     C    21_B     69   71   71     31   52   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    22_B     E    22_B     69   71   71      6   52   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    23_B     E    23_B     69   71   71     21   52   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     H    24_B     H    24_B     69   71   71     27   52   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    25_B     G    25_B     69   71   71     31   52   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    26_B     K    26_B     69   71   71     31   52   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V    27_B     V    27_B     69   71   71     31   52   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    28_B     F    28_B     69   71   71     31   52   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    29_B     K    29_B     69   71   71     31   52   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D    30_B     D    30_B     69   71   71     24   50   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    31_B     E    31_B     69   71   71     31   51   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     Q    32_B     Q    32_B     69   71   71     30   52   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    33_B     I    33_B     69   71   71     31   52   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D    34_B     D    34_B     69   71   71     31   52   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    35_B     G    35_B     69   71   71     31   52   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    36_B     E    36_B     69   71   71     22   52   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    37_B     A    37_B     69   71   71     31   52   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    38_B     F    38_B     69   71   71     31   52   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    39_B     L    39_B     69   71   71     31   52   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    40_B     L    40_B     69   71   71     27   52   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     M    41_B     M    41_B     69   71   71     29   52   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     T    42_B     T    42_B     69   71   71     28   52   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     Q    43_B     Q    43_B     69   71   71     25   52   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     T    44_B     T    44_B     69   71   71     23   52   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D    45_B     D    45_B     69   71   71     20   52   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    46_B     I    46_B     69   71   71     18   52   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V    47_B     V    47_B     69   71   71     19   52   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    48_B     K    48_B     69   71   71     19   42   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    49_B     I    49_B     69   71   71     19   33   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     M    50_B     M    50_B     69   71   71     19   52   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    51_B     S    51_B     69   71   71     19   52   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    52_B     I    52_B     69   71   71     19   52   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    53_B     K    53_B     69   71   71     20   52   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    54_B     E    54_B     69   71   71     20   43   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    55_B     G    55_B     69   71   71     20   42   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     P    56_B     P    56_B     69   71   71     20   52   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    57_B     A    57_B     69   71   71     20   52   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    58_B     E    58_B     69   71   71     20   52   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    59_B     K    59_B     69   71   71     20   50   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    60_B     I    60_B     69   71   71     20   52   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    61_B     F    61_B     69   71   71     31   52   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     N    62_B     N    62_B     69   71   71     20   52   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    63_B     S    63_B     69   71   71     19   45   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    64_B     I    64_B     69   71   71     19   48   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    65_B     L    65_B     69   71   71     20   50   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     M    66_B     M    66_B     69   71   71     17   40   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    67_B     F    67_B     69   71   71     17   37   63   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    68_B     K    68_B     69   71   71      9   33   62   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    69_B     A    69_B     69   71   71      9   33   54   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    70_B     A    70_B     52   71   71      9   29   38   50   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    71_B     E    71_B     51   71   71      9   13   38   50   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_AVERAGE  LCS_A:  98.83  (  96.49  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     31     52     65     68     70     71     71     71     71     71     71     71     71     71     71     71     71     71     71     71 
GDT PERCENT_AT  43.66  73.24  91.55  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
GDT RMS_LOCAL    0.33   0.63   0.82   0.94   1.08   1.10   1.10   1.10   1.10   1.10   1.10   1.10   1.10   1.10   1.10   1.10   1.10   1.10   1.10   1.10
GDT RMS_ALL_AT   1.46   1.27   1.18   1.12   1.11   1.10   1.10   1.10   1.10   1.10   1.10   1.10   1.10   1.10   1.10   1.10   1.10   1.10   1.10   1.10

# Checking swapping
#   possible swapping detected:  D     9_B      D     9_B
#   possible swapping detected:  E    13_B      E    13_B
#   possible swapping detected:  F    14_B      F    14_B
#   possible swapping detected:  E    54_B      E    54_B
#   possible swapping detected:  E    58_B      E    58_B
#   possible swapping detected:  F    67_B      F    67_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    G     1_B      G     1_B     2.253     0    0.448   0.448     4.783   62.619   62.619
LGA    S     2_B      S     2_B     1.305     0    0.011   0.715     3.036   79.286   74.762
LGA    V     3_B      V     3_B     0.898     0    0.047   0.128     1.609   90.476   85.374
LGA    S     4_B      S     4_B     0.924     0    0.032   0.144     1.332   85.952   85.952
LGA    K     5_B      K     5_B     1.130     0    0.045   0.833     5.546   83.690   62.646
LGA    W     6_B      W     6_B     0.962     0    0.028   0.136     1.892   88.214   82.823
LGA    S     7_B      S     7_B     0.754     0    0.033   0.038     0.814   90.476   90.476
LGA    T     8_B      T     8_B     0.502     0    0.016   0.067     0.796   95.238   93.197
LGA    D     9_B      D     9_B     0.254     0    0.022   0.754     3.245  100.000   84.940
LGA    E    10_B      E    10_B     0.658     0    0.034   0.359     2.125   90.476   84.603
LGA    V    11_B      V    11_B     0.474     0    0.016   0.062     0.562   95.238   95.918
LGA    S    12_B      S    12_B     0.518     0    0.032   0.100     0.880   92.857   92.063
LGA    E    13_B      E    13_B     1.042     0    0.015   0.776     4.366   83.690   69.101
LGA    F    14_B      F    14_B     1.063     0    0.012   1.397     7.020   83.690   56.797
LGA    I    15_B      I    15_B     0.663     0    0.011   0.654     2.115   90.476   88.452
LGA    Q    16_B      Q    16_B     1.164     0    0.053   0.159     2.116   83.690   79.630
LGA    S    17_B      S    17_B     1.478     0    0.009   0.013     1.603   81.429   80.000
LGA    L    18_B      L    18_B     1.065     0    0.038   0.089     1.123   81.429   87.143
LGA    P    19_B      P    19_B     1.251     0    0.011   0.387     2.170   81.429   79.048
LGA    G    20_B      G    20_B     1.323     0    0.034   0.034     1.324   81.429   81.429
LGA    C    21_B      C    21_B     0.857     0    0.045   0.047     1.057   88.214   88.968
LGA    E    22_B      E    22_B     1.055     0    0.039   0.780     4.493   85.952   69.841
LGA    E    23_B      E    23_B     0.683     0    0.098   0.830     3.462   90.476   81.164
LGA    H    24_B      H    24_B     0.688     0    0.145   0.140     1.361   92.857   86.905
LGA    G    25_B      G    25_B     0.824     0    0.020   0.020     0.939   90.476   90.476
LGA    K    26_B      K    26_B     1.066     0    0.013   0.772     1.671   81.429   80.476
LGA    V    27_B      V    27_B     1.223     0    0.043   1.056     3.690   83.690   78.571
LGA    F    28_B      F    28_B     0.604     0    0.009   0.092     1.379   90.476   88.009
LGA    K    29_B      K    29_B     0.697     0    0.012   0.814     2.774   85.952   80.106
LGA    D    30_B      D    30_B     1.453     0    0.051   0.074     1.830   79.286   76.071
LGA    E    31_B      E    31_B     1.307     0    0.016   0.137     1.881   81.429   78.571
LGA    Q    32_B      Q    32_B     1.240     0    0.026   0.836     4.265   81.429   68.624
LGA    I    33_B      I    33_B     0.622     0    0.059   0.078     0.772   92.857   94.048
LGA    D    34_B      D    34_B     0.668     0    0.012   0.121     1.421   90.476   88.214
LGA    G    35_B      G    35_B     0.804     0    0.056   0.056     0.804   90.476   90.476
LGA    E    36_B      E    36_B     1.076     0    0.013   0.066     2.298   85.952   76.931
LGA    A    37_B      A    37_B     0.862     0    0.008   0.012     0.885   90.476   90.476
LGA    F    38_B      F    38_B     0.316     0    0.078   0.325     2.106   97.619   86.753
LGA    L    39_B      L    39_B     0.249     0    0.113   0.209     0.765   97.619   96.429
LGA    L    40_B      L    40_B     0.218     0    0.008   0.061     0.623  100.000   96.429
LGA    M    41_B      M    41_B     0.444     0    0.082   0.866     2.012   97.619   87.500
LGA    T    42_B      T    42_B     0.514     0    0.035   0.053     0.636   95.238   93.197
LGA    Q    43_B      Q    43_B     0.535     0    0.009   0.086     1.031   92.857   90.529
LGA    T    44_B      T    44_B     0.538     0    0.044   0.108     0.833   95.238   94.558
LGA    D    45_B      D    45_B     0.519     0    0.016   0.102     0.937   92.857   91.667
LGA    I    46_B      I    46_B     0.569     0    0.032   0.074     0.743   90.476   92.857
LGA    V    47_B      V    47_B     0.863     0    0.041   0.046     1.145   90.476   89.184
LGA    K    48_B      K    48_B     1.336     0    0.060   0.819     5.191   79.286   67.196
LGA    I    49_B      I    49_B     1.287     0    0.039   0.090     1.814   81.429   78.214
LGA    M    50_B      M    50_B     0.895     0    0.026   0.237     1.305   90.476   89.345
LGA    S    51_B      S    51_B     0.849     0    0.022   0.041     1.290   90.476   88.968
LGA    I    52_B      I    52_B     0.509     0    0.037   0.039     0.699   90.476   92.857
LGA    K    53_B      K    53_B     0.905     0    0.020   0.657     2.586   90.476   83.069
LGA    E    54_B      E    54_B     1.160     0    0.013   0.576     2.714   81.429   75.026
LGA    G    55_B      G    55_B     1.285     0    0.067   0.067     1.372   81.429   81.429
LGA    P    56_B      P    56_B     0.900     0    0.043   0.053     0.959   90.476   90.476
LGA    A    57_B      A    57_B     0.716     0    0.032   0.031     0.839   92.857   92.381
LGA    E    58_B      E    58_B     0.860     0    0.028   0.154     1.175   90.476   88.466
LGA    K    59_B      K    59_B     0.980     0    0.015   0.109     1.324   90.476   85.450
LGA    I    60_B      I    60_B     0.574     0    0.014   0.071     0.675   95.238   94.048
LGA    F    61_B      F    61_B     0.286     0    0.064   0.106     0.564  100.000   98.268
LGA    N    62_B      N    62_B     0.580     0    0.006   0.021     1.428   95.238   89.464
LGA    S    63_B      S    63_B     1.020     0    0.015   0.038     1.382   85.952   84.444
LGA    I    64_B      I    64_B     0.865     0    0.009   0.092     1.208   88.214   88.214
LGA    L    65_B      L    65_B     0.544     0    0.029   0.140     0.974   90.476   94.048
LGA    M    66_B      M    66_B     1.245     0    0.016   0.840     2.704   81.548   79.702
LGA    F    67_B      F    67_B     1.614     0    0.018   0.450     2.074   72.976   76.017
LGA    K    68_B      K    68_B     1.756     0    0.024   0.986     2.532   70.833   70.265
LGA    A    69_B      A    69_B     2.059     0    0.080   0.083     2.375   66.786   68.000
LGA    A    70_B      A    70_B     2.927     0    0.154   0.168     3.336   53.571   54.286
LGA    E    71_B      E    71_B     3.211     0    0.022   0.694     3.512   50.000   55.079

# 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):     1.105          1.127                  1.493           86.680   83.221

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   73   71    4.0     71    1.10    92.254    96.868     5.895

LGA_LOCAL      RMSD:   1.105  Number of atoms:   71  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.105  Number of assigned atoms:   71 
Std_ASGN_ATOMS RMSD:   1.105  Standard rmsd on all 71 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.165894 * X  +  -0.978384 * Y  +  -0.123464 * Z  +  26.239763
  Y_new =  -0.395641 * X  +  -0.048648 * Y  +   0.917116 * Z  +  40.315929
  Z_new =  -0.903298 * X  +   0.200992 * Y  +  -0.379018 * Z  +  -8.687488 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.967834  1.127396  2.654003   [DEG: -112.7486   64.5950  152.0632 ]
ZXZ: -3.007775  1.959532 -1.351854   [DEG: -172.3328  112.2729  -77.4555 ]
 
# END of job
