
#######################################################
#                                                     #
#                        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   68 (  529),  selected   67 , name one
# Molecule2: number of CA atoms   67 (  519),  selected   67 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:A  -ch2:A  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    67       2_A - 68_A        0.90     0.90
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    67       2_A - 68_A        0.90     0.90
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    67       2_A - 68_A        0.90     0.90
  LCS_AVERAGE:    100.00

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   67
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     S     2_A     S     2_A     67   67   67     11   23   52   63   65   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     P     3_A     P     3_A     67   67   67     16   42   58   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E     4_A     E     4_A     67   67   67     11   38   58   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E     5_A     E     5_A     67   67   67     11   42   59   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q     6_A     Q     6_A     67   67   67     19   51   61   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K     7_A     K     7_A     67   67   67     27   56   61   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q     8_A     Q     8_A     67   67   67     16   56   61   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     M     9_A     M     9_A     67   67   67     24   56   61   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    10_A     L    10_A     67   67   67     48   56   61   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     G    11_A     G    11_A     67   67   67     50   56   61   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    12_A     E    12_A     67   67   67     50   56   61   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    13_A     A    13_A     67   67   67     50   56   61   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     I    14_A     I    14_A     67   67   67     50   56   61   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Y    15_A     Y    15_A     67   67   67     50   56   61   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     P    16_A     P    16_A     67   67   67     50   56   61   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K    17_A     K    17_A     67   67   67     50   56   61   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    18_A     V    18_A     67   67   67     50   56   61   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    19_A     A    19_A     67   67   67     50   56   61   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    20_A     A    20_A     67   67   67     50   56   61   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     S    21_A     S    21_A     67   67   67     50   56   61   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q    22_A     Q    22_A     67   67   67     50   56   61   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     P    23_A     P    23_A     67   67   67     40   56   61   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    24_A     E    24_A     67   67   67     50   56   61   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    25_A     L    25_A     67   67   67     50   56   61   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    26_A     A    26_A     67   67   67     50   56   61   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     G    27_A     G    27_A     67   67   67     50   56   61   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K    28_A     K    28_A     67   67   67     50   56   61   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    29_A     L    29_A     67   67   67     50   56   61   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     T    30_A     T    30_A     67   67   67     50   56   61   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     G    31_A     G    31_A     67   67   67     50   56   61   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     M    32_A     M    32_A     67   67   67     50   56   61   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     I    33_A     I    33_A     67   67   67     50   56   61   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    34_A     L    34_A     67   67   67     50   56   61   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    35_A     E    35_A     67   67   67     50   56   61   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    36_A     L    36_A     67   67   67     50   56   61   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     P    37_A     P    37_A     67   67   67     50   56   61   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    38_A     V    38_A     67   67   67     50   56   61   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     T    39_A     T    39_A     67   67   67     50   56   61   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    40_A     E    40_A     67   67   67     50   56   61   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    41_A     L    41_A     67   67   67     50   56   61   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    42_A     L    42_A     67   67   67     50   56   61   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     H    43_A     H    43_A     67   67   67     50   56   61   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    44_A     L    44_A     67   67   67     50   56   61   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    45_A     L    45_A     67   67   67     50   56   61   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    46_A     E    46_A     67   67   67     50   56   61   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    47_A     E    47_A     67   67   67     50   56   61   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     S    48_A     S    48_A     67   67   67     50   56   61   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    49_A     E    49_A     67   67   67     50   56   61   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    50_A     A    50_A     67   67   67     50   56   61   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    51_A     L    51_A     67   67   67     50   56   61   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     D    52_A     D    52_A     67   67   67     50   56   61   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    53_A     A    53_A     67   67   67     50   56   61   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K    54_A     K    54_A     67   67   67     50   56   61   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    55_A     V    55_A     67   67   67     50   56   61   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     N    56_A     N    56_A     67   67   67     50   56   61   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    57_A     E    57_A     67   67   67     50   56   61   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    58_A     A    58_A     67   67   67     50   56   61   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    59_A     L    59_A     67   67   67     50   56   61   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    60_A     E    60_A     67   67   67     50   56   61   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    61_A     V    61_A     67   67   67     50   56   61   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    62_A     L    62_A     67   67   67     26   56   61   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K    63_A     K    63_A     67   67   67     32   56   61   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    64_A     E    64_A     67   67   67     50   56   61   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Y    65_A     Y    65_A     67   67   67     50   56   61   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q    66_A     Q    66_A     67   67   67     15   55   59   63   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q    67_A     Q    67_A     67   67   67      5   38   59   63   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     N    68_A     N    68_A     67   67   67      3   55   61   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
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     50     56     61     64     66     67     67     67     67     67     67     67     67     67     67     67     67     67     67     67 
GDT PERCENT_AT  74.63  83.58  91.04  95.52  98.51 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.28   0.34   0.56   0.74   0.82   0.90   0.90   0.90   0.90   0.90   0.90   0.90   0.90   0.90   0.90   0.90   0.90   0.90   0.90   0.90
GDT RMS_ALL_AT   1.03   1.05   0.94   0.91   0.91   0.90   0.90   0.90   0.90   0.90   0.90   0.90   0.90   0.90   0.90   0.90   0.90   0.90   0.90   0.90

# Checking swapping
#   possible swapping detected:  E    35_A      E    35_A
#   possible swapping detected:  E    46_A      E    46_A
#   possible swapping detected:  E    57_A      E    57_A
#   possible swapping detected:  E    64_A      E    64_A
#   possible swapping detected:  Y    65_A      Y    65_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     2_A      S     2_A     3.136     0    0.032   0.052     3.352   55.476   53.651
LGA    P     3_A      P     3_A     2.163     0    0.014   0.026     2.922   66.905   63.810
LGA    E     4_A      E     4_A     2.126     0    0.017   1.036     5.546   68.810   53.915
LGA    E     5_A      E     5_A     1.937     0    0.047   0.660     5.143   72.976   59.259
LGA    Q     6_A      Q     6_A     1.417     0    0.022   0.652     2.343   83.810   78.730
LGA    K     7_A      K     7_A     0.740     0    0.026   0.894     4.650   92.857   75.873
LGA    Q     8_A      Q     8_A     0.994     0    0.016   1.435     5.713   90.595   65.926
LGA    M     9_A      M     9_A     0.776     0    0.028   0.684     1.233   90.476   88.274
LGA    L    10_A      L    10_A     0.450     0    0.035   0.083     1.137   97.619   92.917
LGA    G    11_A      G    11_A     0.628     0    0.077   0.077     0.628   97.619   97.619
LGA    E    12_A      E    12_A     0.356     0    0.029   0.806     3.148  100.000   87.354
LGA    A    13_A      A    13_A     0.241     0    0.037   0.042     0.484  100.000  100.000
LGA    I    14_A      I    14_A     0.165     0    0.022   0.063     0.235  100.000  100.000
LGA    Y    15_A      Y    15_A     0.195     0    0.030   0.191     0.810  100.000   96.825
LGA    P    16_A      P    16_A     0.138     0    0.045   0.040     0.218  100.000  100.000
LGA    K    17_A      K    17_A     0.185     0    0.053   0.723     3.007  100.000   89.471
LGA    V    18_A      V    18_A     0.194     0    0.035   0.055     0.267  100.000  100.000
LGA    A    19_A      A    19_A     0.298     0    0.045   0.046     0.353  100.000  100.000
LGA    A    20_A      A    20_A     0.399     0    0.028   0.036     0.589   97.619   98.095
LGA    S    21_A      S    21_A     0.292     0    0.062   0.076     0.743   97.619   96.825
LGA    Q    22_A      Q    22_A     0.242     0    0.085   0.187     0.713   97.619   95.767
LGA    P    23_A      P    23_A     0.524     0    0.021   0.040     0.638   95.238   94.558
LGA    E    24_A      E    24_A     0.323     0    0.091   0.617     2.193   92.976   89.841
LGA    L    25_A      L    25_A     0.297     0    0.030   0.044     0.551  100.000   98.810
LGA    A    26_A      A    26_A     0.387     0    0.039   0.046     0.516  100.000   98.095
LGA    G    27_A      G    27_A     0.513     0    0.038   0.038     0.513   97.619   97.619
LGA    K    28_A      K    28_A     0.315     0    0.007   1.193     6.092  100.000   74.603
LGA    L    29_A      L    29_A     0.185     0    0.018   0.132     0.884  100.000   97.619
LGA    T    30_A      T    30_A     0.360     0    0.030   0.066     0.599  100.000   98.639
LGA    G    31_A      G    31_A     0.438     0    0.058   0.058     0.438  100.000  100.000
LGA    M    32_A      M    32_A     0.182     0    0.011   0.131     0.597  100.000   98.810
LGA    I    33_A      I    33_A     0.302     0    0.052   0.078     0.526  100.000   98.810
LGA    L    34_A      L    34_A     0.191     0    0.035   0.077     0.483  100.000  100.000
LGA    E    35_A      E    35_A     0.598     0    0.124   1.059     4.751   90.595   68.995
LGA    L    36_A      L    36_A     0.598     0    0.016   0.073     0.660   90.476   92.857
LGA    P    37_A      P    37_A     0.819     0    0.049   0.315     1.711   90.476   86.667
LGA    V    38_A      V    38_A     0.890     0    0.025   0.055     1.014   90.476   89.184
LGA    T    39_A      T    39_A     0.836     0    0.014   0.049     0.880   90.476   90.476
LGA    E    40_A      E    40_A     0.537     0    0.028   0.831     3.757   92.857   81.852
LGA    L    41_A      L    41_A     0.643     0    0.018   0.088     0.713   90.476   91.667
LGA    L    42_A      L    42_A     0.771     0    0.034   0.052     1.213   90.476   87.083
LGA    H    43_A      H    43_A     0.524     0    0.034   1.109     2.665   90.476   85.667
LGA    L    44_A      L    44_A     0.619     0    0.020   0.128     0.745   90.476   92.857
LGA    L    45_A      L    45_A     0.995     0    0.073   1.373     3.082   88.214   78.810
LGA    E    46_A      E    46_A     0.959     0    0.028   0.812     3.209   90.476   73.862
LGA    E    47_A      E    47_A     0.780     0    0.041   1.078     3.990   90.476   75.873
LGA    S    48_A      S    48_A     0.461     0    0.025   0.630     2.493   97.619   92.540
LGA    E    49_A      E    49_A     0.552     0    0.074   0.269     1.368   95.238   89.577
LGA    A    50_A      A    50_A     0.389     0    0.016   0.018     0.501  100.000   98.095
LGA    L    51_A      L    51_A     0.140     0    0.026   0.129     0.588  100.000   98.810
LGA    D    52_A      D    52_A     0.132     0    0.018   0.067     0.180  100.000  100.000
LGA    A    53_A      A    53_A     0.296     0    0.039   0.046     0.571  100.000   98.095
LGA    K    54_A      K    54_A     0.197     0    0.004   0.555     1.428  100.000   94.762
LGA    V    55_A      V    55_A     0.120     0    0.033   0.049     0.199  100.000  100.000
LGA    N    56_A      N    56_A     0.155     0    0.008   0.118     0.344  100.000  100.000
LGA    E    57_A      E    57_A     0.135     0    0.037   0.706     2.363  100.000   85.238
LGA    A    58_A      A    58_A     0.431     0    0.026   0.029     0.555   97.619   96.190
LGA    L    59_A      L    59_A     0.513     0    0.006   0.337     1.055   92.857   91.726
LGA    E    60_A      E    60_A     0.557     0    0.047   0.264     1.904   90.476   86.614
LGA    V    61_A      V    61_A     0.634     0    0.010   0.053     0.913   90.476   90.476
LGA    L    62_A      L    62_A     1.165     0    0.019   1.398     3.583   83.690   76.726
LGA    K    63_A      K    63_A     1.255     0    0.017   0.516     3.251   81.429   74.286
LGA    E    64_A      E    64_A     0.624     0    0.014   0.903     2.474   90.476   80.106
LGA    Y    65_A      Y    65_A     1.181     0    0.023   1.036     6.128   79.405   60.238
LGA    Q    66_A      Q    66_A     2.165     0    0.126   0.177     5.110   66.786   50.582
LGA    Q    67_A      Q    67_A     2.016     0    0.211   0.476     5.144   70.952   56.825
LGA    N    68_A      N    68_A     1.401     0    0.253   1.057     5.164   66.548   61.905

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       67     268    268  100.00     519    519  100.00                67
SUMMARY(RMSD_GDC):     0.903          0.908                  1.586           92.177   86.871

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   68   67    4.0     67    0.90    94.776    97.624     6.683

LGA_LOCAL      RMSD:   0.903  Number of atoms:   67  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.903  Number of assigned atoms:   67 
Std_ASGN_ATOMS RMSD:   0.903  Standard rmsd on all 67 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.915019 * X  +   0.131097 * Y  +   0.381514 * Z  +  -3.531672
  Y_new =   0.397704 * X  +  -0.451649 * Y  +  -0.798652 * Z  + -12.871169
  Z_new =   0.067610 * X  +   0.882512 * Y  +  -0.465405 * Z  +  -0.462599 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.410007 -0.067661  2.056095   [DEG:   23.4917   -3.8767  117.8055 ]
ZXZ:  0.445647  2.054888  0.076461   [DEG:   25.5337  117.7364    4.3809 ]
 
# END of job
