
#######################################################
#                                                     #
#                        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        0.89     0.89
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    67       2_A - 68_A        0.89     0.89
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    67       2_A - 68_A        0.89     0.89
  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   25   51   64   66   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   41   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   59   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   41   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     18   50   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   57   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     13   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   57   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   57   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   57   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   57   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   57   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   57   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   57   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   57   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   57   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   57   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   57   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   57   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   57   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   57   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   57   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   57   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   57   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   57   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   57   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   57   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   57   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   57   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   57   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   57   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   57   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   57   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   57   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   57   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   57   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   57   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   57   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   57   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   57   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   57   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   57   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   57   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   57   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     43   57   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   57   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   57   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   57   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   57   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   57   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   57   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   57   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   57   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   57   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   57   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   57   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   57   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   57   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   57   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   57   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     43   57   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     43   57   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   57   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     47   57   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     13   57   60   64   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      4   54   60   64   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   56   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     57     61     64     66     67     67     67     67     67     67     67     67     67     67     67     67     67     67     67 
GDT PERCENT_AT  74.63  85.07  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   0.38   0.56   0.70   0.80   0.89   0.89   0.89   0.89   0.89   0.89   0.89   0.89   0.89   0.89   0.89   0.89   0.89   0.89   0.89
GDT RMS_ALL_AT   1.01   1.06   0.92   0.92   0.89   0.89   0.89   0.89   0.89   0.89   0.89   0.89   0.89   0.89   0.89   0.89   0.89   0.89   0.89   0.89

# Checking swapping
#   possible swapping detected:  E     4_A      E     4_A
#   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:  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     3.054     0    0.051   0.067     3.229   55.476   54.841
LGA    P     3_A      P     3_A     2.107     0    0.017   0.026     2.828   69.048   65.034
LGA    E     4_A      E     4_A     2.082     0    0.025   0.983     3.633   68.810   63.333
LGA    E     5_A      E     5_A     1.925     0    0.050   0.620     5.032   75.119   59.471
LGA    Q     6_A      Q     6_A     1.407     0    0.024   0.650     2.371   83.810   79.735
LGA    K     7_A      K     7_A     0.742     0    0.030   0.633     2.334   92.857   83.862
LGA    Q     8_A      Q     8_A     0.978     0    0.011   1.492     5.927   90.595   67.196
LGA    M     9_A      M     9_A     0.760     0    0.026   0.681     1.244   90.476   88.274
LGA    L    10_A      L    10_A     0.448     0    0.031   0.077     1.082   97.619   94.107
LGA    G    11_A      G    11_A     0.647     0    0.077   0.077     0.647   97.619   97.619
LGA    E    12_A      E    12_A     0.388     0    0.030   0.807     3.111  100.000   87.354
LGA    A    13_A      A    13_A     0.240     0    0.037   0.041     0.477  100.000  100.000
LGA    I    14_A      I    14_A     0.168     0    0.022   0.064     0.237  100.000  100.000
LGA    Y    15_A      Y    15_A     0.190     0    0.030   0.189     0.834  100.000   96.825
LGA    P    16_A      P    16_A     0.139     0    0.045   0.040     0.220  100.000  100.000
LGA    K    17_A      K    17_A     0.178     0    0.052   0.722     3.018  100.000   89.471
LGA    V    18_A      V    18_A     0.186     0    0.035   0.054     0.263  100.000  100.000
LGA    A    19_A      A    19_A     0.279     0    0.045   0.046     0.334  100.000  100.000
LGA    A    20_A      A    20_A     0.382     0    0.027   0.037     0.563   97.619   98.095
LGA    S    21_A      S    21_A     0.262     0    0.063   0.076     0.719  100.000   98.413
LGA    Q    22_A      Q    22_A     0.205     0    0.084   0.186     0.666   97.619   96.825
LGA    P    23_A      P    23_A     0.496     0    0.022   0.039     0.600   97.619   95.918
LGA    E    24_A      E    24_A     0.352     0    0.091   0.616     2.267   92.976   89.841
LGA    L    25_A      L    25_A     0.303     0    0.029   0.046     0.580  100.000   97.619
LGA    A    26_A      A    26_A     0.377     0    0.039   0.046     0.508  100.000   98.095
LGA    G    27_A      G    27_A     0.501     0    0.038   0.038     0.501   97.619   97.619
LGA    K    28_A      K    28_A     0.309     0    0.008   1.194     6.081  100.000   74.603
LGA    L    29_A      L    29_A     0.162     0    0.018   0.130     0.884  100.000   97.619
LGA    T    30_A      T    30_A     0.345     0    0.029   0.066     0.582  100.000   98.639
LGA    G    31_A      G    31_A     0.421     0    0.058   0.058     0.421  100.000  100.000
LGA    M    32_A      M    32_A     0.166     0    0.010   0.131     0.587  100.000   98.810
LGA    I    33_A      I    33_A     0.296     0    0.051   0.077     0.501  100.000   98.810
LGA    L    34_A      L    34_A     0.187     0    0.034   0.077     0.467  100.000  100.000
LGA    E    35_A      E    35_A     0.588     0    0.120   1.060     4.733   90.595   68.995
LGA    L    36_A      L    36_A     0.586     0    0.013   0.075     0.642   90.476   91.667
LGA    P    37_A      P    37_A     0.802     0    0.048   0.315     1.689   90.476   87.959
LGA    V    38_A      V    38_A     0.881     0    0.024   0.058     1.008   90.476   89.184
LGA    T    39_A      T    39_A     0.822     0    0.015   0.048     0.866   90.476   90.476
LGA    E    40_A      E    40_A     0.531     0    0.030   0.832     3.813   92.857   81.852
LGA    L    41_A      L    41_A     0.633     0    0.019   0.088     0.713   90.476   91.667
LGA    L    42_A      L    42_A     0.775     0    0.035   0.055     1.238   90.476   87.083
LGA    H    43_A      H    43_A     0.536     0    0.034   1.108     2.704   90.476   85.667
LGA    L    44_A      L    44_A     0.624     0    0.019   0.130     0.754   90.476   92.857
LGA    L    45_A      L    45_A     1.000     0    0.072   1.373     3.070   88.214   78.810
LGA    E    46_A      E    46_A     0.991     0    0.029   0.814     3.245   88.214   72.063
LGA    E    47_A      E    47_A     0.806     0    0.041   1.076     3.947   90.476   75.873
LGA    S    48_A      S    48_A     0.477     0    0.024   0.630     2.525   95.238   89.683
LGA    E    49_A      E    49_A     0.579     0    0.075   0.269     1.405   95.238   89.577
LGA    A    50_A      A    50_A     0.382     0    0.016   0.018     0.491  100.000  100.000
LGA    L    51_A      L    51_A     0.139     0    0.026   0.129     0.594  100.000   98.810
LGA    D    52_A      D    52_A     0.153     0    0.018   0.067     0.205  100.000  100.000
LGA    A    53_A      A    53_A     0.332     0    0.037   0.044     0.604  100.000   98.095
LGA    K    54_A      K    54_A     0.158     0    0.004   0.552     1.548  100.000   93.810
LGA    V    55_A      V    55_A     0.074     0    0.035   0.051     0.158  100.000  100.000
LGA    N    56_A      N    56_A     0.211     0    0.011   0.121     0.339  100.000  100.000
LGA    E    57_A      E    57_A     0.180     0    0.046   0.710     2.386  100.000   85.238
LGA    A    58_A      A    58_A     0.480     0    0.013   0.018     0.580   95.238   94.286
LGA    L    59_A      L    59_A     0.548     0    0.032   0.287     1.145   90.476   90.536
LGA    E    60_A      E    60_A     0.569     0    0.086   0.271     2.133   90.476   85.714
LGA    V    61_A      V    61_A     0.652     0    0.019   0.058     0.919   90.476   90.476
LGA    L    62_A      L    62_A     1.122     0    0.012   1.403     3.523   83.690   76.726
LGA    K    63_A      K    63_A     1.186     0    0.010   0.523     3.358   81.429   73.492
LGA    E    64_A      E    64_A     0.565     0    0.029   0.132     0.893   90.476   94.709
LGA    Y    65_A      Y    65_A     1.152     0    0.021   1.047     6.283   81.548   60.952
LGA    Q    66_A      Q    66_A     2.069     0    0.125   0.175     4.979   68.810   53.598
LGA    Q    67_A      Q    67_A     1.911     0    0.213   0.477     4.942   72.976   59.101
LGA    N    68_A      N    68_A     1.420     0    0.259   1.052     5.141   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):     0.885          0.894                  1.516           92.264   87.446

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   68   67    4.0     67    0.89    95.149    97.742     6.801

LGA_LOCAL      RMSD:   0.885  Number of atoms:   67  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.885  Number of assigned atoms:   67 
Std_ASGN_ATOMS RMSD:   0.885  Standard rmsd on all 67 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.951258 * X  +   0.007465 * Y  +   0.308304 * Z  +  -4.212361
  Y_new =   0.274824 * X  +  -0.474110 * Y  +  -0.836476 * Z  + -11.658967
  Z_new =   0.139926 * X  +   0.880434 * Y  +  -0.453053 * Z  +  -1.057090 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.281248 -0.140387  2.046039   [DEG:   16.1143   -8.0436  117.2294 ]
ZXZ:  0.353126  2.040983  0.157610   [DEG:   20.2327  116.9397    9.0304 ]
 
# END of job
