
#######################################################
#                                                     #
#                        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   97 (  681),  selected   64 , name one
# Molecule2: number of CA atoms   64 (  433),  selected   64 , 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:    64      22_A - 85_A        0.83     0.83
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    64      22_A - 85_A        0.83     0.83
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    64      22_A - 85_A        0.83     0.83
  LCS_AVERAGE:    100.00

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   64
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     A    22_A     A    22_A     64   64   64      3    4   60   62   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     D    23_A     D    23_A     64   64   64      3    7   49   62   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    24_A     G    24_A     64   64   64      3    4    6   26   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     D    25_A     D    25_A     64   64   64      3    4    5    5   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    26_A     G    26_A     64   64   64     50   59   60   62   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     Q    27_A     Q    27_A     64   64   64     50   59   60   62   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    28_A     G    28_A     64   64   64     50   59   60   62   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    29_A     L    29_A     64   64   64     50   59   60   62   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     Y    30_A     Y    30_A     64   64   64     50   59   60   62   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    31_A     A    31_A     64   64   64     50   59   60   62   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    32_A     A    32_A     64   64   64     50   59   60   62   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     N    33_A     N    33_A     64   64   64     50   59   60   62   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     C    34_A     C    34_A     64   64   64     50   59   60   62   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    35_A     A    35_A     64   64   64     50   59   60   62   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    36_A     A    36_A     64   64   64     42   59   60   62   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     C    37_A     C    37_A     64   64   64     39   59   60   62   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     H    38_A     H    38_A     64   64   64     39   59   60   62   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    39_A     G    39_A     64   64   64     32   59   60   62   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    40_A     A    40_A     64   64   64     50   59   60   62   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    41_A     L    41_A     64   64   64     50   59   60   62   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    42_A     A    42_A     64   64   64     50   59   60   62   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     T    43_A     T    43_A     64   64   64     50   59   60   62   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    44_A     S    44_A     64   64   64     50   59   60   62   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     E    45_A     E    45_A     64   64   64     29   59   60   62   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     K    46_A     K    46_A     64   64   64     50   59   60   62   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     K    47_A     K    47_A     64   64   64     50   59   60   62   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    48_A     G    48_A     64   64   64     50   59   60   62   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     T    49_A     T    49_A     64   64   64     50   59   60   62   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     T    50_A     T    50_A     64   64   64     50   59   60   62   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    51_A     L    51_A     64   64   64     50   59   60   62   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    52_A     A    52_A     64   64   64     50   59   60   62   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     R    53_A     R    53_A     64   64   64     50   59   60   62   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    54_A     L    54_A     64   64   64     50   59   60   62   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     Q    55_A     Q    55_A     64   64   64     50   59   60   62   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    56_A     S    56_A     64   64   64     50   59   60   62   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    57_A     A    57_A     64   64   64     50   59   60   62   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     V    58_A     V    58_A     64   64   64     50   59   60   62   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    59_A     S    59_A     64   64   64     50   59   60   62   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    60_A     A    60_A     64   64   64     50   59   60   62   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     N    61_A     N    61_A     64   64   64     50   59   60   62   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    62_A     A    62_A     64   64   64     50   59   60   62   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    63_A     G    63_A     64   64   64     50   59   60   62   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    64_A     G    64_A     64   64   64     11   59   60   62   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     M    65_A     M    65_A     64   64   64     12   59   60   62   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    66_A     G    66_A     64   64   64     12   59   60   62   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     F    67_A     F    67_A     64   64   64     12   33   60   62   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    68_A     L    68_A     64   64   64     15   59   60   62   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    69_A     S    69_A     64   64   64     50   59   60   62   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    70_A     S    70_A     64   64   64     50   59   60   62   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    71_A     L    71_A     64   64   64     50   59   60   62   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     T    72_A     T    72_A     64   64   64     50   59   60   62   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    73_A     S    73_A     64   64   64     50   59   60   62   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    74_A     A    74_A     64   64   64     50   59   60   62   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     Q    75_A     Q    75_A     64   64   64     50   59   60   62   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    76_A     L    76_A     64   64   64     50   59   60   62   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     Q    77_A     Q    77_A     64   64   64     50   59   60   62   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    78_A     A    78_A     64   64   64     50   59   60   62   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     I    79_A     I    79_A     64   64   64     50   59   60   62   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     V    80_A     V    80_A     64   64   64     50   59   60   62   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     D    81_A     D    81_A     64   64   64     50   59   60   62   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     V    82_A     V    82_A     64   64   64     50   59   60   62   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    83_A     L    83_A     64   64   64     50   59   60   62   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    84_A     A    84_A     64   64   64     50   59   60   62   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     V    85_A     V    85_A     64   64   64     50   59   60   62   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
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     59     60     62     63     64     64     64     64     64     64     64     64     64     64     64     64     64     64     64 
GDT PERCENT_AT  78.12  92.19  93.75  96.88  98.44 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.29   0.42   0.44   0.59   0.70   0.83   0.83   0.83   0.83   0.83   0.83   0.83   0.83   0.83   0.83   0.83   0.83   0.83   0.83   0.83
GDT RMS_ALL_AT   0.86   0.85   0.85   0.84   0.84   0.83   0.83   0.83   0.83   0.83   0.83   0.83   0.83   0.83   0.83   0.83   0.83   0.83   0.83   0.83

# Checking swapping
#   possible swapping detected:  D    25_A      D    25_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A    22_A      A    22_A     1.698     0    0.609   0.561     3.989   65.000   60.667
LGA    D    23_A      D    23_A     2.406     0    0.100   0.119     3.952   57.738   58.512
LGA    G    24_A      G    24_A     3.599     0    0.672   0.672     3.599   63.690   63.690
LGA    D    25_A      D    25_A     2.976     0    0.367   1.023     5.127   51.310   41.429
LGA    G    26_A      G    26_A     0.383     0    0.098   0.098     0.674   97.619   97.619
LGA    Q    27_A      Q    27_A     0.302     0    0.010   0.767     1.978  100.000   93.968
LGA    G    28_A      G    28_A     0.221     0    0.016   0.016     0.296  100.000  100.000
LGA    L    29_A      L    29_A     0.284     0    0.001   0.079     0.585  100.000   98.810
LGA    Y    30_A      Y    30_A     0.297     0    0.044   0.137     0.542  100.000   99.206
LGA    A    31_A      A    31_A     0.231     0    0.010   0.010     0.310  100.000  100.000
LGA    A    32_A      A    32_A     0.149     0    0.021   0.020     0.208  100.000  100.000
LGA    N    33_A      N    33_A     0.400     0    0.039   0.063     0.593   97.619   98.810
LGA    C    34_A      C    34_A     0.255     0    0.032   0.065     0.359  100.000  100.000
LGA    A    35_A      A    35_A     0.494     0    0.018   0.018     0.764   95.238   96.190
LGA    A    36_A      A    36_A     0.533     0    0.010   0.010     0.705   92.857   92.381
LGA    C    37_A      C    37_A     0.566     0    0.061   0.069     0.780   90.476   92.063
LGA    H    38_A      H    38_A     0.556     0    0.049   0.057     0.753   90.476   93.333
LGA    G    39_A      G    39_A     0.864     0    0.083   0.083     0.864   90.476   90.476
LGA    A    40_A      A    40_A     0.322     0    0.013   0.019     0.534   97.619   98.095
LGA    L    41_A      L    41_A     0.360     0    0.025   0.031     0.570   97.619   98.810
LGA    A    42_A      A    42_A     0.627     0    0.021   0.021     0.730   90.476   90.476
LGA    T    43_A      T    43_A     0.518     0    0.118   0.099     0.833   90.476   90.476
LGA    S    44_A      S    44_A     0.598     0    0.017   0.033     0.687   95.238   93.651
LGA    E    45_A      E    45_A     1.048     0    0.022   1.021     7.411   85.952   57.937
LGA    K    46_A      K    46_A     0.304     0    0.039   0.207     1.395   97.619   92.698
LGA    K    47_A      K    47_A     0.245     0    0.011   0.105     0.390  100.000  100.000
LGA    G    48_A      G    48_A     0.219     0    0.085   0.085     0.624   97.619   97.619
LGA    T    49_A      T    49_A     0.269     0    0.041   0.081     0.399  100.000  100.000
LGA    T    50_A      T    50_A     0.324     0    0.023   0.075     0.823  100.000   95.918
LGA    L    51_A      L    51_A     0.424     0    0.003   0.103     1.083  100.000   94.107
LGA    A    52_A      A    52_A     0.592     0    0.013   0.013     0.696   90.476   90.476
LGA    R    53_A      R    53_A     0.524     0    0.005   0.658     3.069   95.238   77.792
LGA    L    54_A      L    54_A     0.224     0    0.014   0.067     0.327  100.000  100.000
LGA    Q    55_A      Q    55_A     0.172     0    0.003   0.223     0.625  100.000   98.942
LGA    S    56_A      S    56_A     0.208     0    0.033   0.041     0.252  100.000  100.000
LGA    A    57_A      A    57_A     0.200     0    0.008   0.012     0.235  100.000  100.000
LGA    V    58_A      V    58_A     0.304     0    0.008   0.033     0.522  100.000   98.639
LGA    S    59_A      S    59_A     0.213     0    0.008   0.573     2.016  100.000   94.127
LGA    A    60_A      A    60_A     0.157     0    0.020   0.028     0.308  100.000  100.000
LGA    N    61_A      N    61_A     0.323     0    0.063   0.092     1.077  100.000   94.107
LGA    A    62_A      A    62_A     0.183     0    0.030   0.037     0.393  100.000  100.000
LGA    G    63_A      G    63_A     0.168     0    0.072   0.072     0.789   97.619   97.619
LGA    G    64_A      G    64_A     0.904     0    0.024   0.024     1.212   88.214   88.214
LGA    M    65_A      M    65_A     0.913     0    0.071   0.261     1.128   90.476   88.214
LGA    G    66_A      G    66_A     0.724     0    0.018   0.018     0.942   90.476   90.476
LGA    F    67_A      F    67_A     1.280     0    0.030   0.153     2.225   81.429   73.766
LGA    L    68_A      L    68_A     0.946     0    0.035   0.077     1.621   90.476   84.881
LGA    S    69_A      S    69_A     0.451     0    0.044   0.045     0.818   95.238   93.651
LGA    S    70_A      S    70_A     0.629     0    0.018   0.059     0.767   90.476   90.476
LGA    L    71_A      L    71_A     0.542     0    0.013   0.031     0.636   90.476   90.476
LGA    T    72_A      T    72_A     0.500     0    0.012   0.038     0.533   95.238   95.918
LGA    S    73_A      S    73_A     0.457     0    0.012   0.628     2.571  100.000   92.857
LGA    A    74_A      A    74_A     0.138     0    0.021   0.023     0.190  100.000  100.000
LGA    Q    75_A      Q    75_A     0.330     0    0.017   0.054     0.635  100.000   96.825
LGA    L    76_A      L    76_A     0.354     0    0.007   0.073     0.502  100.000   98.810
LGA    Q    77_A      Q    77_A     0.370     0    0.022   0.137     0.551  100.000   98.942
LGA    A    78_A      A    78_A     0.275     0    0.007   0.007     0.329  100.000  100.000
LGA    I    79_A      I    79_A     0.257     0    0.019   0.046     0.367  100.000  100.000
LGA    V    80_A      V    80_A     0.373     0    0.015   0.030     0.382  100.000  100.000
LGA    D    81_A      D    81_A     0.395     0    0.017   0.034     0.814  100.000   95.238
LGA    V    82_A      V    82_A     0.239     0    0.025   1.267     2.665  100.000   88.844
LGA    L    83_A      L    83_A     0.147     0    0.068   0.070     0.320  100.000  100.000
LGA    A    84_A      A    84_A     0.119     0    0.071   0.075     0.441  100.000  100.000
LGA    V    85_A      V    85_A     0.155     0    0.285   1.313     2.908  100.000   88.844

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       64     256    256  100.00     433    433  100.00                64
SUMMARY(RMSD_GDC):     0.831          0.848                  1.179           94.390   92.111

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   97   64    4.0     64    0.83    97.266    98.595     6.876

LGA_LOCAL      RMSD:   0.831  Number of atoms:   64  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.831  Number of assigned atoms:   64 
Std_ASGN_ATOMS RMSD:   0.831  Standard rmsd on all 64 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.323476 * X  +  -0.249039 * Y  +  -0.912876 * Z  +  23.205896
  Y_new =   0.941852 * X  +   0.177502 * Y  +   0.285320 * Z  +  -8.854109
  Z_new =   0.090982 * X  +  -0.952088 * Y  +   0.291976 * Z  +  -8.292377 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.239971 -0.091108 -1.273233   [DEG:   71.0451   -5.2201  -72.9509 ]
ZXZ: -1.873728  1.274504  3.046322   [DEG: -107.3567   73.0237  174.5414 ]
 
# END of job
