
#######################################################
#                                                     #
#                        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   99 (  793),  selected   61 , name one
# Molecule2: number of CA atoms   61 (  480),  selected   61 , 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:    61      32_A - 98_A        1.62     1.62
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    61      32_A - 98_A        1.62     1.62
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    22      32_A - 53_A        0.92     3.97
  LCS_AVERAGE:     32.09

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   61
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    32_A     A    32_A     22   61   61      9   20   31   50   55   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     T    33_A     T    33_A     22   61   61     17   26   41   50   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     M    34_A     M    34_A     22   61   61     17   25   41   50   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    35_A     A    35_A     22   61   61     17   26   45   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    36_A     D    36_A     22   61   61     17   28   45   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    37_A     L    37_A     22   61   61     17   26   41   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    38_A     K    38_A     22   61   61     17   27   45   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     M    39_A     M    39_A     22   61   61     17   28   45   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Q    40_A     Q    40_A     22   61   61     17   28   45   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    41_A     A    41_A     22   61   61     17   28   45   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    42_A     V    42_A     22   61   61     17   28   45   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    43_A     K    43_A     22   61   61     17   28   45   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    44_A     E    44_A     22   61   61     17   28   45   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     I    45_A     I    45_A     22   61   61     17   28   45   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     C    46_A     C    46_A     22   61   61     17   28   45   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Y    47_A     Y    47_A     22   61   61     17   26   44   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    48_A     E    48_A     22   61   61     17   28   45   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    49_A     V    49_A     22   61   61     17   28   45   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    50_A     A    50_A     22   61   61     13   23   38   51   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    51_A     L    51_A     22   61   61      5   20   37   51   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    52_A     A    52_A     22   61   61      3    5    6   18   55   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    53_A     D    53_A     22   61   61      3   12   17   45   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     F    54_A     F    54_A     20   61   61      8   25   44   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    55_A     R    55_A     20   61   61      3    3    6   51   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     H    56_A     H    56_A     21   61   61      8   26   45   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     G    57_A     G    57_A     21   61   61      8   28   45   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    58_A     R    58_A     21   61   61     12   28   45   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    59_A     A    59_A     21   61   61     12   28   45   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    60_A     E    60_A     21   61   61     12   28   45   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     I    61_A     I    61_A     21   61   61     12   27   45   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    62_A     E    62_A     21   61   61     13   25   45   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    63_A     A    63_A     21   61   61     13   28   45   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    64_A     L    64_A     21   61   61     13   28   45   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    65_A     A    65_A     21   61   61     13   28   45   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    66_A     A    66_A     21   61   61     13   28   45   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    67_A     L    67_A     21   61   61     13   28   45   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    68_A     K    68_A     21   61   61     13   28   45   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     M    69_A     M    69_A     21   61   61     13   28   45   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    70_A     R    70_A     21   61   61     13   28   45   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    71_A     E    71_A     21   61   61     12   28   45   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    72_A     L    72_A     21   61   61     13   26   45   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     C    73_A     C    73_A     21   61   61     13   26   45   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    74_A     R    74_A     21   61   61     13   26   45   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     T    75_A     T    75_A     21   61   61     13   26   45   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Y    76_A     Y    76_A     21   61   61      8   26   44   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     G    83_A     G    83_A      4   61   61      3    4    5    9   20   47   55   59   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    84_A     D    84_A     15   61   61      4   11   42   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    85_A     A    85_A     15   61   61     11   26   42   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     W    86_A     W    86_A     15   61   61     11   23   42   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    87_A     R    87_A     15   61   61     11   28   45   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    88_A     A    88_A     15   61   61     11   26   45   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    89_A     V    89_A     15   61   61     11   26   45   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    90_A     A    90_A     15   61   61     11   26   45   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    91_A     R    91_A     15   61   61     13   28   45   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    92_A     D    92_A     15   61   61     14   28   45   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    93_A     V    93_A     15   61   61     11   26   45   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     W    94_A     W    94_A     15   61   61     11   23   45   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    95_A     D    95_A     15   61   61     11   28   45   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     T    96_A     T    96_A     15   61   61     11   26   45   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    97_A     V    97_A     15   61   61     11   26   45   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     G    98_A     G    98_A     15   61   61      4    6   45   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_AVERAGE  LCS_A:  77.36  (  32.09  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     17     28     45     52     57     60     60     60     61     61     61     61     61     61     61     61     61     61     61     61 
GDT PERCENT_AT  27.87  45.90  73.77  85.25  93.44  98.36  98.36  98.36 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.28   0.71   1.05   1.18   1.34   1.47   1.47   1.47   1.62   1.62   1.62   1.62   1.62   1.62   1.62   1.62   1.62   1.62   1.62   1.62
GDT RMS_ALL_AT   3.07   1.68   1.66   1.66   1.63   1.63   1.63   1.63   1.62   1.62   1.62   1.62   1.62   1.62   1.62   1.62   1.62   1.62   1.62   1.62

# Checking swapping
#   possible swapping detected:  E    48_A      E    48_A
#   possible swapping detected:  E    60_A      E    60_A
#   possible swapping detected:  E    62_A      E    62_A
#   possible swapping detected:  Y    76_A      Y    76_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A    32_A      A    32_A     3.240     0    0.350   0.342     5.314   47.738   45.619
LGA    T    33_A      T    33_A     1.971     0    0.021   0.320     2.522   70.833   70.680
LGA    M    34_A      M    34_A     2.034     0    0.038   0.304     3.461   72.976   64.226
LGA    A    35_A      A    35_A     1.281     0    0.093   0.102     1.526   81.548   81.524
LGA    D    36_A      D    36_A     0.835     0    0.096   0.905     4.030   88.214   76.250
LGA    L    37_A      L    37_A     1.685     0    0.041   0.139     3.012   79.286   68.274
LGA    K    38_A      K    38_A     1.138     0    0.086   0.678     4.569   88.333   71.217
LGA    M    39_A      M    39_A     0.428     0    0.020   1.187     7.105   95.238   72.738
LGA    Q    40_A      Q    40_A     1.023     0    0.026   1.455     5.137   88.214   69.418
LGA    A    41_A      A    41_A     0.966     0    0.043   0.046     1.159   90.476   88.667
LGA    V    42_A      V    42_A     0.337     0    0.076   0.141     0.786  100.000   97.279
LGA    K    43_A      K    43_A     0.731     0    0.031   0.130     1.767   92.857   84.603
LGA    E    44_A      E    44_A     1.043     0    0.151   0.532     2.912   81.548   73.228
LGA    I    45_A      I    45_A     0.460     0    0.026   0.116     1.359   97.619   91.786
LGA    C    46_A      C    46_A     0.638     0    0.099   0.125     1.206   90.595   90.556
LGA    Y    47_A      Y    47_A     1.354     0    0.051   1.321    10.034   83.690   45.714
LGA    E    48_A      E    48_A     0.657     0    0.036   0.235     1.140   90.476   89.471
LGA    V    49_A      V    49_A     0.602     0    0.040   0.070     1.119   88.333   87.959
LGA    A    50_A      A    50_A     2.121     0    0.101   0.105     2.620   64.881   63.333
LGA    L    51_A      L    51_A     2.520     0    0.673   1.210     5.676   59.167   53.750
LGA    A    52_A      A    52_A     2.962     0    0.563   0.565     3.815   59.286   56.095
LGA    D    53_A      D    53_A     2.730     0    0.182   0.985     6.457   61.190   44.107
LGA    F    54_A      F    54_A     1.537     0    0.198   1.265     8.988   79.405   43.983
LGA    R    55_A      R    55_A     2.194     0    0.106   0.882     8.140   70.833   36.840
LGA    H    56_A      H    56_A     1.321     0    0.035   0.903     3.164   83.690   72.524
LGA    G    57_A      G    57_A     1.041     0    0.084   0.084     1.082   85.952   85.952
LGA    R    58_A      R    58_A     0.901     0    0.054   1.111     4.974   90.476   75.844
LGA    A    59_A      A    59_A     0.879     0    0.065   0.067     0.978   90.476   90.476
LGA    E    60_A      E    60_A     0.788     0    0.038   0.408     1.721   90.476   85.503
LGA    I    61_A      I    61_A     1.207     0    0.044   0.099     1.539   83.690   81.488
LGA    E    62_A      E    62_A     1.395     0    0.007   0.135     1.856   81.429   77.619
LGA    A    63_A      A    63_A     0.920     0    0.019   0.035     1.121   88.214   88.667
LGA    L    64_A      L    64_A     0.795     0    0.183   0.433     1.568   90.476   87.143
LGA    A    65_A      A    65_A     0.928     0    0.012   0.017     1.131   90.595   88.762
LGA    A    66_A      A    66_A     0.764     0    0.054   0.060     0.956   92.857   92.381
LGA    L    67_A      L    67_A     0.514     0    0.015   0.784     3.200   92.857   83.274
LGA    K    68_A      K    68_A     0.817     0    0.005   0.841     1.447   90.476   88.466
LGA    M    69_A      M    69_A     0.592     0    0.031   0.899     3.306   95.238   82.500
LGA    R    70_A      R    70_A     0.463     0    0.085   1.182     2.411   92.857   83.506
LGA    E    71_A      E    71_A     0.835     0    0.061   1.083     2.940   83.810   75.132
LGA    L    72_A      L    72_A     1.420     0    0.013   0.156     1.843   79.286   77.143
LGA    C    73_A      C    73_A     1.487     0    0.102   0.283     1.706   77.143   77.143
LGA    R    74_A      R    74_A     2.173     0    0.308   0.974     8.222   59.524   44.329
LGA    T    75_A      T    75_A     2.258     0    0.121   0.226     2.424   64.762   64.762
LGA    Y    76_A      Y    76_A     2.419     0    0.694   0.611     3.212   59.167   64.246
LGA    G    83_A      G    83_A     5.557     0    0.106   0.106     5.790   30.833   30.833
LGA    D    84_A      D    84_A     2.442     0    0.296   0.339     3.412   67.262   65.179
LGA    A    85_A      A    85_A     1.927     0    0.045   0.051     2.529   72.976   69.810
LGA    W    86_A      W    86_A     1.719     0    0.126   1.250     7.675   77.143   47.959
LGA    R    87_A      R    87_A     1.078     0    0.037   1.372     2.874   83.690   71.861
LGA    A    88_A      A    88_A     1.406     0    0.137   0.153     1.581   79.286   78.000
LGA    V    89_A      V    89_A     1.182     0    0.103   0.132     1.456   81.429   81.429
LGA    A    90_A      A    90_A     1.083     0    0.041   0.052     1.155   83.690   83.238
LGA    R    91_A      R    91_A     0.667     0    0.009   1.258     8.247   90.476   61.126
LGA    D    92_A      D    92_A     0.798     0    0.068   0.162     1.040   90.476   89.345
LGA    V    93_A      V    93_A     1.124     0    0.010   0.084     1.245   83.690   82.721
LGA    W    94_A      W    94_A     1.396     0    0.024   1.648     5.622   79.286   62.755
LGA    D    95_A      D    95_A     1.103     0    0.215   0.484     1.903   79.286   83.750
LGA    T    96_A      T    96_A     1.489     0    0.116   1.139     3.556   81.429   73.537
LGA    V    97_A      V    97_A     1.455     0    0.542   1.330     2.989   73.214   73.129
LGA    G    98_A      G    98_A     1.576     0    0.692   0.692     3.227   69.286   69.286

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       61     244    244  100.00     480    480  100.00                61
SUMMARY(RMSD_GDC):     1.619          1.592                  2.552           80.486   73.084

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   99   61    4.0     60    1.47    82.377    92.026     3.810

LGA_LOCAL      RMSD:   1.475  Number of atoms:   60  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.627  Number of assigned atoms:   61 
Std_ASGN_ATOMS RMSD:   1.619  Standard rmsd on all 61 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.137668 * X  +  -0.138181 * Y  +  -0.980792 * Z  +  23.943241
  Y_new =   0.937613 * X  +   0.337363 * Y  +   0.084077 * Z  +  39.019951
  Z_new =   0.319265 * X  +  -0.931178 * Y  +   0.176004 * Z  +  15.261580 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.425010 -0.324954 -1.383988   [DEG:   81.6470  -18.6185  -79.2966 ]
ZXZ: -1.656311  1.393870  2.811291   [DEG:  -94.8996   79.8629  161.0751 ]
 
# END of job
