
#######################################################
#                                                     #
#                        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        1.64     1.64
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    61      32_A - 98_A        1.64     1.64
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    24      32_A - 55_A        1.00     2.63
  LCS_AVERAGE:     34.69

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     24   61   61     18   29   42   51   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     T    33_A     T    33_A     24   61   61     20   29   46   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     M    34_A     M    34_A     24   61   61     20   29   46   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    35_A     A    35_A     24   61   61     20   29   46   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    36_A     D    36_A     24   61   61      8   29   46   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    37_A     L    37_A     24   61   61     19   29   46   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    38_A     K    38_A     24   61   61     20   29   46   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     M    39_A     M    39_A     24   61   61     20   29   46   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Q    40_A     Q    40_A     24   61   61     20   29   46   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    41_A     A    41_A     24   61   61     20   29   46   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    42_A     V    42_A     24   61   61     20   29   46   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    43_A     K    43_A     24   61   61     20   29   46   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    44_A     E    44_A     24   61   61     20   29   46   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     I    45_A     I    45_A     24   61   61     20   29   46   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     C    46_A     C    46_A     24   61   61     19   29   46   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Y    47_A     Y    47_A     24   61   61     20   29   46   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    48_A     E    48_A     24   61   61     20   29   46   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    49_A     V    49_A     24   61   61     20   29   46   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    50_A     A    50_A     24   61   61     20   29   46   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    51_A     L    51_A     24   61   61     20   29   46   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    52_A     A    52_A     24   61   61      3    5   13   49   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    53_A     D    53_A     24   61   61      3    3   21   46   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     F    54_A     F    54_A     24   61   61      8   29   46   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    55_A     R    55_A     24   61   61      3    3   25   49   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     H    56_A     H    56_A     22   61   61      8   29   46   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     G    57_A     G    57_A     22   61   61      6   29   46   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    58_A     R    58_A     22   61   61     10   24   46   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    59_A     A    59_A     22   61   61     10   26   46   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    60_A     E    60_A     22   61   61     20   29   46   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     I    61_A     I    61_A     22   61   61     10   29   46   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    62_A     E    62_A     22   61   61      9   24   46   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    63_A     A    63_A     22   61   61     12   28   46   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    64_A     L    64_A     22   61   61     20   29   46   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    65_A     A    65_A     22   61   61     12   29   46   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    66_A     A    66_A     22   61   61     10   24   46   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    67_A     L    67_A     22   61   61     10   23   46   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    68_A     K    68_A     22   61   61      9   26   46   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     M    69_A     M    69_A     22   61   61     10   24   46   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    70_A     R    70_A     22   61   61     10   23   43   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    71_A     E    71_A     22   61   61      8   23   43   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    72_A     L    72_A     22   61   61      8   21   43   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     C    73_A     C    73_A     22   61   61      9   22   36   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    74_A     R    74_A     22   61   61      8   21   31   48   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     T    75_A     T    75_A     22   61   61      8   21   33   48   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Y    76_A     Y    76_A     22   61   61      3   21   31   48   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     G    83_A     G    83_A     22   61   61      0    3    5    6   40   58   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    84_A     D    84_A     21   61   61      4    9   29   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    85_A     A    85_A     15   61   61      4   14   46   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     W    86_A     W    86_A     15   61   61      4   14   21   45   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    87_A     R    87_A     15   61   61     11   29   46   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    88_A     A    88_A     15   61   61     11   29   46   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    89_A     V    89_A     15   61   61     11   29   46   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    90_A     A    90_A     15   61   61     11   29   46   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    91_A     R    91_A     15   61   61     20   29   46   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    92_A     D    92_A     15   61   61     20   29   46   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    93_A     V    93_A     15   61   61     11   29   46   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     W    94_A     W    94_A     15   61   61     11   29   46   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    95_A     D    95_A     15   61   61     11   29   46   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     T    96_A     T    96_A     15   61   61     11   14   42   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    97_A     V    97_A     15   61   61     11   14   46   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     G    98_A     G    98_A     15   61   61      5   14   46   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_AVERAGE  LCS_A:  78.23  (  34.69  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     20     29     46     52     57     60     61     61     61     61     61     61     61     61     61     61     61     61     61     61 
GDT PERCENT_AT  32.79  47.54  75.41  85.25  93.44  98.36 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.31   0.53   1.03   1.25   1.37   1.55   1.64   1.64   1.64   1.64   1.64   1.64   1.64   1.64   1.64   1.64   1.64   1.64   1.64   1.64
GDT RMS_ALL_AT   2.34   2.29   1.89   1.69   1.71   1.64   1.64   1.64   1.64   1.64   1.64   1.64   1.64   1.64   1.64   1.64   1.64   1.64   1.64   1.64

# Checking swapping
#   possible swapping detected:  E    44_A      E    44_A
#   possible swapping detected:  E    60_A      E    60_A
#   possible swapping detected:  E    62_A      E    62_A
#   possible swapping detected:  D    84_A      D    84_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A    32_A      A    32_A     2.569     0    0.488   0.488     3.735   60.952   57.429
LGA    T    33_A      T    33_A     1.907     0    0.109   0.317     2.216   72.857   74.218
LGA    M    34_A      M    34_A     1.894     0    0.031   1.060     2.521   72.857   70.952
LGA    A    35_A      A    35_A     1.516     0    0.066   0.072     1.646   77.143   78.000
LGA    D    36_A      D    36_A     1.266     0    0.109   0.194     2.074   81.429   77.202
LGA    L    37_A      L    37_A     1.747     0    0.042   0.102     2.491   75.000   69.881
LGA    K    38_A      K    38_A     1.367     0    0.136   0.682     2.298   88.333   80.741
LGA    M    39_A      M    39_A     0.527     0    0.035   1.071     4.501   90.476   77.857
LGA    Q    40_A      Q    40_A     1.153     0    0.022   1.232     3.332   83.690   70.053
LGA    A    41_A      A    41_A     0.984     0    0.040   0.040     1.078   88.214   86.857
LGA    V    42_A      V    42_A     0.326     0    0.101   0.167     0.675   95.238   95.918
LGA    K    43_A      K    43_A     0.778     0    0.020   0.084     1.869   90.595   82.646
LGA    E    44_A      E    44_A     1.261     0    0.151   0.269     2.083   77.262   79.630
LGA    I    45_A      I    45_A     0.723     0    0.032   0.100     1.820   90.476   87.143
LGA    C    46_A      C    46_A     0.959     0    0.149   0.829     1.619   83.810   81.587
LGA    Y    47_A      Y    47_A     1.709     0    0.053   1.162    11.341   77.143   38.532
LGA    E    48_A      E    48_A     1.298     0    0.037   0.883     3.373   81.429   69.048
LGA    V    49_A      V    49_A     0.739     0    0.019   0.061     0.948   90.476   94.558
LGA    A    50_A      A    50_A     1.489     0    0.095   0.100     2.129   75.119   74.667
LGA    L    51_A      L    51_A     1.875     0    0.690   0.609     3.133   67.143   70.000
LGA    A    52_A      A    52_A     2.531     0    0.529   0.531     3.238   59.286   58.857
LGA    D    53_A      D    53_A     2.323     0    0.250   0.972     6.361   65.119   48.155
LGA    F    54_A      F    54_A     1.099     0    0.253   1.383     5.225   83.810   66.277
LGA    R    55_A      R    55_A     2.530     0    0.107   0.886     9.374   66.905   31.861
LGA    H    56_A      H    56_A     1.269     0    0.061   0.920     3.231   83.690   75.048
LGA    G    57_A      G    57_A     1.360     0    0.123   0.123     1.360   81.429   81.429
LGA    R    58_A      R    58_A     1.203     0    0.048   1.122     4.706   81.429   73.896
LGA    A    59_A      A    59_A     0.920     0    0.075   0.077     1.044   88.214   88.667
LGA    E    60_A      E    60_A     0.709     0    0.033   0.501     1.449   90.476   86.455
LGA    I    61_A      I    61_A     1.345     0    0.037   0.084     1.819   81.429   77.143
LGA    E    62_A      E    62_A     1.433     0    0.010   0.166     2.070   81.429   74.868
LGA    A    63_A      A    63_A     0.743     0    0.013   0.025     1.017   90.595   90.571
LGA    L    64_A      L    64_A     0.664     0    0.190   0.469     1.623   88.214   86.012
LGA    A    65_A      A    65_A     1.097     0    0.021   0.031     1.527   85.952   83.333
LGA    A    66_A      A    66_A     1.074     0    0.048   0.055     1.290   85.952   85.048
LGA    L    67_A      L    67_A     0.493     0    0.009   0.790     3.751   95.238   84.821
LGA    K    68_A      K    68_A     0.453     0    0.032   0.556     1.513   97.619   88.677
LGA    M    69_A      M    69_A     0.790     0    0.037   0.543     1.878   90.476   87.202
LGA    R    70_A      R    70_A     1.146     0    0.090   1.192     2.857   81.548   76.190
LGA    E    71_A      E    71_A     1.276     0    0.052   1.077     3.830   79.286   68.995
LGA    L    72_A      L    72_A     1.310     0    0.013   0.163     1.841   77.143   82.679
LGA    C    73_A      C    73_A     1.924     0    0.065   0.250     2.566   69.048   68.968
LGA    R    74_A      R    74_A     3.008     0    0.280   0.962     8.764   49.048   36.320
LGA    T    75_A      T    75_A     2.835     0    0.094   0.174     3.193   55.357   57.211
LGA    Y    76_A      Y    76_A     3.044     0    0.537   1.565    10.746   53.571   29.683
LGA    G    83_A      G    83_A     4.288     0    0.200   0.200     5.132   50.238   50.238
LGA    D    84_A      D    84_A     1.823     0    0.597   1.097     4.716   79.762   65.298
LGA    A    85_A      A    85_A     1.136     0    0.046   0.050     1.639   79.286   78.000
LGA    W    86_A      W    86_A     2.182     0    0.108   1.220     9.910   68.810   35.000
LGA    R    87_A      R    87_A     1.610     0    0.014   0.857     2.744   72.857   70.693
LGA    A    88_A      A    88_A     1.552     0    0.132   0.146     1.640   75.000   74.571
LGA    V    89_A      V    89_A     1.211     0    0.086   0.137     1.490   81.429   84.014
LGA    A    90_A      A    90_A     1.606     0    0.050   0.060     1.676   75.000   74.571
LGA    R    91_A      R    91_A     1.355     0    0.012   1.245     6.970   81.429   60.996
LGA    D    92_A      D    92_A     1.379     0    0.065   0.188     1.854   81.429   79.286
LGA    V    93_A      V    93_A     1.388     0    0.017   0.084     1.482   81.429   81.429
LGA    W    94_A      W    94_A     1.676     0    0.013   0.359     1.718   72.857   77.143
LGA    D    95_A      D    95_A     1.437     0    0.253   0.484     2.103   75.119   78.333
LGA    T    96_A      T    96_A     1.755     0    0.114   1.153     3.834   77.143   71.156
LGA    V    97_A      V    97_A     1.417     0    0.562   1.348     2.727   77.262   73.129
LGA    G    98_A      G    98_A     1.546     0    0.094   0.094     1.972   77.143   77.143

# 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):     1.636          1.620                  2.693           78.493   72.726

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   99   61    4.0     61    1.64    83.197    92.458     3.513

LGA_LOCAL      RMSD:   1.636  Number of atoms:   61  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.636  Number of assigned atoms:   61 
Std_ASGN_ATOMS RMSD:   1.636  Standard rmsd on all 61 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.851722 * X  +   0.324613 * Y  +   0.411335 * Z  + -26.242348
  Y_new =   0.139842 * X  +  -0.615712 * Y  +   0.775463 * Z  +  64.757263
  Z_new =   0.504989 * X  +   0.718001 * Y  +   0.479021 * Z  +  -7.834777 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.978857 -0.529369  0.982453   [DEG:  170.6759  -30.3306   56.2904 ]
ZXZ:  2.653893  1.071257  0.612955   [DEG:  152.0569   61.3785   35.1197 ]
 
# END of job
