
#######################################################
#                                                     #
#                        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   61 (  499),  selected   61 , name one
# Molecule2: number of CA atoms  109 (  875),  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:    43      62_A - 104_A       4.93    10.69
  LCS_AVERAGE:     32.67

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    21      84_A - 104_A       1.99    12.73
  LCS_AVERAGE:     11.96

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14      84_A - 97_A        0.92    13.52
  LCS_AVERAGE:      7.73

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     L    44_A     L    44_A      8    8   14      8    8    8    8    8    8    8   10   11   11   12   12   13   14   16   22   24   28   33   34 
LCS_GDT     K    45_A     K    45_A      8    8   14      8    8    8    8    8    8   12   15   17   17   19   20   24   26   27   27   29   31   35   36 
LCS_GDT     N    46_A     N    46_A      8    8   14      8    8    8    8    8    8   12   15   19   20   22   22   24   26   27   27   29   33   36   38 
LCS_GDT     L    47_A     L    47_A      8    8   14      8    8    8    9   11   16   17   18   19   20   22   23   24   26   27   28   30   31   35   38 
LCS_GDT     L    48_A     L    48_A      8    8   14      8    8    8   12   15   16   17   18   19   20   22   23   24   26   27   30   34   36   37   39 
LCS_GDT     K    49_A     K    49_A      8    8   14      8    8    8    8    8    8    8   10   11   11   13   16   21   23   27   28   30   35   37   39 
LCS_GDT     D    50_A     D    50_A      8    8   14      8    8    8    8    8    8    8   17   18   20   22   23   23   26   27   28   31   34   35   39 
LCS_GDT     Q    51_A     Q    51_A      8    8   14      8    8    8    8    8    8    8    8   12   15   17   19   22   25   27   28   30   34   35   37 
LCS_GDT     I    52_A     I    52_A      3    3   14      5    5    5    5    5    6    8   10   12   15   18   21   26   28   31   32   32   34   36   39 
LCS_GDT     P    53_A     P    53_A      4    5   14      5    5    5    5    5   10   11   13   15   17   21   25   26   28   31   32   32   34   35   39 
LCS_GDT     T    54_A     T    54_A      4    5   14      3    4    4    5    8   10   11   13   15   17   21   25   26   28   31   32   32   34   35   37 
LCS_GDT     G    55_A     G    55_A      4    5   14      3    4    4    5    8   10   11   13   15   17   21   25   26   28   31   32   32   34   35   39 
LCS_GDT     S    56_A     S    56_A      4    5   23      3    4    4    5    8   10   11   13   15   17   21   25   26   28   31   32   32   34   35   39 
LCS_GDT     S    57_A     S    57_A      3    5   23      0    3    3    5    5   10   11   13   15   17   21   25   26   28   31   32   32   34   35   39 
LCS_GDT     F    58_A     F    58_A      3    5   23      0    3    3    3    4    5    6   13   15   17   21   25   26   28   31   32   32   34   35   35 
LCS_GDT     F    59_A     F    59_A      3    5   23      3    3    3    4    4    5    8   10   15   17   21   25   26   28   31   32   32   34   35   39 
LCS_GDT     K    60_A     K    60_A      3    5   23      3    3    4    4    4    8   12   15   17   18   20   23   26   28   31   32   33   36   37   39 
LCS_GDT     L    61_A     L    61_A      3    5   40      3    3    7    9   12   13   17   18   18   21   26   28   31   33   38   40   43   44   44   44 
LCS_GDT     P    62_A     P    62_A      4    8   43      3    7   10   12   15   16   19   24   25   28   30   33   36   37   40   41   43   44   44   44 
LCS_GDT     V    63_A     V    63_A      4    8   43      3    7    9   12   15   17   22   24   26   28   30   33   36   37   40   41   43   44   44   44 
LCS_GDT     V    64_A     V    64_A      4    8   43      4    5    7    8   12   14   16   18   25   28   30   33   36   37   40   41   43   44   44   44 
LCS_GDT     F    65_A     F    65_A      4    8   43      4    5    7    8    8    9   15   17   19   20   30   33   36   37   40   41   43   44   44   44 
LCS_GDT     F    66_A     F    66_A      4   13   43      5    5    5   10   15   16   17   18   19   20   23   28   32   36   40   41   43   44   44   44 
LCS_GDT     R    67_A     R    67_A      4   13   43      4    4    5   10   15   16   17   18   19   20   23   28   31   36   39   41   43   44   44   44 
LCS_GDT     V    68_A     V    68_A      7   13   43      5    5    7   11   12   15   17   18   19   20   22   30   32   35   38   40   43   44   44   44 
LCS_GDT     T    69_A     T    69_A      9   13   43      5    6   10   12   15   16   17   18   19   22   26   30   32   36   38   40   43   44   44   44 
LCS_GDT     D    70_A     D    70_A      9   13   43      5    7   10   12   15   16   17   20   25   27   30   33   36   37   40   41   43   44   44   44 
LCS_GDT     N    71_A     N    71_A      9   13   43      5    7   17   19   21   23   25   26   29   30   31   33   36   37   40   41   43   44   44   44 
LCS_GDT     V    72_A     V    72_A      9   13   43      5    7   10   17   20   22   23   26   28   29   31   33   34   37   40   41   43   44   44   44 
LCS_GDT     I    73_A     I    73_A      9   13   43      3   14   17   19   21   24   26   28   29   30   31   33   36   37   40   41   43   44   44   44 
LCS_GDT     V    74_A     V    74_A      9   13   43      3    7   10   12   15   21   23   26   28   30   31   33   34   37   40   41   43   44   44   44 
LCS_GDT     I    75_A     I    75_A      9   13   43      3   12   17   19   21   24   26   28   29   30   31   33   36   37   40   41   43   44   44   44 
LCS_GDT     L    76_A     L    76_A      9   13   43      3   10   17   19   21   24   26   28   29   30   31   33   36   37   40   41   43   44   44   44 
LCS_GDT     L    77_A     L    77_A      9   13   43      3    7   10   12   15   24   26   28   29   30   31   33   36   37   40   41   43   44   44   44 
LCS_GDT     T    78_A     T    78_A      4   13   43      2   10   17   19   21   24   26   28   29   30   31   33   36   37   40   41   43   44   44   44 
LCS_GDT     N    79_A     N    79_A      4    9   43      3    4    4    7   10   19   23   28   29   30   31   33   36   37   40   41   43   44   44   44 
LCS_GDT     E    80_A     E    80_A      4    6   43      3    4   15   18   21   24   26   28   29   30   31   33   36   37   40   41   43   44   44   44 
LCS_GDT     K    81_A     K    81_A      4    6   43      4    8   16   19   21   24   26   28   29   30   31   33   36   37   40   41   43   44   44   44 
LCS_GDT     E    82_A     E    82_A      4    4   43      4    4    5    5    7    9   12   16   23   29   29   31   33   36   40   41   43   44   44   44 
LCS_GDT     N    83_A     N    83_A      4   16   43      4    4    5    5   11   18   22   26   28   30   31   33   36   37   40   41   43   44   44   44 
LCS_GDT     I    84_A     I    84_A     14   21   43      6   14   17   19   21   24   26   28   29   30   31   33   36   37   40   41   43   44   44   44 
LCS_GDT     I    85_A     I    85_A     14   21   43      9   14   17   19   21   24   26   28   29   30   31   33   36   37   40   41   43   44   44   44 
LCS_GDT     L    86_A     L    86_A     14   21   43      9   14   17   19   21   24   26   28   29   30   31   33   36   37   40   41   43   44   44   44 
LCS_GDT     S    87_A     S    87_A     14   21   43      9   14   17   19   21   24   26   28   29   30   31   33   36   37   40   41   43   44   44   44 
LCS_GDT     M    88_A     M    88_A     14   21   43      9   14   17   19   21   24   26   28   29   30   31   33   36   37   40   41   43   44   44   44 
LCS_GDT     F    89_A     F    89_A     14   21   43      9   14   17   19   21   24   26   28   29   30   31   33   36   37   40   41   43   44   44   44 
LCS_GDT     E    90_A     E    90_A     14   21   43      9   14   17   19   21   24   26   28   29   30   31   33   36   37   40   41   43   44   44   44 
LCS_GDT     L    91_A     L    91_A     14   21   43      9   14   17   19   21   24   26   28   29   30   31   33   36   37   40   41   43   44   44   44 
LCS_GDT     F    92_A     F    92_A     14   21   43      9   14   17   19   21   24   26   28   29   30   31   33   36   37   40   41   43   44   44   44 
LCS_GDT     S    93_A     S    93_A     14   21   43      9   14   17   19   21   24   26   28   29   30   31   33   36   37   40   41   43   44   44   44 
LCS_GDT     T    94_A     T    94_A     14   21   43      5   14   17   19   21   24   26   28   29   30   31   33   36   37   40   41   43   44   44   44 
LCS_GDT     Q    95_A     Q    95_A     14   21   43      5   14   17   19   21   24   26   28   29   30   31   33   36   37   40   41   43   44   44   44 
LCS_GDT     F    96_A     F    96_A     14   21   43      6   14   17   19   21   24   26   28   29   30   31   33   36   37   40   41   43   44   44   44 
LCS_GDT     A    97_A     A    97_A     14   21   43      4    9   12   18   21   24   26   28   29   30   31   33   36   37   40   41   43   44   44   44 
LCS_GDT     E    98_A     E    98_A     12   21   43      7    9   12   15   21   24   26   28   29   30   31   33   36   37   40   41   43   44   44   44 
LCS_GDT     K    99_A     K    99_A     12   21   43      7    9   12   18   21   24   26   28   29   30   31   33   36   37   40   41   43   44   44   44 
LCS_GDT     L   100_A     L   100_A     12   21   43      7    9   12   15   21   24   26   28   29   30   31   33   36   37   40   41   43   44   44   44 
LCS_GDT     A   101_A     A   101_A     12   21   43      7    9   12   15   17   22   26   28   29   30   31   33   36   37   40   41   43   44   44   44 
LCS_GDT     L   102_A     L   102_A     12   21   43      7    9   12   15   17   22   26   28   29   29   31   33   36   37   40   41   43   44   44   44 
LCS_GDT     E   103_A     E   103_A     12   21   43      7    9   12   15   17   24   26   28   29   30   31   33   36   37   40   41   43   44   44   44 
LCS_GDT     Y   104_A     Y   104_A     12   21   43      7    9   12   15   17   19   22   26   28   29   31   33   36   37   40   41   43   44   44   44 
LCS_AVERAGE  LCS_A:  17.45  (   7.73   11.96   32.67 )

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      9     14     17     19     21     24     26     28     29     30     31     33     36     37     40     41     43     44     44     44 
GDT PERCENT_AT   8.26  12.84  15.60  17.43  19.27  22.02  23.85  25.69  26.61  27.52  28.44  30.28  33.03  33.94  36.70  37.61  39.45  40.37  40.37  40.37
GDT RMS_LOCAL    0.21   0.70   0.86   1.05   1.33   1.89   2.17   2.39   2.51   2.73   2.85   3.12   3.92   4.01   4.44   4.60   4.93   5.13   5.13   5.13
GDT RMS_ALL_AT  13.95  12.80  12.75  12.65  12.53  11.93  11.70  11.54  11.69  11.93  11.65  11.89  10.54  11.01  10.75  10.66  10.69  10.56  10.56  10.56

# Checking swapping
#   possible swapping detected:  D    50_A      D    50_A
#   possible swapping detected:  F    58_A      F    58_A
#   possible swapping detected:  F    59_A      F    59_A
#   possible swapping detected:  F    65_A      F    65_A
#   possible swapping detected:  E    82_A      E    82_A
#   possible swapping detected:  F    89_A      F    89_A
#   possible swapping detected:  E    90_A      E    90_A
#   possible swapping detected:  E    98_A      E    98_A
#   possible swapping detected:  Y   104_A      Y   104_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    L    44_A      L    44_A    17.886     0    0.145   0.210    20.275    0.000    0.000
LGA    K    45_A      K    45_A    15.278     0    0.047   1.237    16.902    0.000    0.159
LGA    N    46_A      N    46_A    20.912     0    0.086   0.921    25.901    0.000    0.000
LGA    L    47_A      L    47_A    20.924     0    0.033   0.130    24.929    0.000    0.000
LGA    L    48_A      L    48_A    16.009     0    0.013   1.414    17.800    0.000    0.179
LGA    K    49_A      K    49_A    20.053     0    0.161   0.345    23.664    0.000    0.000
LGA    D    50_A      D    50_A    25.072     0    0.191   1.041    27.890    0.000    0.000
LGA    Q    51_A      Q    51_A    22.208     0    0.409   0.905    23.819    0.000    0.000
LGA    I    52_A      I    52_A    18.733     0    0.595   0.910    19.510    0.000    0.000
LGA    P    53_A      P    53_A    22.000     0    0.610   0.616    23.766    0.000    0.000
LGA    T    54_A      T    54_A    20.040     0    0.574   0.542    21.259    0.000    0.000
LGA    G    55_A      G    55_A    16.142     0    0.183   0.183    16.942    0.000    0.000
LGA    S    56_A      S    56_A    17.502     0    0.591   0.575    19.249    0.000    0.000
LGA    S    57_A      S    57_A    19.376     0    0.575   0.905    22.494    0.000    0.000
LGA    F    58_A      F    58_A    21.900     0    0.662   0.916    30.134    0.000    0.000
LGA    F    59_A      F    59_A    18.360     0    0.586   0.672    19.598    0.000    0.000
LGA    K    60_A      K    60_A    19.652     0    0.214   0.995    28.218    0.000    0.000
LGA    L    61_A      L    61_A    13.451     0    0.127   1.368    15.937    0.000    0.179
LGA    P    62_A      P    62_A    10.272     0    0.598   0.543    12.591    4.048    2.517
LGA    V    63_A      V    63_A     8.931     0    0.113   0.142    11.632    1.071    1.020
LGA    V    64_A      V    64_A     9.484     0    0.610   0.667    11.824    2.381    1.973
LGA    F    65_A      F    65_A     9.776     0    0.033   1.139    10.079    0.476    2.597
LGA    F    66_A      F    66_A    10.225     0    0.038   1.388    16.563    0.000    0.043
LGA    R    67_A      R    67_A    11.102     0    0.311   1.455    13.473    0.000    0.000
LGA    V    68_A      V    68_A    11.250     0    0.625   1.034    14.989    0.000    0.680
LGA    T    69_A      T    69_A    12.024     0    0.086   0.998    14.074    1.905    1.088
LGA    D    70_A      D    70_A     8.208     0    0.025   0.080    12.947   18.571    9.464
LGA    N    71_A      N    71_A     4.927     0    0.024   0.202    11.421   21.905   12.679
LGA    V    72_A      V    72_A     6.770     0    0.035   0.092    11.561   19.524   11.224
LGA    I    73_A      I    73_A     2.691     0    0.010   1.203     5.666   38.214   48.690
LGA    V    74_A      V    74_A     5.922     0    0.035   0.053    10.550   31.786   18.639
LGA    I    75_A      I    75_A     1.438     0    0.012   0.163     5.972   55.000   50.774
LGA    L    76_A      L    76_A     2.987     0    0.114   1.325     9.600   69.286   39.821
LGA    L    77_A      L    77_A     2.806     0    0.060   0.080     9.647   59.524   35.417
LGA    T    78_A      T    78_A     0.888     0    0.172   1.039     5.028   62.976   53.197
LGA    N    79_A      N    79_A     4.359     0    0.593   1.245     9.422   54.048   31.429
LGA    E    80_A      E    80_A     3.138     0    0.152   1.010     6.077   42.381   36.667
LGA    K    81_A      K    81_A     3.027     0    0.610   0.993     4.560   43.929   62.963
LGA    E    82_A      E    82_A     8.666     0    0.041   0.846    17.064    7.024    3.122
LGA    N    83_A      N    83_A     6.773     0    0.126   1.100    10.443   25.238   14.167
LGA    I    84_A      I    84_A     0.896     0    0.595   1.033     5.412   84.048   64.048
LGA    I    85_A      I    85_A     1.345     0    0.044   0.110     2.149   83.690   77.262
LGA    L    86_A      L    86_A     0.620     0    0.049   1.396     4.797   95.238   73.393
LGA    S    87_A      S    87_A     0.911     0    0.029   0.061     1.563   88.333   84.603
LGA    M    88_A      M    88_A     1.542     0    0.010   1.626     5.217   75.000   62.440
LGA    F    89_A      F    89_A     1.400     0    0.036   1.147     6.173   79.286   56.494
LGA    E    90_A      E    90_A     0.874     0    0.010   0.801     3.410   83.810   75.344
LGA    L    91_A      L    91_A     2.306     0    0.028   1.402     4.686   64.881   60.714
LGA    F    92_A      F    92_A     2.633     0    0.026   1.230     6.046   59.048   48.571
LGA    S    93_A      S    93_A     2.452     0    0.019   0.605     2.818   60.952   60.952
LGA    T    94_A      T    94_A     2.465     0    0.050   0.088     2.946   60.952   62.585
LGA    Q    95_A      Q    95_A     2.556     0    0.041   0.093     2.933   57.143   57.143
LGA    F    96_A      F    96_A     2.610     0    0.110   0.507     6.406   65.000   42.381
LGA    A    97_A      A    97_A     1.261     0    0.015   0.016     2.283   77.262   78.095
LGA    E    98_A      E    98_A     2.421     0    0.096   0.196     6.700   67.024   44.497
LGA    K    99_A      K    99_A     1.345     0    0.078   0.159     5.522   81.548   61.376
LGA    L   100_A      L   100_A     1.742     0    0.068   0.145     3.127   71.310   65.238
LGA    A   101_A      A   101_A     3.450     0    0.197   0.192     5.629   41.429   43.143
LGA    L   102_A      L   102_A     4.012     0    0.103   0.140     5.484   40.476   37.500
LGA    E   103_A      E   103_A     2.940     0    0.142   1.146     3.962   48.452   51.005
LGA    Y   104_A      Y   104_A     5.436     0    0.278   1.213    12.726   23.095   12.698

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       61     244    244  100.00     499    499  100.00               109
SUMMARY(RMSD_GDC):     9.054          9.013                  9.933           18.048   15.213

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   61  109    4.0     28    2.39    23.394    20.819     1.123

LGA_LOCAL      RMSD:   2.394  Number of atoms:   28  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  11.541  Number of assigned atoms:   61 
Std_ASGN_ATOMS RMSD:   9.054  Standard rmsd on all 61 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.311766 * X  +   0.856702 * Y  +   0.410931 * Z  + -35.114368
  Y_new =  -0.916901 * X  +  -0.157837 * Y  +  -0.366579 * Z  +  71.639557
  Z_new =  -0.249189 * X  +  -0.491069 * Y  +   0.834719 * Z  +  14.884251 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.898554  0.251842 -0.531776   [DEG: -108.7791   14.4295  -30.4685 ]
ZXZ:  0.842380  0.583174 -2.672010   [DEG:   48.2648   33.4134 -153.0949 ]
 
# END of job
