
#######################################################
#                                                     #
#                        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:    45      32_A - 76_A        4.84     7.20
  LCS_AVERAGE:     65.17

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    21      56_A - 76_A        1.73    10.61
  LCS_AVERAGE:     29.70

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    20      57_A - 76_A        0.84    11.37
  LCS_AVERAGE:     23.41

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      4   18   45      3    4   10   17   22   26   28   32   33   36   39   41   42   45   47   48   51   52   53   54 
LCS_GDT     T    33_A     T    33_A     15   19   45      6   13   16   20   22   26   28   32   33   36   39   41   42   45   47   48   51   52   53   54 
LCS_GDT     M    34_A     M    34_A     15   19   45      5   13   16   20   22   26   28   32   33   36   39   41   42   45   47   48   51   52   53   54 
LCS_GDT     A    35_A     A    35_A     15   19   45      5   13   16   20   22   26   28   32   33   36   39   41   42   45   47   48   51   52   53   54 
LCS_GDT     D    36_A     D    36_A     15   19   45      5   13   16   20   22   26   28   32   33   36   39   41   42   45   47   48   51   52   53   54 
LCS_GDT     L    37_A     L    37_A     15   19   45      6   13   16   20   22   26   28   32   33   36   39   41   42   45   47   48   51   52   53   54 
LCS_GDT     K    38_A     K    38_A     15   19   45      6   13   16   20   22   26   28   32   33   36   39   41   42   45   47   48   51   52   53   54 
LCS_GDT     M    39_A     M    39_A     15   19   45      6   13   16   20   22   26   28   32   33   36   39   41   42   45   47   48   51   52   53   54 
LCS_GDT     Q    40_A     Q    40_A     15   19   45      6   12   16   20   22   26   28   32   33   36   39   41   42   45   47   48   51   52   53   54 
LCS_GDT     A    41_A     A    41_A     15   19   45      6   13   16   20   22   26   28   32   33   36   39   41   42   45   47   48   51   52   53   54 
LCS_GDT     V    42_A     V    42_A     15   19   45      6   13   16   20   22   26   28   32   33   36   39   41   42   45   47   48   51   52   53   54 
LCS_GDT     K    43_A     K    43_A     15   19   45      6   13   16   20   22   26   28   32   33   36   39   41   42   45   47   48   51   52   53   54 
LCS_GDT     E    44_A     E    44_A     15   19   45      4   13   16   20   22   26   28   32   33   36   39   41   42   45   47   48   51   52   53   54 
LCS_GDT     I    45_A     I    45_A     15   19   45      5   13   16   20   22   26   28   32   33   36   39   41   42   45   47   48   51   52   53   54 
LCS_GDT     C    46_A     C    46_A     15   19   45      5   13   16   20   22   26   28   32   33   36   39   41   42   45   47   48   51   52   53   54 
LCS_GDT     Y    47_A     Y    47_A     15   19   45      3   10   16   20   22   26   28   32   33   36   39   41   42   45   47   48   51   52   53   54 
LCS_GDT     E    48_A     E    48_A      6   19   45      4   11   15   19   22   26   28   32   33   36   39   41   42   45   47   48   51   52   53   54 
LCS_GDT     V    49_A     V    49_A      6   19   45      4    6    7    8   12   24   28   32   33   36   39   41   42   45   47   48   51   52   53   54 
LCS_GDT     A    50_A     A    50_A      6   19   45      4    6    9   11   17   23   28   32   33   36   39   41   42   45   47   48   51   52   53   54 
LCS_GDT     L    51_A     L    51_A      6   19   45      4    7   16   20   22   26   28   32   33   36   39   41   42   45   47   48   51   52   53   54 
LCS_GDT     A    52_A     A    52_A      6   11   45      3    5    7   14   18   26   28   32   33   36   39   41   42   45   47   48   51   52   53   54 
LCS_GDT     D    53_A     D    53_A      3    6   45      3   10   16   20   22   26   28   32   33   36   39   41   42   45   47   48   51   52   53   54 
LCS_GDT     F    54_A     F    54_A      4    6   45      3    3    4    6   11   15   19   29   33   36   39   41   42   45   47   48   51   52   53   54 
LCS_GDT     R    55_A     R    55_A      4    6   45      3    3    4    5   10   17   21   26   33   36   39   41   42   45   47   48   51   52   53   54 
LCS_GDT     H    56_A     H    56_A      4   21   45      3    3    4    5    7   10   17   24   27   31   33   36   41   44   46   48   51   52   53   54 
LCS_GDT     G    57_A     G    57_A     20   21   45     10   16   19   20   21   23   24   26   27   31   32   35   38   41   44   47   50   52   53   54 
LCS_GDT     R    58_A     R    58_A     20   21   45      9   16   19   20   21   23   24   26   27   31   33   36   39   42   46   48   51   52   53   54 
LCS_GDT     A    59_A     A    59_A     20   21   45     10   16   19   20   21   23   24   26   28   31   34   38   41   44   46   48   51   52   53   54 
LCS_GDT     E    60_A     E    60_A     20   21   45     10   16   19   20   21   23   24   26   28   31   35   39   42   44   46   48   51   52   53   54 
LCS_GDT     I    61_A     I    61_A     20   21   45     10   16   19   20   21   23   24   26   28   31   34   38   42   44   46   48   51   52   53   54 
LCS_GDT     E    62_A     E    62_A     20   21   45     10   16   19   20   21   23   24   26   28   31   36   39   42   44   46   48   51   52   53   54 
LCS_GDT     A    63_A     A    63_A     20   21   45     10   16   19   20   21   23   24   26   30   35   39   40   42   44   47   48   51   52   53   54 
LCS_GDT     L    64_A     L    64_A     20   21   45     10   16   19   20   21   23   24   26   30   36   39   40   42   45   47   48   51   52   53   54 
LCS_GDT     A    65_A     A    65_A     20   21   45     10   16   19   20   21   23   24   26   30   36   39   40   42   45   47   48   51   52   53   54 
LCS_GDT     A    66_A     A    66_A     20   21   45     10   16   19   20   21   23   24   28   33   36   39   41   42   45   47   48   51   52   53   54 
LCS_GDT     L    67_A     L    67_A     20   21   45     10   16   19   20   22   26   28   31   33   36   39   41   42   45   47   48   51   52   53   54 
LCS_GDT     K    68_A     K    68_A     20   21   45     10   16   19   20   22   26   28   31   33   36   39   41   42   45   47   48   51   52   53   54 
LCS_GDT     M    69_A     M    69_A     20   21   45      9   16   19   20   22   26   28   31   33   36   39   41   42   45   47   48   51   52   53   54 
LCS_GDT     R    70_A     R    70_A     20   21   45     10   16   19   20   22   26   28   32   33   36   39   41   42   45   47   48   51   52   53   54 
LCS_GDT     E    71_A     E    71_A     20   21   45      9   16   19   20   22   26   28   32   33   36   39   41   42   45   47   48   51   52   53   54 
LCS_GDT     L    72_A     L    72_A     20   21   45      7   16   19   20   22   26   28   32   33   36   39   41   42   45   47   48   51   52   53   54 
LCS_GDT     C    73_A     C    73_A     20   21   45      7   16   19   20   22   26   28   32   33   36   39   41   42   45   47   48   51   52   53   54 
LCS_GDT     R    74_A     R    74_A     20   21   45      7   16   19   20   22   26   28   32   33   36   39   41   42   45   47   48   51   52   53   54 
LCS_GDT     T    75_A     T    75_A     20   21   45      7   15   19   20   21   26   28   32   33   36   39   41   42   45   47   48   51   52   53   54 
LCS_GDT     Y    76_A     Y    76_A     20   21   45      7   16   19   20   21   26   28   32   33   36   39   41   42   45   47   48   51   52   53   54 
LCS_GDT     G    83_A     G    83_A      4   16   25      0    3    8    9   12   19   24   27   31   33   34   38   39   43   43   46   46   48   51   52 
LCS_GDT     D    84_A     D    84_A     11   16   25      3    5    9   14   18   26   28   31   33   34   36   39   41   43   44   46   48   49   51   53 
LCS_GDT     A    85_A     A    85_A     13   16   25      3    9   13   14   15   16   23   27   30   33   35   38   41   43   44   46   47   49   51   53 
LCS_GDT     W    86_A     W    86_A     13   16   25      3   11   13   14   18   22   25   30   32   34   36   38   41   43   44   46   47   49   51   53 
LCS_GDT     R    87_A     R    87_A     13   16   25      4   11   13   17   22   26   28   32   33   36   39   41   42   45   46   48   49   52   53   54 
LCS_GDT     A    88_A     A    88_A     13   16   25      4   11   13   14   21   25   28   32   33   36   39   41   42   45   47   48   51   52   53   54 
LCS_GDT     V    89_A     V    89_A     13   16   25      4   11   13   14   15   26   28   32   33   36   39   41   42   45   47   48   51   52   53   54 
LCS_GDT     A    90_A     A    90_A     13   16   25      4   11   15   20   22   26   28   32   33   36   39   41   42   45   47   48   51   52   53   54 
LCS_GDT     R    91_A     R    91_A     13   16   25      4   11   14   18   22   26   28   31   33   36   39   41   42   45   47   48   51   52   53   54 
LCS_GDT     D    92_A     D    92_A     13   16   25      5   11   13   14   15   16   26   31   33   36   39   41   42   45   47   48   51   52   53   54 
LCS_GDT     V    93_A     V    93_A     13   16   25      5   11   13   15   22   26   28   31   33   36   39   41   42   45   47   48   51   52   53   54 
LCS_GDT     W    94_A     W    94_A     13   16   25      5   11   13   16   22   24   25   27   31   35   39   40   42   45   47   48   51   52   53   54 
LCS_GDT     D    95_A     D    95_A     13   16   25      5   11   13   14   15   16   18   25   28   35   39   40   42   44   47   48   51   52   53   54 
LCS_GDT     T    96_A     T    96_A     13   16   25      5   11   13   14   15   16   18   23   28   32   38   40   42   44   47   48   51   52   53   54 
LCS_GDT     V    97_A     V    97_A     13   16   25      3   10   13   14   15   16   18   19   22   28   32   38   41   44   46   48   51   52   53   54 
LCS_GDT     G    98_A     G    98_A     13   16   25      3    5   12   14   15   16   18   19   21   25   27   29   31   37   43   46   47   50   51   54 
LCS_AVERAGE  LCS_A:  39.42  (  23.41   29.70   65.17 )

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     10     16     19     20     22     26     28     32     33     36     39     41     42     45     47     48     51     52     53     54 
GDT PERCENT_AT  16.39  26.23  31.15  32.79  36.07  42.62  45.90  52.46  54.10  59.02  63.93  67.21  68.85  73.77  77.05  78.69  83.61  85.25  86.89  88.52
GDT RMS_LOCAL    0.28   0.56   0.76   0.84   1.43   1.92   2.06   2.45   2.53   2.92   3.17   3.43   3.57   3.97   4.31   4.41   4.89   5.01   5.17   5.30
GDT RMS_ALL_AT  11.22  10.99  11.24  11.37   7.92   7.42   8.43   8.42   8.34   7.45   7.61   7.36   7.21   6.98   6.80   6.82   6.73   6.70   6.75   6.70

# 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:  D    92_A      D    92_A
#   possible swapping detected:  D    95_A      D    95_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A    32_A      A    32_A     1.971     0    0.429   0.399     3.079   71.548   68.667
LGA    T    33_A      T    33_A     1.823     0    0.121   0.180     3.399   77.262   66.599
LGA    M    34_A      M    34_A     1.566     0    0.082   0.981     5.086   72.857   58.988
LGA    A    35_A      A    35_A     1.555     0    0.068   0.090     1.669   75.000   74.571
LGA    D    36_A      D    36_A     1.634     0    0.208   0.670     3.120   72.857   73.274
LGA    L    37_A      L    37_A     2.576     0    0.025   0.396     3.623   62.857   56.488
LGA    K    38_A      K    38_A     1.745     0    0.130   0.955     7.122   79.643   56.455
LGA    M    39_A      M    39_A     1.240     0    0.061   0.598     5.518   81.548   62.619
LGA    Q    40_A      Q    40_A     2.189     0    0.072   1.310     5.690   70.833   54.180
LGA    A    41_A      A    41_A     1.373     0    0.041   0.060     2.008   81.548   78.190
LGA    V    42_A      V    42_A     1.699     0    0.181   0.277     4.177   77.262   64.762
LGA    K    43_A      K    43_A     2.098     0    0.120   0.565     5.159   70.833   59.048
LGA    E    44_A      E    44_A     1.180     0    0.044   0.304     2.236   85.952   78.730
LGA    I    45_A      I    45_A     0.973     0    0.085   0.164     1.355   85.952   85.952
LGA    C    46_A      C    46_A     1.090     0    0.215   0.846     1.909   88.333   84.603
LGA    Y    47_A      Y    47_A     1.041     0    0.236   0.341     1.780   85.952   83.095
LGA    E    48_A      E    48_A     2.148     0    0.081   0.499     8.386   68.929   42.381
LGA    V    49_A      V    49_A     4.261     0    0.042   0.100     7.092   39.405   30.136
LGA    A    50_A      A    50_A     4.681     0    0.036   0.045     5.382   37.381   35.143
LGA    L    51_A      L    51_A     1.439     0    0.159   1.250     6.160   81.905   61.250
LGA    A    52_A      A    52_A     3.367     0    0.295   0.283     5.877   61.190   53.238
LGA    D    53_A      D    53_A     2.366     0    0.466   0.857     5.447   54.643   49.524
LGA    F    54_A      F    54_A     7.987     0    0.541   0.682    13.124    7.500    2.771
LGA    R    55_A      R    55_A    10.146     0    0.260   0.998    14.233    0.714    0.909
LGA    H    56_A      H    56_A    15.814     0    0.593   0.621    18.887    0.000    0.000
LGA    G    57_A      G    57_A    19.451     0    0.619   0.619    19.451    0.000    0.000
LGA    R    58_A      R    58_A    18.667     0    0.056   1.393    24.129    0.000    0.000
LGA    A    59_A      A    59_A    19.240     0    0.049   0.052    20.503    0.000    0.000
LGA    E    60_A      E    60_A    17.384     0    0.040   0.597    21.041    0.000    0.000
LGA    I    61_A      I    61_A    14.685     0    0.050   1.398    16.087    0.000    0.000
LGA    E    62_A      E    62_A    14.574     0    0.050   0.713    19.016    0.000    0.000
LGA    A    63_A      A    63_A    13.818     0    0.020   0.023    14.821    0.000    0.000
LGA    L    64_A      L    64_A    11.696     0    0.220   0.353    12.633    0.119    0.060
LGA    A    65_A      A    65_A     9.955     0    0.052   0.057    10.878    2.262    1.810
LGA    A    66_A      A    66_A     8.955     0    0.079   0.100     9.688    5.952    4.857
LGA    L    67_A      L    67_A     7.867     0    0.019   0.501     8.838   10.595    6.726
LGA    K    68_A      K    68_A     6.196     0    0.068   1.127     7.166   23.452   17.989
LGA    M    69_A      M    69_A     4.816     0    0.103   0.755     8.025   34.524   23.095
LGA    R    70_A      R    70_A     3.863     0    0.075   0.900    10.939   52.619   23.333
LGA    E    71_A      E    71_A     3.238     0    0.127   0.982     6.244   55.476   40.794
LGA    L    72_A      L    72_A     2.407     0    0.012   0.965     5.469   73.452   58.810
LGA    C    73_A      C    73_A     1.608     0    0.094   0.150     4.594   75.119   64.841
LGA    R    74_A      R    74_A     2.332     0    0.234   1.263     5.807   55.595   51.515
LGA    T    75_A      T    75_A     3.880     0    0.120   0.292     5.027   42.262   40.272
LGA    Y    76_A      Y    76_A     4.141     0    0.706   1.043     7.610   34.524   27.778
LGA    G    83_A      G    83_A     8.663     0    0.548   0.548     8.722    4.405    4.405
LGA    D    84_A      D    84_A     5.886     0    0.189   0.718     6.746   18.333   29.881
LGA    A    85_A      A    85_A     7.520     0    0.151   0.160     8.726   10.952    9.333
LGA    W    86_A      W    86_A     6.417     0    0.048   1.246    10.210   27.738    9.592
LGA    R    87_A      R    87_A     2.970     0    0.091   0.805     9.922   57.619   34.978
LGA    A    88_A      A    88_A     2.928     0    0.134   0.152     4.599   52.857   50.952
LGA    V    89_A      V    89_A     3.337     0    0.078   0.108     5.795   57.381   45.646
LGA    A    90_A      A    90_A     2.248     0    0.060   0.087     4.659   55.238   52.857
LGA    R    91_A      R    91_A     6.269     0    0.069   0.732     9.971   18.095    8.745
LGA    D    92_A      D    92_A     7.312     0    0.148   0.875     9.043    9.643    7.917
LGA    V    93_A      V    93_A     5.607     0    0.044   1.222     8.294   14.405   27.823
LGA    W    94_A      W    94_A     9.585     0    0.084   1.148    16.301    1.905    0.544
LGA    D    95_A      D    95_A    13.418     0    0.139   0.781    16.142    0.000    0.000
LGA    T    96_A      T    96_A    13.219     0    0.073   1.127    14.217    0.000    0.000
LGA    V    97_A      V    97_A    12.869     0    0.517   1.284    14.078    0.000    0.408
LGA    G    98_A      G    98_A    17.063     0    0.321   0.321    18.231    0.000    0.000

# 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):     6.573          6.440                  7.213           39.122   33.222

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   99   61    4.0     32    2.45    47.541    43.921     1.257

LGA_LOCAL      RMSD:   2.445  Number of atoms:   32  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   8.418  Number of assigned atoms:   61 
Std_ASGN_ATOMS RMSD:   6.573  Standard rmsd on all 61 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.779179 * X  +  -0.084296 * Y  +  -0.621107 * Z  +   1.631718
  Y_new =  -0.467351 * X  +   0.738457 * Y  +   0.486070 * Z  +  21.014069
  Z_new =   0.417687 * X  +   0.669011 * Y  +  -0.614786 * Z  + -10.680294 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.601321 -0.430898  2.313982   [DEG: -149.0447  -24.6886  132.5814 ]
ZXZ: -2.234829  2.232911  0.558121   [DEG: -128.0463  127.9364   31.9780 ]
 
# END of job
