
#######################################################
#                                                     #
#                        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   65 (  516),  selected   51 , name one
# Molecule2: number of CA atoms   51 (  404),  selected   51 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:C  -ch2:C  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    40       6_C - 45_C        4.52     8.37
  LONGEST_CONTINUOUS_SEGMENT:    40       7_C - 46_C        4.58     8.29
  LONGEST_CONTINUOUS_SEGMENT:    40       8_C - 47_C        5.00     8.18
  LCS_AVERAGE:     74.01

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    18       9_C - 26_C        1.89     8.62
  LONGEST_CONTINUOUS_SEGMENT:    18      10_C - 27_C        1.98     8.80
  LCS_AVERAGE:     23.53

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8       8_C - 15_C        0.73     8.41
  LONGEST_CONTINUOUS_SEGMENT:     8       9_C - 16_C        0.97     8.40
  LCS_AVERAGE:     10.73

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   51
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     P     6_C     P     6_C      3    6   40      3    3    3    4    5    6    7    8    9   13   15   16   18   28   28   30   30   36   39   40 
LCS_GDT     T     7_C     T     7_C      5   14   40      3    4    5    7   13   14   19   21   23   28   28   31   35   37   38   42   42   43   43   45 
LCS_GDT     K     8_C     K     8_C      8   17   40      4    7    9   13   17   22   24   26   30   34   36   37   37   39   40   42   42   43   43   45 
LCS_GDT     I     9_C     I     9_C      8   18   40      4    7    9   15   19   22   24   27   30   34   36   37   37   39   40   42   42   43   43   45 
LCS_GDT     L    10_C     L    10_C      8   18   40      5    7   11   17   19   22   24   27   30   34   36   37   37   39   40   42   42   43   43   45 
LCS_GDT     P    11_C     P    11_C      8   18   40      5    8   11   17   19   22   24   27   30   34   36   37   37   39   40   42   42   43   43   45 
LCS_GDT     C    12_C     C    12_C      8   18   40      5    8   11   17   19   22   24   27   30   34   36   37   37   39   40   42   42   43   43   45 
LCS_GDT     P    13_C     P    13_C      8   18   40      5    8   11   17   19   22   24   27   30   34   36   37   37   39   40   42   42   43   43   45 
LCS_GDT     R    14_C     R    14_C      8   18   40      5    7   10   17   19   22   24   27   30   34   36   37   37   39   40   42   42   43   43   45 
LCS_GDT     C    15_C     C    15_C      8   18   40      3    7   11   17   19   22   24   27   30   34   36   37   37   39   40   42   42   43   43   45 
LCS_GDT     N    16_C     N    16_C      8   18   40      3    5   10   17   19   22   24   27   30   34   36   37   37   39   40   42   42   43   43   45 
LCS_GDT     S    17_C     S    17_C      3   18   40      3    3    7   12   19   21   24   27   30   34   36   37   37   39   40   42   42   43   43   45 
LCS_GDT     M    18_C     M    18_C      4   18   40      3    5   11   17   19   22   24   27   30   34   36   37   37   39   40   42   42   43   43   45 
LCS_GDT     E    19_C     E    19_C      4   18   40      3    4    6    9   18   21   24   27   30   34   36   37   37   39   40   42   42   43   43   45 
LCS_GDT     T    20_C     T    20_C      5   18   40      4    8   11   17   19   22   24   27   30   34   36   37   37   39   40   42   42   43   43   45 
LCS_GDT     K    21_C     K    21_C      5   18   40      4    8   11   17   19   22   24   27   30   34   36   37   37   39   40   42   42   43   43   45 
LCS_GDT     F    22_C     F    22_C      5   18   40      5    8   11   17   19   22   24   27   30   34   36   37   37   39   40   42   42   43   43   45 
LCS_GDT     C    23_C     C    23_C      5   18   40      5    7    9   17   19   22   24   27   30   34   36   37   37   39   40   42   42   43   43   45 
LCS_GDT     Y    24_C     Y    24_C      5   18   40      4    6   11   17   19   22   24   27   30   34   36   37   37   39   40   42   42   43   43   45 
LCS_GDT     Y    25_C     Y    25_C      4   18   40      3    6    9   12   19   21   24   27   30   34   36   37   37   39   40   42   42   43   43   45 
LCS_GDT     N    26_C     N    26_C      4   18   40      3    8   11   17   19   21   24   27   30   34   36   37   37   39   40   42   42   43   43   45 
LCS_GDT     N    27_C     N    27_C      4   18   40      3    4    8   16   19   21   24   27   30   34   36   37   37   39   40   42   42   43   43   45 
LCS_GDT     Y    28_C     Y    28_C      4   10   40      3    4    5    8   10   14   18   21   29   34   36   37   37   39   40   42   42   43   43   45 
LCS_GDT     N    29_C     N    29_C      7   10   40      5    5    7    8   11   16   18   26   30   34   36   37   37   39   40   42   42   43   43   45 
LCS_GDT     V    30_C     V    30_C      7   10   40      5    5    7    8   11   13   17   20   23   31   36   37   37   39   40   42   42   43   43   45 
LCS_GDT     N    31_C     N    31_C      7   10   40      5    5    7    8   11   14   18   22   30   32   36   37   37   39   40   42   42   43   43   45 
LCS_GDT     Q    32_C     Q    32_C      7   10   40      5    5    7    9   13   21   23   27   30   34   36   37   37   39   40   42   42   43   43   45 
LCS_GDT     P    33_C     P    33_C      7   10   40      5    5    7    8   13   16   22   27   30   34   36   37   37   39   40   42   42   43   43   45 
LCS_GDT     R    34_C     R    34_C      7   10   40      3    7    9   15   19   22   24   27   30   34   36   37   37   39   40   42   42   43   43   45 
LCS_GDT     H    35_C     H    35_C      7   10   40      5    7    9   17   19   22   24   27   30   34   36   37   37   39   40   42   42   43   43   45 
LCS_GDT     F    36_C     F    36_C      5    9   40      4    7   10   17   19   22   24   27   30   34   36   37   37   39   40   42   42   43   43   45 
LCS_GDT     C    37_C     C    37_C      5    9   40      5    8   11   17   19   22   24   27   30   34   36   37   37   39   40   42   42   43   43   45 
LCS_GDT     K    38_C     K    38_C      5    8   40      5    7    9   13   19   22   24   27   30   34   36   37   37   39   40   42   42   43   43   45 
LCS_GDT     A    39_C     A    39_C      5    8   40      4    5    7   10   13   17   20   22   27   32   36   37   37   39   40   42   42   43   43   45 
LCS_GDT     C    40_C     C    40_C      5    8   40      3    5    8   11   18   22   24   26   29   34   36   37   37   39   40   42   42   43   43   45 
LCS_GDT     Q    41_C     Q    41_C      5    8   40      4    5    8   11   17   22   23   26   29   34   36   37   37   39   40   42   42   43   43   45 
LCS_GDT     R    42_C     R    42_C      3    4   40      3    3    3    8   12   16   23   27   30   34   36   37   37   39   40   42   42   43   43   45 
LCS_GDT     Y    43_C     Y    43_C      3    4   40      1    3    3    3    6    9   11   12   22   34   36   37   37   39   40   41   42   43   43   45 
LCS_GDT     W    44_C     W    44_C      3    6   40      3    4    4    7   12   16   22   27   30   34   36   37   37   39   40   42   42   43   43   45 
LCS_GDT     T    45_C     T    45_C      6    6   40      3    5    6    6   11   13   16   17   21   26   29   35   37   39   40   42   42   43   43   45 
LCS_GDT     S    46_C     S    46_C      6    6   40      3    5    6    6    7    9   10   12   14   16   17   18   21   27   28   31   34   36   39   44 
LCS_GDT     G    47_C     G    47_C      6    6   40      3    5    6    6    7    9   11   12   14   17   21   23   25   27   30   33   39   40   42   45 
LCS_GDT     G    48_C     G    48_C      6    7   33      3    5    6    6    8   12   14   17   21   27   28   35   37   39   40   42   42   43   43   45 
LCS_GDT     T    49_C     T    49_C      6    8   32      3    5    6    6    8    9   11   14   18   22   25   32   36   38   40   42   42   43   43   45 
LCS_GDT     M    50_C     M    50_C      6    8   31      3    4    6    6    8    9   11   14   15   19   21   25   30   37   39   42   42   43   43   45 
LCS_GDT     R    51_C     R    51_C      4    8   30      3    4    6    6    8    9   11   14   15   19   21   25   30   37   39   42   42   43   43   45 
LCS_GDT     S    52_C     S    52_C      4    8   27      3    4    5    6    8    9   11   12   14   16   17   22   25   28   29   31   34   37   42   45 
LCS_GDT     V    53_C     V    53_C      4    8   26      3    4    6    6    8    9   11   12   14   17   20   22   25   28   30   33   39   41   43   45 
LCS_GDT     P    54_C     P    54_C      4    8   22      3    4    6    6    8    9   11   12   14   17   20   22   25   26   28   33   40   41   42   45 
LCS_GDT     I    55_C     I    55_C      4    8   22      3    4    5    6    8    9   10   12   14   16   17   18   21   24   28   30   34   37   41   42 
LCS_GDT     G    56_C     G    56_C      3    8   22      0    3    6    6    8    8    9   10   13   16   16   18   20   23   28   30   34   36   40   41 
LCS_AVERAGE  LCS_A:  36.09  (  10.73   23.53   74.01 )

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      5      8     11     17     19     22     24     27     30     34     36     37     37     39     40     42     42     43     43     45 
GDT PERCENT_AT   9.80  15.69  21.57  33.33  37.25  43.14  47.06  52.94  58.82  66.67  70.59  72.55  72.55  76.47  78.43  82.35  82.35  84.31  84.31  88.24
GDT RMS_LOCAL    0.24   0.68   1.05   1.45   1.58   2.00   2.12   2.51   2.83   3.20   3.44   3.59   3.59   4.10   4.38   5.04   4.80   5.08   5.08   5.93
GDT RMS_ALL_AT  10.02   9.04   8.86   8.81   8.99   8.96   8.82   8.57   8.56   8.62   8.60   8.61   8.61   8.30   8.11   7.63   7.88   7.70   7.70   7.28

# Checking swapping
#   possible swapping detected:  Y    24_C      Y    24_C
#   possible swapping detected:  Y    28_C      Y    28_C
#   possible swapping detected:  F    36_C      F    36_C
#   possible swapping detected:  Y    43_C      Y    43_C

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    P     6_C      P     6_C    15.101     2    0.116   0.169    16.983    0.000    0.000
LGA    T     7_C      T     7_C     8.670     0    0.689   0.968    10.779    5.000    8.095
LGA    K     8_C      K     8_C     4.392     4    0.038   0.046     5.705   33.333   19.630
LGA    I     9_C      I     9_C     2.851     0    0.117   1.463     7.373   61.190   47.560
LGA    L    10_C      L    10_C     1.848     0    0.023   0.086     2.252   68.810   68.810
LGA    P    11_C      P    11_C     1.451     0    0.084   0.444     2.283   77.143   75.374
LGA    C    12_C      C    12_C     1.627     0    0.024   0.120     2.476   79.286   75.794
LGA    P    13_C      P    13_C     1.439     0    0.024   0.165     1.772   75.000   74.082
LGA    R    14_C      R    14_C     2.109     0    0.062   1.316     4.831   68.810   59.827
LGA    C    15_C      C    15_C     1.481     0    0.673   0.612     3.419   71.429   74.762
LGA    N    16_C      N    16_C     1.533     0    0.660   1.129     5.461   77.381   59.167
LGA    S    17_C      S    17_C     3.230     0    0.106   0.722     7.799   59.405   43.651
LGA    M    18_C      M    18_C     1.043     0    0.692   0.912     8.218   69.286   48.988
LGA    E    19_C      E    19_C     3.508     4    0.414   0.430     5.512   59.405   28.783
LGA    T    20_C      T    20_C     0.704     0    0.083   1.009     4.596   85.952   73.265
LGA    K    21_C      K    21_C     1.817     0    0.100   1.404     5.154   79.405   59.259
LGA    F    22_C      F    22_C     1.181     0    0.020   0.064     1.850   77.143   79.957
LGA    C    23_C      C    23_C     1.862     0    0.587   0.611     4.695   64.881   64.841
LGA    Y    24_C      Y    24_C     1.321     0    0.602   1.295    12.272   81.786   37.063
LGA    Y    25_C      Y    25_C     3.268     0    0.033   1.139    13.647   53.810   21.746
LGA    N    26_C      N    26_C     0.553     0    0.207   0.354     2.596   83.810   79.643
LGA    N    27_C      N    27_C     3.484     0    0.427   1.116     6.105   40.833   43.810
LGA    Y    28_C      Y    28_C     6.252     0    0.444   1.358    12.539   20.714    8.651
LGA    N    29_C      N    29_C     6.048     0    0.298   0.947     6.500   18.214   34.524
LGA    V    30_C      V    30_C     8.866     0    0.106   1.017    13.623    4.405    2.517
LGA    N    31_C      N    31_C     7.113     0    0.226   1.139     9.081   14.643   11.310
LGA    Q    32_C      Q    32_C     3.471     0    0.320   1.225     8.395   43.690   34.021
LGA    P    33_C      P    33_C     4.973     0    0.159   0.452     7.429   46.190   31.633
LGA    R    34_C      R    34_C     3.543     0    0.555   1.041    14.691   52.143   20.823
LGA    H    35_C      H    35_C     2.140     0    0.079   0.383     3.616   57.500   57.381
LGA    F    36_C      F    36_C     1.878     0    0.056   1.162     9.449   81.548   41.602
LGA    C    37_C      C    37_C     1.118     0    0.301   1.028     2.205   77.381   77.302
LGA    K    38_C      K    38_C     3.288     0    0.147   1.053    10.147   41.905   25.767
LGA    A    39_C      A    39_C     6.158     0    0.105   0.118     6.984   20.833   19.333
LGA    C    40_C      C    40_C     4.715     0    0.183   0.797     5.914   29.048   39.127
LGA    Q    41_C      Q    41_C     5.003     0    0.409   1.129     8.566   31.548   20.265
LGA    R    42_C      R    42_C     4.200     0    0.587   1.214    11.091   30.476   15.541
LGA    Y    43_C      Y    43_C     5.676     0    0.570   1.359    15.403   29.286   11.429
LGA    W    44_C      W    44_C     4.800     0    0.588   0.474    10.416   21.190   15.102
LGA    T    45_C      T    45_C     8.733     0    0.619   1.030    11.864    3.214    1.973
LGA    S    46_C      S    46_C    15.343     0    0.020   0.043    19.624    0.000    0.000
LGA    G    47_C      G    47_C    16.994     0    0.681   0.681    16.994    0.000    0.000
LGA    G    48_C      G    48_C    10.665     0    0.066   0.066    13.201    0.000    0.000
LGA    T    49_C      T    49_C    11.111     0    0.605   0.575    12.708    0.119    0.136
LGA    M    50_C      M    50_C    13.023     0    0.083   0.931    17.813    0.000    0.000
LGA    R    51_C      R    51_C    14.600     0    0.047   1.062    16.240    0.000    0.000
LGA    S    52_C      S    52_C    16.559     0    0.264   0.537    17.787    0.000    0.000
LGA    V    53_C      V    53_C    17.242     0    0.064   0.089    17.318    0.000    0.000
LGA    P    54_C      P    54_C    18.037     0    0.666   0.573    18.441    0.000    0.000
LGA    I    55_C      I    55_C    19.211     0    0.248   1.178    23.430    0.000    0.000
LGA    G    56_C      G    56_C    20.385     0    0.193   0.193    20.385    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       51     204    204  100.00     404    404  100.00                51
SUMMARY(RMSD_GDC):     7.209          7.166                  7.833           39.160   31.618

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   65   51    4.0     27    2.51    46.078    42.329     1.034

LGA_LOCAL      RMSD:   2.510  Number of atoms:   27  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   8.565  Number of assigned atoms:   51 
Std_ASGN_ATOMS RMSD:   7.209  Standard rmsd on all 51 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.936868 * X  +   0.183840 * Y  +  -0.297459 * Z  + -42.425659
  Y_new =   0.112631 * X  +  -0.646673 * Y  +  -0.754406 * Z  + -33.429161
  Z_new =  -0.331048 * X  +  -0.740282 * Y  +   0.585141 * Z  +  18.624113 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  3.021946  0.337414 -0.901918   [DEG:  173.1447   19.3324  -51.6761 ]
ZXZ: -0.375579  0.945743 -2.721076   [DEG:  -21.5191   54.1871 -155.9062 ]
 
# END of job
