
#######################################################
#                                                     #
#                        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:    38       7_C - 44_C        4.95     6.85
  LONGEST_CONTINUOUS_SEGMENT:    38       8_C - 45_C        5.00     6.78
  LCS_AVERAGE:     67.13

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    16       7_C - 22_C        1.90     9.01
  LCS_AVERAGE:     20.95

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13       9_C - 21_C        0.99     8.87
  LCS_AVERAGE:     13.80

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    4   33      3    3    3    6    8    9   13   15   18   20   21   24   26   27   29   30   38   40   44   46 
LCS_GDT     T     7_C     T     7_C      3   16   38      3    3    4    6   13   16   17   20   23   26   31   36   38   39   43   45   45   46   47   48 
LCS_GDT     K     8_C     K     8_C      3   16   38      3    3    3    4    4    9   15   18   23   24   29   34   38   39   43   45   45   46   47   48 
LCS_GDT     I     9_C     I     9_C     13   16   38      7   11   12   14   15   17   18   22   27   32   35   38   39   40   43   45   45   46   47   48 
LCS_GDT     L    10_C     L    10_C     13   16   38      7   11   12   14   15   17   19   22   27   32   35   38   39   40   43   45   45   46   47   48 
LCS_GDT     P    11_C     P    11_C     13   16   38      7   11   12   14   15   17   19   22   27   32   35   38   39   40   43   45   45   46   47   48 
LCS_GDT     C    12_C     C    12_C     13   16   38      4   11   12   14   15   17   19   22   27   32   35   38   39   40   43   45   45   46   47   48 
LCS_GDT     P    13_C     P    13_C     13   16   38      4   11   12   14   15   17   19   21   27   32   35   38   39   40   43   45   45   46   47   48 
LCS_GDT     R    14_C     R    14_C     13   16   38      6   11   12   14   15   17   18   20   24   32   35   38   39   40   43   45   45   46   47   48 
LCS_GDT     C    15_C     C    15_C     13   16   38      7   11   12   14   15   17   18   20   25   32   35   38   39   40   43   45   45   46   47   48 
LCS_GDT     N    16_C     N    16_C     13   16   38      7   11   12   14   15   17   19   21   27   32   35   38   39   40   43   45   45   46   47   48 
LCS_GDT     S    17_C     S    17_C     13   16   38      6   11   12   14   15   17   19   21   27   32   35   38   39   40   43   45   45   46   47   48 
LCS_GDT     M    18_C     M    18_C     13   16   38      7   11   12   14   15   17   19   22   27   32   35   38   39   40   43   45   45   46   47   48 
LCS_GDT     E    19_C     E    19_C     13   16   38      7   11   12   14   15   17   19   22   27   32   35   38   39   40   43   45   45   46   47   48 
LCS_GDT     T    20_C     T    20_C     13   16   38      4    9   12   14   15   17   19   22   27   32   35   38   39   40   43   45   45   46   47   48 
LCS_GDT     K    21_C     K    21_C     13   16   38      3    8   12   14   15   16   17   20   25   32   35   38   39   40   43   45   45   46   47   48 
LCS_GDT     F    22_C     F    22_C     10   16   38      3    3   12   14   15   16   17   20   25   32   35   38   39   40   43   45   45   46   47   48 
LCS_GDT     C    23_C     C    23_C      5   15   38      3    4    5    6   12   13   16   22   27   32   35   38   39   40   43   45   45   46   47   48 
LCS_GDT     Y    24_C     Y    24_C      5   12   38      3    4    5    7   12   14   17   22   27   32   35   38   39   40   43   45   45   46   47   48 
LCS_GDT     Y    25_C     Y    25_C      5   12   38      3    4    5    7   12   13   17   22   27   32   35   38   39   40   43   45   45   46   47   48 
LCS_GDT     N    26_C     N    26_C      5   12   38      3    6    7    9   12   14   17   22   27   32   35   38   39   40   43   45   45   46   47   48 
LCS_GDT     N    27_C     N    27_C      5   12   38      3    4    5    6    9   13   16   22   27   32   35   38   39   40   43   45   45   46   47   48 
LCS_GDT     Y    28_C     Y    28_C      8   12   38      3    6    8    9   12   14   19   22   27   31   35   38   39   40   43   45   45   46   47   48 
LCS_GDT     N    29_C     N    29_C      8   12   38      4    6    8    9   12   14   19   22   27   31   35   38   39   40   43   45   45   46   47   48 
LCS_GDT     V    30_C     V    30_C      8   12   38      4    6    8    9   12   15   19   22   27   32   35   38   39   40   43   45   45   46   47   48 
LCS_GDT     N    31_C     N    31_C      8   12   38      4    6    8    9   12   15   19   22   27   32   35   38   39   40   43   45   45   46   47   48 
LCS_GDT     Q    32_C     Q    32_C      8   12   38      4    6    8    9   12   15   19   22   27   32   35   38   39   40   43   45   45   46   47   48 
LCS_GDT     P    33_C     P    33_C      8   12   38      4    6    8    9   12   15   19   22   27   32   35   38   39   40   43   45   45   46   47   48 
LCS_GDT     R    34_C     R    34_C      8   12   38      4    6    8    9   12   12   18   20   26   30   35   38   39   40   43   45   45   46   47   48 
LCS_GDT     H    35_C     H    35_C      8   12   38      4    6    8    9   12   12   18   22   27   32   35   38   39   40   43   45   45   46   47   48 
LCS_GDT     F    36_C     F    36_C      5    9   38      4    4    6    7    9   11   18   21   27   32   35   38   39   40   43   45   45   46   47   48 
LCS_GDT     C    37_C     C    37_C      5    8   38      4    7   12   13   15   17   19   21   27   32   35   38   39   40   43   45   45   46   47   48 
LCS_GDT     K    38_C     K    38_C      5    8   38      4    6   12   13   14   17   18   20   23   30   35   38   39   40   43   45   45   46   47   48 
LCS_GDT     A    39_C     A    39_C      5    8   38      4    6    6    8   11   17   17   19   23   24   26   30   35   40   43   45   45   46   47   48 
LCS_GDT     C    40_C     C    40_C      5    8   38      4    6   12   13   14   17   17   19   23   24   26   30   35   39   43   45   45   46   47   48 
LCS_GDT     Q    41_C     Q    41_C      5    8   38      4    6    6    8   14   17   17   19   23   24   26   28   33   38   41   43   44   46   47   48 
LCS_GDT     R    42_C     R    42_C      3    4   38      3    3    3    3    6    9   17   18   20   24   30   36   39   40   43   45   45   46   47   48 
LCS_GDT     Y    43_C     Y    43_C      3    4   38      1    3    3    6    6   10   15   18   24   32   35   38   39   40   43   45   45   46   47   48 
LCS_GDT     W    44_C     W    44_C      3    3   38      3    3    4    6    6    8   15   17   19   26   33   38   39   40   43   45   45   46   47   48 
LCS_GDT     T    45_C     T    45_C      4    5   38      4    4    4    6    6    8   15   17   19   20   24   28   34   38   41   45   45   46   47   48 
LCS_GDT     S    46_C     S    46_C      4    5   21      4    4    4    6    8    8    9   11   13   15   20   21   22   23   25   28   28   31   32   38 
LCS_GDT     G    47_C     G    47_C      4    5   21      4    4    4    6    6    7    7    8   10   11   13   14   16   21   22   27   30   33   34   38 
LCS_GDT     G    48_C     G    48_C      4    5   21      4    4    4    6    8    8   12   17   19   20   24   28   31   35   39   42   44   46   47   48 
LCS_GDT     T    49_C     T    49_C      4    5   21      3    3    4    5    8    8   12   17   19   22   29   34   39   40   42   45   45   46   47   48 
LCS_GDT     M    50_C     M    50_C      4    5   21      3    3    4    6    9   12   16   20   27   32   35   38   39   40   43   45   45   46   47   48 
LCS_GDT     R    51_C     R    51_C      4    6   21      3    3    4    5    6    7   12   14   20   22   33   38   39   40   43   45   45   46   47   48 
LCS_GDT     S    52_C     S    52_C      3    6   21      3    3    4    5    8    8   12   17   27   32   35   38   39   40   43   45   45   46   47   48 
LCS_GDT     V    53_C     V    53_C      3    6   21      4    5    7    9   11   15   19   22   27   32   35   38   39   40   43   45   45   46   47   48 
LCS_GDT     P    54_C     P    54_C      3    6   21      4    5    7    9   11   16   19   22   27   32   35   38   39   40   43   45   45   46   47   48 
LCS_GDT     I    55_C     I    55_C      3    6   21      4    5    7    9   11   16   19   22   27   32   35   38   39   40   43   45   45   46   47   48 
LCS_GDT     G    56_C     G    56_C      3    6   21      2    3    5    6   11   14   17   20   23   29   32   36   38   39   41   43   45   46   47   48 
LCS_AVERAGE  LCS_A:  33.96  (  13.80   20.95   67.13 )

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      7     11     12     14     15     17     19     22     27     32     35     38     39     40     43     45     45     46     47     48 
GDT PERCENT_AT  13.73  21.57  23.53  27.45  29.41  33.33  37.25  43.14  52.94  62.75  68.63  74.51  76.47  78.43  84.31  88.24  88.24  90.20  92.16  94.12
GDT RMS_LOCAL    0.27   0.54   0.68   1.10   1.31   1.64   2.55   3.09   3.35   3.76   3.90   4.16   4.28   4.41   4.81   5.11   5.07   5.22   5.34   5.56
GDT RMS_ALL_AT   9.23   9.14   9.03   8.67   8.86  10.97   7.16   7.32   7.12   6.82   6.88   6.80   6.78   6.79   6.77   6.65   6.72   6.65   6.67   6.61

# Checking swapping
#   possible swapping detected:  F    22_C      F    22_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    13.998     2    0.185   0.213    15.771    0.000    0.000
LGA    T     7_C      T     7_C     8.280     0    0.169   0.198    10.308    4.881    6.327
LGA    K     8_C      K     8_C     9.048     4    0.577   0.556    11.484    5.833    2.593
LGA    I     9_C      I     9_C     3.003     0    0.623   1.243     5.503   52.738   50.655
LGA    L    10_C      L    10_C     2.248     0    0.027   0.089     4.179   64.762   57.560
LGA    P    11_C      P    11_C     2.515     0    0.100   0.402     3.422   55.476   58.367
LGA    C    12_C      C    12_C     4.196     0    0.108   0.517     5.234   38.929   36.508
LGA    P    13_C      P    13_C     4.773     0    0.024   0.126     5.740   26.429   30.204
LGA    R    14_C      R    14_C     6.740     0    0.039   0.828     7.399   14.524   12.900
LGA    C    15_C      C    15_C     6.486     0    0.047   0.153     6.486   17.143   17.143
LGA    N    16_C      N    16_C     5.017     0    0.170   1.154     7.643   28.810   22.798
LGA    S    17_C      S    17_C     4.443     0    0.085   0.678     5.468   42.143   37.698
LGA    M    18_C      M    18_C     2.405     0    0.199   0.732     4.000   63.095   54.107
LGA    E    19_C      E    19_C     1.486     4    0.256   0.259     2.000   77.143   43.333
LGA    T    20_C      T    20_C     2.716     0    0.124   1.079     5.119   57.262   48.912
LGA    K    21_C      K    21_C     5.048     0    0.515   0.873     6.476   26.667   42.275
LGA    F    22_C      F    22_C     5.141     0    0.095   1.471     8.157   39.881   21.126
LGA    C    23_C      C    23_C     4.024     0    0.554   0.582     6.368   38.690   32.222
LGA    Y    24_C      Y    24_C     3.532     0    0.043   1.414    10.067   43.333   28.810
LGA    Y    25_C      Y    25_C     3.644     0    0.203   0.201     4.491   45.000   41.310
LGA    N    26_C      N    26_C     2.936     0    0.046   0.889     3.311   55.357   56.310
LGA    N    27_C      N    27_C     3.975     0    0.567   0.873     8.853   43.690   27.679
LGA    Y    28_C      Y    28_C     3.402     0    0.122   1.311     5.586   45.357   41.746
LGA    N    29_C      N    29_C     3.135     0    0.135   0.945     6.477   59.286   43.452
LGA    V    30_C      V    30_C     3.499     0    0.106   1.239     6.980   48.333   37.075
LGA    N    31_C      N    31_C     3.757     0    0.181   0.350     6.554   50.238   36.250
LGA    Q    32_C      Q    32_C     2.239     0    0.176   0.280     3.622   64.762   62.487
LGA    P    33_C      P    33_C     3.310     0    0.143   0.174     4.770   43.690   41.837
LGA    R    34_C      R    34_C     4.972     0    0.179   0.873    13.557   35.833   15.498
LGA    H    35_C      H    35_C     4.219     0    0.115   0.313     4.696   34.286   38.476
LGA    F    36_C      F    36_C     4.498     0    0.084   1.228    13.127   35.714   15.801
LGA    C    37_C      C    37_C     4.616     0    0.301   0.655     7.544   23.214   25.238
LGA    K    38_C      K    38_C     7.510     0    0.114   0.974    10.565    6.429    6.667
LGA    A    39_C      A    39_C    10.269     0    0.101   0.119    11.983    0.714    0.571
LGA    C    40_C      C    40_C    10.292     0    0.208   0.798    11.456    0.119    3.016
LGA    Q    41_C      Q    41_C    10.956     0    0.409   1.243    14.152    0.000    0.000
LGA    R    42_C      R    42_C     9.909     0    0.592   1.149    18.634    0.952    0.346
LGA    Y    43_C      Y    43_C     6.603     0    0.566   1.328    10.425    8.810   14.008
LGA    W    44_C      W    44_C     8.302     0    0.617   0.983    11.502    4.048    3.333
LGA    T    45_C      T    45_C    10.997     0    0.585   1.042    15.097    0.119    0.068
LGA    S    46_C      S    46_C    17.627     0    0.559   0.773    19.536    0.000    0.000
LGA    G    47_C      G    47_C    19.415     0    0.194   0.194    19.415    0.000    0.000
LGA    G    48_C      G    48_C    14.188     0    0.637   0.637    15.597    0.000    0.000
LGA    T    49_C      T    49_C    11.666     0    0.069   0.943    12.859    0.833    0.476
LGA    M    50_C      M    50_C     7.020     0    0.021   0.504     9.099    6.429    7.619
LGA    R    51_C      R    51_C     7.733     0    0.630   1.683    17.133   15.952    6.061
LGA    S    52_C      S    52_C     5.274     0    0.106   0.702     8.832   30.952   23.333
LGA    V    53_C      V    53_C     1.505     0    0.376   1.373     4.700   68.929   60.272
LGA    P    54_C      P    54_C     1.798     0    0.036   0.529     3.972   75.000   65.442
LGA    I    55_C      I    55_C     1.618     0    0.201   1.363     6.549   65.357   50.179
LGA    G    56_C      G    56_C     4.973     0    0.109   0.109     8.416   23.333   23.333

# 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):     6.547          6.586                  7.059           31.186   26.498

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   65   51    4.0     22    3.09    45.098    39.793     0.691

LGA_LOCAL      RMSD:   3.085  Number of atoms:   22  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   7.323  Number of assigned atoms:   51 
Std_ASGN_ATOMS RMSD:   6.547  Standard rmsd on all 51 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.515038 * X  +  -0.832420 * Y  +  -0.204482 * Z  + -29.818203
  Y_new =  -0.367951 * X  +   0.430163 * Y  +  -0.824362 * Z  +  -8.293975
  Z_new =   0.774175 * X  +  -0.349338 * Y  +  -0.527840 * Z  +   0.684430 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.521257 -0.885411 -2.556949   [DEG: -144.4574  -50.7303 -146.5024 ]
ZXZ: -0.243142  2.126852  1.994680   [DEG:  -13.9310  121.8596  114.2868 ]
 
# END of job
