
#######################################################
#                                                     #
#                        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   42 (  348),  selected   41 , name one
# Molecule2: number of CA atoms   41 (  336),  selected   41 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:B  -ch2:B  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    41       2_B - 42_B        3.65     3.65
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    34       3_B - 36_B        1.97     4.17
  LONGEST_CONTINUOUS_SEGMENT:    34       4_B - 37_B        2.00     4.18
  LONGEST_CONTINUOUS_SEGMENT:    34       5_B - 38_B        1.98     4.25
  LCS_AVERAGE:     78.29

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    22       6_B - 27_B        0.97     5.27
  LONGEST_CONTINUOUS_SEGMENT:    22       7_B - 28_B        0.97     5.45
  LCS_AVERAGE:     43.78

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   41
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     2_B     A     2_B      3   24   41      3    3   12   20   23   25   29   33   36   37   37   38   38   40   40   40   41   41   41   41 
LCS_GDT     S     3_B     S     3_B      4   34   41      3    4    4   20   23   26   32   33   36   37   37   38   38   40   40   40   41   41   41   41 
LCS_GDT     Q     4_B     Q     4_B      4   34   41      3    4    4   20   23   25   30   33   36   37   37   38   38   40   40   40   41   41   41   41 
LCS_GDT     R     5_B     R     5_B     21   34   41      5   11   21   24   29   31   32   33   36   37   37   38   38   40   40   40   41   41   41   41 
LCS_GDT     L     6_B     L     6_B     22   34   41      5   18   23   26   29   31   32   33   36   37   37   38   38   40   40   40   41   41   41   41 
LCS_GDT     F     7_B     F     7_B     22   34   41      5   18   23   26   29   31   32   33   36   37   37   38   38   40   40   40   41   41   41   41 
LCS_GDT     V     8_B     V     8_B     22   34   41      5   18   23   26   29   31   32   33   36   37   37   38   38   40   40   40   41   41   41   41 
LCS_GDT     L     9_B     L     9_B     22   34   41     16   18   23   26   29   31   32   33   36   37   37   38   38   40   40   40   41   41   41   41 
LCS_GDT     D    10_B     D    10_B     22   34   41     16   18   23   26   29   31   32   33   36   37   37   38   38   40   40   40   41   41   41   41 
LCS_GDT     N    11_B     N    11_B     22   34   41     16   18   23   26   29   31   32   33   36   37   37   38   38   40   40   40   41   41   41   41 
LCS_GDT     E    12_B     E    12_B     22   34   41     16   18   23   26   29   31   32   33   36   37   37   38   38   40   40   40   41   41   41   41 
LCS_GDT     R    13_B     R    13_B     22   34   41     16   18   23   26   29   31   32   33   36   37   37   38   38   40   40   40   41   41   41   41 
LCS_GDT     Y    14_B     Y    14_B     22   34   41     16   18   23   26   29   31   32   33   36   37   37   38   38   40   40   40   41   41   41   41 
LCS_GDT     D    15_B     D    15_B     22   34   41     16   18   23   26   29   31   32   33   36   37   37   38   38   40   40   40   41   41   41   41 
LCS_GDT     S    16_B     S    16_B     22   34   41     16   18   23   26   29   31   32   33   36   37   37   38   38   40   40   40   41   41   41   41 
LCS_GDT     F    17_B     F    17_B     22   34   41     16   18   23   26   29   31   32   33   36   37   37   38   38   40   40   40   41   41   41   41 
LCS_GDT     I    18_B     I    18_B     22   34   41     16   18   23   26   29   31   32   33   36   37   37   38   38   40   40   40   41   41   41   41 
LCS_GDT     T    19_B     T    19_B     22   34   41     16   18   23   26   29   31   32   33   36   37   37   38   38   40   40   40   41   41   41   41 
LCS_GDT     Q    20_B     Q    20_B     22   34   41     16   18   23   26   29   31   32   33   36   37   37   38   38   40   40   40   41   41   41   41 
LCS_GDT     L    21_B     L    21_B     22   34   41     16   18   23   26   29   31   32   33   36   37   37   38   38   40   40   40   41   41   41   41 
LCS_GDT     E    22_B     E    22_B     22   34   41     16   18   23   26   29   31   32   33   36   37   37   38   38   40   40   40   41   41   41   41 
LCS_GDT     A    23_B     A    23_B     22   34   41     16   18   23   26   29   31   32   33   36   37   37   38   38   40   40   40   41   41   41   41 
LCS_GDT     P    24_B     P    24_B     22   34   41     16   18   23   26   29   31   32   33   36   37   37   38   38   40   40   40   41   41   41   41 
LCS_GDT     V    25_B     V    25_B     22   34   41      3    3   23   26   29   31   32   33   36   37   37   38   38   40   40   40   41   41   41   41 
LCS_GDT     Q    26_B     Q    26_B     22   34   41     10   13   14   15   24   29   32   33   36   37   37   38   38   40   40   40   41   41   41   41 
LCS_GDT     N    27_B     N    27_B     22   34   41     11   18   23   26   29   31   32   33   36   37   37   38   38   40   40   40   41   41   41   41 
LCS_GDT     A    28_B     A    28_B     22   34   41     11   13   20   26   29   31   32   33   36   37   37   38   38   40   40   40   41   41   41   41 
LCS_GDT     E    29_B     E    29_B     15   34   41     11   18   23   26   29   31   32   33   36   37   37   38   38   40   40   40   41   41   41   41 
LCS_GDT     G    30_B     G    30_B     15   34   41     11   13   15   26   29   31   32   33   36   37   37   38   38   40   40   40   41   41   41   41 
LCS_GDT     R    31_B     R    31_B     15   34   41     11   13   23   26   29   31   32   33   36   37   37   38   38   40   40   40   41   41   41   41 
LCS_GDT     E    32_B     E    32_B     15   34   41     12   18   23   26   29   31   32   33   36   37   37   38   38   40   40   40   41   41   41   41 
LCS_GDT     R    33_B     R    33_B     15   34   41     11   13   15   26   29   31   32   33   36   37   37   38   38   40   40   40   41   41   41   41 
LCS_GDT     L    34_B     L    34_B     15   34   41     11   13   14   22   29   31   32   33   36   37   37   38   38   40   40   40   41   41   41   41 
LCS_GDT     M    35_B     M    35_B     15   34   41     11   17   23   26   29   31   32   33   36   37   37   38   38   40   40   40   41   41   41   41 
LCS_GDT     A    36_B     A    36_B     15   34   41     11   13   14   22   29   31   32   33   36   37   37   38   38   40   40   40   41   41   41   41 
LCS_GDT     V    37_B     V    37_B     15   34   41     11   13   14   15   20   29   32   33   36   37   37   38   38   40   40   40   41   41   41   41 
LCS_GDT     K    38_B     K    38_B     15   34   41      7   13   14   15   15   20   29   32   34   37   37   38   38   40   40   40   41   41   41   41 
LCS_GDT     P    39_B     P    39_B     15   17   41      4    9   14   15   15   16   16   19   25   31   34   38   38   40   40   40   41   41   41   41 
LCS_GDT     E    40_B     E    40_B     15   17   41      4    5    6   13   15   16   16   16   17   18   19   23   30   34   37   40   41   41   41   41 
LCS_GDT     W    41_B     W    41_B     15   17   41      4   13   14   15   15   16   16   16   18   21   29   32   35   40   40   40   41   41   41   41 
LCS_GDT     K    42_B     K    42_B      3   17   41      0    3    3    3    4    4    4   12   17   18   22   32   35   40   40   40   41   41   41   41 
LCS_AVERAGE  LCS_A:  74.02  (  43.78   78.29  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     16     18     23     26     29     31     32     33     36     37     37     38     38     40     40     40     41     41     41     41 
GDT PERCENT_AT  39.02  43.90  56.10  63.41  70.73  75.61  78.05  80.49  87.80  90.24  90.24  92.68  92.68  97.56  97.56  97.56 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.28   0.46   0.81   0.97   1.20   1.40   1.53   1.79   2.24   2.41   2.41   2.71   2.71   3.29   3.29   3.29   3.65   3.65   3.65   3.65
GDT RMS_ALL_AT   4.15   4.45   4.94   4.70   4.69   4.52   4.56   4.27   3.99   3.90   3.90   3.79   3.79   3.66   3.66   3.66   3.65   3.65   3.65   3.65

# Checking swapping
#   possible swapping detected:  F     7_B      F     7_B
#   possible swapping detected:  F    17_B      F    17_B
#   possible swapping detected:  E    22_B      E    22_B
#   possible swapping detected:  E    29_B      E    29_B
#   possible swapping detected:  E    40_B      E    40_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A     2_B      A     2_B     6.666     0    0.538   0.550     7.899   27.976   23.810
LGA    S     3_B      S     3_B     4.889     0    0.523   0.438     6.089   35.714   35.238
LGA    Q     4_B      Q     4_B     5.518     0    0.252   0.558    13.650   28.095   13.069
LGA    R     5_B      R     5_B     2.751     0    0.648   1.114    12.978   60.952   28.961
LGA    L     6_B      L     6_B     1.923     0    0.139   1.381     4.318   68.810   60.655
LGA    F     7_B      F     7_B     1.518     0    0.142   0.158     1.795   72.857   78.312
LGA    V     8_B      V     8_B     1.412     0    0.037   1.194     3.236   81.429   75.714
LGA    L     9_B      L     9_B     0.474     0    0.029   0.125     0.713   95.238   92.857
LGA    D    10_B      D    10_B     0.430     0    0.085   0.632     1.423  100.000   95.357
LGA    N    11_B      N    11_B     0.417     0    0.026   0.959     2.825  100.000   87.738
LGA    E    12_B      E    12_B     0.610     0    0.049   1.124     6.615   90.476   65.714
LGA    R    13_B      R    13_B     0.535     0    0.015   1.129     2.636   92.857   83.506
LGA    Y    14_B      Y    14_B     0.389     0    0.040   0.164     0.901  100.000   95.238
LGA    D    15_B      D    15_B     0.399     0    0.018   0.455     1.356  100.000   96.488
LGA    S    16_B      S    16_B     0.329     0    0.023   0.174     0.736  100.000   98.413
LGA    F    17_B      F    17_B     0.405     0    0.031   0.253     1.015  100.000   94.026
LGA    I    18_B      I    18_B     0.436     0    0.017   0.118     0.811   97.619   96.429
LGA    T    19_B      T    19_B     0.537     0    0.021   0.245     0.824   92.857   91.837
LGA    Q    20_B      Q    20_B     0.698     0    0.010   1.150     3.291   90.476   81.058
LGA    L    21_B      L    21_B     0.905     0    0.018   1.320     3.059   90.476   82.083
LGA    E    22_B      E    22_B     0.780     0    0.114   0.749     2.313   90.476   81.746
LGA    A    23_B      A    23_B     0.538     0    0.088   0.124     0.662   92.857   92.381
LGA    P    24_B      P    24_B     0.546     0    0.049   0.359     1.359   88.214   87.891
LGA    V    25_B      V    25_B     1.637     0    0.092   1.272     4.703   77.262   66.190
LGA    Q    26_B      Q    26_B     3.862     0    0.680   1.180     9.500   37.976   24.656
LGA    N    27_B      N    27_B     2.161     0    0.165   0.170     2.539   66.786   65.833
LGA    A    28_B      A    28_B     2.444     0    0.045   0.045     3.303   70.952   66.762
LGA    E    29_B      E    29_B     1.210     0    0.054   0.849     3.183   83.690   69.101
LGA    G    30_B      G    30_B     1.842     0    0.123   0.123     1.948   77.262   77.262
LGA    R    31_B      R    31_B     1.624     0    0.041   0.983     6.181   81.667   53.983
LGA    E    32_B      E    32_B     0.952     0    0.042   0.849     5.571   83.810   61.958
LGA    R    33_B      R    33_B     2.338     0    0.055   1.171     3.886   61.190   57.359
LGA    L    34_B      L    34_B     2.790     0    0.028   1.391     6.827   60.952   50.179
LGA    M    35_B      M    35_B     1.122     0    0.065   1.014     7.015   77.143   63.512
LGA    A    36_B      A    36_B     3.132     0    0.043   0.041     4.732   47.381   46.571
LGA    V    37_B      V    37_B     4.942     0    0.044   0.094     6.228   31.548   28.707
LGA    K    38_B      K    38_B     6.368     4    0.143   0.162     9.426   11.786    6.349
LGA    P    39_B      P    39_B     9.265     0    0.096   0.138    10.098    2.500    6.327
LGA    E    40_B      E    40_B    12.874     0    0.442   1.072    20.922    0.000    0.000
LGA    W    41_B      W    41_B    11.796     0    0.696   1.370    13.282    0.000    0.034
LGA    K    42_B      K    42_B    10.545     0    0.546   1.276    15.194    2.857    1.270

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       41     164    164  100.00     336    336  100.00                41
SUMMARY(RMSD_GDC):     3.648          3.589                  4.757           67.613   60.599

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   42   41    4.0     33    1.79    71.341    76.557     1.750

LGA_LOCAL      RMSD:   1.786  Number of atoms:   33  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   4.268  Number of assigned atoms:   41 
Std_ASGN_ATOMS RMSD:   3.648  Standard rmsd on all 41 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.513233 * X  +   0.567629 * Y  +  -0.643731 * Z  +   8.794535
  Y_new =   0.140289 * X  +  -0.684478 * Y  +  -0.715408 * Z  + -25.383730
  Z_new =  -0.846706 * X  +  -0.457479 * Y  +   0.271664 * Z  +  45.764931 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.874767  1.009763 -1.034927   [DEG:  164.7120   57.8552  -59.2969 ]
ZXZ: -0.732710  1.295674 -2.066166   [DEG:  -41.9812   74.2367 -118.3826 ]
 
# END of job
