
#######################################################
#                                                     #
#                        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        1.61     1.61
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    41       2_B - 42_B        1.61     1.61
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    37       2_B - 38_B        0.94     1.66
  LONGEST_CONTINUOUS_SEGMENT:    37       3_B - 39_B        0.95     1.63
  LCS_AVERAGE:     86.44

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     37   41   41      3   11   18   35   37   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     S     3_B     S     3_B     37   41   41      4   23   34   36   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     Q     4_B     Q     4_B     37   41   41      4   29   34   36   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     R     5_B     R     5_B     37   41   41     17   30   34   36   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     L     6_B     L     6_B     37   41   41      5   30   34   36   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     F     7_B     F     7_B     37   41   41     17   30   34   36   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     V     8_B     V     8_B     37   41   41     16   30   34   36   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     L     9_B     L     9_B     37   41   41     17   30   34   36   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     D    10_B     D    10_B     37   41   41     17   30   34   36   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     N    11_B     N    11_B     37   41   41     17   30   34   36   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     E    12_B     E    12_B     37   41   41     17   30   34   36   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     R    13_B     R    13_B     37   41   41     17   30   34   36   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     Y    14_B     Y    14_B     37   41   41     17   30   34   36   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     D    15_B     D    15_B     37   41   41     17   30   34   36   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     S    16_B     S    16_B     37   41   41     17   30   34   36   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     F    17_B     F    17_B     37   41   41     17   30   34   36   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     I    18_B     I    18_B     37   41   41     17   30   34   36   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     T    19_B     T    19_B     37   41   41     17   30   34   36   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     Q    20_B     Q    20_B     37   41   41     17   30   34   36   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     L    21_B     L    21_B     37   41   41     12   30   34   36   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     E    22_B     E    22_B     37   41   41     17   30   34   36   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     A    23_B     A    23_B     37   41   41     17   30   34   36   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     P    24_B     P    24_B     37   41   41     17   30   34   36   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     V    25_B     V    25_B     37   41   41      3   24   34   36   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     Q    26_B     Q    26_B     37   41   41      3   16   32   36   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     N    27_B     N    27_B     37   41   41     12   30   34   36   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     A    28_B     A    28_B     37   41   41     12   30   34   36   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     E    29_B     E    29_B     37   41   41     11   30   34   36   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     G    30_B     G    30_B     37   41   41     15   30   34   36   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     R    31_B     R    31_B     37   41   41     17   30   34   36   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     E    32_B     E    32_B     37   41   41     17   30   34   36   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     R    33_B     R    33_B     37   41   41     17   30   34   36   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     L    34_B     L    34_B     37   41   41     12   30   34   36   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     M    35_B     M    35_B     37   41   41     13   30   34   36   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     A    36_B     A    36_B     37   41   41     13   30   34   36   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     V    37_B     V    37_B     37   41   41     12   29   34   36   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     K    38_B     K    38_B     37   41   41     12   26   34   36   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     P    39_B     P    39_B     37   41   41      3   14   19   35   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     E    40_B     E    40_B     23   41   41      3    7   15   21   35   38   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     W    41_B     W    41_B     21   41   41      3   14   27   36   38   39   40   40   40   40   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     K    42_B     K    42_B      3   41   41      0    3    3    3    4    4    4    4   13   40   41   41   41   41   41   41   41   41   41   41 
LCS_AVERAGE  LCS_A:  95.48  (  86.44  100.00  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     17     30     34     36     38     39     40     40     40     40     41     41     41     41     41     41     41     41     41     41 
GDT PERCENT_AT  41.46  73.17  82.93  87.80  92.68  95.12  97.56  97.56  97.56  97.56 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.27   0.60   0.73   0.84   1.03   1.12   1.27   1.27   1.27   1.27   1.61   1.61   1.61   1.61   1.61   1.61   1.61   1.61   1.61   1.61
GDT RMS_ALL_AT   1.73   1.66   1.67   1.65   1.62   1.62   1.63   1.63   1.63   1.63   1.61   1.61   1.61   1.61   1.61   1.61   1.61   1.61   1.61   1.61

# Checking swapping
#   possible swapping detected:  E    12_B      E    12_B
#   possible swapping detected:  Y    14_B      Y    14_B
#   possible swapping detected:  E    29_B      E    29_B
#   possible swapping detected:  E    32_B      E    32_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     3.003     0    0.321   0.438     5.041   41.190   47.524
LGA    S     3_B      S     3_B     2.048     0    0.134   0.522     2.228   70.952   68.889
LGA    Q     4_B      Q     4_B     1.434     0    0.015   0.263     2.234   77.143   72.063
LGA    R     5_B      R     5_B     0.718     0    0.100   0.360     1.851   90.476   84.762
LGA    L     6_B      L     6_B     0.945     0    0.066   0.133     1.803   83.810   81.548
LGA    F     7_B      F     7_B     0.444     0    0.028   0.140     0.764   92.857   94.805
LGA    V     8_B      V     8_B     0.712     0    0.041   1.153     2.269   92.857   84.490
LGA    L     9_B      L     9_B     0.531     0    0.025   0.134     0.903   90.476   90.476
LGA    D    10_B      D    10_B     0.649     0    0.043   0.588     1.684   90.476   86.071
LGA    N    11_B      N    11_B     0.257     0    0.074   0.871     2.494   97.619   89.821
LGA    E    12_B      E    12_B     0.542     0    0.039   1.163     6.432   92.857   68.519
LGA    R    13_B      R    13_B     0.785     0    0.051   1.095     3.258   90.476   77.532
LGA    Y    14_B      Y    14_B     0.470     0    0.050   0.073     0.548  100.000   97.619
LGA    D    15_B      D    15_B     0.137     0    0.020   0.431     0.969  100.000   97.619
LGA    S    16_B      S    16_B     0.297     0    0.014   0.769     2.356  100.000   94.127
LGA    F    17_B      F    17_B     0.294     0    0.018   0.190     0.962  100.000   95.671
LGA    I    18_B      I    18_B     0.207     0    0.031   0.121     0.430  100.000  100.000
LGA    T    19_B      T    19_B     0.149     0    0.016   0.237     0.997  100.000   98.639
LGA    Q    20_B      Q    20_B     0.388     0    0.036   1.080     3.202  100.000   87.249
LGA    L    21_B      L    21_B     0.803     0    0.015   1.305     3.130   90.476   83.214
LGA    E    22_B      E    22_B     0.880     0    0.023   0.740     1.656   88.214   83.492
LGA    A    23_B      A    23_B     0.608     0    0.095   0.112     0.777   92.857   92.381
LGA    P    24_B      P    24_B     0.724     0    0.013   0.323     1.520   90.476   87.959
LGA    V    25_B      V    25_B     1.482     0    0.131   1.276     3.776   77.143   72.313
LGA    Q    26_B      Q    26_B     1.936     0    0.618   1.165     5.290   58.571   54.392
LGA    N    27_B      N    27_B     1.118     0    0.129   0.121     1.701   88.214   82.679
LGA    A    28_B      A    28_B     0.955     0    0.112   0.124     1.049   90.595   88.762
LGA    E    29_B      E    29_B     1.056     0    0.086   0.560     3.155   88.333   73.757
LGA    G    30_B      G    30_B     0.695     0    0.104   0.104     0.803   92.857   92.857
LGA    R    31_B      R    31_B     0.349     0    0.050   1.039     3.217   97.619   87.792
LGA    E    32_B      E    32_B     0.143     0    0.099   0.800     2.957  100.000   87.460
LGA    R    33_B      R    33_B     0.266     0    0.050   1.310     4.381   95.238   79.004
LGA    L    34_B      L    34_B     0.803     0    0.012   0.065     1.346   88.214   85.952
LGA    M    35_B      M    35_B     0.739     0    0.028   0.934     2.705   88.214   85.179
LGA    A    36_B      A    36_B     0.653     0    0.015   0.025     0.970   90.476   92.381
LGA    V    37_B      V    37_B     1.031     0    0.066   0.086     1.480   83.690   84.014
LGA    K    38_B      K    38_B     1.414     4    0.102   0.116     3.055   69.405   38.042
LGA    P    39_B      P    39_B     2.624     0    0.085   0.350     2.769   62.976   65.034
LGA    E    40_B      E    40_B     3.821     0    0.386   0.493     9.702   51.905   27.090
LGA    W    41_B      W    41_B     2.523     0    0.650   0.930     4.907   50.238   47.721
LGA    K    42_B      K    42_B     6.709     0    0.152   1.019    13.749   14.881    6.772

# 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):     1.608          1.696                  2.472           84.434   78.431

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   42   41    4.0     40    1.27    89.634    94.480     2.921

LGA_LOCAL      RMSD:   1.269  Number of atoms:   40  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.634  Number of assigned atoms:   41 
Std_ASGN_ATOMS RMSD:   1.608  Standard rmsd on all 41 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.315699 * X  +  -0.193015 * Y  +   0.929021 * Z  +  21.553886
  Y_new =   0.241315 * X  +   0.930567 * Y  +   0.275340 * Z  + -10.699058
  Z_new =  -0.917661 * X  +   0.311111 * Y  +  -0.247202 * Z  +  36.037868 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.488950  1.162152  2.242223   [DEG:  142.6064   66.5864  128.4699 ]
ZXZ:  1.858925  1.820588 -1.243931   [DEG:  106.5086  104.3120  -71.2720 ]
 
# END of job
