
#######################################################
#                                                     #
#                        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 (  334),  selected   39 , name one
# Molecule2: number of CA atoms   61 (  480),  selected   39 , 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:    26      51_A - 76_A        4.70    17.37
  LCS_AVERAGE:     39.97

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    21      56_A - 76_A        1.78    19.63
  LCS_AVERAGE:     28.71

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    20      57_A - 76_A        0.77    20.20
  LCS_AVERAGE:     25.77

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   39
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     K    38_A     K    38_A     14   15   21      9   13   13   13   14   15   17   17   18   18   18   18   20   20   21   21   21   21   23   23 
LCS_GDT     M    39_A     M    39_A     14   15   21      9   13   13   13   14   15   17   17   18   18   18   18   20   20   21   21   21   21   23   23 
LCS_GDT     Q    40_A     Q    40_A     14   15   21      9   13   13   13   14   15   17   17   18   18   18   18   20   20   21   21   21   21   23   23 
LCS_GDT     A    41_A     A    41_A     14   15   21      9   13   13   13   14   15   17   17   18   18   18   18   20   20   21   21   21   21   23   23 
LCS_GDT     V    42_A     V    42_A     14   15   21      9   13   13   13   14   15   17   17   18   18   18   18   20   20   21   21   21   21   23   23 
LCS_GDT     K    43_A     K    43_A     14   15   21      9   13   13   13   14   15   17   17   18   18   18   18   20   20   21   21   21   21   23   23 
LCS_GDT     E    44_A     E    44_A     14   15   21      9   13   13   13   14   15   17   17   18   18   18   18   20   20   21   21   21   21   23   23 
LCS_GDT     I    45_A     I    45_A     14   15   21      9   13   13   13   14   15   17   17   18   18   18   18   20   20   21   21   21   21   23   23 
LCS_GDT     C    46_A     C    46_A     14   15   21      9   13   13   13   14   15   17   17   18   18   18   18   20   20   21   21   21   21   23   23 
LCS_GDT     Y    47_A     Y    47_A     14   15   21      6   13   13   13   14   15   17   17   18   18   18   18   20   20   21   21   21   21   24   25 
LCS_GDT     E    48_A     E    48_A     14   15   21      6   13   13   13   14   15   17   17   18   18   18   18   20   20   21   21   21   21   24   25 
LCS_GDT     V    49_A     V    49_A     14   15   21      8   13   13   13   14   15   17   17   18   18   18   18   20   20   21   22   23   26   27   27 
LCS_GDT     A    50_A     A    50_A     14   15   23      8   13   13   13   14   15   17   17   18   18   18   18   20   20   21   22   25   26   27   27 
LCS_GDT     L    51_A     L    51_A     14   15   26      4    4    4    7   14   15   17   17   18   18   18   18   20   21   22   25   25   26   27   27 
LCS_GDT     A    52_A     A    52_A      4   15   26      4    4    6    9   13   14   17   17   18   20   22   24   25   25   25   25   25   26   27   27 
LCS_GDT     D    53_A     D    53_A      4    6   26      4    4    5    6    8   10   12   17   18   20   22   24   25   25   25   25   25   26   27   27 
LCS_GDT     F    54_A     F    54_A      3    6   26      3    3    5    7   13   14   17   17   18   20   22   24   25   25   25   25   25   26   27   27 
LCS_GDT     R    55_A     R    55_A      3    5   26      3    3   10   12   14   15   17   17   18   20   22   24   25   25   25   25   25   26   27   27 
LCS_GDT     H    56_A     H    56_A      3   21   26      3    3    4    6    9   12   16   21   21   21   22   24   25   25   25   25   25   26   27   27 
LCS_GDT     G    57_A     G    57_A     20   21   26      7   13   20   20   20   20   20   21   21   21   22   24   25   25   25   25   25   26   27   27 
LCS_GDT     R    58_A     R    58_A     20   21   26      7   16   20   20   20   20   20   21   21   21   22   24   25   25   25   25   25   26   27   27 
LCS_GDT     A    59_A     A    59_A     20   21   26     11   18   20   20   20   20   20   21   21   21   22   24   25   25   25   25   25   26   27   27 
LCS_GDT     E    60_A     E    60_A     20   21   26     10   18   20   20   20   20   20   21   21   21   22   24   25   25   25   25   25   26   27   27 
LCS_GDT     I    61_A     I    61_A     20   21   26     11   18   20   20   20   20   20   21   21   21   22   24   25   25   25   25   25   26   27   27 
LCS_GDT     E    62_A     E    62_A     20   21   26     12   18   20   20   20   20   20   21   21   21   22   24   25   25   25   25   25   26   27   27 
LCS_GDT     A    63_A     A    63_A     20   21   26     12   18   20   20   20   20   20   21   21   21   22   24   25   25   25   25   25   26   27   27 
LCS_GDT     L    64_A     L    64_A     20   21   26     12   18   20   20   20   20   20   21   21   21   22   24   25   25   25   25   25   26   27   27 
LCS_GDT     A    65_A     A    65_A     20   21   26     12   18   20   20   20   20   20   21   21   21   22   24   25   25   25   25   25   26   27   27 
LCS_GDT     A    66_A     A    66_A     20   21   26     12   18   20   20   20   20   20   21   21   21   22   24   25   25   25   25   25   26   27   27 
LCS_GDT     L    67_A     L    67_A     20   21   26     12   18   20   20   20   20   20   21   21   21   22   24   25   25   25   25   25   26   27   27 
LCS_GDT     K    68_A     K    68_A     20   21   26     12   18   20   20   20   20   20   21   21   21   22   24   25   25   25   25   25   26   27   27 
LCS_GDT     M    69_A     M    69_A     20   21   26     12   18   20   20   20   20   20   21   21   21   22   24   25   25   25   25   25   26   27   27 
LCS_GDT     R    70_A     R    70_A     20   21   26     12   18   20   20   20   20   20   21   21   21   22   24   25   25   25   25   25   26   27   27 
LCS_GDT     E    71_A     E    71_A     20   21   26     12   18   20   20   20   20   20   21   21   21   22   24   25   25   25   25   25   26   27   27 
LCS_GDT     L    72_A     L    72_A     20   21   26     12   18   20   20   20   20   20   21   21   21   22   24   25   25   25   25   25   26   27   27 
LCS_GDT     C    73_A     C    73_A     20   21   26     12   18   20   20   20   20   20   21   21   21   22   24   25   25   25   25   25   26   27   27 
LCS_GDT     R    74_A     R    74_A     20   21   26      9   18   20   20   20   20   20   21   21   21   22   24   25   25   25   25   25   26   27   27 
LCS_GDT     T    75_A     T    75_A     20   21   26      6   18   20   20   20   20   20   21   21   21   22   24   25   25   25   25   25   26   27   27 
LCS_GDT     Y    76_A     Y    76_A     20   21   26      3   18   20   20   20   20   20   21   21   21   21   24   25   25   25   25   25   26   26   27 
LCS_AVERAGE  LCS_A:  31.48  (  25.77   28.71   39.97 )

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     12     18     20     20     20     20     20     21     21     21     22     24     25     25     25     25     25     26     27     27 
GDT PERCENT_AT  19.67  29.51  32.79  32.79  32.79  32.79  32.79  34.43  34.43  34.43  36.07  39.34  40.98  40.98  40.98  40.98  40.98  42.62  44.26  44.26
GDT RMS_LOCAL    0.28   0.58   0.77   0.77   0.77   0.77   0.77   1.78   1.78   1.78   3.27   3.70   4.03   4.03   4.03   4.03   4.03   4.70   5.50   5.22
GDT RMS_ALL_AT  20.73  20.50  20.20  20.20  20.20  20.20  20.20  19.63  19.63  19.63  18.57  18.21  17.81  17.81  17.81  17.81  17.81  17.37  16.51  16.97

# Checking swapping
#   possible swapping detected:  Y    47_A      Y    47_A
#   possible swapping detected:  E    48_A      E    48_A
#   possible swapping detected:  D    53_A      D    53_A
#   possible swapping detected:  E    60_A      E    60_A
#   possible swapping detected:  E    62_A      E    62_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    K    38_A      K    38_A    43.812     0    0.095   0.718    46.342    0.000    0.000
LGA    M    39_A      M    39_A    44.162     0    0.032   0.830    49.318    0.000    0.000
LGA    Q    40_A      Q    40_A    42.944     0    0.021   0.275    44.692    0.000    0.000
LGA    A    41_A      A    41_A    37.384     0    0.020   0.030    39.823    0.000    0.000
LGA    V    42_A      V    42_A    34.648     0    0.079   0.091    36.246    0.000    0.000
LGA    K    43_A      K    43_A    35.178     0    0.014   0.156    46.524    0.000    0.000
LGA    E    44_A      E    44_A    32.079     0    0.152   1.069    38.294    0.000    0.000
LGA    I    45_A      I    45_A    27.138     0    0.039   0.082    29.478    0.000    0.000
LGA    C    46_A      C    46_A    26.195     0    0.099   0.174    28.995    0.000    0.000
LGA    Y    47_A      Y    47_A    25.659     0    0.137   1.387    27.164    0.000    0.000
LGA    E    48_A      E    48_A    21.722     0    0.107   0.920    25.813    0.000    0.000
LGA    V    49_A      V    49_A    18.461     0    0.175   1.282    19.875    0.000    0.000
LGA    A    50_A      A    50_A    20.631     0    0.417   0.443    22.745    0.000    0.000
LGA    L    51_A      L    51_A    20.656     0    0.023   0.189    26.884    0.000    0.000
LGA    A    52_A      A    52_A    14.459     0    0.035   0.045    16.919    0.000    0.000
LGA    D    53_A      D    53_A    13.201     0    0.593   0.859    15.863    0.000    0.000
LGA    F    54_A      F    54_A    10.947     0    0.417   1.516    15.531    0.714    0.260
LGA    R    55_A      R    55_A    11.413     0    0.067   1.597    19.810    1.071    0.390
LGA    H    56_A      H    56_A     6.690     0    0.567   1.392     8.894   18.452   10.571
LGA    G    57_A      G    57_A     0.864     0    0.588   0.588     2.482   81.786   81.786
LGA    R    58_A      R    58_A     0.862     0    0.039   1.098     3.572   90.476   81.299
LGA    A    59_A      A    59_A     0.810     0    0.044   0.041     0.982   90.476   90.476
LGA    E    60_A      E    60_A     1.023     0    0.027   0.399     2.159   83.690   77.725
LGA    I    61_A      I    61_A     0.844     0    0.025   0.079     0.976   90.476   90.476
LGA    E    62_A      E    62_A     0.591     0    0.024   0.696     2.619   90.476   81.111
LGA    A    63_A      A    63_A     1.344     0    0.012   0.015     1.704   81.429   79.714
LGA    L    64_A      L    64_A     1.513     0    0.182   0.453     3.111   79.286   71.190
LGA    A    65_A      A    65_A     0.963     0    0.007   0.023     1.331   88.214   88.667
LGA    A    66_A      A    66_A     0.716     0    0.053   0.056     1.076   92.857   90.571
LGA    L    67_A      L    67_A     1.270     0    0.014   0.804     2.244   83.690   77.262
LGA    K    68_A      K    68_A     1.246     0    0.051   1.152     5.300   85.952   73.016
LGA    M    69_A      M    69_A     0.666     0    0.051   0.942     4.486   92.857   79.940
LGA    R    70_A      R    70_A     0.693     0    0.098   1.264     4.044   92.857   78.615
LGA    E    71_A      E    71_A     1.038     0    0.100   1.342     4.106   88.214   73.228
LGA    L    72_A      L    72_A     1.068     0    0.048   0.227     1.978   85.952   80.476
LGA    C    73_A      C    73_A     1.014     0    0.081   0.243     1.427   83.690   82.937
LGA    R    74_A      R    74_A     0.931     0    0.270   1.454    10.252   83.810   52.554
LGA    T    75_A      T    75_A     0.990     0    0.084   0.328     1.208   85.952   85.306
LGA    Y    76_A      Y    76_A     1.605     0    0.678   0.698     2.127   75.000   71.548

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       39     156    156  100.00     314    314  100.00                61
SUMMARY(RMSD_GDC):    13.774         13.529                 14.367           28.646   26.215

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   42   61    4.0     21    1.78    34.426    33.141     1.119

LGA_LOCAL      RMSD:   1.777  Number of atoms:   21  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  19.628  Number of assigned atoms:   39 
Std_ASGN_ATOMS RMSD:  13.774  Standard rmsd on all 39 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.812481 * X  +   0.297105 * Y  +   0.501602 * Z  +  69.380432
  Y_new =  -0.576763 * X  +  -0.284237 * Y  +  -0.765868 * Z  + 134.520645
  Z_new =  -0.084969 * X  +  -0.911558 * Y  +   0.402296 * Z  +  97.859856 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.524267  0.085072 -1.155177   [DEG: -144.6299    4.8743  -66.1868 ]
ZXZ:  0.579844  1.156773 -3.048648   [DEG:   33.2226   66.2782 -174.6747 ]
 
# END of job
