
#######################################################
#                                                     #
#                        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   39 (  329),  selected   39 , name one
# Molecule2: number of CA atoms   39 (  326),  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:    39       1_A - 39_A        0.72     0.72
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    39       1_A - 39_A        0.72     0.72
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    39       1_A - 39_A        0.72     0.72
  LCS_AVERAGE:    100.00

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     D     1_A     D     1_A     39   39   39     24   36   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     K     2_A     K     2_A     39   39   39     21   36   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     L     3_A     L     3_A     39   39   39     20   36   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     W     4_A     W     4_A     39   39   39     25   36   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     I     5_A     I     5_A     39   39   39     10   36   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     L     6_A     L     6_A     39   39   39     19   36   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     Q     7_A     Q     7_A     39   39   39     26   36   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     K     8_A     K     8_A     39   39   39     17   36   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     I     9_A     I     9_A     39   39   39     25   36   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     Y    10_A     Y    10_A     39   39   39     26   36   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     E    11_A     E    11_A     39   39   39     26   36   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     I    12_A     I    12_A     39   39   39     26   36   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     M    13_A     M    13_A     39   39   39     26   36   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     V    14_A     V    14_A     39   39   39     26   36   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     R    15_A     R    15_A     39   39   39     26   36   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     L    16_A     L    16_A     39   39   39     26   36   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     D    17_A     D    17_A     39   39   39     26   36   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     E    18_A     E    18_A     39   39   39     16   36   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     E    19_A     E    19_A     39   39   39     17   36   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     G    20_A     G    20_A     39   39   39     26   36   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     H    21_A     H    21_A     39   39   39     26   36   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     G    22_A     G    22_A     39   39   39     26   36   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     E    23_A     E    23_A     39   39   39     26   36   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     A    24_A     A    24_A     39   39   39     26   36   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     S    25_A     S    25_A     39   39   39     26   36   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     L    26_A     L    26_A     39   39   39     26   36   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     M    27_A     M    27_A     39   39   39     26   36   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     V    28_A     V    28_A     39   39   39     26   36   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     S    29_A     S    29_A     39   39   39     26   36   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     D    30_A     D    30_A     39   39   39     26   36   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     L    31_A     L    31_A     39   39   39     26   36   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     I    32_A     I    32_A     39   39   39     26   36   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     Y    33_A     Y    33_A     39   39   39     26   36   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     E    34_A     E    34_A     39   39   39     26   36   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     F    35_A     F    35_A     39   39   39     26   36   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     M    36_A     M    36_A     39   39   39     26   36   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     K    37_A     K    37_A     39   39   39     26   36   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     R    38_A     R    38_A     39   39   39      3   31   38   38   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     D    39_A     D    39_A     39   39   39      3    5   30   37   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_AVERAGE  LCS_A: 100.00  ( 100.00  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     26     36     38     38     39     39     39     39     39     39     39     39     39     39     39     39     39     39     39     39 
GDT PERCENT_AT  66.67  92.31  97.44  97.44 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.30   0.50   0.59   0.59   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72
GDT RMS_ALL_AT   0.77   0.75   0.73   0.73   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72   0.72

# Checking swapping
#   possible swapping detected:  D     1_A      D     1_A
#   possible swapping detected:  E    11_A      E    11_A
#   possible swapping detected:  E    18_A      E    18_A
#   possible swapping detected:  E    19_A      E    19_A
#   possible swapping detected:  E    23_A      E    23_A
#   possible swapping detected:  Y    33_A      Y    33_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    D     1_A      D     1_A     0.694     0    0.500   1.129     4.251   84.048   64.702
LGA    K     2_A      K     2_A     0.847     0    0.041   1.191     7.236   90.476   64.762
LGA    L     3_A      L     3_A     0.763     0    0.055   1.177     4.422   90.476   75.476
LGA    W     4_A      W     4_A     0.595     0    0.005   1.490     9.694   90.476   52.483
LGA    I     5_A      I     5_A     1.415     0    0.080   1.455     5.956   83.690   67.143
LGA    L     6_A      L     6_A     0.793     0    0.000   0.097     1.533   95.238   89.524
LGA    Q     7_A      Q     7_A     0.175     0    0.054   0.224     0.915  100.000   95.767
LGA    K     8_A      K     8_A     0.953     0    0.118   1.180     9.525   90.476   57.937
LGA    I     9_A      I     9_A     0.477     0    0.037   0.540     1.046   97.619   92.917
LGA    Y    10_A      Y    10_A     0.074     0    0.034   0.096     0.268  100.000  100.000
LGA    E    11_A      E    11_A     0.370     0    0.013   0.759     2.225  100.000   85.979
LGA    I    12_A      I    12_A     0.483     0    0.048   0.873     2.234  100.000   88.690
LGA    M    13_A      M    13_A     0.215     0    0.046   0.656     1.933  100.000   90.893
LGA    V    14_A      V    14_A     0.455     0    0.041   0.947     2.740  100.000   87.483
LGA    R    15_A      R    15_A     0.417     0    0.050   0.573     1.481  100.000   91.472
LGA    L    16_A      L    16_A     0.245     0    0.051   0.208     0.965  100.000   96.429
LGA    D    17_A      D    17_A     0.599     0    0.026   0.362     1.511   92.857   87.202
LGA    E    18_A      E    18_A     1.131     0    0.059   0.802     5.771   85.952   57.460
LGA    E    19_A      E    19_A     1.075     0    0.278   0.938     3.608   88.333   70.317
LGA    G    20_A      G    20_A     0.580     0    0.078   0.078     1.082   90.595   90.595
LGA    H    21_A      H    21_A     0.593     0    0.491   1.222     3.107   78.095   76.190
LGA    G    22_A      G    22_A     0.398     0    0.169   0.169     0.408  100.000  100.000
LGA    E    23_A      E    23_A     0.429     0    0.051   0.714     3.137  100.000   88.254
LGA    A    24_A      A    24_A     0.300     0    0.062   0.057     0.404  100.000  100.000
LGA    S    25_A      S    25_A     0.183     0    0.044   0.577     2.038  100.000   94.127
LGA    L    26_A      L    26_A     0.307     0    0.049   0.939     2.384  100.000   91.012
LGA    M    27_A      M    27_A     0.367     0    0.046   0.948     4.390  100.000   85.595
LGA    V    28_A      V    28_A     0.350     0    0.000   1.084     2.833  100.000   88.844
LGA    S    29_A      S    29_A     0.447     0    0.077   0.678     2.562  100.000   91.270
LGA    D    30_A      D    30_A     0.330     0    0.075   0.074     0.662  100.000   96.429
LGA    L    31_A      L    31_A     0.322     0    0.000   0.150     1.289  100.000   94.107
LGA    I    32_A      I    32_A     0.201     0    0.028   0.116     0.765  100.000   97.619
LGA    Y    33_A      Y    33_A     0.433     0    0.047   1.288     6.623  100.000   69.722
LGA    E    34_A      E    34_A     0.342     0    0.014   0.203     1.901  100.000   88.889
LGA    F    35_A      F    35_A     0.323     0    0.047   0.683     1.836  100.000   91.645
LGA    M    36_A      M    36_A     0.281     0    0.137   0.791     2.175   92.976   88.571
LGA    K    37_A      K    37_A     0.520     0    0.190   1.346     5.079   90.595   77.989
LGA    R    38_A      R    38_A     1.212     0    0.048   1.074     2.390   77.381   77.013
LGA    D    39_A      D    39_A     2.533     3    0.356   0.383     4.918   69.048   38.452

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       39     156    156  100.00     326    326  100.00                39
SUMMARY(RMSD_GDC):     0.719          0.741                  2.079           94.573   83.153

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   39   39    4.0     39    0.72    97.436    99.022     4.760

LGA_LOCAL      RMSD:   0.719  Number of atoms:   39  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.719  Number of assigned atoms:   39 
Std_ASGN_ATOMS RMSD:   0.719  Standard rmsd on all 39 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.063976 * X  +  -0.014825 * Y  +  -0.997841 * Z  + 261.682892
  Y_new =  -0.227028 * X  +   0.973888 * Y  +   0.000087 * Z  + -136.510025
  Z_new =   0.971785 * X  +   0.226543 * Y  +  -0.065672 * Z  + -233.355164 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.845473 -1.332683  1.852948   [DEG: -105.7378  -76.3571  106.1661 ]
ZXZ: -1.570883  1.636515  1.341766   [DEG:  -90.0050   93.7654   76.8775 ]
 
# END of job
