
#######################################################
#                                                     #
#                        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        0.73     0.73
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    39       1_A - 39_A        0.73     0.73
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    39       1_A - 39_A        0.73     0.73
  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   37   38   39   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     24   37   38   39   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     24   37   38   39   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     24   37   38   39   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     14   37   38   39   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     24   37   38   39   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     24   37   38   39   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     24   37   38   39   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     24   37   38   39   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     24   37   38   39   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     24   37   38   39   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     24   37   38   39   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     24   37   38   39   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     24   37   38   39   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     24   37   38   39   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     18   37   38   39   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     18   37   38   39   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     24   37   38   39   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     19   37   38   39   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     14   37   38   39   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      7   37   38   39   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     24   37   38   39   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     24   37   38   39   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     24   37   38   39   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     24   37   38   39   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     24   37   38   39   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     24   37   38   39   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     23   37   38   39   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     11   37   38   39   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     24   37   38   39   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     24   37   38   39   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     11   37   38   39   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     10   37   38   39   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     24   37   38   39   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     17   37   38   39   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     17   37   38   39   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     17   37   38   39   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     10   36   38   39   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    3    3   39   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     24     37     38     39     39     39     39     39     39     39     39     39     39     39     39     39     39     39     39     39 
GDT PERCENT_AT  61.54  94.87  97.44 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.34   0.56   0.58   0.73   0.73   0.73   0.73   0.73   0.73   0.73   0.73   0.73   0.73   0.73   0.73   0.73   0.73   0.73   0.73   0.73
GDT RMS_ALL_AT   0.81   0.76   0.75   0.73   0.73   0.73   0.73   0.73   0.73   0.73   0.73   0.73   0.73   0.73   0.73   0.73   0.73   0.73   0.73   0.73

# Checking swapping
#   possible swapping detected:  E    19_A      E    19_A
#   possible swapping detected:  E    34_A      E    34_A
#   possible swapping detected:  F    35_A      F    35_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    D     1_A      D     1_A     0.269     0    0.266   1.452     5.632   93.214   66.667
LGA    K     2_A      K     2_A     0.387     0    0.054   0.752     2.007  100.000   91.852
LGA    L     3_A      L     3_A     0.640     0    0.051   1.077     3.241   90.476   82.202
LGA    W     4_A      W     4_A     0.616     0    0.060   1.239     8.162   90.476   52.041
LGA    I     5_A      I     5_A     1.040     0    0.069   1.471     5.292   88.214   72.917
LGA    L     6_A      L     6_A     0.413     0    0.019   0.076     1.078   97.619   92.917
LGA    Q     7_A      Q     7_A     0.422     0    0.053   1.149     6.437  100.000   72.063
LGA    K     8_A      K     8_A     0.586     0    0.089   0.267     2.291   95.238   86.720
LGA    I     9_A      I     9_A     0.377     0    0.003   0.673     1.958  100.000   95.417
LGA    Y    10_A      Y    10_A     0.437     0    0.041   0.713     6.757  100.000   62.143
LGA    E    11_A      E    11_A     0.491     0    0.055   0.772     2.327  100.000   89.841
LGA    I    12_A      I    12_A     0.276     0    0.021   0.414     1.808  100.000   94.286
LGA    M    13_A      M    13_A     0.230     0    0.055   1.023     2.807  100.000   86.845
LGA    V    14_A      V    14_A     0.448     0    0.047   0.077     1.142  100.000   94.626
LGA    R    15_A      R    15_A     0.167     0    0.000   1.234     7.352   97.619   67.186
LGA    L    16_A      L    16_A     0.715     0    0.000   0.318     1.342   90.476   89.345
LGA    D    17_A      D    17_A     0.820     0    0.000   0.144     1.011   90.476   89.345
LGA    E    18_A      E    18_A     0.281     0    0.056   0.555     3.519  100.000   79.471
LGA    E    19_A      E    19_A     0.576     0    0.234   0.877     5.151   88.452   67.196
LGA    G    20_A      G    20_A     1.036     0    0.074   0.074     1.274   83.690   83.690
LGA    H    21_A      H    21_A     0.878     0    0.053   0.919     3.452   92.857   82.429
LGA    G    22_A      G    22_A     0.504     0    0.033   0.033     0.594   95.238   95.238
LGA    E    23_A      E    23_A     0.255     0    0.035   0.455     1.303  100.000   94.762
LGA    A    24_A      A    24_A     0.473     0    0.068   0.057     0.659   97.619   96.190
LGA    S    25_A      S    25_A     0.219     0    0.031   0.078     0.385  100.000  100.000
LGA    L    26_A      L    26_A     0.602     0    0.085   0.990     4.627   92.857   75.952
LGA    M    27_A      M    27_A     0.656     0    0.046   1.098     2.502   90.476   81.964
LGA    V    28_A      V    28_A     0.798     0    0.040   1.085     2.248   88.214   81.837
LGA    S    29_A      S    29_A     0.865     0    0.035   0.489     2.062   90.476   86.190
LGA    D    30_A      D    30_A     0.623     0    0.077   0.687     2.670   92.857   81.131
LGA    L    31_A      L    31_A     0.553     0    0.000   0.932     3.685   90.476   78.155
LGA    I    32_A      I    32_A     0.750     0    0.055   0.576     2.043   90.476   87.321
LGA    Y    33_A      Y    33_A     0.762     0    0.114   1.447    11.276   95.238   47.778
LGA    E    34_A      E    34_A     0.375     0    0.081   1.215     3.937  100.000   76.032
LGA    F    35_A      F    35_A     0.355     0    0.000   1.160     5.234   97.619   72.900
LGA    M    36_A      M    36_A     0.532     0    0.090   1.163     3.300   95.238   81.369
LGA    K    37_A      K    37_A     0.663     0    0.112   0.877     4.950   90.476   76.720
LGA    R    38_A      R    38_A     0.805     0    0.109   1.087     4.679   83.810   73.463
LGA    D    39_A      D    39_A     2.748     3    0.044   0.046     3.742   64.881   37.857

# 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):     0.733          0.717                  2.325           93.712   80.104

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   39   39    4.0     39    0.73    98.718    99.404     4.684

LGA_LOCAL      RMSD:   0.733  Number of atoms:   39  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.733  Number of assigned atoms:   39 
Std_ASGN_ATOMS RMSD:   0.733  Standard rmsd on all 39 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.179857 * X  +  -0.402871 * Y  +  -0.897411 * Z  + 328.047974
  Y_new =  -0.954578 * X  +   0.291793 * Y  +   0.060321 * Z  + 122.440536
  Z_new =   0.237556 * X  +   0.867498 * Y  +  -0.437052 * Z  + -107.527786 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.757028 -0.239850  2.037486   [DEG: -100.6703  -13.7424  116.7393 ]
ZXZ: -1.637912  2.023115  0.267288   [DEG:  -93.8454  115.9160   15.3145 ]
 
# END of job
