
#######################################################
#                                                     #
#                        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        0.89     0.89
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    39       1_A - 39_A        0.89     0.89
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    39       1_A - 39_A        0.89     0.89
  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      6   20   36   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     13   22   36   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     13   31   36   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     13   32   36   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     13   31   36   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     13   32   36   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   32   36   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     16   32   36   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   32   36   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   32   36   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   32   36   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   32   36   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   32   36   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   32   36   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   32   36   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     24   32   36   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     10   32   36   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     12   31   36   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      9   32   36   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     19   32   36   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      8   29   36   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     23   32   36   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   32   36   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   32   36   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   32   36   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   32   36   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   32   36   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     24   32   36   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     24   32   36   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   32   36   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   32   36   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     24   32   36   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     24   32   36   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   32   36   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     24   32   36   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     24   32   36   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     24   32   36   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     23   32   36   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    4   34   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     32     36     39     39     39     39     39     39     39     39     39     39     39     39     39     39     39     39     39 
GDT PERCENT_AT  61.54  82.05  92.31 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.35   0.56   0.72   0.89   0.89   0.89   0.89   0.89   0.89   0.89   0.89   0.89   0.89   0.89   0.89   0.89   0.89   0.89   0.89   0.89
GDT RMS_ALL_AT   1.04   0.96   0.91   0.89   0.89   0.89   0.89   0.89   0.89   0.89   0.89   0.89   0.89   0.89   0.89   0.89   0.89   0.89   0.89   0.89

# Checking swapping
#   possible swapping detected:  D     1_A      D     1_A
#   possible swapping detected:  E    11_A      E    11_A
#   possible swapping detected:  E    19_A      E    19_A
#   possible swapping detected:  E    23_A      E    23_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     1.817     0    0.095   1.029     2.408   75.000   71.964
LGA    K     2_A      K     2_A     1.921     0    0.075   0.774     5.203   77.143   61.111
LGA    L     3_A      L     3_A     1.122     0    0.041   0.071     2.002   85.952   79.464
LGA    W     4_A      W     4_A     0.760     0    0.000   1.655     7.250   90.476   64.694
LGA    I     5_A      I     5_A     1.298     0    0.053   0.569     4.127   85.952   74.940
LGA    L     6_A      L     6_A     0.558     0    0.000   0.846     3.929   95.238   82.560
LGA    Q     7_A      Q     7_A     0.412     0    0.000   0.371     1.622   95.238   88.624
LGA    K     8_A      K     8_A     0.997     0    0.071   1.073     8.852   90.476   59.524
LGA    I     9_A      I     9_A     0.618     0    0.028   1.014     2.736   90.476   79.881
LGA    Y    10_A      Y    10_A     0.515     0    0.052   0.142     1.857   92.857   86.071
LGA    E    11_A      E    11_A     0.944     0    0.000   1.047     3.062   90.476   80.053
LGA    I    12_A      I    12_A     0.715     0    0.037   0.246     1.781   95.238   89.524
LGA    M    13_A      M    13_A     0.360     0    0.035   0.943     2.411  100.000   91.190
LGA    V    14_A      V    14_A     0.722     0    0.033   0.972     3.139   90.476   79.932
LGA    R    15_A      R    15_A     0.717     0    0.000   1.352     5.511   95.238   71.905
LGA    L    16_A      L    16_A     0.452     0    0.000   0.118     1.168   97.619   92.917
LGA    D    17_A      D    17_A     0.917     0    0.019   0.371     2.273   90.476   80.655
LGA    E    18_A      E    18_A     1.278     0    0.055   0.391     4.822   85.952   64.868
LGA    E    19_A      E    19_A     1.014     0    0.255   1.147     4.183   88.333   67.302
LGA    G    20_A      G    20_A     0.967     0    0.070   0.070     1.947   86.190   86.190
LGA    H    21_A      H    21_A     1.514     0    0.142   0.942     5.645   81.548   61.476
LGA    G    22_A      G    22_A     0.890     0    0.029   0.029     1.109   90.595   90.595
LGA    E    23_A      E    23_A     0.689     0    0.039   0.836     2.556   92.857   82.011
LGA    A    24_A      A    24_A     0.569     0    0.047   0.044     0.707   95.238   94.286
LGA    S    25_A      S    25_A     0.104     0    0.032   0.600     1.877  100.000   95.476
LGA    L    26_A      L    26_A     0.248     0    0.039   0.878     3.356  100.000   84.940
LGA    M    27_A      M    27_A     0.374     0    0.066   0.789     3.369  100.000   83.988
LGA    V    28_A      V    28_A     0.464     0    0.054   1.080     2.451   97.619   89.728
LGA    S    29_A      S    29_A     0.540     0    0.054   0.084     0.985   92.857   92.063
LGA    D    30_A      D    30_A     0.358     0    0.066   0.161     0.774  100.000   98.810
LGA    L    31_A      L    31_A     0.414     0    0.028   0.959     3.673  100.000   82.917
LGA    I    32_A      I    32_A     0.358     0    0.000   0.908     2.739   97.619   86.726
LGA    Y    33_A      Y    33_A     0.489     0    0.000   0.189     2.091   97.619   87.063
LGA    E    34_A      E    34_A     0.521     0    0.044   1.118     3.528   97.619   80.847
LGA    F    35_A      F    35_A     0.335     0    0.047   1.171     6.128  100.000   67.186
LGA    M    36_A      M    36_A     0.246     0    0.137   0.811     3.513   95.238   81.548
LGA    K    37_A      K    37_A     0.656     0    0.133   0.684     2.987   90.595   82.116
LGA    R    38_A      R    38_A     0.986     0    0.133   1.505     4.546   77.738   68.831
LGA    D    39_A      D    39_A     1.953     3    0.443   0.537     2.192   72.976   44.583

# 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):     0.888          0.851                  2.007           91.767   79.707

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   39   39    4.0     39    0.89    95.513    98.009     3.949

LGA_LOCAL      RMSD:   0.888  Number of atoms:   39  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.888  Number of assigned atoms:   39 
Std_ASGN_ATOMS RMSD:   0.888  Standard rmsd on all 39 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.102896 * X  +  -0.465840 * Y  +  -0.878866 * Z  + 321.028564
  Y_new =  -0.983055 * X  +   0.182384 * Y  +   0.018422 * Z  + 160.632355
  Z_new =   0.151710 * X  +   0.865869 * Y  +  -0.476713 * Z  + -79.595963 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.675086 -0.152298  2.074069   [DEG:  -95.9754   -8.7260  118.8354 ]
ZXZ: -1.591755  2.067708  0.173450   [DEG:  -91.2008  118.4709    9.9380 ]
 
# END of job
