
#######################################################
#                                                     #
#                        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   53 (  410),  selected   49 , name one
# Molecule2: number of CA atoms   49 (  370),  selected   49 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:F  -ch2:F  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    49       1_F - 49_F        1.26     1.26
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    49       1_F - 49_F        1.26     1.26
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    47       2_F - 48_F        0.94     1.30
  LONGEST_CONTINUOUS_SEGMENT:    47       3_F - 49_F        0.93     1.31
  LCS_AVERAGE:     94.13

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   49
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     M     1_F     M     1_F      4   49   49      3    4    9   14   19   38   47   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     G     2_F     G     2_F     47   49   49      4   11   35   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     K     3_F     K     3_F     47   49   49      6   42   44   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     I     4_F     I     4_F     47   49   49     29   42   44   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     K     5_F     K     5_F     47   49   49     31   42   44   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     R     6_F     R     6_F     47   49   49     31   42   44   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     F     7_F     F     7_F     47   49   49     31   42   44   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     F     8_F     F     8_F     47   49   49     31   42   44   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     A     9_F     A     9_F     47   49   49     31   42   44   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     K    10_F     K    10_F     47   49   49     25   42   44   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     D    11_F     D    11_F     47   49   49      6   42   44   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     M    12_F     M    12_F     47   49   49     31   42   44   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     R    13_F     R    13_F     47   49   49     31   42   44   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     A    14_F     A    14_F     47   49   49     31   42   44   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     A    15_F     A    15_F     47   49   49     31   42   44   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     L    16_F     L    16_F     47   49   49     31   42   44   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     A    17_F     A    17_F     47   49   49     31   42   44   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     Q    18_F     Q    18_F     47   49   49     31   42   44   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     V    19_F     V    19_F     47   49   49     31   42   44   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     K    20_F     K    20_F     47   49   49     31   42   44   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     D    21_F     D    21_F     47   49   49     31   42   44   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     T    22_F     T    22_F     47   49   49     31   42   44   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     L    23_F     L    23_F     47   49   49     31   42   44   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     G    24_F     G    24_F     47   49   49     31   42   44   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     S    25_F     S    25_F     47   49   49      4   42   44   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     D    26_F     D    26_F     47   49   49     31   42   44   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     A    27_F     A    27_F     47   49   49      9   41   44   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     V    28_F     V    28_F     47   49   49     31   42   44   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     I    29_F     I    29_F     47   49   49     31   42   44   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     M    30_F     M    30_F     47   49   49     31   42   44   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     S    31_F     S    31_F     47   49   49      9   42   44   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     N    32_F     N    32_F     47   49   49     12   42   44   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     K    33_F     K    33_F     47   49   49     31   42   44   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     K    34_F     K    34_F     47   49   49      5   42   44   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     V    35_F     V    35_F     47   49   49     11   42   44   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     N    36_F     N    36_F     47   49   49     29   42   44   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     G    37_F     G    37_F     47   49   49     31   42   44   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     G    38_F     G    38_F     47   49   49     31   42   44   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     I    39_F     I    39_F     47   49   49     31   42   44   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     E    40_F     E    40_F     47   49   49     31   42   44   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     I    41_F     I    41_F     47   49   49     29   42   44   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     V    42_F     V    42_F     47   49   49     31   42   44   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     A    43_F     A    43_F     47   49   49     31   42   44   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     A    44_F     A    44_F     47   49   49     31   42   44   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     V    45_F     V    45_F     47   49   49     31   42   44   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     L    46_F     L    46_F     47   49   49     11   41   44   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     E    47_F     E    47_F     47   49   49      3    7   34   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     H    48_F     H    48_F     47   49   49      3    3   10   16   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     H    49_F     H    49_F     47   49   49      1    9   21   46   47   48   48   49   49   49   49   49   49   49   49   49   49   49   49   49 
LCS_AVERAGE  LCS_A:  98.04  (  94.13  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     31     42     44     46     47     48     48     49     49     49     49     49     49     49     49     49     49     49     49     49 
GDT PERCENT_AT  63.27  85.71  89.80  93.88  95.92  97.96  97.96 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.35   0.52   0.58   0.79   0.90   1.00   1.00   1.26   1.26   1.26   1.26   1.26   1.26   1.26   1.26   1.26   1.26   1.26   1.26   1.26
GDT RMS_ALL_AT   1.48   1.44   1.42   1.35   1.31   1.28   1.28   1.26   1.26   1.26   1.26   1.26   1.26   1.26   1.26   1.26   1.26   1.26   1.26   1.26

# Checking swapping
#   possible swapping detected:  F     7_F      F     7_F
#   possible swapping detected:  D    21_F      D    21_F
#   possible swapping detected:  D    26_F      D    26_F
#   possible swapping detected:  E    40_F      E    40_F
#   possible swapping detected:  E    47_F      E    47_F

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    M     1_F      M     1_F     5.185     0    0.128   1.106     7.674   32.024   24.524
LGA    G     2_F      G     2_F     2.281     0    0.087   0.087     3.426   63.095   63.095
LGA    K     3_F      K     3_F     0.872     0    0.164   1.074     6.277   88.214   67.407
LGA    I     4_F      I     4_F     0.871     0    0.076   0.148     1.500   83.810   84.881
LGA    K     5_F      K     5_F     0.622     0    0.029   1.138     2.733   92.857   80.423
LGA    R     6_F      R     6_F     0.779     0    0.011   1.276     6.266   90.476   73.506
LGA    F     7_F      F     7_F     0.600     0    0.016   0.071     0.757   90.476   91.342
LGA    F     8_F      F     8_F     0.472     0    0.012   1.296     7.121   97.619   62.035
LGA    A     9_F      A     9_F     0.285     0    0.036   0.045     0.579   97.619   98.095
LGA    K    10_F      K    10_F     0.388     0    0.027   1.067     4.936   97.619   79.206
LGA    D    11_F      D    11_F     1.152     0    0.083   0.960     2.941   90.595   81.905
LGA    M    12_F      M    12_F     0.373     0    0.011   1.147     4.179   97.619   85.357
LGA    R    13_F      R    13_F     0.539     0    0.054   1.554     8.076   92.857   59.913
LGA    A    14_F      A    14_F     0.558     0    0.015   0.024     0.627   90.476   90.476
LGA    A    15_F      A    15_F     0.459     0    0.065   0.075     0.508   97.619   96.190
LGA    L    16_F      L    16_F     0.366     0    0.021   1.101     2.322   95.238   87.619
LGA    A    17_F      A    17_F     0.817     0    0.047   0.053     0.950   90.476   90.476
LGA    Q    18_F      Q    18_F     0.852     0    0.037   0.430     1.800   90.476   88.519
LGA    V    19_F      V    19_F     0.643     0    0.035   0.073     0.704   90.476   91.837
LGA    K    20_F      K    20_F     0.533     0    0.013   0.638     2.836   90.476   79.365
LGA    D    21_F      D    21_F     0.783     0    0.025   0.483     1.841   90.476   88.274
LGA    T    22_F      T    22_F     0.845     0    0.142   1.128     2.578   90.476   83.197
LGA    L    23_F      L    23_F     0.901     0    0.158   1.118     3.123   90.476   82.083
LGA    G    24_F      G    24_F     0.874     0    0.084   0.084     1.051   90.595   90.595
LGA    S    25_F      S    25_F     1.106     0    0.103   0.111     1.942   85.952   81.587
LGA    D    26_F      D    26_F     0.653     0    0.545   0.595     2.202   90.595   80.774
LGA    A    27_F      A    27_F     1.541     0    0.200   0.261     2.166   70.833   71.238
LGA    V    28_F      V    28_F     1.155     0    0.023   0.069     1.357   81.429   81.429
LGA    I    29_F      I    29_F     0.927     0    0.023   0.621     2.834   88.214   84.048
LGA    M    30_F      M    30_F     1.080     0    0.049   0.850     3.498   83.690   78.631
LGA    S    31_F      S    31_F     0.978     0    0.036   0.574     2.454   88.214   83.175
LGA    N    32_F      N    32_F     1.202     0    0.501   0.998     2.808   77.619   76.369
LGA    K    33_F      K    33_F     0.158     0    0.046   0.891     3.282   95.238   81.481
LGA    K    34_F      K    34_F     1.047     0    0.084   0.786     3.214   85.952   74.392
LGA    V    35_F      V    35_F     0.873     0    0.037   1.206     3.300   88.214   79.728
LGA    N    36_F      N    36_F     0.464     0    0.073   1.222     4.920   95.238   78.095
LGA    G    37_F      G    37_F     0.389     0    0.207   0.207     0.919   97.619   97.619
LGA    G    38_F      G    38_F     0.587     0    0.076   0.076     0.719   90.476   90.476
LGA    I    39_F      I    39_F     0.535     0    0.083   1.495     3.740   95.238   79.583
LGA    E    40_F      E    40_F     0.514     0    0.095   0.514     1.601   90.595   87.566
LGA    I    41_F      I    41_F     0.901     0    0.038   1.245     3.470   90.476   82.024
LGA    V    42_F      V    42_F     0.542     0    0.043   1.063     2.743   90.476   83.401
LGA    A    43_F      A    43_F     0.802     0    0.057   0.061     0.982   90.476   90.476
LGA    A    44_F      A    44_F     1.059     0    0.021   0.021     1.239   83.690   83.238
LGA    V    45_F      V    45_F     0.909     0    0.036   0.957     3.029   92.976   82.313
LGA    L    46_F      L    46_F     0.772     0    0.594   1.129     4.621   76.429   63.214
LGA    E    47_F      E    47_F     1.973     0    0.405   0.923     4.920   62.143   55.767
LGA    H    48_F      H    48_F     2.858     0    0.310   1.141    11.564   71.310   32.143
LGA    H    49_F      H    49_F     2.398     0    0.082   1.299     7.305   65.119   41.524

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       49     196    196  100.00     370    370  100.00                49
SUMMARY(RMSD_GDC):     1.261          1.276                  2.435           86.742   78.380

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   53   49    4.0     49    1.26    94.898    97.172     3.601

LGA_LOCAL      RMSD:   1.261  Number of atoms:   49  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.261  Number of assigned atoms:   49 
Std_ASGN_ATOMS RMSD:   1.261  Standard rmsd on all 49 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.865261 * X  +  -0.034337 * Y  +   0.500145 * Z  +  52.556480
  Y_new =   0.313173 * X  +   0.816058 * Y  +  -0.485770 * Z  + -80.439842
  Z_new =  -0.391467 * X  +   0.576949 * Y  +   0.716856 * Z  +  -3.652229 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.347272  0.402226  0.677681   [DEG:   19.8972   23.0458   38.8283 ]
ZXZ:  0.799978  0.771514 -0.596159   [DEG:   45.8353   44.2045  -34.1574 ]
 
# END of job
