
#######################################################
#                                                     #
#                        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        1.60     1.60
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    49       1_F - 49_F        1.60     1.60
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    46       2_F - 47_F        0.83     1.65
  LCS_AVERAGE:     88.75

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      7   49   49      3    7   11   18   31   43   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     G     2_F     G     2_F     46   49   49      4   12   32   45   46   46   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     K     3_F     K     3_F     46   49   49      6   41   44   45   46   46   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     I     4_F     I     4_F     46   49   49     26   41   44   45   46   46   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     K     5_F     K     5_F     46   49   49     29   41   44   45   46   46   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     R     6_F     R     6_F     46   49   49     29   41   44   45   46   46   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     F     7_F     F     7_F     46   49   49     29   41   44   45   46   46   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     F     8_F     F     8_F     46   49   49     29   41   44   45   46   46   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     A     9_F     A     9_F     46   49   49     29   41   44   45   46   46   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     K    10_F     K    10_F     46   49   49     22   41   44   45   46   46   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     D    11_F     D    11_F     46   49   49      6   41   44   45   46   46   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     M    12_F     M    12_F     46   49   49     29   41   44   45   46   46   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     R    13_F     R    13_F     46   49   49     29   41   44   45   46   46   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     A    14_F     A    14_F     46   49   49     29   41   44   45   46   46   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     A    15_F     A    15_F     46   49   49     29   41   44   45   46   46   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     L    16_F     L    16_F     46   49   49     29   41   44   45   46   46   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     A    17_F     A    17_F     46   49   49     29   41   44   45   46   46   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     Q    18_F     Q    18_F     46   49   49     29   41   44   45   46   46   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     V    19_F     V    19_F     46   49   49     29   41   44   45   46   46   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     K    20_F     K    20_F     46   49   49     29   41   44   45   46   46   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     D    21_F     D    21_F     46   49   49     29   41   44   45   46   46   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     T    22_F     T    22_F     46   49   49     29   41   44   45   46   46   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     L    23_F     L    23_F     46   49   49     29   41   44   45   46   46   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     G    24_F     G    24_F     46   49   49     29   41   44   45   46   46   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     S    25_F     S    25_F     46   49   49     28   41   44   45   46   46   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     D    26_F     D    26_F     46   49   49     15   41   44   45   46   46   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     A    27_F     A    27_F     46   49   49      7   39   44   45   46   46   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     V    28_F     V    28_F     46   49   49     20   41   44   45   46   46   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     I    29_F     I    29_F     46   49   49     29   41   44   45   46   46   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     M    30_F     M    30_F     46   49   49     29   41   44   45   46   46   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     S    31_F     S    31_F     46   49   49      7   41   44   45   46   46   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     N    32_F     N    32_F     46   49   49      9   41   44   45   46   46   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     K    33_F     K    33_F     46   49   49     29   41   44   45   46   46   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     K    34_F     K    34_F     46   49   49      4   41   44   45   46   46   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     V    35_F     V    35_F     46   49   49      4   41   44   45   46   46   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     N    36_F     N    36_F     46   49   49      3   41   44   45   46   46   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     G    37_F     G    37_F     46   49   49     29   41   44   45   46   46   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     G    38_F     G    38_F     46   49   49     29   41   44   45   46   46   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     I    39_F     I    39_F     46   49   49     29   41   44   45   46   46   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     E    40_F     E    40_F     46   49   49     29   41   44   45   46   46   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     I    41_F     I    41_F     46   49   49     29   41   44   45   46   46   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     V    42_F     V    42_F     46   49   49     29   41   44   45   46   46   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     A    43_F     A    43_F     46   49   49     29   41   44   45   46   46   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     A    44_F     A    44_F     46   49   49     29   41   44   45   46   46   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     V    45_F     V    45_F     46   49   49     29   41   44   45   46   46   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     L    46_F     L    46_F     46   49   49      4   38   44   45   46   46   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     E    47_F     E    47_F     46   49   49      4   33   44   45   46   46   47   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     H    48_F     H    48_F      5   49   49      3    4    5    7    8   24   46   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_GDT     H    49_F     H    49_F      3   49   49      0    3    6    8   10   25   45   47   48   49   49   49   49   49   49   49   49   49   49   49 
LCS_AVERAGE  LCS_A:  96.25  (  88.75  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     29     41     44     45     46     46     47     47     48     49     49     49     49     49     49     49     49     49     49     49 
GDT PERCENT_AT  59.18  83.67  89.80  91.84  93.88  93.88  95.92  95.92  97.96 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.31   0.50   0.62   0.68   0.83   0.83   1.11   1.11   1.40   1.60   1.60   1.60   1.60   1.60   1.60   1.60   1.60   1.60   1.60   1.60
GDT RMS_ALL_AT   1.72   1.73   1.69   1.66   1.65   1.65   1.67   1.67   1.62   1.60   1.60   1.60   1.60   1.60   1.60   1.60   1.60   1.60   1.60   1.60

# 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     4.785     0    0.120   1.070     6.018   36.071   35.119
LGA    G     2_F      G     2_F     2.733     0    0.033   0.033     3.493   59.167   59.167
LGA    K     3_F      K     3_F     0.755     0    0.104   1.022     5.654   88.214   67.989
LGA    I     4_F      I     4_F     0.543     0    0.080   0.133     1.017   90.476   89.345
LGA    K     5_F      K     5_F     0.407     0    0.017   1.018     2.596  100.000   81.640
LGA    R     6_F      R     6_F     0.693     0    0.023   1.005     6.333   90.476   66.147
LGA    F     7_F      F     7_F     0.574     0    0.012   0.077     0.979   90.476   90.476
LGA    F     8_F      F     8_F     0.571     0    0.027   1.299     7.013   90.476   60.433
LGA    A     9_F      A     9_F     0.344     0    0.078   0.108     0.555   97.619   98.095
LGA    K    10_F      K    10_F     0.512     0    0.022   1.026     4.850   95.238   77.143
LGA    D    11_F      D    11_F     1.131     0    0.087   0.777     2.377   90.595   83.988
LGA    M    12_F      M    12_F     0.583     0    0.031   1.109     4.055   95.238   82.976
LGA    R    13_F      R    13_F     0.389     0    0.047   1.562     7.794  100.000   65.455
LGA    A    14_F      A    14_F     0.343     0    0.002   0.005     0.352  100.000  100.000
LGA    A    15_F      A    15_F     0.321     0    0.050   0.053     0.411  100.000  100.000
LGA    L    16_F      L    16_F     0.124     0    0.010   1.096     2.343  100.000   90.000
LGA    A    17_F      A    17_F     0.590     0    0.012   0.014     0.693   92.857   92.381
LGA    Q    18_F      Q    18_F     0.687     0    0.026   0.511     2.209   90.476   88.677
LGA    V    19_F      V    19_F     0.447     0    0.018   0.038     0.474  100.000  100.000
LGA    K    20_F      K    20_F     0.187     0    0.027   0.929     4.004  100.000   84.127
LGA    D    21_F      D    21_F     0.551     0    0.011   0.488     1.560   92.857   89.464
LGA    T    22_F      T    22_F     0.676     0    0.057   1.076     2.418   90.476   84.286
LGA    L    23_F      L    23_F     0.589     0    0.070   1.041     2.745   92.857   85.298
LGA    G    24_F      G    24_F     0.562     0    0.070   0.070     0.729   92.857   92.857
LGA    S    25_F      S    25_F     0.495     0    0.109   0.623     3.228   97.619   88.492
LGA    D    26_F      D    26_F     1.044     0    0.511   1.192     5.551   85.952   68.155
LGA    A    27_F      A    27_F     1.671     0    0.113   0.160     1.997   72.857   72.857
LGA    V    28_F      V    28_F     1.196     0    0.066   0.104     1.504   85.952   82.789
LGA    I    29_F      I    29_F     0.758     0    0.027   0.656     3.048   90.476   85.417
LGA    M    30_F      M    30_F     0.886     0    0.054   0.696     2.001   90.476   86.131
LGA    S    31_F      S    31_F     0.882     0    0.035   0.781     3.631   85.952   78.095
LGA    N    32_F      N    32_F     1.282     0    0.448   0.486     2.695   77.619   79.583
LGA    K    33_F      K    33_F     0.515     0    0.035   0.925     3.408   90.476   78.519
LGA    K    34_F      K    34_F     0.969     0    0.055   0.726     2.985   88.214   79.048
LGA    V    35_F      V    35_F     0.890     0    0.036   1.200     3.269   92.857   82.381
LGA    N    36_F      N    36_F     0.711     0    0.115   1.196     5.507   90.595   68.988
LGA    G    37_F      G    37_F     0.486     0    0.216   0.216     0.705   97.619   97.619
LGA    G    38_F      G    38_F     0.484     0    0.047   0.047     0.554   97.619   97.619
LGA    I    39_F      I    39_F     0.467     0    0.041   1.317     2.927   95.238   81.548
LGA    E    40_F      E    40_F     0.552     0    0.056   0.471     1.670   92.857   89.577
LGA    I    41_F      I    41_F     0.789     0    0.022   1.236     3.248   90.476   79.881
LGA    V    42_F      V    42_F     0.342     0    0.049   1.147     2.642   95.238   86.122
LGA    A    43_F      A    43_F     0.693     0    0.051   0.060     0.819   90.476   90.476
LGA    A    44_F      A    44_F     0.590     0    0.034   0.050     0.694   90.476   90.476
LGA    V    45_F      V    45_F     0.769     0    0.034   1.293     3.228   90.476   81.020
LGA    L    46_F      L    46_F     1.595     0    0.591   0.989     4.783   62.619   58.452
LGA    E    47_F      E    47_F     1.596     0    0.450   0.876     5.333   61.190   53.280
LGA    H    48_F      H    48_F     5.724     0    0.170   1.170    13.692   24.286   10.190
LGA    H    49_F      H    49_F     6.829     0    0.085   1.177     9.050   10.238    9.095

# 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):     1.597          1.678                  2.639           86.210   78.385

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   53   49    4.0     47    1.11    92.857    96.053     3.898

LGA_LOCAL      RMSD:   1.106  Number of atoms:   47  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.671  Number of assigned atoms:   49 
Std_ASGN_ATOMS RMSD:   1.597  Standard rmsd on all 49 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.568075 * X  +   0.042177 * Y  +  -0.821896 * Z  +  51.840416
  Y_new =   0.026060 * X  +  -0.997263 * Y  +  -0.069189 * Z  + -86.456398
  Z_new =  -0.822564 * X  +  -0.060723 * Y  +   0.565421 * Z  +  -4.307805 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  3.095750  0.965906 -0.106985   [DEG:  177.3734   55.3423   -6.1298 ]
ZXZ: -1.486812  0.969853 -1.644485   [DEG:  -85.1881   55.5685  -94.2220 ]
 
# END of job
