
#######################################################
#                                                     #
#                        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        1.78     1.78
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    49       1_F - 49_F        1.78     1.78
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    46       2_F - 47_F        0.88     1.82
  LONGEST_CONTINUOUS_SEGMENT:    46       3_F - 48_F        0.99     1.81
  LCS_AVERAGE:     90.34

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    3    6    9   16   28   39   45   47   47   47   48   49   49   49   49   49   49   49   49 
LCS_GDT     G     2_F     G     2_F     46   49   49      3   10   25   43   45   46   46   46   48   48   48   48   49   49   49   49   49   49   49   49 
LCS_GDT     K     3_F     K     3_F     46   49   49      6   39   45   45   45   46   46   47   48   48   48   48   49   49   49   49   49   49   49   49 
LCS_GDT     I     4_F     I     4_F     46   49   49     10   40   45   45   45   46   46   47   48   48   48   48   49   49   49   49   49   49   49   49 
LCS_GDT     K     5_F     K     5_F     46   49   49     27   40   45   45   45   46   46   47   48   48   48   48   49   49   49   49   49   49   49   49 
LCS_GDT     R     6_F     R     6_F     46   49   49     27   40   45   45   45   46   46   47   48   48   48   48   49   49   49   49   49   49   49   49 
LCS_GDT     F     7_F     F     7_F     46   49   49     27   40   45   45   45   46   46   47   48   48   48   48   49   49   49   49   49   49   49   49 
LCS_GDT     F     8_F     F     8_F     46   49   49     27   40   45   45   45   46   46   47   48   48   48   48   49   49   49   49   49   49   49   49 
LCS_GDT     A     9_F     A     9_F     46   49   49     27   40   45   45   45   46   46   47   48   48   48   48   49   49   49   49   49   49   49   49 
LCS_GDT     K    10_F     K    10_F     46   49   49     15   40   45   45   45   46   46   47   48   48   48   48   49   49   49   49   49   49   49   49 
LCS_GDT     D    11_F     D    11_F     46   49   49     27   40   45   45   45   46   46   47   48   48   48   48   49   49   49   49   49   49   49   49 
LCS_GDT     M    12_F     M    12_F     46   49   49     27   40   45   45   45   46   46   47   48   48   48   48   49   49   49   49   49   49   49   49 
LCS_GDT     R    13_F     R    13_F     46   49   49     27   40   45   45   45   46   46   47   48   48   48   48   49   49   49   49   49   49   49   49 
LCS_GDT     A    14_F     A    14_F     46   49   49     27   40   45   45   45   46   46   47   48   48   48   48   49   49   49   49   49   49   49   49 
LCS_GDT     A    15_F     A    15_F     46   49   49     27   40   45   45   45   46   46   47   48   48   48   48   49   49   49   49   49   49   49   49 
LCS_GDT     L    16_F     L    16_F     46   49   49     27   40   45   45   45   46   46   47   48   48   48   48   49   49   49   49   49   49   49   49 
LCS_GDT     A    17_F     A    17_F     46   49   49     27   40   45   45   45   46   46   47   48   48   48   48   49   49   49   49   49   49   49   49 
LCS_GDT     Q    18_F     Q    18_F     46   49   49     27   40   45   45   45   46   46   47   48   48   48   48   49   49   49   49   49   49   49   49 
LCS_GDT     V    19_F     V    19_F     46   49   49     27   40   45   45   45   46   46   47   48   48   48   48   49   49   49   49   49   49   49   49 
LCS_GDT     K    20_F     K    20_F     46   49   49     27   40   45   45   45   46   46   47   48   48   48   48   49   49   49   49   49   49   49   49 
LCS_GDT     D    21_F     D    21_F     46   49   49     27   40   45   45   45   46   46   47   48   48   48   48   49   49   49   49   49   49   49   49 
LCS_GDT     T    22_F     T    22_F     46   49   49     27   40   45   45   45   46   46   47   48   48   48   48   49   49   49   49   49   49   49   49 
LCS_GDT     L    23_F     L    23_F     46   49   49     27   40   45   45   45   46   46   47   48   48   48   48   49   49   49   49   49   49   49   49 
LCS_GDT     G    24_F     G    24_F     46   49   49     27   40   45   45   45   46   46   47   48   48   48   48   49   49   49   49   49   49   49   49 
LCS_GDT     S    25_F     S    25_F     46   49   49     10   40   45   45   45   46   46   47   48   48   48   48   49   49   49   49   49   49   49   49 
LCS_GDT     D    26_F     D    26_F     46   49   49     24   39   45   45   45   46   46   47   48   48   48   48   49   49   49   49   49   49   49   49 
LCS_GDT     A    27_F     A    27_F     46   49   49      6   36   45   45   45   46   46   47   48   48   48   48   49   49   49   49   49   49   49   49 
LCS_GDT     V    28_F     V    28_F     46   49   49     10   40   45   45   45   46   46   47   48   48   48   48   49   49   49   49   49   49   49   49 
LCS_GDT     I    29_F     I    29_F     46   49   49     27   40   45   45   45   46   46   47   48   48   48   48   49   49   49   49   49   49   49   49 
LCS_GDT     M    30_F     M    30_F     46   49   49     27   40   45   45   45   46   46   47   48   48   48   48   49   49   49   49   49   49   49   49 
LCS_GDT     S    31_F     S    31_F     46   49   49     10   40   45   45   45   46   46   47   48   48   48   48   49   49   49   49   49   49   49   49 
LCS_GDT     N    32_F     N    32_F     46   49   49     22   40   45   45   45   46   46   47   48   48   48   48   49   49   49   49   49   49   49   49 
LCS_GDT     K    33_F     K    33_F     46   49   49     27   40   45   45   45   46   46   47   48   48   48   48   49   49   49   49   49   49   49   49 
LCS_GDT     K    34_F     K    34_F     46   49   49      3   40   45   45   45   46   46   47   48   48   48   48   49   49   49   49   49   49   49   49 
LCS_GDT     V    35_F     V    35_F     46   49   49      3   28   45   45   45   46   46   47   48   48   48   48   49   49   49   49   49   49   49   49 
LCS_GDT     N    36_F     N    36_F     46   49   49      4   34   45   45   45   46   46   47   48   48   48   48   49   49   49   49   49   49   49   49 
LCS_GDT     G    37_F     G    37_F     46   49   49     27   40   45   45   45   46   46   47   48   48   48   48   49   49   49   49   49   49   49   49 
LCS_GDT     G    38_F     G    38_F     46   49   49     27   40   45   45   45   46   46   47   48   48   48   48   49   49   49   49   49   49   49   49 
LCS_GDT     I    39_F     I    39_F     46   49   49      8   40   45   45   45   46   46   47   48   48   48   48   49   49   49   49   49   49   49   49 
LCS_GDT     E    40_F     E    40_F     46   49   49     27   40   45   45   45   46   46   47   48   48   48   48   49   49   49   49   49   49   49   49 
LCS_GDT     I    41_F     I    41_F     46   49   49     13   40   45   45   45   46   46   47   48   48   48   48   49   49   49   49   49   49   49   49 
LCS_GDT     V    42_F     V    42_F     46   49   49     27   40   45   45   45   46   46   47   48   48   48   48   49   49   49   49   49   49   49   49 
LCS_GDT     A    43_F     A    43_F     46   49   49     27   40   45   45   45   46   46   47   48   48   48   48   49   49   49   49   49   49   49   49 
LCS_GDT     A    44_F     A    44_F     46   49   49     27   40   45   45   45   46   46   47   48   48   48   48   49   49   49   49   49   49   49   49 
LCS_GDT     V    45_F     V    45_F     46   49   49     27   40   45   45   45   46   46   47   48   48   48   48   49   49   49   49   49   49   49   49 
LCS_GDT     L    46_F     L    46_F     46   49   49     18   40   45   45   45   46   46   47   48   48   48   48   49   49   49   49   49   49   49   49 
LCS_GDT     E    47_F     E    47_F     46   49   49      3   40   45   45   45   46   46   47   48   48   48   48   49   49   49   49   49   49   49   49 
LCS_GDT     H    48_F     H    48_F     46   49   49      3    4    5   10   18   45   46   47   48   48   48   48   49   49   49   49   49   49   49   49 
LCS_GDT     H    49_F     H    49_F      3   49   49      0    3    3    9   11   25   38   47   48   48   48   48   49   49   49   49   49   49   49   49 
LCS_AVERAGE  LCS_A:  96.78  (  90.34  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     27     40     45     45     45     46     46     47     48     48     48     48     49     49     49     49     49     49     49     49 
GDT PERCENT_AT  55.10  81.63  91.84  91.84  91.84  93.88  93.88  95.92  97.96  97.96  97.96  97.96 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.34   0.53   0.67   0.67   0.67   0.88   0.88   1.31   1.45   1.45   1.45   1.45   1.78   1.78   1.78   1.78   1.78   1.78   1.78   1.78
GDT RMS_ALL_AT   1.85   1.84   1.83   1.83   1.83   1.82   1.82   1.85   1.81   1.81   1.81   1.81   1.78   1.78   1.78   1.78   1.78   1.78   1.78   1.78

# 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    47_F      E    47_F

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    M     1_F      M     1_F     8.043     0    0.206   1.189    10.002    9.524    7.679
LGA    G     2_F      G     2_F     4.668     0    0.077   0.077     6.022   30.833   30.833
LGA    K     3_F      K     3_F     1.943     0    0.189   1.142     6.362   73.214   55.185
LGA    I     4_F      I     4_F     1.217     0    0.076   0.141     2.001   85.952   79.464
LGA    K     5_F      K     5_F     0.607     0    0.024   0.721     1.936   92.857   87.566
LGA    R     6_F      R     6_F     0.276     0    0.014   1.158     7.488  100.000   67.879
LGA    F     7_F      F     7_F     0.384     0    0.001   0.122     0.554  100.000   98.268
LGA    F     8_F      F     8_F     0.641     0    0.046   1.205     5.643   90.476   68.615
LGA    A     9_F      A     9_F     0.711     0    0.055   0.081     0.843   90.476   90.476
LGA    K    10_F      K    10_F     1.042     0    0.032   1.277     5.730   88.214   72.857
LGA    D    11_F      D    11_F     0.235     0    0.038   0.558     1.512  100.000   91.905
LGA    M    12_F      M    12_F     0.288     0    0.023   1.090     3.606  100.000   88.512
LGA    R    13_F      R    13_F     0.222     0    0.049   1.823     8.012  100.000   62.944
LGA    A    14_F      A    14_F     0.280     0    0.015   0.034     0.303  100.000  100.000
LGA    A    15_F      A    15_F     0.185     0    0.065   0.077     0.271  100.000  100.000
LGA    L    16_F      L    16_F     0.366     0    0.015   1.092     2.576  100.000   89.048
LGA    A    17_F      A    17_F     0.390     0    0.055   0.057     0.509   97.619   98.095
LGA    Q    18_F      Q    18_F     0.150     0    0.039   0.352     1.540  100.000   94.868
LGA    V    19_F      V    19_F     0.580     0    0.041   0.085     0.791   92.857   91.837
LGA    K    20_F      K    20_F     0.837     0    0.010   1.122     4.503   90.476   77.143
LGA    D    21_F      D    21_F     0.631     0    0.020   0.497     1.739   90.476   88.274
LGA    T    22_F      T    22_F     0.653     0    0.137   1.116     2.738   88.214   81.905
LGA    L    23_F      L    23_F     0.475     0    0.147   1.114     2.396   92.976   87.679
LGA    G    24_F      G    24_F     0.614     0    0.053   0.053     1.131   88.214   88.214
LGA    S    25_F      S    25_F     1.224     0    0.066   0.677     3.458   83.690   77.698
LGA    D    26_F      D    26_F     1.336     0    0.523   1.256     4.471   77.262   69.583
LGA    A    27_F      A    27_F     1.275     0    0.213   0.280     1.721   79.286   79.714
LGA    V    28_F      V    28_F     0.532     0    0.021   0.063     0.699   90.476   94.558
LGA    I    29_F      I    29_F     0.690     0    0.013   0.613     2.872   90.476   86.310
LGA    M    30_F      M    30_F     0.597     0    0.045   0.746     2.151   90.476   86.131
LGA    S    31_F      S    31_F     0.666     0    0.035   0.623     2.834   90.476   84.921
LGA    N    32_F      N    32_F     0.958     0    0.424   1.220     3.782   81.786   73.810
LGA    K    33_F      K    33_F     0.515     0    0.125   1.151     5.303   88.214   76.190
LGA    K    34_F      K    34_F     0.972     0    0.059   0.351     1.466   88.214   85.450
LGA    V    35_F      V    35_F     1.631     0    0.044   1.240     3.349   77.143   69.796
LGA    N    36_F      N    36_F     1.685     0    0.122   1.218     6.616   77.143   56.190
LGA    G    37_F      G    37_F     0.865     0    0.246   0.246     1.274   85.952   85.952
LGA    G    38_F      G    38_F     0.600     0    0.065   0.065     0.612   90.476   90.476
LGA    I    39_F      I    39_F     0.920     0    0.120   1.492     3.572   88.214   74.940
LGA    E    40_F      E    40_F     0.540     0    0.075   0.623     1.727   88.214   87.566
LGA    I    41_F      I    41_F     0.572     0    0.049   1.217     3.157   95.238   85.536
LGA    V    42_F      V    42_F     0.479     0    0.060   1.068     2.288  100.000   88.571
LGA    A    43_F      A    43_F     0.674     0    0.067   0.071     0.807   90.476   90.476
LGA    A    44_F      A    44_F     0.895     0    0.019   0.022     0.999   90.476   90.476
LGA    V    45_F      V    45_F     0.706     0    0.031   1.278     3.164   90.476   81.020
LGA    L    46_F      L    46_F     0.220     0    0.616   0.945     3.799   81.190   76.369
LGA    E    47_F      E    47_F     0.827     0    0.378   0.790     3.596   76.310   72.169
LGA    H    48_F      H    48_F     4.352     0    0.238   1.194    12.406   39.405   17.190
LGA    H    49_F      H    49_F     5.653     0    0.180   1.286     7.949   18.929   16.810

# 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):     1.776          1.849                  2.766           84.742   77.493

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   53   49    4.0     47    1.31    92.347    95.551     3.323

LGA_LOCAL      RMSD:   1.314  Number of atoms:   47  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.850  Number of assigned atoms:   49 
Std_ASGN_ATOMS RMSD:   1.776  Standard rmsd on all 49 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.182977 * X  +   0.974825 * Y  +   0.127418 * Z  +  51.107571
  Y_new =  -0.365817 * X  +   0.187811 * Y  +  -0.911540 * Z  + -82.808632
  Z_new =  -0.912522 * X  +   0.120180 * Y  +   0.390973 * Z  +  -4.625893 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.106998  1.149409  0.298219   [DEG:  -63.4263   65.8563   17.0867 ]
ZXZ:  0.138883  1.169108 -1.439849   [DEG:    7.9574   66.9850  -82.4973 ]
 
# END of job
