
#######################################################
#                                                     #
#                        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   42 (  348),  selected   41 , name one
# Molecule2: number of CA atoms   41 (  336),  selected   41 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:B  -ch2:B  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    41       2_B - 42_B        3.72     3.72
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    34       3_B - 36_B        1.99     4.23
  LONGEST_CONTINUOUS_SEGMENT:    34       4_B - 37_B        1.99     4.24
  LONGEST_CONTINUOUS_SEGMENT:    34       5_B - 38_B        1.99     4.28
  LCS_AVERAGE:     78.29

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    23       6_B - 28_B        0.99     5.36
  LCS_AVERAGE:     44.38

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   41
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     A     2_B     A     2_B      3   24   41      3    3    3    5   20   24   26   29   33   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     S     3_B     S     3_B      4   34   41      3    4    4    5   19   24   30   33   35   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     Q     4_B     Q     4_B      4   34   41      3    4    4    4    6   24   26   33   35   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     R     5_B     R     5_B     21   34   41      4    9   18   23   29   31   32   33   35   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     L     6_B     L     6_B     23   34   41      4   20   23   26   29   31   32   33   35   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     F     7_B     F     7_B     23   34   41      4   20   23   26   29   31   32   33   35   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     V     8_B     V     8_B     23   34   41     12   20   23   26   29   31   32   33   35   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     L     9_B     L     9_B     23   34   41     16   20   23   26   29   31   32   33   35   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     D    10_B     D    10_B     23   34   41     16   20   23   26   29   31   32   33   35   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     N    11_B     N    11_B     23   34   41     16   20   23   26   29   31   32   33   35   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     E    12_B     E    12_B     23   34   41     16   20   23   26   29   31   32   33   35   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     R    13_B     R    13_B     23   34   41     16   20   23   26   29   31   32   33   35   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     Y    14_B     Y    14_B     23   34   41     16   20   23   26   29   31   32   33   35   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     D    15_B     D    15_B     23   34   41     16   20   23   26   29   31   32   33   35   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     S    16_B     S    16_B     23   34   41     16   20   23   26   29   31   32   33   35   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     F    17_B     F    17_B     23   34   41     16   20   23   26   29   31   32   33   35   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     I    18_B     I    18_B     23   34   41     16   20   23   26   29   31   32   33   35   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     T    19_B     T    19_B     23   34   41     16   20   23   26   29   31   32   33   35   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     Q    20_B     Q    20_B     23   34   41     16   20   23   26   29   31   32   33   35   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     L    21_B     L    21_B     23   34   41     16   20   23   26   29   31   32   33   35   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     E    22_B     E    22_B     23   34   41     16   20   23   26   29   31   32   33   35   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     A    23_B     A    23_B     23   34   41     16   20   23   26   29   31   32   33   35   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     P    24_B     P    24_B     23   34   41     16   20   23   26   29   31   32   33   35   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     V    25_B     V    25_B     23   34   41      3    3   23   26   29   31   32   33   35   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     Q    26_B     Q    26_B     23   34   41     10   13   15   15   24   29   32   33   35   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     N    27_B     N    27_B     23   34   41     11   18   23   26   29   31   32   33   35   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     A    28_B     A    28_B     23   34   41     11   13   20   26   29   31   32   33   35   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     E    29_B     E    29_B     14   34   41     11   19   23   26   29   31   32   33   35   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     G    30_B     G    30_B     14   34   41     11   13   15   26   29   31   32   33   35   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     R    31_B     R    31_B     14   34   41     11   13   23   26   29   31   32   33   35   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     E    32_B     E    32_B     14   34   41     11   20   23   26   29   31   32   33   35   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     R    33_B     R    33_B     14   34   41     11   13   16   26   29   31   32   33   35   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     L    34_B     L    34_B     14   34   41     11   13   15   22   29   31   32   33   35   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     M    35_B     M    35_B     14   34   41     11   16   23   26   29   31   32   33   35   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     A    36_B     A    36_B     14   34   41     11   13   15   23   29   31   32   33   35   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     V    37_B     V    37_B     14   34   41     11   13   15   15   20   29   32   33   35   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     K    38_B     K    38_B     14   34   41      6   13   15   15   15   20   29   32   34   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     P    39_B     P    39_B     14   17   41      4    9   15   15   15   16   16   19   25   31   33   38   38   39   40   40   41   41   41   41 
LCS_GDT     E    40_B     E    40_B     14   17   41      4    5    6   13   15   16   16   16   17   18   19   23   27   34   36   39   41   41   41   41 
LCS_GDT     W    41_B     W    41_B     14   17   41      4   13   15   15   15   16   16   16   18   21   29   32   35   39   40   40   41   41   41   41 
LCS_GDT     K    42_B     K    42_B      3   17   41      2    3    3    3    4    4    4   11   17   18   22   32   35   39   40   40   41   41   41   41 
LCS_AVERAGE  LCS_A:  74.22  (  44.38   78.29  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     16     20     23     26     29     31     32     33     35     36     37     38     38     39     40     40     41     41     41     41 
GDT PERCENT_AT  39.02  48.78  56.10  63.41  70.73  75.61  78.05  80.49  85.37  87.80  90.24  92.68  92.68  95.12  97.56  97.56 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.27   0.57   0.79   0.96   1.21   1.41   1.54   1.74   2.13   2.32   2.48   2.78   2.78   3.07   3.36   3.36   3.72   3.72   3.72   3.72
GDT RMS_ALL_AT   4.16   4.79   4.94   4.70   4.70   4.54   4.58   4.43   4.14   4.04   3.97   3.86   3.86   3.79   3.74   3.74   3.72   3.72   3.72   3.72

# Checking swapping
#   possible swapping detected:  F     7_B      F     7_B
#   possible swapping detected:  F    17_B      F    17_B
#   possible swapping detected:  E    22_B      E    22_B
#   possible swapping detected:  E    29_B      E    29_B
#   possible swapping detected:  E    40_B      E    40_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A     2_B      A     2_B     8.698     0    0.544   0.556    10.133   12.262    9.810
LGA    S     3_B      S     3_B     6.254     0    0.498   0.425     7.619   23.452   23.571
LGA    Q     4_B      Q     4_B     6.428     0    0.048   0.276    12.697   19.762    9.418
LGA    R     5_B      R     5_B     2.418     0    0.659   1.227     6.572   62.857   38.615
LGA    L     6_B      L     6_B     1.456     0    0.157   1.396     4.444   77.143   65.060
LGA    F     7_B      F     7_B     1.251     0    0.139   0.191     1.758   79.286   78.312
LGA    V     8_B      V     8_B     0.983     0    0.044   1.193     2.338   85.952   79.252
LGA    L     9_B      L     9_B     0.798     0    0.026   0.121     1.107   90.476   85.952
LGA    D    10_B      D    10_B     0.885     0    0.085   0.629     1.652   90.476   87.143
LGA    N    11_B      N    11_B     0.449     0    0.026   0.961     3.040   92.857   83.274
LGA    E    12_B      E    12_B     0.816     0    0.048   1.124     6.690   90.476   63.915
LGA    R    13_B      R    13_B     0.868     0    0.015   1.129     2.908   90.476   80.260
LGA    Y    14_B      Y    14_B     0.545     0    0.041   0.163     1.276   95.238   89.048
LGA    D    15_B      D    15_B     0.421     0    0.017   0.455     1.354  100.000   95.298
LGA    S    16_B      S    16_B     0.450     0    0.022   0.173     0.689  100.000   96.825
LGA    F    17_B      F    17_B     0.537     0    0.032   0.252     1.156   92.857   89.740
LGA    I    18_B      I    18_B     0.489     0    0.015   0.120     0.738  100.000   97.619
LGA    T    19_B      T    19_B     0.399     0    0.022   0.244     0.802   97.619   95.918
LGA    Q    20_B      Q    20_B     0.645     0    0.010   1.148     3.041   90.476   81.058
LGA    L    21_B      L    21_B     0.962     0    0.018   1.319     2.996   90.476   81.964
LGA    E    22_B      E    22_B     0.839     0    0.113   0.748     1.988   90.476   84.550
LGA    A    23_B      A    23_B     0.504     0    0.087   0.123     0.906   90.476   92.381
LGA    P    24_B      P    24_B     0.579     0    0.049   0.361     1.519   86.071   87.959
LGA    V    25_B      V    25_B     1.911     0    0.091   1.272     4.911   75.000   63.741
LGA    Q    26_B      Q    26_B     3.832     0    0.680   1.181     9.371   37.976   24.762
LGA    N    27_B      N    27_B     2.048     0    0.164   0.167     2.299   66.786   67.798
LGA    A    28_B      A    28_B     2.606     0    0.046   0.046     3.524   66.905   62.190
LGA    E    29_B      E    29_B     1.417     0    0.054   0.849     3.503   81.548   66.614
LGA    G    30_B      G    30_B     1.713     0    0.124   0.124     1.872   77.262   77.262
LGA    R    31_B      R    31_B     1.679     0    0.040   0.982     6.444   83.810   53.593
LGA    E    32_B      E    32_B     0.940     0    0.042   0.849     5.751   83.810   61.958
LGA    R    33_B      R    33_B     2.186     0    0.055   1.171     4.113   67.024   58.961
LGA    L    34_B      L    34_B     2.751     0    0.029   1.391     6.810   60.952   51.131
LGA    M    35_B      M    35_B     1.158     0    0.068   1.022     7.389   79.286   62.976
LGA    A    36_B      A    36_B     2.814     0    0.044   0.043     4.417   52.619   52.095
LGA    V    37_B      V    37_B     4.786     0    0.045   0.098     6.173   33.095   29.592
LGA    K    38_B      K    38_B     6.154     4    0.142   0.161     9.274   11.786    6.720
LGA    P    39_B      P    39_B     9.308     0    0.096   0.137    10.053    2.500    5.306
LGA    E    40_B      E    40_B    12.788     0    0.442   1.073    20.769    0.000    0.000
LGA    W    41_B      W    41_B    11.943     0    0.696   1.370    13.912    0.000    0.000
LGA    K    42_B      K    42_B    10.832     0    0.542   1.272    15.642    2.619    1.164

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       41     164    164  100.00     336    336  100.00                41
SUMMARY(RMSD_GDC):     3.719          3.665                  4.628           66.638   59.581

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   42   41    4.0     33    1.74    72.561    76.653     1.793

LGA_LOCAL      RMSD:   1.741  Number of atoms:   33  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   4.429  Number of assigned atoms:   41 
Std_ASGN_ATOMS RMSD:   3.719  Standard rmsd on all 41 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.824002 * X  +   0.064063 * Y  +  -0.562953 * Z  +   6.307972
  Y_new =   0.315578 * X  +  -0.877093 * Y  +   0.362103 * Z  + -24.098534
  Z_new =  -0.470565 * X  +  -0.476029 * Y  +  -0.742944 * Z  +  46.488510 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.365750  0.489931 -2.571759   [DEG:   20.9559   28.0710 -147.3510 ]
ZXZ: -2.142391  2.408254 -2.361967   [DEG: -122.7500  137.9828 -135.3307 ]
 
# END of job
