
#######################################################
#                                                     #
#                        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:    27       4_B - 30_B        4.97    16.71
  LONGEST_CONTINUOUS_SEGMENT:    27       5_B - 31_B        4.78    16.08
  LCS_AVERAGE:     63.06

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    20       7_B - 26_B        1.85    17.19
  LONGEST_CONTINUOUS_SEGMENT:    20       8_B - 27_B        1.84    16.91
  LCS_AVERAGE:     41.23

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    16       9_B - 24_B        0.96    17.27
  LCS_AVERAGE:     30.46

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    6   22      0    0    4    5    7    8    9   11   11   13   13   13   13   15   15   16   19   19   20   21 
LCS_GDT     S     3_B     S     3_B      4    6   26      1    3    4    5    7    9   11   13   15   16   18   19   21   21   23   25   25   25   27   28 
LCS_GDT     Q     4_B     Q     4_B      4    7   27      0    3    4    5    7    8   11   13   15   16   18   19   21   21   23   25   25   26   27   28 
LCS_GDT     R     5_B     R     5_B      6   13   27      3    4    6    8   12   12   15   16   20   20   21   22   23   23   24   25   26   27   27   28 
LCS_GDT     L     6_B     L     6_B      6   13   27      3    5    6    8   10   11   13   15   16   19   19   21   23   23   23   25   26   27   27   28 
LCS_GDT     F     7_B     F     7_B      7   20   27      3    5    7   10   12   15   17   19   20   20   21   22   23   23   24   25   26   27   27   28 
LCS_GDT     V     8_B     V     8_B     12   20   27      3    5    9   12   16   18   19   19   20   20   21   22   23   23   24   25   26   27   27   28 
LCS_GDT     L     9_B     L     9_B     16   20   27      4   13   15   16   18   18   19   19   20   20   21   22   23   23   24   25   26   27   27   28 
LCS_GDT     D    10_B     D    10_B     16   20   27      4   14   15   16   18   18   19   19   20   20   21   22   23   23   24   25   26   27   27   28 
LCS_GDT     N    11_B     N    11_B     16   20   27     12   14   15   16   18   18   19   19   20   20   21   22   23   23   24   25   26   27   27   28 
LCS_GDT     E    12_B     E    12_B     16   20   27     12   14   15   16   18   18   19   19   20   20   21   22   23   23   24   25   26   27   27   28 
LCS_GDT     R    13_B     R    13_B     16   20   27     12   14   15   16   18   18   19   19   20   20   21   22   23   23   24   25   26   27   27   28 
LCS_GDT     Y    14_B     Y    14_B     16   20   27     12   14   15   16   18   18   19   19   20   20   21   22   23   23   24   25   26   27   27   28 
LCS_GDT     D    15_B     D    15_B     16   20   27     12   14   15   16   18   18   19   19   20   20   21   22   23   23   24   25   26   27   27   28 
LCS_GDT     S    16_B     S    16_B     16   20   27     12   14   15   16   18   18   19   19   20   20   21   22   23   23   24   25   26   27   27   28 
LCS_GDT     F    17_B     F    17_B     16   20   27     12   14   15   16   18   18   19   19   20   20   21   22   23   23   24   25   26   27   27   28 
LCS_GDT     I    18_B     I    18_B     16   20   27     12   14   15   16   18   18   19   19   20   20   21   22   23   23   24   25   26   27   27   28 
LCS_GDT     T    19_B     T    19_B     16   20   27     12   14   15   16   18   18   19   19   20   20   21   22   23   23   24   25   26   27   27   28 
LCS_GDT     Q    20_B     Q    20_B     16   20   27     12   14   15   16   18   18   19   19   20   20   21   22   23   23   24   25   26   27   27   28 
LCS_GDT     L    21_B     L    21_B     16   20   27     12   14   15   16   18   18   19   19   20   20   21   22   23   23   24   25   26   27   27   28 
LCS_GDT     E    22_B     E    22_B     16   20   27     12   14   15   16   18   18   19   19   20   20   21   22   23   23   24   25   26   27   27   28 
LCS_GDT     A    23_B     A    23_B     16   20   27     10   14   15   16   18   18   19   19   20   20   21   22   23   23   24   25   26   27   27   28 
LCS_GDT     P    24_B     P    24_B     16   20   27      3    3   13   16   18   18   19   19   20   20   21   22   23   23   24   25   26   27   27   28 
LCS_GDT     V    25_B     V    25_B     15   20   27      3    3   11   16   18   18   19   19   20   20   21   22   23   23   24   25   26   27   27   28 
LCS_GDT     Q    26_B     Q    26_B     11   20   27      2   10   15   16   18   18   19   19   20   20   21   22   23   23   24   25   26   27   27   28 
LCS_GDT     N    27_B     N    27_B     13   20   27      5   11   12   14   15   15   17   19   20   20   21   22   23   23   24   25   26   27   27   28 
LCS_GDT     A    28_B     A    28_B     13   16   27      5   11   13   14   15   15   16   17   18   20   20   21   21   23   24   24   26   27   27   28 
LCS_GDT     E    29_B     E    29_B     13   16   27      6   11   13   14   15   15   16   16   17   18   19   20   21   22   24   24   26   27   27   28 
LCS_GDT     G    30_B     G    30_B     13   16   27      6   11   13   14   15   15   16   16   17   17   18   18   19   21   23   24   26   27   27   28 
LCS_GDT     R    31_B     R    31_B     13   16   27      6   11   13   14   15   15   16   16   17   17   18   19   19   21   23   24   26   27   27   27 
LCS_GDT     E    32_B     E    32_B     13   16   26      6   11   13   14   15   15   16   16   17   17   18   18   18   19   21   22   23   24   25   27 
LCS_GDT     R    33_B     R    33_B     13   16   23      6   11   13   14   15   15   16   16   17   17   18   18   18   19   20   21   21   22   23   25 
LCS_GDT     L    34_B     L    34_B     13   16   23      6   11   13   14   15   15   16   16   17   17   18   18   18   19   20   21   21   22   23   24 
LCS_GDT     M    35_B     M    35_B     13   16   23      6   11   13   14   15   15   16   16   17   17   18   18   18   19   20   21   21   22   23   24 
LCS_GDT     A    36_B     A    36_B     13   16   23      6   11   13   14   15   15   16   16   17   17   18   18   18   19   20   21   21   22   22   23 
LCS_GDT     V    37_B     V    37_B     13   16   23      3   11   13   14   15   15   16   16   17   17   18   18   18   19   20   20   21   22   22   23 
LCS_GDT     K    38_B     K    38_B     13   16   23      3   10   13   14   15   15   16   16   17   17   18   18   18   19   20   20   21   22   22   23 
LCS_GDT     P    39_B     P    39_B     13   16   23      3    5   13   14   15   15   16   16   17   17   18   18   18   19   20   20   21   22   22   23 
LCS_GDT     E    40_B     E    40_B     13   16   23      1    5   13   14   15   15   16   16   17   17   18   18   18   19   20   20   21   22   22   23 
LCS_GDT     W    41_B     W    41_B      6   16   23      0    4    6   12   15   15   15   16   17   17   18   18   18   19   20   20   21   22   22   23 
LCS_GDT     K    42_B     K    42_B      0    4   23      0    0    3    3    4    4    4    6    6   12   16   17   17   18   19   20   21   22   22   23 
LCS_AVERAGE  LCS_A:  44.91  (  30.46   41.23   63.06 )

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     12     14     15     16     18     18     19     19     20     20     21     22     23     23     24     25     26     27     27     28 
GDT PERCENT_AT  29.27  34.15  36.59  39.02  43.90  43.90  46.34  46.34  48.78  48.78  51.22  53.66  56.10  56.10  58.54  60.98  63.41  65.85  65.85  68.29
GDT RMS_LOCAL    0.35   0.46   0.57   0.90   1.17   1.17   1.47   1.47   1.84   1.84   2.16   2.63   3.01   3.01   3.68   4.29   4.53   4.78   4.78   5.40
GDT RMS_ALL_AT  17.55  17.53  17.58  17.13  16.94  16.94  17.05  17.05  16.91  16.91  17.06  17.34  17.49  17.49  16.51  18.40  15.96  16.08  16.08  17.13

# Checking swapping
#   possible swapping detected:  F     7_B      F     7_B
#   possible swapping detected:  D    10_B      D    10_B
#   possible swapping detected:  E    12_B      E    12_B
#   possible swapping detected:  D    15_B      D    15_B
#   possible swapping detected:  F    17_B      F    17_B
#   possible swapping detected:  E    29_B      E    29_B
#   possible swapping detected:  E    32_B      E    32_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A     2_B      A     2_B    24.075     0    0.659   0.650    25.893    0.000    0.000
LGA    S     3_B      S     3_B    17.295     0    0.564   0.739    19.732    0.000    0.000
LGA    Q     4_B      Q     4_B    15.641     0    0.349   1.173    18.276    0.000    0.000
LGA    R     5_B      R     5_B     8.787     0    0.133   0.956    11.504    7.857    6.970
LGA    L     6_B      L     6_B     8.922     0    0.043   0.078    11.085    4.643    2.440
LGA    F     7_B      F     7_B     5.422     0    0.038   1.250     6.781   25.595   30.476
LGA    V     8_B      V     8_B     3.847     0    0.153   1.150     6.082   43.452   39.660
LGA    L     9_B      L     9_B     1.765     0    0.116   0.353     2.963   70.833   68.869
LGA    D    10_B      D    10_B     1.273     0    0.103   1.281     4.891   85.952   72.321
LGA    N    11_B      N    11_B     0.849     0    0.067   0.886     3.086   90.476   84.286
LGA    E    12_B      E    12_B     0.433     0    0.049   0.923     3.020  100.000   85.397
LGA    R    13_B      R    13_B     0.368     0    0.038   1.084     6.130  100.000   71.775
LGA    Y    14_B      Y    14_B     0.414     0    0.061   0.184     0.981  100.000   95.238
LGA    D    15_B      D    15_B     0.282     0    0.062   0.952     2.919  100.000   85.893
LGA    S    16_B      S    16_B     0.699     0    0.061   0.600     1.233   92.857   90.556
LGA    F    17_B      F    17_B     0.810     0    0.059   0.368     1.320   90.476   85.541
LGA    I    18_B      I    18_B     0.320     0    0.047   0.089     0.673  100.000   96.429
LGA    T    19_B      T    19_B     0.667     0    0.041   0.219     0.924   90.476   91.837
LGA    Q    20_B      Q    20_B     0.680     0    0.058   1.094     3.262   90.476   82.011
LGA    L    21_B      L    21_B     0.642     0    0.072   0.323     1.285   92.857   88.274
LGA    E    22_B      E    22_B     0.784     0    0.195   0.794     2.208   90.476   82.698
LGA    A    23_B      A    23_B     0.574     0    0.249   0.332     2.173   84.048   83.524
LGA    P    24_B      P    24_B     2.769     0    0.092   0.417     4.487   75.476   62.789
LGA    V    25_B      V    25_B     2.295     0    0.087   1.001     7.010   65.119   46.190
LGA    Q    26_B      Q    26_B     1.928     0    0.168   0.870     7.110   63.690   43.810
LGA    N    27_B      N    27_B     5.810     0    0.493   0.633     9.605   20.476   13.750
LGA    A    28_B      A    28_B     9.152     0    0.089   0.084    11.801    2.857    2.286
LGA    E    29_B      E    29_B    11.235     0    0.085   0.562    13.508    0.119    0.423
LGA    G    30_B      G    30_B    11.252     0    0.116   0.116    13.678    0.000    0.000
LGA    R    31_B      R    31_B    12.021     0    0.200   0.980    14.478    0.000    4.069
LGA    E    32_B      E    32_B    16.583     0    0.092   1.137    19.753    0.000    0.000
LGA    R    33_B      R    33_B    18.391     0    0.317   1.033    21.392    0.000    0.000
LGA    L    34_B      L    34_B    19.004     0    0.616   1.451    20.472    0.000    0.000
LGA    M    35_B      M    35_B    20.736     0    0.239   1.033    22.170    0.000    0.000
LGA    A    36_B      A    36_B    24.820     0    0.127   0.130    28.283    0.000    0.000
LGA    V    37_B      V    37_B    26.783     0    0.193   0.303    29.316    0.000    0.000
LGA    K    38_B      K    38_B    32.415     4    0.179   0.188    35.120    0.000    0.000
LGA    P    39_B      P    39_B    34.623     0    0.623   0.633    38.820    0.000    0.000
LGA    E    40_B      E    40_B    40.472     0    0.143   0.979    44.636    0.000    0.000
LGA    W    41_B      W    41_B    40.898     0    0.594   1.351    43.825    0.000    0.000
LGA    K    42_B      K    42_B    41.819     0    0.061   1.156    45.683    0.000    0.000

# 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):    12.848         12.764                 13.062           41.176   37.012

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   42   41    4.0     19    1.47    45.122    44.784     1.211

LGA_LOCAL      RMSD:   1.469  Number of atoms:   19  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  17.045  Number of assigned atoms:   41 
Std_ASGN_ATOMS RMSD:  12.848  Standard rmsd on all 41 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.135588 * X  +  -0.900697 * Y  +   0.412747 * Z  +  39.913601
  Y_new =  -0.122980 * X  +  -0.428673 * Y  +  -0.895051 * Z  + -18.132189
  Z_new =   0.983103 * X  +   0.070599 * Y  +  -0.168891 * Z  +  49.071789 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.736675 -1.386706  2.745654   [DEG:  -42.2084  -79.4524  157.3144 ]
ZXZ:  0.432083  1.740501  1.499107   [DEG:   24.7565   99.7233   85.8925 ]
 
# END of job
