
#######################################################
#                                                     #
#                        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:    39       4_B - 42_B        4.90     6.00
  LCS_AVERAGE:     94.71

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    25       3_B - 27_B        1.86    10.90
  LONGEST_CONTINUOUS_SEGMENT:    25       4_B - 28_B        1.96     9.72
  LCS_AVERAGE:     52.05

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    22       6_B - 27_B        0.86     9.95
  LCS_AVERAGE:     41.52

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      4   14   34      3    4    4    8   11   13   13   16   16   18   20   21   22   26   26   27   28   28   32   32 
LCS_GDT     S     3_B     S     3_B      4   25   37      3    4    4    7   11   13   15   18   20   24   25   25   26   29   29   31   33   34   35   36 
LCS_GDT     Q     4_B     Q     4_B     14   25   39      3    9   13   16   24   24   24   24   25   26   27   29   30   33   36   38   38   38   39   39 
LCS_GDT     R     5_B     R     5_B     16   25   39      4    9   13   18   24   24   24   24   25   26   28   29   31   34   37   38   38   38   39   39 
LCS_GDT     L     6_B     L     6_B     22   25   39      4   11   21   22   24   24   24   24   25   26   29   32   35   36   37   38   38   38   39   39 
LCS_GDT     F     7_B     F     7_B     22   25   39     10   19   21   22   24   24   24   24   25   26   29   32   35   36   37   38   38   38   39   39 
LCS_GDT     V     8_B     V     8_B     22   25   39      4   19   21   22   24   24   24   24   25   26   29   32   35   36   37   38   38   38   39   39 
LCS_GDT     L     9_B     L     9_B     22   25   39     10   19   21   22   24   24   24   24   25   26   29   32   35   36   37   38   38   38   39   39 
LCS_GDT     D    10_B     D    10_B     22   25   39     10   19   21   22   24   24   24   24   25   26   29   32   35   36   37   38   38   38   39   39 
LCS_GDT     N    11_B     N    11_B     22   25   39     10   19   21   22   24   24   24   24   25   26   29   32   35   36   37   38   38   38   39   39 
LCS_GDT     E    12_B     E    12_B     22   25   39     10   19   21   22   24   24   24   24   25   26   29   32   35   36   37   38   38   38   39   39 
LCS_GDT     R    13_B     R    13_B     22   25   39     10   19   21   22   24   24   24   24   25   26   29   32   35   36   37   38   38   38   39   39 
LCS_GDT     Y    14_B     Y    14_B     22   25   39     10   19   21   22   24   24   24   24   25   26   29   32   35   36   37   38   38   38   39   39 
LCS_GDT     D    15_B     D    15_B     22   25   39     10   19   21   22   24   24   24   24   25   26   29   32   35   36   37   38   38   38   39   39 
LCS_GDT     S    16_B     S    16_B     22   25   39     10   19   21   22   24   24   24   24   25   26   29   32   35   36   37   38   38   38   39   39 
LCS_GDT     F    17_B     F    17_B     22   25   39      9   19   21   22   24   24   24   24   25   26   29   32   35   36   37   38   38   38   39   39 
LCS_GDT     I    18_B     I    18_B     22   25   39     10   19   21   22   24   24   24   24   25   26   29   32   35   36   37   38   38   38   39   39 
LCS_GDT     T    19_B     T    19_B     22   25   39     10   19   21   22   24   24   24   24   25   26   29   32   35   36   37   38   38   38   39   39 
LCS_GDT     Q    20_B     Q    20_B     22   25   39      9   19   21   22   24   24   24   24   25   26   29   32   35   36   37   38   38   38   39   39 
LCS_GDT     L    21_B     L    21_B     22   25   39     10   19   21   22   24   24   24   24   25   26   29   32   35   36   37   38   38   38   39   39 
LCS_GDT     E    22_B     E    22_B     22   25   39     10   19   21   22   24   24   24   24   25   26   29   32   35   36   37   38   38   38   39   39 
LCS_GDT     A    23_B     A    23_B     22   25   39      8   19   21   22   24   24   24   24   25   26   29   32   35   36   37   38   38   38   39   39 
LCS_GDT     P    24_B     P    24_B     22   25   39     10   19   21   22   24   24   24   24   25   26   29   32   35   36   37   38   38   38   39   39 
LCS_GDT     V    25_B     V    25_B     22   25   39      8   19   21   22   24   24   24   24   25   26   29   32   35   36   37   38   38   38   39   39 
LCS_GDT     Q    26_B     Q    26_B     22   25   39      3    6   21   22   24   24   24   24   25   26   29   32   35   36   37   38   38   38   39   39 
LCS_GDT     N    27_B     N    27_B     22   25   39     10   19   21   22   24   24   24   24   25   26   29   32   35   36   37   38   38   38   39   39 
LCS_GDT     A    28_B     A    28_B     13   25   39      9   12   15   16   17   20   21   23   25   26   29   32   35   36   37   38   38   38   39   39 
LCS_GDT     E    29_B     E    29_B     13   16   39      8   12   15   16   17   20   21   23   25   26   29   32   35   36   37   38   38   38   39   39 
LCS_GDT     G    30_B     G    30_B     13   16   39      9   12   15   16   17   20   21   23   25   26   29   32   35   36   37   38   38   38   39   39 
LCS_GDT     R    31_B     R    31_B     13   16   39      9   12   15   16   17   20   21   23   25   26   29   32   35   36   37   38   38   38   39   39 
LCS_GDT     E    32_B     E    32_B     13   16   39      9   12   15   16   17   20   21   23   25   26   29   32   35   36   37   38   38   38   39   39 
LCS_GDT     R    33_B     R    33_B     13   16   39      9   12   15   16   17   20   21   23   25   26   29   32   35   36   37   38   38   38   39   39 
LCS_GDT     L    34_B     L    34_B     13   16   39      9   12   15   16   17   20   21   23   25   26   29   32   35   36   37   38   38   38   39   39 
LCS_GDT     M    35_B     M    35_B     13   16   39      9   12   15   16   17   20   21   23   25   26   29   32   35   36   37   38   38   38   39   39 
LCS_GDT     A    36_B     A    36_B     13   16   39      9   12   15   16   17   20   21   23   25   26   29   32   35   36   37   38   38   38   39   39 
LCS_GDT     V    37_B     V    37_B     13   16   39      8   12   15   16   17   20   21   23   25   26   29   32   35   36   37   38   38   38   39   39 
LCS_GDT     K    38_B     K    38_B     13   16   39      3   11   14   16   17   19   21   22   25   26   28   30   35   36   37   38   38   38   39   39 
LCS_GDT     P    39_B     P    39_B     13   16   39      9   11   15   16   17   20   21   23   25   26   28   32   35   36   37   38   38   38   39   39 
LCS_GDT     E    40_B     E    40_B     13   16   39      3   11   15   16   17   20   21   23   25   26   28   32   35   36   37   38   38   38   39   39 
LCS_GDT     W    41_B     W    41_B      4   16   39      3    3    9   14   17   20   21   23   25   26   29   32   35   36   37   38   38   38   39   39 
LCS_GDT     K    42_B     K    42_B      3    3   39      3    3    3    3    3    4    4    4    4    6    9   10   21   23   24   26   34   38   39   39 
LCS_AVERAGE  LCS_A:  62.76  (  41.52   52.05   94.71 )

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     10     19     21     22     24     24     24     24     25     26     29     32     35     36     37     38     38     38     39     39 
GDT PERCENT_AT  24.39  46.34  51.22  53.66  58.54  58.54  58.54  58.54  60.98  63.41  70.73  78.05  85.37  87.80  90.24  92.68  92.68  92.68  95.12  95.12
GDT RMS_LOCAL    0.31   0.57   0.71   0.86   1.28   1.28   1.28   1.28   1.96   2.46   3.60   3.89   4.19   4.29   4.48   4.71   4.71   4.71   4.90   4.90
GDT RMS_ALL_AT   9.50   9.45   9.68   9.95  10.63  10.63  10.63  10.63   9.72   8.84   6.25   6.24   6.53   6.34   6.15   6.01   6.01   6.01   6.00   6.00

# 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:  F    17_B      F    17_B
#   possible swapping detected:  E    22_B      E    22_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    11.153     0    0.463   0.483    12.366    0.714    0.571
LGA    S     3_B      S     3_B     7.108     0    0.282   0.686    10.921   12.857    9.048
LGA    Q     4_B      Q     4_B     3.312     0    0.165   1.179     4.445   46.786   57.778
LGA    R     5_B      R     5_B     2.536     0    0.105   1.314     3.518   60.952   58.095
LGA    L     6_B      L     6_B     1.433     0    0.119   0.162     1.708   79.286   78.214
LGA    F     7_B      F     7_B     0.700     0    0.138   0.180     2.161   85.952   82.468
LGA    V     8_B      V     8_B     1.970     0    0.055   1.154     4.404   72.857   64.490
LGA    L     9_B      L     9_B     0.967     0    0.053   0.194     1.355   85.952   88.214
LGA    D    10_B      D    10_B     0.699     0    0.052   1.148     4.094   95.238   81.786
LGA    N    11_B      N    11_B     0.594     0    0.091   0.256     0.711   95.238   95.238
LGA    E    12_B      E    12_B     0.566     0    0.050   1.145     5.075   92.857   74.497
LGA    R    13_B      R    13_B     0.618     0    0.039   0.966     2.910   90.476   81.861
LGA    Y    14_B      Y    14_B     0.694     0    0.025   0.119     0.765   90.476   95.238
LGA    D    15_B      D    15_B     0.679     0    0.041   0.495     1.362   90.476   88.214
LGA    S    16_B      S    16_B     0.792     0    0.086   0.644     1.537   90.476   87.540
LGA    F    17_B      F    17_B     0.990     0    0.035   0.359     2.200   90.476   80.909
LGA    I    18_B      I    18_B     0.758     0    0.030   0.906     2.001   90.476   82.857
LGA    T    19_B      T    19_B     0.808     0    0.040   0.953     2.496   88.214   82.993
LGA    Q    20_B      Q    20_B     1.130     0    0.035   0.244     2.038   83.690   76.825
LGA    L    21_B      L    21_B     0.861     0    0.084   0.857     3.279   90.476   82.083
LGA    E    22_B      E    22_B     0.877     0    0.538   0.710     2.354   81.786   77.831
LGA    A    23_B      A    23_B     1.246     0    0.069   0.067     1.472   81.429   81.429
LGA    P    24_B      P    24_B     0.959     0    0.047   0.079     1.086   88.214   87.891
LGA    V    25_B      V    25_B     0.928     0    0.057   0.198     1.886   83.810   81.565
LGA    Q    26_B      Q    26_B     1.498     0    0.061   0.710     7.356   81.548   54.868
LGA    N    27_B      N    27_B     0.940     0    0.310   0.830     5.072   62.619   68.988
LGA    A    28_B      A    28_B     8.222     0    0.649   0.615    10.013    7.024    5.619
LGA    E    29_B      E    29_B    10.159     0    0.079   0.954    11.853    0.357    0.212
LGA    G    30_B      G    30_B    11.434     0    0.095   0.095    12.130    0.000    0.000
LGA    R    31_B      R    31_B    10.442     0    0.053   1.196    12.881    0.000    0.823
LGA    E    32_B      E    32_B    13.065     0    0.081   0.978    15.416    0.000    0.000
LGA    R    33_B      R    33_B    15.087     0    0.057   1.436    17.404    0.000    0.000
LGA    L    34_B      L    34_B    14.611     0    0.030   1.410    16.100    0.000    0.000
LGA    M    35_B      M    35_B    15.231     0    0.089   1.306    17.703    0.000    0.000
LGA    A    36_B      A    36_B    17.912     0    0.184   0.184    19.407    0.000    0.000
LGA    V    37_B      V    37_B    19.498     0    0.020   1.135    20.114    0.000    0.000
LGA    K    38_B      K    38_B    21.390     4    0.271   0.332    22.874    0.000    0.000
LGA    P    39_B      P    39_B    22.041     0    0.050   0.129    22.972    0.000    0.000
LGA    E    40_B      E    40_B    24.335     0    0.479   0.951    27.600    0.000    0.000
LGA    W    41_B      W    41_B    21.727     0    0.139   1.149    23.650    0.000    0.000
LGA    K    42_B      K    42_B    21.299     0    0.515   1.180    21.683    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):     5.875          5.765                  5.925           49.286   46.540

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   42   41    4.0     24    1.28    62.805    60.360     1.739

LGA_LOCAL      RMSD:   1.280  Number of atoms:   24  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  10.628  Number of assigned atoms:   41 
Std_ASGN_ATOMS RMSD:   5.875  Standard rmsd on all 41 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.912230 * X  +  -0.341251 * Y  +   0.226681 * Z  +  14.917046
  Y_new =  -0.049334 * X  +   0.640792 * Y  +   0.766128 * Z  + -37.758636
  Z_new =  -0.406698 * X  +   0.687701 * Y  +  -0.601385 * Z  +  83.414970 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -3.087564  0.418836  2.289335   [DEG: -176.9044   23.9976  131.1692 ]
ZXZ:  2.853921  2.216030 -0.534062   [DEG:  163.5176  126.9691  -30.5995 ]
 
# END of job
