
#######################################################
#                                                     #
#                        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   57 (  477),  selected   57 , name one
# Molecule2: number of CA atoms   58 (  481),  selected   57 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:A  -ch2:A  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    28      30_A - 57_A        4.55    15.03
  LCS_AVERAGE:     42.86

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    24      34_A - 57_A        1.45    15.26
  LCS_AVERAGE:     31.91

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    23      35_A - 57_A        0.38    15.26
  LCS_AVERAGE:     28.58

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   57
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     1_A     A     1_A      3   14   17      3    3    3    4    7   18   27   34   38   39   40   41   41   41   43   43   43   44   45   45 
LCS_GDT     E     2_A     E     2_A     13   14   17     29   33   35   36   36   36   36   36   38   39   40   41   41   41   43   43   43   44   45   45 
LCS_GDT     Y     3_A     Y     3_A     13   14   17     29   33   35   36   36   36   36   36   38   39   40   41   41   41   43   43   43   44   45   45 
LCS_GDT     V     4_A     V     4_A     13   14   17     29   33   35   36   36   36   36   36   38   39   40   41   41   41   43   43   43   44   45   45 
LCS_GDT     R     5_A     R     5_A     13   14   17     29   33   35   36   36   36   36   36   38   39   40   41   41   41   43   43   43   44   45   45 
LCS_GDT     A     6_A     A     6_A     13   14   17     29   33   35   36   36   36   36   36   38   39   40   41   41   41   43   43   43   44   45   45 
LCS_GDT     L     7_A     L     7_A     13   14   17     29   33   35   36   36   36   36   36   38   39   40   41   41   41   43   43   43   44   45   45 
LCS_GDT     F     8_A     F     8_A     13   14   17     29   33   35   36   36   36   36   36   38   39   40   41   41   41   43   43   43   44   45   45 
LCS_GDT     D     9_A     D     9_A     13   14   17     20   33   35   36   36   36   36   36   38   39   40   41   41   41   43   43   43   44   45   45 
LCS_GDT     H    10_A     H    10_A     13   14   17     20   33   35   36   36   36   36   36   38   39   40   41   41   41   43   43   43   44   45   45 
LCS_GDT     T    11_A     T    11_A     13   14   17     29   33   35   36   36   36   36   36   38   39   40   41   41   41   43   43   43   44   45   45 
LCS_GDT     G    12_A     G    12_A     13   14   21      3   24   35   36   36   36   36   36   38   39   40   41   41   41   43   43   43   44   45   45 
LCS_GDT     H    13_A     H    13_A     13   14   25      3    3   28   36   36   36   36   36   38   39   40   41   41   41   43   43   43   44   45   45 
LCS_GDT     D    14_A     D    14_A     13   14   25     28   33   35   36   36   36   36   36   38   39   40   41   41   41   43   43   43   44   45   45 
LCS_GDT     E    15_A     E    15_A      3   16   25      3    3    3    5   22   28   31   34   38   39   40   41   41   41   43   43   43   44   45   45 
LCS_GDT     Q    16_A     Q    16_A     15   16   25     13   14   14   14   15   15   23   24   28   33   40   41   41   41   43   43   43   44   45   45 
LCS_GDT     E    17_A     E    17_A     15   16   25     10   14   14   14   15   15   16   18   20   22   22   22   26   31   37   40   42   44   45   45 
LCS_GDT     L    18_A     L    18_A     15   16   25     13   14   14   14   15   15   16   18   20   22   22   22   22   23   23   24   27   31   35   37 
LCS_GDT     P    19_A     P    19_A     15   16   25     13   14   14   14   15   15   16   18   20   22   22   22   22   23   23   24   25   28   28   29 
LCS_GDT     F    20_A     F    20_A     15   16   25     13   14   14   14   15   15   16   18   20   22   22   22   22   23   23   24   25   28   28   29 
LCS_GDT     K    21_A     K    21_A     15   16   25     13   14   14   14   15   15   16   18   20   22   22   22   22   23   23   24   25   28   28   29 
LCS_GDT     K    22_A     K    22_A     15   16   25     13   14   14   14   15   15   16   18   20   22   22   22   22   23   23   24   25   28   28   29 
LCS_GDT     G    23_A     G    23_A     15   16   25     13   14   14   14   15   15   16   18   20   22   22   22   22   23   23   24   25   28   28   29 
LCS_GDT     E    24_A     E    24_A     15   16   25     13   14   14   14   15   15   16   18   20   22   22   22   22   23   23   24   25   28   28   29 
LCS_GDT     I    25_A     I    25_A     15   16   25     13   14   14   14   15   15   16   18   20   22   22   22   22   23   23   24   25   28   28   29 
LCS_GDT     L    26_A     L    26_A     15   16   25     13   14   14   14   15   15   16   18   20   22   22   22   22   23   23   24   25   28   28   29 
LCS_GDT     R    27_A     R    27_A     15   16   25     13   14   14   14   15   15   16   18   20   22   22   22   22   23   23   24   25   28   28   29 
LCS_GDT     I    28_A     I    28_A     15   16   25     13   14   14   14   15   15   16   18   20   22   22   22   22   23   23   25   28   30   34   35 
LCS_GDT     R    29_A     R    29_A     15   16   25     13   14   14   14   15   15   16   18   20   22   22   22   22   23   28   31   32   33   35   41 
LCS_GDT     D    30_A     D    30_A     15   16   28      3    3    7   14   15   15   16   18   20   22   22   24   27   30   40   40   42   44   45   45 
LCS_GDT     K    31_A     K    31_A      4   16   28      3    3    4    5    6   11   15   18   20   22   23   26   27   37   43   43   43   44   45   45 
LCS_GDT     P    32_A     P    32_A      4    6   28      3    3    4    5    7   11   16   18   20   22   30   35   38   41   43   43   43   44   45   45 
LCS_GDT     E    33_A     E    33_A      4    5   28      3    3    4    5    6    9   15   27   35   37   38   41   41   41   43   43   43   44   45   45 
LCS_GDT     E    34_A     E    34_A      4   24   28      3    4    5    5    5    9   23   28   37   39   40   41   41   41   43   43   43   44   45   45 
LCS_GDT     Q    35_A     Q    35_A     23   24   28      5   14   35   36   36   36   36   36   38   39   40   41   41   41   43   43   43   44   45   45 
LCS_GDT     L    36_A     L    36_A     23   24   28     29   33   35   36   36   36   36   36   38   39   40   41   41   41   43   43   43   44   45   45 
LCS_GDT     W    37_A     W    37_A     23   24   28     29   33   35   36   36   36   36   36   38   39   40   41   41   41   43   43   43   44   45   45 
LCS_GDT     N    38_A     N    38_A     23   24   28     29   33   35   36   36   36   36   36   38   39   40   41   41   41   43   43   43   44   45   45 
LCS_GDT     A    39_A     A    39_A     23   24   28     29   33   35   36   36   36   36   36   38   39   40   41   41   41   43   43   43   44   45   45 
LCS_GDT     E    40_A     E    40_A     23   24   28     29   33   35   36   36   36   36   36   38   39   40   41   41   41   43   43   43   44   45   45 
LCS_GDT     N    41_A     N    41_A     23   24   28     29   33   35   36   36   36   36   36   38   39   40   41   41   41   43   43   43   44   45   45 
LCS_GDT     V    42_A     V    42_A     23   24   28     29   33   35   36   36   36   36   36   38   39   40   41   41   41   43   43   43   44   45   45 
LCS_GDT     E    43_A     E    43_A     23   24   28     29   33   35   36   36   36   36   36   38   39   40   41   41   41   43   43   43   44   45   45 
LCS_GDT     G    44_A     G    44_A     23   24   28     29   33   35   36   36   36   36   36   38   39   40   41   41   41   43   43   43   44   45   45 
LCS_GDT     K    45_A     K    45_A     23   24   28     29   33   35   36   36   36   36   36   38   39   40   41   41   41   43   43   43   44   45   45 
LCS_GDT     R    46_A     R    46_A     23   24   28     29   33   35   36   36   36   36   36   38   39   40   41   41   41   43   43   43   44   45   45 
LCS_GDT     G    47_A     G    47_A     23   24   28     29   33   35   36   36   36   36   36   38   39   40   41   41   41   43   43   43   44   45   45 
LCS_GDT     L    48_A     L    48_A     23   24   28     29   33   35   36   36   36   36   36   38   39   40   41   41   41   43   43   43   44   45   45 
LCS_GDT     I    49_A     I    49_A     23   24   28     29   33   35   36   36   36   36   36   38   39   40   41   41   41   43   43   43   44   45   45 
LCS_GDT     H    50_A     H    50_A     23   24   28     29   33   35   36   36   36   36   36   38   39   40   41   41   41   43   43   43   44   45   45 
LCS_GDT     V    51_A     V    51_A     23   24   28     29   33   35   36   36   36   36   36   38   39   40   41   41   41   43   43   43   44   45   45 
LCS_GDT     V    52_A     V    52_A     23   24   28     29   33   35   36   36   36   36   36   38   39   40   41   41   41   43   43   43   44   45   45 
LCS_GDT     L    53_A     L    53_A     23   24   28     29   33   35   36   36   36   36   36   38   39   40   41   41   41   43   43   43   44   45   45 
LCS_GDT     V    54_A     V    54_A     23   24   28     29   33   35   36   36   36   36   36   38   39   40   41   41   41   43   43   43   44   45   45 
LCS_GDT     E    55_A     E    55_A     23   24   28     29   33   35   36   36   36   36   36   38   39   40   41   41   41   43   43   43   44   45   45 
LCS_GDT     K    56_A     K    56_A     23   24   28     29   33   35   36   36   36   36   36   38   39   40   41   41   41   43   43   43   44   45   45 
LCS_GDT     Y    57_A     Y    57_A     23   24   28     29   33   35   36   36   36   36   36   38   39   40   41   41   41   43   43   43   44   45   45 
LCS_AVERAGE  LCS_A:  34.45  (  28.58   31.91   42.86 )

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     33     35     36     36     36     36     36     38     39     40     41     41     41     43     43     43     44     45     45 
GDT PERCENT_AT  50.00  56.90  60.34  62.07  62.07  62.07  62.07  62.07  65.52  67.24  68.97  70.69  70.69  70.69  74.14  74.14  74.14  75.86  77.59  77.59
GDT RMS_LOCAL    0.24   0.34   0.53   0.68   0.68   0.68   0.68   0.68   1.73   2.00   2.35   2.72   2.72   2.72   3.62   3.62   3.62   3.97   4.38   4.38
GDT RMS_ALL_AT  15.28  15.28  15.29  15.30  15.30  15.30  15.30  15.30  15.14  15.11  15.00  14.98  14.98  14.98  14.85  14.85  14.85  14.72  14.62  14.62

# Checking swapping
#   possible swapping detected:  Y     3_A      Y     3_A
#   possible swapping detected:  F     8_A      F     8_A
#   possible swapping detected:  D    14_A      D    14_A
#   possible swapping detected:  F    20_A      F    20_A
#   possible swapping detected:  D    30_A      D    30_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A     1_A      A     1_A     7.497     0    0.483   0.543     9.016   16.071   13.429
LGA    E     2_A      E     2_A     0.418     0    0.666   1.142     6.496   87.500   57.407
LGA    Y     3_A      Y     3_A     0.304     0    0.052   0.171     1.660  100.000   89.246
LGA    V     4_A      V     4_A     0.092     0    0.032   0.040     0.141  100.000  100.000
LGA    R     5_A      R     5_A     0.031     0    0.018   1.150     2.789  100.000   87.143
LGA    A     6_A      A     6_A     0.272     0    0.064   0.064     0.378  100.000  100.000
LGA    L     7_A      L     7_A     0.231     0    0.035   0.084     0.590  100.000   98.810
LGA    F     8_A      F     8_A     0.417     0    0.019   0.153     0.505  100.000   98.268
LGA    D     9_A      D     9_A     0.537     0    0.091   0.293     1.096   90.476   89.345
LGA    H    10_A      H    10_A     0.664     0    0.046   1.085     2.587   90.476   82.714
LGA    T    11_A      T    11_A     0.465     0    0.655   0.955     2.785   86.905   81.156
LGA    G    12_A      G    12_A     1.704     0    0.145   0.145     1.704   75.000   75.000
LGA    H    13_A      H    13_A     2.510     0    0.591   1.238     4.277   57.500   53.190
LGA    D    14_A      D    14_A     0.717     0    0.060   1.260     4.759   63.333   58.571
LGA    E    15_A      E    15_A     6.995     0    0.669   0.785    13.774   16.905    8.201
LGA    Q    16_A      Q    16_A     8.728     0    0.662   1.398    13.856    2.619    1.376
LGA    E    17_A      E    17_A    12.082     0    0.049   1.023    15.808    0.000    0.000
LGA    L    18_A      L    18_A    19.213     0    0.066   1.347    23.609    0.000    0.000
LGA    P    19_A      P    19_A    24.557     0    0.014   0.068    27.415    0.000    0.000
LGA    F    20_A      F    20_A    30.514     0    0.027   1.445    32.607    0.000    0.000
LGA    K    21_A      K    21_A    37.245     0    0.027   0.182    39.690    0.000    0.000
LGA    K    22_A      K    22_A    40.389     0    0.094   0.444    49.623    0.000    0.000
LGA    G    23_A      G    23_A    42.366     0    0.033   0.033    42.366    0.000    0.000
LGA    E    24_A      E    24_A    38.564     0    0.060   1.036    39.479    0.000    0.000
LGA    I    25_A      I    25_A    36.447     0    0.070   0.620    41.185    0.000    0.000
LGA    L    26_A      L    26_A    30.068     0    0.016   0.058    32.108    0.000    0.000
LGA    R    27_A      R    27_A    28.390     0    0.039   0.163    32.729    0.000    0.000
LGA    I    28_A      I    28_A    21.350     0    0.011   0.065    24.078    0.000    0.000
LGA    R    29_A      R    29_A    21.074     0    0.631   1.230    27.956    0.000    0.000
LGA    D    30_A      D    30_A    16.990     0    0.663   1.149    20.696    0.000    0.000
LGA    K    31_A      K    31_A    14.950     0    0.329   0.303    22.606    0.000    0.000
LGA    P    32_A      P    32_A    13.497     0    0.136   0.412    15.841    0.000    0.000
LGA    E    33_A      E    33_A    10.599     0    0.702   1.309    13.354    0.476    0.212
LGA    E    34_A      E    34_A     7.083     0    0.236   0.889     7.737   15.119   11.958
LGA    Q    35_A      Q    35_A     1.273     0    0.640   0.588     5.885   79.881   61.217
LGA    L    36_A      L    36_A     0.382     0    0.166   1.188     2.974   92.976   82.143
LGA    W    37_A      W    37_A     0.347     0    0.015   0.213     1.147  100.000   91.939
LGA    N    38_A      N    38_A     0.394     0    0.037   0.894     2.909   97.619   85.536
LGA    A    39_A      A    39_A     0.036     0    0.045   0.068     0.194  100.000  100.000
LGA    E    40_A      E    40_A     0.081     0    0.014   0.413     1.369  100.000   93.757
LGA    N    41_A      N    41_A     0.249     0    0.014   0.107     0.610   97.619   98.810
LGA    V    42_A      V    42_A     0.541     0    0.064   1.068     2.865   90.476   80.952
LGA    E    43_A      E    43_A     0.694     0    0.021   0.419     1.779   90.476   90.635
LGA    G    44_A      G    44_A     0.576     0    0.021   0.021     0.576   90.476   90.476
LGA    K    45_A      K    45_A     0.497     0    0.025   0.842     5.665  100.000   72.169
LGA    R    46_A      R    46_A     0.352     0    0.046   0.167     0.482  100.000  100.000
LGA    G    47_A      G    47_A     0.462     0    0.054   0.054     0.462  100.000  100.000
LGA    L    48_A      L    48_A     0.448     0    0.032   0.081     0.838  100.000   96.429
LGA    I    49_A      I    49_A     0.421     0    0.071   0.116     0.515  100.000   98.810
LGA    H    50_A      H    50_A     0.606     0    0.035   0.248     1.707   90.476   84.238
LGA    V    51_A      V    51_A     0.553     0    0.024   0.096     0.723   95.238   93.197
LGA    V    52_A      V    52_A     0.371     0    0.012   0.053     0.618  100.000   97.279
LGA    L    53_A      L    53_A     0.348     0    0.018   0.118     0.580  100.000   97.619
LGA    V    54_A      V    54_A     0.234     0    0.053   0.067     0.304  100.000  100.000
LGA    E    55_A      E    55_A     0.255     0    0.021   0.052     0.562  100.000   98.942
LGA    K    56_A      K    56_A     0.455     0    0.011   0.553     1.829  100.000   90.847
LGA    Y    57_A      Y    57_A     0.419     0    0.564   0.469     2.507   88.810   77.738

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       57     228    228  100.00     477    477  100.00                58
SUMMARY(RMSD_GDC):    13.117         13.047                 13.385           58.904   54.979

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   57   58    4.0     36    0.68    63.793    56.276     4.590

LGA_LOCAL      RMSD:   0.684  Number of atoms:   36  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  15.300  Number of assigned atoms:   57 
Std_ASGN_ATOMS RMSD:  13.117  Standard rmsd on all 57 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.910060 * X  +   0.313209 * Y  +  -0.271461 * Z  + -25.164133
  Y_new =   0.387518 * X  +   0.410626 * Y  +  -0.825358 * Z  +   8.254241
  Z_new =  -0.147041 * X  +  -0.856321 * Y  +  -0.495068 * Z  +   1.488698 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.739031  0.147576 -2.094983   [DEG:  156.9349    8.4555 -120.0337 ]
ZXZ: -0.317756  2.088710 -2.971539   [DEG:  -18.2061  119.6743 -170.2566 ]
 
# END of job
