
#######################################################
#                                                     #
#                        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   58 (  482),  selected   58 , name one
# Molecule2: number of CA atoms  141 ( 1112),  selected   58 , 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:    34      37_A - 70_A        4.59    15.42
  LCS_AVERAGE:     21.55

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    16      28_A - 43_A        1.90    14.43
  LCS_AVERAGE:      9.02

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14      29_A - 42_A        0.58    13.87
  LCS_AVERAGE:      6.66

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   58
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     V    13_A     V    13_A      3    4   14      3    3    4    4    5    6    8   11   13   14   14   16   21   22   22   26   28   32   34   39 
LCS_GDT     N    14_A     N    14_A      3    4   14      3    3    4    5    8   10   14   17   18   19   21   21   22   23   24   26   28   31   34   36 
LCS_GDT     D    15_A     D    15_A      3    4   14      3    3    4    5    5    6    8   17   19   19   21   21   22   25   26   27   28   30   33   36 
LCS_GDT     F    16_A     F    16_A      6    7   14      5    6    6    7    7   13   15   17   19   19   21   21   23   25   26   27   28   30   30   32 
LCS_GDT     L    17_A     L    17_A      6    7   14      5    6    6    7    7   14   15   17   19   19   20   21   23   25   26   27   28   35   40   42 
LCS_GDT     A    18_A     A    18_A      6    7   14      5    6    6    7    7    8   10   14   16   17   19   19   22   24   26   27   28   34   40   42 
LCS_GDT     E    19_A     E    19_A      6    7   14      5    6    6    7    7    8    8   14   16   16   19   20   23   25   26   29   29   35   38   42 
LCS_GDT     I    20_A     I    20_A      6    7   16      5    6    6    7    7    8    8   11   13   14   14   16   23   25   26   27   28   35   40   42 
LCS_GDT     F    21_A     F    21_A      6    7   24      4    6    6    7    7    8   10   11   16   17   19   23   26   32   37   37   40   40   42   42 
LCS_GDT     K    22_A     K    22_A      5    7   24      3    4    5    7    7    8    8   11   13   14   18   23   27   33   37   37   40   40   42   42 
LCS_GDT     K    23_A     K    23_A      4    5   24      3    4    4    5    5    6    8   11   13   20   22   24   28   33   37   37   40   40   42   42 
LCS_GDT     I    24_A     I    24_A      5    6   24      3    4    5    5    5    6    8   11   13   21   24   26   28   33   37   37   40   40   42   42 
LCS_GDT     G    25_A     G    25_A      5    6   33      4    4    5    5    5   12   19   20   21   22   24   25   25   28   31   35   40   40   42   42 
LCS_GDT     S    26_A     S    26_A      5    6   33      4    4    6   11   15   17   19   20   22   22   25   28   28   33   37   37   40   40   42   42 
LCS_GDT     K    27_A     K    27_A      5    6   33      4    4   11   14   16   17   18   20   22   24   27   28   29   33   37   37   40   40   42   42 
LCS_GDT     E    28_A     E    28_A      5   16   33      4    4    5    6    8   13   18   20   21   24   27   28   29   33   37   37   40   40   42   42 
LCS_GDT     N    29_A     N    29_A     14   16   33      7   13   14   15   15   17   19   20   21   23   27   28   29   30   37   37   40   40   42   42 
LCS_GDT     T    30_A     T    30_A     14   16   33      7   13   14   15   15   17   19   20   21   24   27   28   29   33   37   37   40   40   42   42 
LCS_GDT     K    31_A     K    31_A     14   16   33     11   13   14   15   15   17   19   20   21   22   24   25   27   28   30   32   35   40   42   42 
LCS_GDT     E    32_A     E    32_A     14   16   33      8   13   14   15   15   17   19   20   21   22   25   28   29   30   37   37   40   40   42   42 
LCS_GDT     G    33_A     G    33_A     14   16   33     11   13   14   15   16   17   19   20   22   24   27   28   29   33   37   37   40   40   42   42 
LCS_GDT     L    34_A     L    34_A     14   16   33     11   13   14   15   15   17   19   20   21   24   27   28   29   33   37   37   40   40   42   42 
LCS_GDT     A    35_A     A    35_A     14   16   33     11   13   14   15   15   17   19   20   21   23   27   28   29   33   37   37   40   40   42   42 
LCS_GDT     E    36_A     E    36_A     14   16   33     11   13   14   15   16   17   19   20   22   24   27   28   29   33   37   37   40   40   42   42 
LCS_GDT     L    37_A     L    37_A     14   16   34     11   13   14   15   15   17   19   20   22   24   27   29   30   33   37   37   40   40   42   42 
LCS_GDT     Y    38_A     Y    38_A     14   16   34     11   13   14   15   15   17   19   20   22   27   28   31   31   33   37   37   40   40   42   42 
LCS_GDT     E    39_A     E    39_A     14   16   34     11   13   14   15   16   17   19   20   22   24   27   29   30   33   37   37   40   40   42   42 
LCS_GDT     Y    40_A     Y    40_A     14   16   34     11   13   14   15   15   17   19   20   22   24   27   28   30   33   37   37   40   40   42   42 
LCS_GDT     K    41_A     K    41_A     14   16   34     11   13   14   15   15   17   19   20   21   28   29   31   31   33   37   37   40   40   42   42 
LCS_GDT     K    42_A     K    42_A     14   16   34     11   13   14   15   15   17   19   20   22   28   29   31   31   33   37   37   40   40   42   42 
LCS_GDT     K    43_A     K    43_A      4   16   34      4    7   11   14   16   17   19   20   22   28   29   31   31   33   37   37   40   40   42   42 
LCS_GDT     Y    44_A     Y    44_A      4   15   34      3   11   11   14   16   17   19   20   22   28   29   31   31   33   37   37   40   40   42   42 
LCS_GDT     S    45_A     S    45_A      4   15   34      3    3    5    5    9   16   19   20   22   28   29   31   31   33   37   37   40   40   42   42 
LCS_GDT     D    46_A     D    46_A     10   15   34      7   11   11   14   16   17   19   20   22   27   29   31   31   33   37   37   40   40   42   42 
LCS_GDT     A    47_A     A    47_A     10   15   34      7   11   11   14   16   17   19   20   22   27   29   31   31   33   37   37   40   40   42   42 
LCS_GDT     D    48_A     D    48_A     10   15   34      7   11   11   14   16   17   19   20   22   28   29   31   31   33   37   37   40   40   42   42 
LCS_GDT     I    49_A     I    49_A     10   15   34      7   11   11   14   16   17   19   20   22   28   29   31   31   33   37   37   40   40   42   42 
LCS_GDT     E    50_A     E    50_A     10   15   34      4   11   11   14   16   17   19   20   22   28   29   31   31   33   37   37   40   40   42   42 
LCS_GDT     P    51_A     P    51_A     10   15   34      6   11   11   14   16   17   19   20   22   28   29   31   31   33   37   37   40   40   42   42 
LCS_GDT     F    52_A     F    52_A     10   15   34      6   11   11   14   16   17   19   20   22   28   29   31   31   33   37   37   40   40   42   42 
LCS_GDT     L    53_A     L    53_A     10   15   34      7   11   11   14   16   17   19   20   22   28   29   31   31   33   37   37   40   40   42   42 
LCS_GDT     K    54_A     K    54_A     10   15   34      7   11   11   14   16   17   19   20   22   28   29   31   31   33   37   37   40   40   42   42 
LCS_GDT     N    55_A     N    55_A     10   15   34      7   11   11   14   16   17   19   20   22   28   29   31   31   33   37   37   40   40   42   42 
LCS_GDT     S    56_A     S    56_A      4   15   34      3    4    4    9   13   17   19   20   22   28   29   31   31   33   37   37   40   40   42   42 
LCS_GDT     S    57_A     S    57_A     12   15   34      5   11   11   13   13   16   19   20   22   28   29   31   31   33   37   37   40   40   42   42 
LCS_GDT     Q    58_A     Q    58_A     12   14   34      5   11   11   13   13   14   15   19   22   28   29   31   31   33   37   37   40   40   42   42 
LCS_GDT     F    59_A     F    59_A     12   14   34      5   11   11   13   13   14   15   17   22   28   29   31   31   33   34   36   40   40   42   42 
LCS_GDT     F    60_A     F    60_A     12   14   34      5   11   11   13   13   14   15   19   22   28   29   31   31   33   37   37   40   40   42   42 
LCS_GDT     Q    61_A     Q    61_A     12   14   34      7   11   11   13   13   14   15   19   22   28   29   31   31   33   34   36   40   40   42   42 
LCS_GDT     S    62_A     S    62_A     12   14   34      7   11   11   13   13   15   17   17   21   28   29   31   31   33   34   34   34   34   37   37 
LCS_GDT     Y    63_A     Y    63_A     12   14   34      7   11   11   15   15   16   17   19   22   28   29   31   31   33   34   34   34   34   37   37 
LCS_GDT     V    64_A     V    64_A     12   14   34      7   11   11   13   15   16   17   19   22   28   29   31   31   33   34   34   38   40   42   42 
LCS_GDT     E    65_A     E    65_A     12   14   34      7   11   11   13   13   14   15   19   21   28   29   31   31   33   34   34   34   34   35   36 
LCS_GDT     R    66_A     R    66_A     12   14   34      7   11   11   15   15   17   19   20   21   28   29   31   31   32   34   34   34   34   35   36 
LCS_GDT     G    67_A     G    67_A     12   14   34      7   11   11   13   13   17   19   20   22   28   29   31   31   33   34   34   34   34   35   36 
LCS_GDT     L    68_A     L    68_A     12   14   34      3    4   10   13   13   14   15   19   22   28   29   31   31   33   34   34   34   34   35   36 
LCS_GDT     R    69_A     R    69_A      5   14   34      3    4    5    9   13   14   15   17   20   28   29   31   31   33   34   34   34   34   35   36 
LCS_GDT     V    70_A     V    70_A      5   14   34      3    4    5    6   10   13   15   19   22   28   29   31   31   33   34   34   34   34   35   36 
LCS_AVERAGE  LCS_A:  12.41  (   6.66    9.02   21.55 )

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     11     13     14     15     16     17     19     20     22     28     29     31     31     33     37     37     40     40     42     42 
GDT PERCENT_AT   7.80   9.22   9.93  10.64  11.35  12.06  13.48  14.18  15.60  19.86  20.57  21.99  21.99  23.40  26.24  26.24  28.37  28.37  29.79  29.79
GDT RMS_LOCAL    0.31   0.44   0.58   0.79   1.50   1.73   2.01   2.21   2.57   3.91   3.96   4.11   4.11   4.50   5.36   5.36   5.85   5.85   6.15   6.15
GDT RMS_ALL_AT  13.92  13.88  13.87  13.63  11.50  15.64  15.73  15.82  11.22  15.92  15.91  15.83  15.83  15.18  10.84  10.84  10.77  10.77  10.77  10.77

# Checking swapping
#   possible swapping detected:  D    15_A      D    15_A
#   possible swapping detected:  F    16_A      F    16_A
#   possible swapping detected:  F    21_A      F    21_A
#   possible swapping detected:  E    32_A      E    32_A
#   possible swapping detected:  E    39_A      E    39_A
#   possible swapping detected:  Y    40_A      Y    40_A
#   possible swapping detected:  D    46_A      D    46_A
#   possible swapping detected:  D    48_A      D    48_A
#   possible swapping detected:  E    50_A      E    50_A
#   possible swapping detected:  F    59_A      F    59_A
#   possible swapping detected:  Y    63_A      Y    63_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    V    13_A      V    13_A    26.551     0    0.094   1.226    29.113    0.000    0.000
LGA    N    14_A      N    14_A    25.553     0    0.195   1.118    29.821    0.000    0.000
LGA    D    15_A      D    15_A    24.224     0    0.599   1.404    27.984    0.000    0.000
LGA    F    16_A      F    16_A    19.782     0    0.579   1.558    21.755    0.000    0.000
LGA    L    17_A      L    17_A    16.325     0    0.037   0.112    17.586    0.000    0.000
LGA    A    18_A      A    18_A    15.799     0    0.124   0.125    16.347    0.000    0.000
LGA    E    19_A      E    19_A    18.023     0    0.034   0.118    21.545    0.000    0.000
LGA    I    20_A      I    20_A    17.406     0    0.118   1.267    18.381    0.000    0.000
LGA    F    21_A      F    21_A    13.522     0    0.591   0.702    15.508    0.000    0.000
LGA    K    22_A      K    22_A    13.544     0    0.201   0.770    21.872    0.000    0.000
LGA    K    23_A      K    23_A    12.542     0    0.235   1.103    23.177    0.238    0.106
LGA    I    24_A      I    24_A     6.268     0    0.616   0.591     8.563   18.095   19.702
LGA    G    25_A      G    25_A     3.374     0    0.195   0.195     4.188   46.905   46.905
LGA    S    26_A      S    26_A     2.285     0    0.033   0.635     3.717   62.976   57.540
LGA    K    27_A      K    27_A     5.221     0    0.231   0.966     8.966   29.048   16.455
LGA    E    28_A      E    28_A     4.253     0    0.591   1.134    11.715   51.071   25.608
LGA    N    29_A      N    29_A     2.434     0    0.584   0.865     5.548   66.786   46.548
LGA    T    30_A      T    30_A     2.704     0    0.039   0.787     4.070   60.952   56.531
LGA    K    31_A      K    31_A     1.749     0    0.037   0.992     4.708   77.381   62.116
LGA    E    32_A      E    32_A     0.290     0    0.059   1.006     3.732   90.595   81.534
LGA    G    33_A      G    33_A     1.813     0    0.045   0.045     2.036   72.976   72.976
LGA    L    34_A      L    34_A     1.755     0    0.025   0.054     3.523   77.143   64.583
LGA    A    35_A      A    35_A     0.776     0    0.073   0.082     1.339   90.476   88.667
LGA    E    36_A      E    36_A     1.815     0    0.027   0.256     4.428   75.238   58.413
LGA    L    37_A      L    37_A     1.861     0    0.032   0.104     4.391   77.143   62.024
LGA    Y    38_A      Y    38_A     0.862     0    0.048   1.457     5.266   88.214   70.992
LGA    E    39_A      E    39_A     2.004     0    0.049   0.094     4.019   70.952   57.196
LGA    Y    40_A      Y    40_A     2.121     0    0.037   0.180     4.200   70.833   57.183
LGA    K    41_A      K    41_A     0.520     0    0.042   0.564     6.239   95.238   70.159
LGA    K    42_A      K    42_A     1.384     0    0.576   0.813     4.146   70.476   68.360
LGA    K    43_A      K    43_A     3.331     0    0.600   0.853     6.738   38.333   33.016
LGA    Y    44_A      Y    44_A    10.762     0    0.207   1.235    13.295    1.190    0.397
LGA    S    45_A      S    45_A    11.553     0    0.410   0.554    14.789    0.000    0.000
LGA    D    46_A      D    46_A    16.813     0    0.365   1.245    20.785    0.000    0.000
LGA    A    47_A      A    47_A    20.396     0    0.094   0.101    22.457    0.000    0.000
LGA    D    48_A      D    48_A    19.182     0    0.031   1.270    20.781    0.000    0.000
LGA    I    49_A      I    49_A    19.156     0    0.073   0.080    22.801    0.000    0.000
LGA    E    50_A      E    50_A    25.198     0    0.034   1.341    30.390    0.000    0.000
LGA    P    51_A      P    51_A    28.714     0    0.113   0.155    29.289    0.000    0.000
LGA    F    52_A      F    52_A    25.149     0    0.059   1.507    26.448    0.000    0.000
LGA    L    53_A      L    53_A    26.705     0    0.181   0.203    29.984    0.000    0.000
LGA    K    54_A      K    54_A    32.275     0    0.175   0.630    36.102    0.000    0.000
LGA    N    55_A      N    55_A    31.448     0    0.598   0.579    32.145    0.000    0.000
LGA    S    56_A      S    56_A    29.827     0    0.070   0.647    30.334    0.000    0.000
LGA    S    57_A      S    57_A    26.546     0    0.629   0.616    27.913    0.000    0.000
LGA    Q    58_A      Q    58_A    24.088     0    0.041   0.965    30.087    0.000    0.000
LGA    F    59_A      F    59_A    20.822     0    0.018   1.198    22.918    0.000    0.000
LGA    F    60_A      F    60_A    17.193     0    0.120   1.213    19.184    0.000    0.000
LGA    Q    61_A      Q    61_A    15.349     0    0.122   1.061    20.973    0.000    0.000
LGA    S    62_A      S    62_A    11.763     0    0.013   0.083    14.501    1.905    1.270
LGA    Y    63_A      Y    63_A     8.558     0    0.025   1.372    12.640   11.905    3.968
LGA    V    64_A      V    64_A     6.195     0    0.046   1.011     8.930   22.619   14.422
LGA    E    65_A      E    65_A     7.170     0    0.092   1.070    14.654   17.738    8.042
LGA    R    66_A      R    66_A     1.057     0    0.038   1.135     8.787   61.905   43.636
LGA    G    67_A      G    67_A     3.021     0    0.090   0.090     5.835   49.048   49.048
LGA    L    68_A      L    68_A     6.091     0    0.094   0.238    10.762   15.833   19.524
LGA    R    69_A      R    69_A    11.582     0    0.585   1.059    17.385    0.357    0.130
LGA    V    70_A      V    70_A    14.747     0    0.690   0.914    18.046    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       58     232    232  100.00     482    482  100.00               141
SUMMARY(RMSD_GDC):    10.484         10.334                 11.678           10.735    8.915

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   58  141    4.0     20    2.21    15.071    13.759     0.866

LGA_LOCAL      RMSD:   2.209  Number of atoms:   20  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  15.820  Number of assigned atoms:   58 
Std_ASGN_ATOMS RMSD:  10.484  Standard rmsd on all 58 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.032979 * X  +   0.294076 * Y  +  -0.955213 * Z  + -17.491093
  Y_new =   0.790195 * X  +   0.577524 * Y  +   0.205080 * Z  +   3.243279
  Z_new =   0.611968 * X  +  -0.761568 * Y  +  -0.213331 * Z  +  -9.789859 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.529086 -0.658546 -1.843917   [DEG:   87.6101  -37.7319 -105.6487 ]
ZXZ: -1.782282  1.785780  2.464683   [DEG: -102.1172  102.3176  141.2159 ]
 
# END of job
