
#######################################################
#                                                     #
#                        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   65 (  516),  selected   51 , name one
# Molecule2: number of CA atoms   51 (  404),  selected   51 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:C  -ch2:C  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    51       6_C - 56_C        4.82     4.82
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    40       7_C - 46_C        2.00     5.84
  LCS_AVERAGE:     66.51

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    18       7_C - 24_C        0.72     6.30
  LCS_AVERAGE:     23.84

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   51
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     P     6_C     P     6_C      3   20   51      3    3    3    4    5   33   37   38   41   45   46   47   47   47   48   49   49   49   49   50 
LCS_GDT     T     7_C     T     7_C     18   40   51     15   27   30   34   35   39   43   43   43   45   46   47   47   47   48   49   49   49   49   50 
LCS_GDT     K     8_C     K     8_C     18   40   51     20   27   30   34   35   39   43   43   43   45   46   47   47   47   48   49   49   49   49   50 
LCS_GDT     I     9_C     I     9_C     18   40   51     20   27   30   34   35   39   43   43   43   45   46   47   47   47   48   49   49   49   49   50 
LCS_GDT     L    10_C     L    10_C     18   40   51     20   27   30   34   35   39   43   43   43   45   46   47   47   47   48   49   49   49   49   50 
LCS_GDT     P    11_C     P    11_C     18   40   51     20   27   30   34   35   39   43   43   43   45   46   47   47   47   48   49   49   49   49   50 
LCS_GDT     C    12_C     C    12_C     18   40   51     20   27   30   34   35   39   43   43   43   45   46   47   47   47   48   49   49   49   49   50 
LCS_GDT     P    13_C     P    13_C     18   40   51     18   27   30   34   35   39   43   43   43   45   46   47   47   47   48   49   49   49   49   50 
LCS_GDT     R    14_C     R    14_C     18   40   51     20   27   30   34   35   39   43   43   43   45   46   47   47   47   48   49   49   49   49   50 
LCS_GDT     C    15_C     C    15_C     18   40   51     20   27   30   34   35   39   43   43   43   45   46   47   47   47   48   49   49   49   49   50 
LCS_GDT     N    16_C     N    16_C     18   40   51     20   27   30   34   35   39   43   43   43   45   46   47   47   47   48   49   49   49   49   50 
LCS_GDT     S    17_C     S    17_C     18   40   51     20   27   30   34   35   39   43   43   43   45   46   47   47   47   48   49   49   49   49   50 
LCS_GDT     M    18_C     M    18_C     18   40   51     20   27   30   34   35   39   43   43   43   45   46   47   47   47   48   49   49   49   49   50 
LCS_GDT     E    19_C     E    19_C     18   40   51     20   27   30   34   35   39   43   43   43   45   46   47   47   47   48   49   49   49   49   50 
LCS_GDT     T    20_C     T    20_C     18   40   51     20   27   30   34   35   39   43   43   43   45   46   47   47   47   48   49   49   49   49   50 
LCS_GDT     K    21_C     K    21_C     18   40   51     10   27   30   34   35   39   43   43   43   45   46   47   47   47   48   49   49   49   49   50 
LCS_GDT     F    22_C     F    22_C     18   40   51      7   27   30   34   35   39   43   43   43   45   46   47   47   47   48   49   49   49   49   50 
LCS_GDT     C    23_C     C    23_C     18   40   51      5   27   30   34   35   39   43   43   43   45   46   47   47   47   48   49   49   49   49   50 
LCS_GDT     Y    24_C     Y    24_C     18   40   51      3   14   30   34   35   39   43   43   43   45   46   47   47   47   48   49   49   49   49   50 
LCS_GDT     Y    25_C     Y    25_C      4   40   51      3    4    5   12   13   35   43   43   43   45   46   47   47   47   48   49   49   49   49   50 
LCS_GDT     N    26_C     N    26_C      4   40   51      3    6    7   17   29   39   43   43   43   45   46   47   47   47   48   49   49   49   49   50 
LCS_GDT     N    27_C     N    27_C      4   40   51      3    4    5   12   35   39   43   43   43   45   46   47   47   47   48   49   49   49   49   50 
LCS_GDT     Y    28_C     Y    28_C      4   40   51      3    4   22   31   35   39   43   43   43   45   46   47   47   47   48   49   49   49   49   50 
LCS_GDT     N    29_C     N    29_C      7   40   51      3    4   10   16   25   39   43   43   43   45   46   47   47   47   48   49   49   49   49   50 
LCS_GDT     V    30_C     V    30_C      7   40   51      4    8   12   20   32   39   43   43   43   45   46   47   47   47   48   49   49   49   49   50 
LCS_GDT     N    31_C     N    31_C      7   40   51      3    8   12   20   32   39   43   43   43   45   46   47   47   47   48   49   49   49   49   50 
LCS_GDT     Q    32_C     Q    32_C      7   40   51      5   14   27   34   35   39   43   43   43   45   46   47   47   47   48   49   49   49   49   50 
LCS_GDT     P    33_C     P    33_C     14   40   51      5   14   30   34   35   39   43   43   43   45   46   47   47   47   48   49   49   49   49   50 
LCS_GDT     R    34_C     R    34_C     14   40   51      7   25   30   34   35   39   43   43   43   45   46   47   47   47   48   49   49   49   49   50 
LCS_GDT     H    35_C     H    35_C     14   40   51     20   27   30   34   35   39   43   43   43   45   46   47   47   47   48   49   49   49   49   50 
LCS_GDT     F    36_C     F    36_C     14   40   51     20   27   30   34   35   39   43   43   43   45   46   47   47   47   48   49   49   49   49   50 
LCS_GDT     C    37_C     C    37_C     14   40   51     20   27   30   34   35   39   43   43   43   45   46   47   47   47   48   49   49   49   49   50 
LCS_GDT     K    38_C     K    38_C     14   40   51     20   27   30   34   35   39   43   43   43   45   46   47   47   47   48   49   49   49   49   50 
LCS_GDT     A    39_C     A    39_C     14   40   51      9   27   30   34   35   39   43   43   43   45   46   47   47   47   48   49   49   49   49   50 
LCS_GDT     C    40_C     C    40_C     14   40   51      9   27   30   34   35   39   43   43   43   45   46   47   47   47   48   49   49   49   49   50 
LCS_GDT     Q    41_C     Q    41_C     14   40   51     20   27   30   34   35   39   43   43   43   45   46   47   47   47   48   49   49   49   49   50 
LCS_GDT     R    42_C     R    42_C     14   40   51     20   27   30   34   35   39   43   43   43   45   46   47   47   47   48   49   49   49   49   50 
LCS_GDT     Y    43_C     Y    43_C     14   40   51     20   27   30   34   35   39   43   43   43   45   46   47   47   47   48   49   49   49   49   50 
LCS_GDT     W    44_C     W    44_C     14   40   51     20   27   30   34   35   39   43   43   43   45   46   47   47   47   48   49   49   49   49   50 
LCS_GDT     T    45_C     T    45_C     14   40   51      3   21   30   34   35   39   43   43   43   45   46   47   47   47   48   49   49   49   49   50 
LCS_GDT     S    46_C     S    46_C     14   40   51      3   25   30   34   35   39   43   43   43   45   46   47   47   47   48   49   49   49   49   50 
LCS_GDT     G    47_C     G    47_C     14   20   51      3   16   28   34   35   39   43   43   43   45   46   47   47   47   48   49   49   49   49   50 
LCS_GDT     G    48_C     G    48_C      4   20   51      3    8   12   22   31   37   43   43   43   45   46   47   47   47   48   49   49   49   49   50 
LCS_GDT     T    49_C     T    49_C      4   20   51      1    8   14   23   31   39   43   43   43   45   46   47   47   47   48   49   49   49   49   50 
LCS_GDT     M    50_C     M    50_C      3    8   51      0    3    4    7   13   17   25   33   37   44   46   47   47   47   48   49   49   49   49   50 
LCS_GDT     R    51_C     R    51_C      3    7   51      3    3    3    4   11   18   30   36   43   45   46   47   47   47   48   49   49   49   49   50 
LCS_GDT     S    52_C     S    52_C      5    7   51      3    5    5    5    8   12   22   25   35   40   45   47   47   47   48   49   49   49   49   50 
LCS_GDT     V    53_C     V    53_C      5    7   51      3    5    5    5    8   12   14   16   20   24   29   38   41   47   48   49   49   49   49   50 
LCS_GDT     P    54_C     P    54_C      5    7   51      3    5    5    5    8   12   14   16   20   24   28   36   38   44   48   49   49   49   49   50 
LCS_GDT     I    55_C     I    55_C      5    7   51      3    5    5    5    8    9   13   15   17   22   24   30   32   32   38   42   43   47   49   50 
LCS_GDT     G    56_C     G    56_C      5    7   51      3    5    5    5    8    9   11   12   12   18   19   22   23   25   33   33   35   37   44   49 
LCS_AVERAGE  LCS_A:  63.45  (  23.84   66.51  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     20     27     30     34     35     39     43     43     43     45     46     47     47     47     48     49     49     49     49     50 
GDT PERCENT_AT  39.22  52.94  58.82  66.67  68.63  76.47  84.31  84.31  84.31  88.24  90.20  92.16  92.16  92.16  94.12  96.08  96.08  96.08  96.08  98.04
GDT RMS_LOCAL    0.33   0.55   0.70   1.07   1.16   1.77   2.13   2.13   2.13   2.45   2.66   2.94   2.94   2.94   3.36   3.77   3.77   3.77   3.77   4.24
GDT RMS_ALL_AT   6.59   6.41   6.24   5.88   5.93   5.69   5.63   5.63   5.63   5.48   5.38   5.23   5.23   5.23   5.07   4.94   4.94   4.94   4.94   4.86

# Checking swapping
#   possible swapping detected:  F    22_C      F    22_C
#   possible swapping detected:  Y    43_C      Y    43_C

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    P     6_C      P     6_C     5.474     2    0.626   0.604     6.488   24.048   16.190
LGA    T     7_C      T     7_C     2.159     0    0.335   0.285     2.331   66.786   68.231
LGA    K     8_C      K     8_C     1.919     4    0.067   0.069     2.108   68.810   37.778
LGA    I     9_C      I     9_C     1.320     0    0.047   0.139     1.473   81.429   83.690
LGA    L    10_C      L    10_C     1.578     0    0.034   0.091     2.628   81.548   73.214
LGA    P    11_C      P    11_C     1.321     0    0.016   0.065     1.948   79.286   76.531
LGA    C    12_C      C    12_C     1.376     0    0.082   0.109     2.061   75.119   77.222
LGA    P    13_C      P    13_C     2.221     0    0.010   0.088     2.552   64.881   64.830
LGA    R    14_C      R    14_C     2.394     0    0.190   0.981     3.175   61.071   62.771
LGA    C    15_C      C    15_C     2.093     0    0.019   0.203     2.191   66.786   70.238
LGA    N    16_C      N    16_C     1.805     0    0.148   0.260     2.372   70.833   68.810
LGA    S    17_C      S    17_C     1.173     0    0.046   0.121     1.305   85.952   84.444
LGA    M    18_C      M    18_C     0.355     0    0.042   0.646     1.807   95.238   88.393
LGA    E    19_C      E    19_C     0.788     4    0.062   0.062     1.032   90.476   49.259
LGA    T    20_C      T    20_C     0.778     0    0.006   0.113     0.969   90.476   90.476
LGA    K    21_C      K    21_C     1.307     0    0.046   0.458     1.940   79.286   75.714
LGA    F    22_C      F    22_C     1.278     0    0.079   1.242     7.292   77.143   52.251
LGA    C    23_C      C    23_C     2.048     0    0.576   0.613     4.544   58.452   63.254
LGA    Y    24_C      Y    24_C     1.415     0    0.048   1.419    11.897   64.286   30.833
LGA    Y    25_C      Y    25_C     4.279     0    0.527   1.246     7.136   44.048   27.103
LGA    N    26_C      N    26_C     3.798     0    0.598   0.693     7.149   42.024   31.548
LGA    N    27_C      N    27_C     2.714     0    0.216   0.206     5.261   49.881   46.845
LGA    Y    28_C      Y    28_C     2.586     0    0.401   1.275    11.524   54.048   26.865
LGA    N    29_C      N    29_C     3.999     0    0.483   0.660     9.133   46.190   27.202
LGA    V    30_C      V    30_C     3.231     0    0.086   1.178     5.606   51.786   50.476
LGA    N    31_C      N    31_C     3.089     0    0.709   0.809     6.147   48.571   39.702
LGA    Q    32_C      Q    32_C     1.437     0    0.021   0.121     2.452   83.690   74.074
LGA    P    33_C      P    33_C     0.255     0    0.083   0.376     1.571   92.857   89.388
LGA    R    34_C      R    34_C     0.868     0    0.057   1.021     4.271   88.333   85.022
LGA    H    35_C      H    35_C     2.083     0    0.170   1.088     4.104   68.810   61.381
LGA    F    36_C      F    36_C     1.468     0    0.039   0.082     1.819   79.286   76.753
LGA    C    37_C      C    37_C     0.633     0    0.030   0.844     2.812   88.214   83.413
LGA    K    38_C      K    38_C     1.667     0    0.105   0.448     2.443   72.976   70.212
LGA    A    39_C      A    39_C     2.074     0    0.174   0.192     2.170   70.833   69.619
LGA    C    40_C      C    40_C     1.766     0    0.012   0.813     3.934   77.143   70.794
LGA    Q    41_C      Q    41_C     1.136     0    0.061   0.063     2.550   88.333   77.143
LGA    R    42_C      R    42_C     0.146     0    0.061   1.495     6.644  100.000   69.654
LGA    Y    43_C      Y    43_C     1.494     0    0.060   0.103     2.183   77.143   72.937
LGA    W    44_C      W    44_C     2.259     0    0.673   0.532     4.849   56.548   71.327
LGA    T    45_C      T    45_C     1.870     0    0.220   1.131     3.861   68.929   64.150
LGA    S    46_C      S    46_C     2.077     0    0.072   0.099     2.673   72.976   67.698
LGA    G    47_C      G    47_C     1.755     0    0.263   0.263     2.191   68.810   68.810
LGA    G    48_C      G    48_C     3.690     0    0.659   0.659     6.098   38.690   38.690
LGA    T    49_C      T    49_C     3.622     0    0.691   1.123     6.660   39.048   34.830
LGA    M    50_C      M    50_C     8.083     0    0.680   1.431    13.083    7.024    3.512
LGA    R    51_C      R    51_C     6.996     0    0.673   1.166    10.053   10.119    9.740
LGA    S    52_C      S    52_C    10.409     0    0.554   0.769    14.426    0.357    0.238
LGA    V    53_C      V    53_C    13.643     0    0.124   1.173    15.537    0.000    0.000
LGA    P    54_C      P    54_C    15.318     0    0.090   0.182    16.754    0.000    0.000
LGA    I    55_C      I    55_C    17.338     0    0.119   1.326    19.776    0.000    0.000
LGA    G    56_C      G    56_C    21.075     0    0.700   0.700    21.194    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       51     204    204  100.00     404    404  100.00                51
SUMMARY(RMSD_GDC):     4.821          4.932                  5.269           60.168   53.789

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   65   51    4.0     43    2.13    75.000    74.592     1.925

LGA_LOCAL      RMSD:   2.134  Number of atoms:   43  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   5.625  Number of assigned atoms:   51 
Std_ASGN_ATOMS RMSD:   4.821  Standard rmsd on all 51 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.346564 * X  +  -0.846976 * Y  +  -0.403145 * Z  + -16.231165
  Y_new =   0.611031 * X  +   0.122249 * Y  +  -0.782110 * Z  + -34.370968
  Z_new =   0.711712 * X  +  -0.517385 * Y  +   0.475162 * Z  +   2.112610 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.086733 -0.791933 -0.827913   [DEG:  119.5610  -45.3744  -47.4359 ]
ZXZ: -0.475937  1.075649  2.199387   [DEG:  -27.2692   61.6301  126.0156 ]
 
# END of job
