
#######################################################
#                                                     #
#                        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:    32       7_C - 38_C        4.99     6.97
  LONGEST_CONTINUOUS_SEGMENT:    32       8_C - 39_C        4.97     7.15
  LCS_AVERAGE:     55.25

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13       7_C - 19_C        2.00    11.26
  LONGEST_CONTINUOUS_SEGMENT:    13       8_C - 20_C        1.58    10.62
  LONGEST_CONTINUOUS_SEGMENT:    13       9_C - 21_C        1.92     9.82
  LONGEST_CONTINUOUS_SEGMENT:    13      10_C - 22_C        1.69     9.66
  LCS_AVERAGE:     17.49

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11       8_C - 18_C        0.97    11.02
  LONGEST_CONTINUOUS_SEGMENT:    11       9_C - 19_C        0.87    10.35
  LCS_AVERAGE:     12.57

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    9   24      0    3    3    7   11   14   15   18   20   22   24   28   30   34   38   42   44   46   47   48 
LCS_GDT     T     7_C     T     7_C      3   13   32      3    3    3    4    7   10   11   16   19   21   24   28   30   35   40   42   44   46   47   48 
LCS_GDT     K     8_C     K     8_C     11   13   32      3    6   11   14   15   17   19   20   21   24   28   32   36   38   41   42   44   46   47   48 
LCS_GDT     I     9_C     I     9_C     11   13   32      3    7   11   14   15   17   19   20   25   27   29   33   36   38   41   42   44   46   47   48 
LCS_GDT     L    10_C     L    10_C     11   13   32      7    9   11   14   15   17   19   20   25   27   29   33   36   38   41   42   44   46   47   48 
LCS_GDT     P    11_C     P    11_C     11   13   32      7    9   11   14   15   17   19   20   25   27   29   33   36   38   41   42   44   46   47   48 
LCS_GDT     C    12_C     C    12_C     11   13   32      7    9   11   14   15   17   19   20   25   27   29   33   36   38   41   42   44   46   47   48 
LCS_GDT     P    13_C     P    13_C     11   13   32      7    9   11   14   15   17   19   20   21   27   29   33   36   38   41   42   44   46   47   48 
LCS_GDT     R    14_C     R    14_C     11   13   32      7    9   11   14   15   17   19   20   21   24   29   33   36   38   41   42   44   46   47   48 
LCS_GDT     C    15_C     C    15_C     11   13   32      7    9   11   14   15   17   19   20   21   25   29   33   36   38   41   42   44   46   47   48 
LCS_GDT     N    16_C     N    16_C     11   13   32      7    9   11   14   15   17   19   20   25   27   29   33   36   38   41   42   44   46   47   48 
LCS_GDT     S    17_C     S    17_C     11   13   32      4    9   11   14   15   17   19   20   25   27   29   33   36   38   41   42   44   46   47   48 
LCS_GDT     M    18_C     M    18_C     11   13   32      4    9   11   14   15   17   19   20   25   27   29   33   36   38   41   42   44   46   47   48 
LCS_GDT     E    19_C     E    19_C     11   13   32      4    9   11   13   15   17   19   20   25   27   29   33   36   38   41   42   44   46   47   48 
LCS_GDT     T    20_C     T    20_C      8   13   32      3    5    8   11   12   13   14   20   21   26   29   33   36   38   41   42   44   46   47   48 
LCS_GDT     K    21_C     K    21_C      8   13   32      3    5    8   11   12   12   14   15   19   22   26   33   36   38   41   42   44   46   47   48 
LCS_GDT     F    22_C     F    22_C      7   13   32      3    4    8   11   12   12   14   15   19   22   26   33   36   38   41   42   44   46   47   48 
LCS_GDT     C    23_C     C    23_C      5    8   32      3    5    5    5    7    8   13   15   25   27   29   33   36   38   41   42   44   46   47   48 
LCS_GDT     Y    24_C     Y    24_C      5    8   32      3    5    5    5    7    8   13   15   25   27   29   33   36   38   41   42   44   46   47   48 
LCS_GDT     Y    25_C     Y    25_C      5    8   32      3    5    5    5    7    8   13   15   25   27   29   33   36   38   41   42   44   46   47   48 
LCS_GDT     N    26_C     N    26_C      5    8   32      3    7    7   10   10   11   13   17   25   27   29   33   36   38   41   42   44   46   47   48 
LCS_GDT     N    27_C     N    27_C      5    8   32      3    4    5   10   10   11   12   16   20   25   29   33   36   38   41   42   44   46   47   48 
LCS_GDT     Y    28_C     Y    28_C      3    6   32      3    3    6    9    9   10   14   17   25   27   29   33   36   38   41   42   44   46   47   48 
LCS_GDT     N    29_C     N    29_C      3    5   32      3    6    7    9    9   10   14   17   25   27   29   33   36   38   41   42   44   46   47   48 
LCS_GDT     V    30_C     V    30_C      3    5   32      0    3    3    4    6    8   11   13   17   24   27   32   36   38   41   42   44   46   47   48 
LCS_GDT     N    31_C     N    31_C      4    5   32      3    3    4    5    6    8   13   17   25   27   29   33   36   38   41   42   44   46   47   48 
LCS_GDT     Q    32_C     Q    32_C      4    5   32      3    7    7   10   10   11   14   17   25   27   29   33   36   38   41   42   44   46   47   48 
LCS_GDT     P    33_C     P    33_C      4    6   32      3    3    4    6    7   10   13   17   25   27   29   33   36   38   41   42   44   46   47   48 
LCS_GDT     R    34_C     R    34_C      5    8   32      3    5    5    8    9   11   14   18   21   24   28   32   36   38   41   42   44   46   47   48 
LCS_GDT     H    35_C     H    35_C      5    8   32      3    5    5    8    9   17   19   20   25   27   29   33   36   38   41   42   44   46   47   48 
LCS_GDT     F    36_C     F    36_C      5    8   32      3    5    5    8    9   11   19   20   22   27   29   33   36   38   41   42   44   46   47   48 
LCS_GDT     C    37_C     C    37_C      5    8   32      4    9   11   14   15   17   19   20   25   27   29   33   36   38   41   42   44   46   47   48 
LCS_GDT     K    38_C     K    38_C      5    8   32      4    7   10   14   15   17   19   20   21   24   29   33   36   38   41   42   44   46   47   48 
LCS_GDT     A    39_C     A    39_C      5    8   32      4    5    6    8    9   15   19   20   21   22   24   28   29   35   40   42   43   46   47   48 
LCS_GDT     C    40_C     C    40_C      5    8   21      4    5    8   14   15   17   19   20   21   22   24   28   29   33   35   42   43   46   47   48 
LCS_GDT     Q    41_C     Q    41_C      5    8   21      3    5    6   14   15   17   19   20   21   22   24   25   29   33   35   40   43   46   47   48 
LCS_GDT     R    42_C     R    42_C      3    4   21      3    3    3    3    6    8   14   18   21   24   29   32   35   38   41   42   44   46   47   48 
LCS_GDT     Y    43_C     Y    43_C      3    4   21      1    3    4    5    9   10   13   17   19   26   29   33   36   38   41   42   44   46   47   48 
LCS_GDT     W    44_C     W    44_C      3    3   21      3    3    4    7    9   11   13   17   19   26   29   33   36   38   41   42   44   46   47   48 
LCS_GDT     T    45_C     T    45_C      3    5   21      3    3    4    5    8   11   13   17   19   22   26   32   36   38   40   42   44   46   47   48 
LCS_GDT     S    46_C     S    46_C      4    7   21      3    3    4    6    8   10   14   17   18   18   22   23   26   28   28   29   30   35   39   44 
LCS_GDT     G    47_C     G    47_C      4    7   21      4    4    5    5    8   10   14   17   18   18   22   23   25   28   28   29   30   34   39   43 
LCS_GDT     G    48_C     G    48_C      4    8   21      4    4    5    6    9   11   14   17   18   19   22   25   28   32   36   40   42   44   47   48 
LCS_GDT     T    49_C     T    49_C      7    8   21      4    6    7    9    9   11   14   17   19   26   29   32   36   38   41   42   44   46   47   48 
LCS_GDT     M    50_C     M    50_C      7    8   21      4    6    7   10   10   11   14   17   25   27   29   33   36   38   41   42   44   46   47   48 
LCS_GDT     R    51_C     R    51_C      7    8   21      4    7    7   10   10   11   14   17   25   27   29   33   36   38   41   42   44   46   47   48 
LCS_GDT     S    52_C     S    52_C      7    8   21      4    7    7   10   10   11   14   17   25   27   29   33   36   38   41   42   44   46   47   48 
LCS_GDT     V    53_C     V    53_C      7    8   21      4    7    7   10   10   11   14   17   25   27   29   33   36   38   41   42   44   46   47   48 
LCS_GDT     P    54_C     P    54_C      7    8   21      3    7    7   10   10   11   14   17   25   27   29   33   36   38   41   42   44   46   47   48 
LCS_GDT     I    55_C     I    55_C      7    8   21      3    7    7   10   10   11   14   17   25   27   29   33   36   38   41   42   44   46   47   48 
LCS_GDT     G    56_C     G    56_C      7    8   21      0    4    6   10   10   11   14   16   18   20   23   26   29   33   37   40   42   45   45   47 
LCS_AVERAGE  LCS_A:  28.44  (  12.57   17.49   55.25 )

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      7      9     11     14     15     17     19     20     25     27     29     33     36     38     41     42     44     46     47     48 
GDT PERCENT_AT  13.73  17.65  21.57  27.45  29.41  33.33  37.25  39.22  49.02  52.94  56.86  64.71  70.59  74.51  80.39  82.35  86.27  90.20  92.16  94.12
GDT RMS_LOCAL    0.27   0.46   0.82   1.31   1.42   1.71   1.95   2.25   3.70   3.82   3.99   4.35   4.55   4.73   5.03   5.10   5.34   5.59   5.72   5.90
GDT RMS_ALL_AT  10.07  10.02  10.42  11.52  11.45  11.50  11.51  11.48   6.85   6.85   6.79   6.70   6.69   6.68   6.68   6.66   6.66   6.67   6.69   6.63

# Checking swapping
#   possible swapping detected:  F    22_C      F    22_C
#   possible swapping detected:  Y    25_C      Y    25_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     5.809     2    0.648   0.605     9.081   14.762   11.497
LGA    T     7_C      T     7_C     7.562     0    0.689   1.393    10.186   19.167   11.361
LGA    K     8_C      K     8_C     2.213     4    0.577   0.589     4.252   59.881   32.963
LGA    I     9_C      I     9_C     1.521     0    0.058   0.145     3.021   75.000   70.179
LGA    L    10_C      L    10_C     1.914     0    0.030   0.983     5.229   77.143   64.286
LGA    P    11_C      P    11_C     1.869     0    0.070   0.199     2.334   68.810   67.075
LGA    C    12_C      C    12_C     1.037     0    0.043   0.134     1.251   81.429   82.937
LGA    P    13_C      P    13_C     1.649     0    0.084   0.185     1.950   77.143   75.306
LGA    R    14_C      R    14_C     0.838     0    0.017   1.264     9.011   85.952   54.156
LGA    C    15_C      C    15_C     1.471     0    0.176   0.580     2.040   79.286   74.444
LGA    N    16_C      N    16_C     1.748     0    0.150   1.068     5.398   79.405   63.571
LGA    S    17_C      S    17_C     1.098     0    0.083   0.169     2.092   81.429   78.651
LGA    M    18_C      M    18_C     1.464     0    0.222   1.410     5.354   81.548   69.048
LGA    E    19_C      E    19_C     2.940     4    0.337   0.344     4.273   52.262   27.354
LGA    T    20_C      T    20_C     5.159     0    0.048   1.007     6.889   29.286   27.687
LGA    K    21_C      K    21_C     8.397     0    0.559   1.268    13.026    4.405    2.487
LGA    F    22_C      F    22_C     8.892     0    0.096   1.453    10.809    3.333    1.299
LGA    C    23_C      C    23_C     7.187     0    0.598   0.620     7.880    8.571   10.794
LGA    Y    24_C      Y    24_C     9.667     0    0.043   1.322    10.721    1.310    5.873
LGA    Y    25_C      Y    25_C    10.417     0    0.181   1.378    13.185    0.000    0.000
LGA    N    26_C      N    26_C    10.493     0    0.184   0.514    11.185    0.000    0.000
LGA    N    27_C      N    27_C    11.062     0    0.373   0.898    14.797    0.000    3.095
LGA    Y    28_C      Y    28_C    16.641     0    0.690   1.213    18.727    0.000    0.000
LGA    N    29_C      N    29_C    19.474     0    0.574   0.678    22.145    0.000    0.000
LGA    V    30_C      V    30_C    21.447     0    0.581   0.951    26.016    0.000    0.000
LGA    N    31_C      N    31_C    17.867     0    0.703   1.001    22.288    0.000    0.000
LGA    Q    32_C      Q    32_C    11.521     0    0.419   1.265    15.257    0.119    0.053
LGA    P    33_C      P    33_C     8.924     0    0.625   0.549    10.560   10.714    6.259
LGA    R    34_C      R    34_C     5.295     0    0.166   0.949    11.893   19.762    9.957
LGA    H    35_C      H    35_C     2.973     0    0.035   1.268     4.762   48.571   50.095
LGA    F    36_C      F    36_C     3.432     0    0.141   1.156     9.817   59.405   28.658
LGA    C    37_C      C    37_C     0.964     0    0.364   0.741     2.407   86.190   81.825
LGA    K    38_C      K    38_C     0.970     0    0.154   0.826     6.981   77.738   55.661
LGA    A    39_C      A    39_C     3.080     0    0.100   0.118     3.814   55.476   53.048
LGA    C    40_C      C    40_C     1.524     0    0.233   0.830     1.762   72.857   74.286
LGA    Q    41_C      Q    41_C     2.117     0    0.416   1.454     5.903   72.976   48.942
LGA    R    42_C      R    42_C     5.774     0    0.575   1.122    15.561   20.000    8.355
LGA    Y    43_C      Y    43_C    10.879     0    0.590   1.330    18.264    1.190    0.397
LGA    W    44_C      W    44_C    11.854     0    0.550   1.343    16.556    0.000    0.000
LGA    T    45_C      T    45_C    15.352     0    0.606   0.527    18.655    0.000    0.000
LGA    S    46_C      S    46_C    21.566     0    0.620   0.533    25.085    0.000    0.000
LGA    G    47_C      G    47_C    24.483     0    0.681   0.681    25.419    0.000    0.000
LGA    G    48_C      G    48_C    22.734     0    0.079   0.079    22.865    0.000    0.000
LGA    T    49_C      T    49_C    18.436     0    0.239   1.088    21.612    0.000    0.000
LGA    M    50_C      M    50_C    14.495     0    0.052   0.564    16.147    0.000    0.000
LGA    R    51_C      R    51_C    15.637     0    0.043   1.355    24.216    0.000    0.000
LGA    S    52_C      S    52_C    15.290     0    0.174   0.285    16.682    0.000    0.000
LGA    V    53_C      V    53_C    14.979     0    0.050   1.151    15.683    0.000    0.000
LGA    P    54_C      P    54_C    16.650     0    0.180   0.271    17.844    0.000    0.000
LGA    I    55_C      I    55_C    15.281     0    0.118   0.629    17.498    0.000    0.000
LGA    G    56_C      G    56_C    18.605     0    0.077   0.077    19.672    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):     6.565          6.573                  7.359           29.512   24.541

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   65   51    4.0     20    2.25    41.667    36.339     0.850

LGA_LOCAL      RMSD:   2.252  Number of atoms:   20  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  11.481  Number of assigned atoms:   51 
Std_ASGN_ATOMS RMSD:   6.565  Standard rmsd on all 51 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.332689 * X  +   0.215139 * Y  +   0.918168 * Z  + -59.948284
  Y_new =  -0.906054 * X  +  -0.342908 * Y  +  -0.247952 * Z  +   6.603974
  Z_new =   0.261503 * X  +  -0.914401 * Y  +   0.309009 * Z  +  -1.849004 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.922698 -0.264579 -1.244909   [DEG: -110.1625  -15.1593  -71.3280 ]
ZXZ:  1.307037  1.256645  2.863044   [DEG:   74.8877   72.0005  164.0404 ]
 
# END of job
