
#######################################################
#                                                     #
#                        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   48 (  395),  selected   48 , name one
# Molecule2: number of CA atoms   51 (  404),  selected   48 , 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:    48       6_C - 53_C        3.32     3.32
  LCS_AVERAGE:     94.12

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    39       9_C - 47_C        1.95     3.69
  LCS_AVERAGE:     66.91

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15      32_C - 46_C        0.90     3.56
  LCS_AVERAGE:     20.18

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   48
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   14   48      0    3    3   11   13   21   24   32   37   44   46   46   46   46   48   48   48   48   48   48 
LCS_GDT     T     7_C     T     7_C      5   18   48      1    4    8   11   16   24   36   41   43   44   46   46   46   46   48   48   48   48   48   48 
LCS_GDT     K     8_C     K     8_C      7   20   48      3    4    8   11   26   33   37   41   43   44   46   46   46   46   48   48   48   48   48   48 
LCS_GDT     I     9_C     I     9_C     12   39   48      3    6   15   29   32   36   37   41   43   44   46   46   46   46   48   48   48   48   48   48 
LCS_GDT     L    10_C     L    10_C     13   39   48      9   18   27   30   34   36   37   41   43   44   46   46   46   46   48   48   48   48   48   48 
LCS_GDT     P    11_C     P    11_C     13   39   48     10   18   27   30   34   36   37   41   43   44   46   46   46   46   48   48   48   48   48   48 
LCS_GDT     C    12_C     C    12_C     13   39   48     10   18   27   30   34   36   37   41   43   44   46   46   46   46   48   48   48   48   48   48 
LCS_GDT     P    13_C     P    13_C     13   39   48     10   18   27   30   34   36   37   41   43   44   46   46   46   46   48   48   48   48   48   48 
LCS_GDT     R    14_C     R    14_C     13   39   48      4   18   27   30   34   36   37   41   43   44   46   46   46   46   48   48   48   48   48   48 
LCS_GDT     C    15_C     C    15_C     13   39   48     10   18   27   30   34   36   37   41   43   44   46   46   46   46   48   48   48   48   48   48 
LCS_GDT     N    16_C     N    16_C     13   39   48     10   18   27   30   34   36   37   41   43   44   46   46   46   46   48   48   48   48   48   48 
LCS_GDT     S    17_C     S    17_C     13   39   48     10   18   27   30   34   36   37   41   43   44   46   46   46   46   48   48   48   48   48   48 
LCS_GDT     M    18_C     M    18_C     13   39   48      5   18   27   30   34   36   37   41   43   44   46   46   46   46   48   48   48   48   48   48 
LCS_GDT     E    19_C     E    19_C     13   39   48      5   15   27   30   34   36   37   41   43   44   46   46   46   46   48   48   48   48   48   48 
LCS_GDT     T    20_C     T    20_C     13   39   48      6   17   27   30   34   36   37   41   43   44   46   46   46   46   48   48   48   48   48   48 
LCS_GDT     K    21_C     K    21_C     13   39   48      6   14   27   30   34   36   37   41   43   44   46   46   46   46   48   48   48   48   48   48 
LCS_GDT     F    22_C     F    22_C     13   39   48      6   17   27   30   34   36   37   41   43   44   46   46   46   46   48   48   48   48   48   48 
LCS_GDT     C    23_C     C    23_C      5   39   48      2    4   26   30   34   36   37   41   43   44   46   46   46   46   48   48   48   48   48   48 
LCS_GDT     Y    24_C     Y    24_C      5   39   48      3    5   26   30   34   36   37   41   43   44   46   46   46   46   48   48   48   48   48   48 
LCS_GDT     Y    25_C     Y    25_C      5   39   48      3   11   18   26   34   36   37   41   43   44   46   46   46   46   48   48   48   48   48   48 
LCS_GDT     N    26_C     N    26_C      4   39   48      3    4    4    6    7   15   36   41   43   44   46   46   46   46   48   48   48   48   48   48 
LCS_GDT     N    27_C     N    27_C      4   39   48      3   17   27   30   34   36   37   41   43   44   46   46   46   46   48   48   48   48   48   48 
LCS_GDT     Y    28_C     Y    28_C      4   39   48      3    3    4   10   16   33   36   38   40   43   46   46   46   46   48   48   48   48   48   48 
LCS_GDT     N    29_C     N    29_C      3   39   48      3    5   23   30   34   36   37   41   43   44   46   46   46   46   48   48   48   48   48   48 
LCS_GDT     V    30_C     V    30_C      3   39   48      3    6   19   29   34   36   37   38   41   43   46   46   46   46   48   48   48   48   48   48 
LCS_GDT     N    31_C     N    31_C      6   39   48      3    5   10   19   20   35   37   41   43   44   46   46   46   46   48   48   48   48   48   48 
LCS_GDT     Q    32_C     Q    32_C     15   39   48      3   14   22   30   34   36   37   41   43   44   46   46   46   46   48   48   48   48   48   48 
LCS_GDT     P    33_C     P    33_C     15   39   48      5   17   27   30   34   36   37   41   43   44   46   46   46   46   48   48   48   48   48   48 
LCS_GDT     R    34_C     R    34_C     15   39   48      7   17   27   30   34   36   37   41   43   44   46   46   46   46   48   48   48   48   48   48 
LCS_GDT     H    35_C     H    35_C     15   39   48     10   18   27   30   34   36   37   41   43   44   46   46   46   46   48   48   48   48   48   48 
LCS_GDT     F    36_C     F    36_C     15   39   48     10   18   27   30   34   36   37   41   43   44   46   46   46   46   48   48   48   48   48   48 
LCS_GDT     C    37_C     C    37_C     15   39   48     10   18   27   30   34   36   37   41   43   44   46   46   46   46   48   48   48   48   48   48 
LCS_GDT     K    38_C     K    38_C     15   39   48     10   18   27   30   34   36   37   41   43   44   46   46   46   46   48   48   48   48   48   48 
LCS_GDT     A    39_C     A    39_C     15   39   48      3   18   27   30   34   36   37   41   43   44   46   46   46   46   48   48   48   48   48   48 
LCS_GDT     C    40_C     C    40_C     15   39   48      4   18   27   30   34   36   37   41   43   44   46   46   46   46   48   48   48   48   48   48 
LCS_GDT     Q    41_C     Q    41_C     15   39   48      4   18   27   30   34   36   37   41   43   44   46   46   46   46   48   48   48   48   48   48 
LCS_GDT     R    42_C     R    42_C     15   39   48      4   16   27   30   34   36   37   41   43   44   46   46   46   46   48   48   48   48   48   48 
LCS_GDT     Y    43_C     Y    43_C     15   39   48      6   18   27   30   34   36   37   41   43   44   46   46   46   46   48   48   48   48   48   48 
LCS_GDT     W    44_C     W    44_C     15   39   48      5   18   27   30   34   36   37   41   43   44   46   46   46   46   48   48   48   48   48   48 
LCS_GDT     T    45_C     T    45_C     15   39   48      6   17   27   30   34   36   37   41   43   44   46   46   46   46   48   48   48   48   48   48 
LCS_GDT     S    46_C     S    46_C     15   39   48      4   12   22   30   34   36   37   41   43   44   46   46   46   46   48   48   48   48   48   48 
LCS_GDT     G    47_C     G    47_C      6   39   48      3    4   10   19   34   36   37   41   43   44   46   46   46   46   48   48   48   48   48   48 
LCS_GDT     G    48_C     G    48_C      3   22   48      3    3    3    4   16   29   37   41   43   44   46   46   46   46   48   48   48   48   48   48 
LCS_GDT     T    49_C     T    49_C      5   19   48      4    4    5   11   19   26   37   41   43   44   46   46   46   46   48   48   48   48   48   48 
LCS_GDT     M    50_C     M    50_C      5    6   48      4    4    5    7   15   21   29   38   43   44   46   46   46   46   48   48   48   48   48   48 
LCS_GDT     R    51_C     R    51_C      5    6   48      4    4    5    5    6   21   32   38   43   44   46   46   46   46   48   48   48   48   48   48 
LCS_GDT     S    52_C     S    52_C      5    6   48      4    4    5    5    6    6    6    7    7   35   38   39   42   46   48   48   48   48   48   48 
LCS_GDT     V    53_C     V    53_C      5    6   48      3    4    5    5    8   14   19   26   33   36   38   41   44   46   48   48   48   48   48   48 
LCS_AVERAGE  LCS_A:  60.40  (  20.18   66.91   94.12 )

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     18     27     30     34     36     37     41     43     44     46     46     46     46     48     48     48     48     48     48 
GDT PERCENT_AT  19.61  35.29  52.94  58.82  66.67  70.59  72.55  80.39  84.31  86.27  90.20  90.20  90.20  90.20  94.12  94.12  94.12  94.12  94.12  94.12
GDT RMS_LOCAL    0.33   0.69   1.00   1.15   1.42   1.54   1.75   2.25   2.52   2.64   2.81   2.81   2.81   2.81   3.32   3.32   3.32   3.32   3.32   3.32
GDT RMS_ALL_AT   4.31   4.10   3.79   3.75   3.68   3.75   3.56   3.39   3.33   3.34   3.36   3.36   3.36   3.36   3.32   3.32   3.32   3.32   3.32   3.32

# Checking swapping
#   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     6.266     2    0.064   0.100     6.800   22.024   15.646
LGA    T     7_C      T     7_C     4.755     0    0.668   0.590     7.693   47.262   32.381
LGA    K     8_C      K     8_C     3.636     4    0.189   0.276     4.735   39.048   21.481
LGA    I     9_C      I     9_C     2.841     0    0.565   1.460     7.945   57.262   44.702
LGA    L    10_C      L    10_C     1.622     0    0.051   1.348     4.838   72.857   60.595
LGA    P    11_C      P    11_C     1.591     0    0.088   0.351     1.960   72.857   74.082
LGA    C    12_C      C    12_C     1.277     0    0.017   0.852     3.155   81.429   76.190
LGA    P    13_C      P    13_C     1.895     0    0.106   0.136     2.396   70.833   68.231
LGA    R    14_C      R    14_C     2.222     0    0.340   0.908     4.795   61.071   51.905
LGA    C    15_C      C    15_C     1.509     0    0.086   0.854     2.325   79.286   77.222
LGA    N    16_C      N    16_C     1.230     0    0.089   0.236     2.273   79.286   76.131
LGA    S    17_C      S    17_C     0.602     0    0.072   0.132     0.789   95.238   93.651
LGA    M    18_C      M    18_C     1.361     0    0.107   0.655     3.507   77.381   70.417
LGA    E    19_C      E    19_C     2.294     4    0.349   0.366     2.875   68.810   36.931
LGA    T    20_C      T    20_C     0.797     0    0.034   1.024     2.952   85.952   78.367
LGA    K    21_C      K    21_C     0.744     0    0.000   0.462     2.952   90.476   82.910
LGA    F    22_C      F    22_C     0.727     0    0.114   1.008     5.939   85.952   61.602
LGA    C    23_C      C    23_C     2.764     0    0.566   1.062     4.589   54.643   51.984
LGA    Y    24_C      Y    24_C     2.592     0    0.029   1.408    13.767   63.214   25.833
LGA    Y    25_C      Y    25_C     2.879     0    0.061   1.319    15.630   68.929   26.111
LGA    N    26_C      N    26_C     4.238     0    0.666   0.603    10.305   43.452   24.881
LGA    N    27_C      N    27_C     1.947     0    0.299   0.966     3.934   59.762   56.786
LGA    Y    28_C      Y    28_C     5.350     0    0.395   1.189    13.477   37.500   13.690
LGA    N    29_C      N    29_C     2.931     0    0.651   0.814     6.678   48.571   37.917
LGA    V    30_C      V    30_C     4.492     0    0.417   0.432     8.585   45.357   30.680
LGA    N    31_C      N    31_C     3.484     0    0.097   1.209     5.250   52.262   45.893
LGA    Q    32_C      Q    32_C     1.195     0    0.402   1.168     4.847   83.690   66.455
LGA    P    33_C      P    33_C     0.307     0    0.106   0.406     1.036   95.357   94.626
LGA    R    34_C      R    34_C     0.375     0    0.065   1.459     7.634   95.238   66.234
LGA    H    35_C      H    35_C     0.603     0    0.011   1.014     2.731   97.619   82.190
LGA    F    36_C      F    36_C     0.419     0    0.052   0.434     1.439   97.619   94.892
LGA    C    37_C      C    37_C     0.672     0    0.062   0.885     1.883   83.810   83.095
LGA    K    38_C      K    38_C     1.763     0    0.063   0.471     2.873   71.071   67.672
LGA    A    39_C      A    39_C     1.797     0    0.329   0.343     2.251   77.143   74.667
LGA    C    40_C      C    40_C     2.011     0    0.062   0.747     3.464   68.810   65.000
LGA    Q    41_C      Q    41_C     1.482     0    0.000   0.803     3.706   79.286   69.735
LGA    R    42_C      R    42_C     1.073     0    0.050   1.381     3.378   88.214   72.814
LGA    Y    43_C      Y    43_C     0.680     0    0.156   0.175     1.444   90.476   87.460
LGA    W    44_C      W    44_C     1.278     0    0.044   1.084     7.626   81.429   47.279
LGA    T    45_C      T    45_C     0.992     0    0.165   1.155     2.934   85.952   78.367
LGA    S    46_C      S    46_C     1.341     0    0.629   0.743     1.941   81.548   78.651
LGA    G    47_C      G    47_C     2.673     0    0.663   0.663     2.673   73.452   73.452
LGA    G    48_C      G    48_C     4.105     0    0.688   0.688     5.525   36.786   36.786
LGA    T    49_C      T    49_C     5.072     0    0.688   1.016     8.514   26.667   21.156
LGA    M    50_C      M    50_C     6.258     0    0.039   0.496    12.209   17.262    9.286
LGA    R    51_C      R    51_C     5.838     0    0.092   1.025     9.317   14.405   17.749
LGA    S    52_C      S    52_C     9.341     0    0.235   0.530    10.103    2.857    1.984
LGA    V    53_C      V    53_C     9.670     0    0.609   1.460    11.271    0.595    0.952

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       48     192    192  100.00     385    385  100.00                51
SUMMARY(RMSD_GDC):     3.316          3.275                  4.578           60.980   51.504

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   48   51    4.0     41    2.25    67.157    70.589     1.742

LGA_LOCAL      RMSD:   2.254  Number of atoms:   41  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   3.386  Number of assigned atoms:   48 
Std_ASGN_ATOMS RMSD:   3.316  Standard rmsd on all 48 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.262786 * X  +  -0.963929 * Y  +   0.042245 * Z  + 147.932404
  Y_new =  -0.948931 * X  +  -0.250280 * Y  +   0.192069 * Z  + 180.323929
  Z_new =  -0.174568 * X  +  -0.090560 * Y  +  -0.980472 * Z  + 247.120255 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.300638  0.175467 -3.049490   [DEG:  -74.5211   10.0535 -174.7229 ]
ZXZ:  2.925093  2.943643 -2.049347   [DEG:  167.5955  168.6583 -117.4189 ]
 
# END of job
