
#######################################################
#                                                     #
#                        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:    49       6_C - 54_C        4.96     6.23
  LCS_AVERAGE:     93.46

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    45       6_C - 50_C        1.90     7.07
  LCS_AVERAGE:     79.70

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    21      28_C - 48_C        0.96     7.21
  LONGEST_CONTINUOUS_SEGMENT:    21      29_C - 49_C        0.98     7.10
  LCS_AVERAGE:     30.53

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   45   49      3   14   34   38   40   41   43   44   44   44   45   45   45   45   46   46   46   47   47   48 
LCS_GDT     T     7_C     T     7_C      3   45   49      3    3    9   13   17   37   43   44   44   44   45   45   45   45   46   46   46   47   47   48 
LCS_GDT     K     8_C     K     8_C     17   45   49      8   26   34   38   40   41   43   44   44   44   45   45   45   45   46   46   46   47   47   48 
LCS_GDT     I     9_C     I     9_C     17   45   49      8   32   34   38   40   41   43   44   44   44   45   45   45   45   46   46   46   47   47   48 
LCS_GDT     L    10_C     L    10_C     17   45   49     21   32   34   38   40   41   43   44   44   44   45   45   45   45   46   46   46   47   47   48 
LCS_GDT     P    11_C     P    11_C     17   45   49     21   32   34   38   40   41   43   44   44   44   45   45   45   45   46   46   46   47   47   48 
LCS_GDT     C    12_C     C    12_C     17   45   49     21   32   34   38   40   41   43   44   44   44   45   45   45   45   46   46   46   47   47   48 
LCS_GDT     P    13_C     P    13_C     17   45   49     21   32   34   38   40   41   43   44   44   44   45   45   45   45   46   46   46   47   47   48 
LCS_GDT     R    14_C     R    14_C     17   45   49     21   32   34   38   40   41   43   44   44   44   45   45   45   45   46   46   46   47   47   48 
LCS_GDT     C    15_C     C    15_C     17   45   49     20   32   34   38   40   41   43   44   44   44   45   45   45   45   46   46   46   47   47   48 
LCS_GDT     N    16_C     N    16_C     17   45   49     20   32   34   38   40   41   43   44   44   44   45   45   45   45   46   46   46   47   47   48 
LCS_GDT     S    17_C     S    17_C     17   45   49     21   32   34   38   40   41   43   44   44   44   45   45   45   45   46   46   46   47   47   48 
LCS_GDT     M    18_C     M    18_C     17   45   49     21   32   34   38   40   41   43   44   44   44   45   45   45   45   46   46   46   47   47   48 
LCS_GDT     E    19_C     E    19_C     17   45   49     19   32   34   38   40   41   43   44   44   44   45   45   45   45   46   46   46   47   47   48 
LCS_GDT     T    20_C     T    20_C     17   45   49     21   32   34   38   40   41   43   44   44   44   45   45   45   45   46   46   46   47   47   48 
LCS_GDT     K    21_C     K    21_C     17   45   49     21   32   34   38   40   41   43   44   44   44   45   45   45   45   46   46   46   47   47   48 
LCS_GDT     F    22_C     F    22_C     17   45   49     21   32   34   38   40   41   43   44   44   44   45   45   45   45   46   46   46   47   47   48 
LCS_GDT     C    23_C     C    23_C     17   45   49     21   32   34   38   40   41   43   44   44   44   45   45   45   45   46   46   46   47   47   48 
LCS_GDT     Y    24_C     Y    24_C     17   45   49     20   32   34   38   40   41   43   44   44   44   45   45   45   45   46   46   46   47   47   48 
LCS_GDT     Y    25_C     Y    25_C      3   45   49      3    3    5    7   36   40   42   44   44   44   45   45   45   45   46   46   46   47   47   48 
LCS_GDT     N    26_C     N    26_C      3   45   49      4   12   24   36   40   41   43   44   44   44   45   45   45   45   46   46   46   47   47   48 
LCS_GDT     N    27_C     N    27_C      3   45   49      3    3    4    5    8   40   43   44   44   44   45   45   45   45   46   46   46   47   47   48 
LCS_GDT     Y    28_C     Y    28_C     21   45   49      3    6   30   38   40   41   43   44   44   44   45   45   45   45   46   46   46   47   47   48 
LCS_GDT     N    29_C     N    29_C     21   45   49      3   14   34   38   40   41   43   44   44   44   45   45   45   45   46   46   46   47   47   48 
LCS_GDT     V    30_C     V    30_C     21   45   49     15   30   34   38   40   41   43   44   44   44   45   45   45   45   46   46   46   47   47   48 
LCS_GDT     N    31_C     N    31_C     21   45   49      3   26   34   38   40   41   43   44   44   44   45   45   45   45   46   46   46   47   47   48 
LCS_GDT     Q    32_C     Q    32_C     21   45   49      9   32   34   38   40   41   43   44   44   44   45   45   45   45   46   46   46   47   47   48 
LCS_GDT     P    33_C     P    33_C     21   45   49     14   32   34   38   40   41   43   44   44   44   45   45   45   45   46   46   46   47   47   48 
LCS_GDT     R    34_C     R    34_C     21   45   49     21   32   34   38   40   41   43   44   44   44   45   45   45   45   46   46   46   47   47   48 
LCS_GDT     H    35_C     H    35_C     21   45   49     21   32   34   38   40   41   43   44   44   44   45   45   45   45   46   46   46   47   47   48 
LCS_GDT     F    36_C     F    36_C     21   45   49     21   32   34   38   40   41   43   44   44   44   45   45   45   45   46   46   46   47   47   48 
LCS_GDT     C    37_C     C    37_C     21   45   49     21   32   34   38   40   41   43   44   44   44   45   45   45   45   46   46   46   47   47   48 
LCS_GDT     K    38_C     K    38_C     21   45   49     21   32   34   38   40   41   43   44   44   44   45   45   45   45   46   46   46   47   47   48 
LCS_GDT     A    39_C     A    39_C     21   45   49     21   32   34   38   40   41   43   44   44   44   45   45   45   45   46   46   46   47   47   48 
LCS_GDT     C    40_C     C    40_C     21   45   49     21   32   34   38   40   41   43   44   44   44   45   45   45   45   46   46   46   47   47   48 
LCS_GDT     Q    41_C     Q    41_C     21   45   49     21   32   34   38   40   41   43   44   44   44   45   45   45   45   46   46   46   47   47   48 
LCS_GDT     R    42_C     R    42_C     21   45   49     21   32   34   38   40   41   43   44   44   44   45   45   45   45   46   46   46   47   47   48 
LCS_GDT     Y    43_C     Y    43_C     21   45   49     21   32   34   38   40   41   43   44   44   44   45   45   45   45   46   46   46   47   47   48 
LCS_GDT     W    44_C     W    44_C     21   45   49     21   32   34   38   40   41   43   44   44   44   45   45   45   45   46   46   46   47   47   48 
LCS_GDT     T    45_C     T    45_C     21   45   49     21   32   34   38   40   41   43   44   44   44   45   45   45   45   46   46   46   47   47   48 
LCS_GDT     S    46_C     S    46_C     21   45   49      9   32   34   38   40   41   43   44   44   44   45   45   45   45   46   46   46   47   47   48 
LCS_GDT     G    47_C     G    47_C     21   45   49      4   32   34   38   40   41   43   44   44   44   45   45   45   45   46   46   46   47   47   48 
LCS_GDT     G    48_C     G    48_C     21   45   49      4   25   34   37   40   41   43   44   44   44   45   45   45   45   46   46   46   47   47   48 
LCS_GDT     T    49_C     T    49_C     21   45   49      8   14   34   38   40   41   43   44   44   44   45   45   45   45   46   46   46   47   47   48 
LCS_GDT     M    50_C     M    50_C      4   45   49      4    4    4    7   14   18   29   39   43   44   45   45   45   45   46   46   46   47   47   48 
LCS_GDT     R    51_C     R    51_C      4    8   49      4    4    4    6    7   11   13   13   14   18   21   28   37   45   46   46   46   47   47   48 
LCS_GDT     S    52_C     S    52_C      4    8   49      4    4    4    6    7    8   11   12   14   15   18   18   20   22   24   29   33   39   44   48 
LCS_GDT     V    53_C     V    53_C      4    8   49      4    4    4    6    8   11   13   13   14   16   18   22   27   30   32   38   43   47   47   48 
LCS_GDT     P    54_C     P    54_C      4    8   49      4    4    4    6    8   11   13   13   14   16   18   18   20   21   22   23   25   29   36   40 
LCS_GDT     I    55_C     I    55_C      4    8   15      3    4    4    6    8   11   13   13   14   16   18   18   20   21   22   23   25   29   34   40 
LCS_GDT     G    56_C     G    56_C      4    8   15      3    4    4    6    8   11   13   13   14   16   18   18   20   21   22   23   25   26   27   35 
LCS_AVERAGE  LCS_A:  67.90  (  30.53   79.70   93.46 )

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     21     32     34     38     40     41     43     44     44     44     45     45     45     45     46     46     46     47     47     48 
GDT PERCENT_AT  41.18  62.75  66.67  74.51  78.43  80.39  84.31  86.27  86.27  86.27  88.24  88.24  88.24  88.24  90.20  90.20  90.20  92.16  92.16  94.12
GDT RMS_LOCAL    0.29   0.51   0.63   0.92   1.03   1.14   1.41   1.55   1.55   1.55   1.90   1.90   1.90   1.90   2.62   2.62   2.62   3.48   3.48   4.16
GDT RMS_ALL_AT   7.14   7.11   7.10   7.14   7.12   7.16   7.18   7.21   7.21   7.21   7.07   7.07   7.07   7.07   6.86   6.86   6.86   6.61   6.61   6.42

# Checking swapping
#   possible swapping detected:  F    22_C      F    22_C
#   possible swapping detected:  Y    25_C      Y    25_C
#   possible swapping detected:  Y    28_C      Y    28_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     2.133     2    0.025   0.030     4.461   52.262   35.170
LGA    T     7_C      T     7_C     4.250     0    0.465   1.013     8.766   47.262   31.224
LGA    K     8_C      K     8_C     1.796     4    0.331   0.437     3.025   70.833   37.037
LGA    I     9_C      I     9_C     1.127     0    0.061   0.746     4.263   83.690   77.083
LGA    L    10_C      L    10_C     0.592     0    0.024   0.119     0.975   90.476   91.667
LGA    P    11_C      P    11_C     0.347     0    0.014   0.036     0.506   97.619   98.639
LGA    C    12_C      C    12_C     0.546     0    0.064   0.100     0.816   92.857   92.063
LGA    P    13_C      P    13_C     0.568     0    0.013   0.247     1.628   92.857   88.027
LGA    R    14_C      R    14_C     0.633     0    0.189   0.979     2.780   88.214   84.199
LGA    C    15_C      C    15_C     0.678     0    0.021   0.200     0.777   90.476   92.063
LGA    N    16_C      N    16_C     0.577     0    0.142   0.254     0.777   90.476   90.476
LGA    S    17_C      S    17_C     0.450     0    0.039   0.116     0.779   95.238   95.238
LGA    M    18_C      M    18_C     0.474     0    0.029   0.408     1.115   97.619   94.107
LGA    E    19_C      E    19_C     0.616     4    0.059   0.058     0.863   92.857   51.323
LGA    T    20_C      T    20_C     0.451     0    0.015   0.069     0.704   92.857   94.558
LGA    K    21_C      K    21_C     0.451     0    0.087   0.545     2.346   97.619   84.021
LGA    F    22_C      F    22_C     0.251     0    0.041   1.297     7.465   92.857   59.221
LGA    C    23_C      C    23_C     0.931     0    0.068   0.067     1.292   85.952   84.444
LGA    Y    24_C      Y    24_C     1.439     0    0.701   1.366    12.525   75.357   33.373
LGA    Y    25_C      Y    25_C     4.481     0    0.583   1.441    15.489   48.690   17.817
LGA    N    26_C      N    26_C     2.961     0    0.579   0.597     5.654   53.810   45.060
LGA    N    27_C      N    27_C     3.588     0    0.303   0.420     8.272   55.595   33.512
LGA    Y    28_C      Y    28_C     2.118     0    0.171   0.171     7.146   69.048   39.444
LGA    N    29_C      N    29_C     1.758     0    0.297   0.749     2.477   72.976   70.893
LGA    V    30_C      V    30_C     1.002     0    0.136   1.189     3.404   79.286   73.333
LGA    N    31_C      N    31_C     1.660     0    0.027   0.363     4.327   77.143   63.810
LGA    Q    32_C      Q    32_C     1.234     0    0.029   0.689     1.539   79.286   81.534
LGA    P    33_C      P    33_C     1.041     0    0.029   0.396     1.727   81.429   81.497
LGA    R    34_C      R    34_C     0.748     0    0.080   0.908     5.889   88.214   68.528
LGA    H    35_C      H    35_C     0.616     0    0.045   0.280     1.509   90.476   86.000
LGA    F    36_C      F    36_C     0.550     0    0.039   0.135     0.952   90.476   90.476
LGA    C    37_C      C    37_C     0.592     0    0.029   0.788     3.178   90.476   83.730
LGA    K    38_C      K    38_C     0.596     0    0.081   0.450     1.674   90.476   90.635
LGA    A    39_C      A    39_C     0.508     0    0.190   0.205     0.779   92.857   92.381
LGA    C    40_C      C    40_C     0.766     0    0.033   0.031     0.900   90.476   90.476
LGA    Q    41_C      Q    41_C     0.752     0    0.062   0.072     1.096   90.476   86.455
LGA    R    42_C      R    42_C     0.476     0    0.064   1.495     6.678   92.857   66.926
LGA    Y    43_C      Y    43_C     0.621     0    0.043   0.085     0.957   90.476   90.476
LGA    W    44_C      W    44_C     0.420     0    0.049   0.114     0.606   95.238   97.279
LGA    T    45_C      T    45_C     0.952     0    0.080   0.156     1.346   88.214   86.599
LGA    S    46_C      S    46_C     0.999     0    0.136   0.566     2.556   85.952   80.397
LGA    G    47_C      G    47_C     1.362     0    0.285   0.285     2.989   71.190   71.190
LGA    G    48_C      G    48_C     2.491     0    0.096   0.096     2.795   69.048   69.048
LGA    T    49_C      T    49_C     1.719     0    0.636   0.617     4.148   64.167   59.524
LGA    M    50_C      M    50_C     7.752     0    0.699   1.482    11.949    8.452    4.464
LGA    R    51_C      R    51_C    13.271     0    0.383   1.542    16.307    0.000    0.000
LGA    S    52_C      S    52_C    19.032     0    0.111   0.204    23.596    0.000    0.000
LGA    V    53_C      V    53_C    17.578     0    0.452   0.572    19.809    0.000    0.000
LGA    P    54_C      P    54_C    23.243     0    0.227   0.444    24.838    0.000    0.000
LGA    I    55_C      I    55_C    22.402     0    0.080   1.341    25.197    0.000    0.000
LGA    G    56_C      G    56_C    24.350     0    0.677   0.677    24.350    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):     6.098          6.085                  6.417           71.258   63.440

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   65   51    4.0     44    1.55    78.431    80.039     2.659

LGA_LOCAL      RMSD:   1.555  Number of atoms:   44  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   7.207  Number of assigned atoms:   51 
Std_ASGN_ATOMS RMSD:   6.098  Standard rmsd on all 51 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.616367 * X  +  -0.006904 * Y  +  -0.787429 * Z  + -23.855375
  Y_new =  -0.628004 * X  +   0.607597 * Y  +   0.486248 * Z  + -31.784800
  Z_new =   0.475082 * X  +   0.794216 * Y  +  -0.378839 * Z  +  -1.613723 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.346843 -0.495057  2.015873   [DEG: -134.4642  -28.3647  115.5010 ]
ZXZ: -2.123994  1.959337  0.539078   [DEG: -121.6959  112.2618   30.8869 ]
 
# END of job
