
#######################################################
#                                                     #
#                        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:    50       6_C - 55_C        4.70     5.13
  LCS_AVERAGE:     96.73

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    44       6_C - 49_C        1.93     6.03
  LCS_AVERAGE:     75.89

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    21      28_C - 48_C        0.92     6.25
  LCS_AVERAGE:     29.03

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   44   50      3    3    6    7   11   13   34   41   42   44   44   45   46   46   46   46   47   49   50   51 
LCS_GDT     T     7_C     T     7_C      7   44   50      3    7   17   28   35   40   41   42   43   44   44   45   46   46   46   46   47   49   50   51 
LCS_GDT     K     8_C     K     8_C      7   44   50      3    6   17   28   35   40   41   42   43   44   44   45   46   46   46   46   47   49   50   51 
LCS_GDT     I     9_C     I     9_C     16   44   50      3    9   23   35   36   40   41   42   43   44   44   45   46   46   46   46   47   49   50   51 
LCS_GDT     L    10_C     L    10_C     16   44   50     13   32   34   35   37   40   41   42   43   44   44   45   46   46   46   46   47   49   50   51 
LCS_GDT     P    11_C     P    11_C     16   44   50     19   32   34   35   37   40   41   42   43   44   44   45   46   46   46   46   47   49   50   51 
LCS_GDT     C    12_C     C    12_C     16   44   50     17   32   34   35   37   40   41   42   43   44   44   45   46   46   46   46   47   49   50   51 
LCS_GDT     P    13_C     P    13_C     16   44   50     15   32   34   35   37   40   41   42   43   44   44   45   46   46   46   46   47   49   50   51 
LCS_GDT     R    14_C     R    14_C     16   44   50     15   32   34   35   37   40   41   42   43   44   44   45   46   46   46   46   47   49   50   51 
LCS_GDT     C    15_C     C    15_C     16   44   50     15   32   34   35   37   40   41   42   43   44   44   45   46   46   46   46   47   49   50   51 
LCS_GDT     N    16_C     N    16_C     16   44   50     19   32   34   35   37   40   41   42   43   44   44   45   46   46   46   46   47   49   50   51 
LCS_GDT     S    17_C     S    17_C     16   44   50     19   32   34   35   37   40   41   42   43   44   44   45   46   46   46   46   47   49   50   51 
LCS_GDT     M    18_C     M    18_C     16   44   50     19   32   34   35   37   40   41   42   43   44   44   45   46   46   46   46   47   49   50   51 
LCS_GDT     E    19_C     E    19_C     16   44   50     19   32   34   35   37   40   41   42   43   44   44   45   46   46   46   46   47   49   50   51 
LCS_GDT     T    20_C     T    20_C     16   44   50     19   32   34   35   37   40   41   42   43   44   44   45   46   46   46   46   47   49   50   51 
LCS_GDT     K    21_C     K    21_C     16   44   50     19   32   34   35   37   40   41   42   43   44   44   45   46   46   46   46   47   49   50   51 
LCS_GDT     F    22_C     F    22_C     16   44   50     19   32   34   35   37   40   41   42   43   44   44   45   46   46   46   46   47   49   50   51 
LCS_GDT     C    23_C     C    23_C     16   44   50     19   32   34   35   37   40   41   42   43   44   44   45   46   46   46   46   47   49   50   51 
LCS_GDT     Y    24_C     Y    24_C     16   44   50     16   32   34   35   37   40   41   42   43   44   44   45   46   46   46   46   47   49   50   51 
LCS_GDT     Y    25_C     Y    25_C      3   44   50      3    3    4    7   27   33   38   40   43   44   44   45   46   46   46   46   47   49   50   51 
LCS_GDT     N    26_C     N    26_C      3   44   50      3    3   16   24   36   38   41   42   43   44   44   45   46   46   46   46   47   49   50   51 
LCS_GDT     N    27_C     N    27_C      3   44   50      3    3    3    5   34   40   41   42   43   44   44   45   46   46   46   46   47   49   50   51 
LCS_GDT     Y    28_C     Y    28_C     21   44   50      3   22   34   35   37   40   41   42   43   44   44   45   46   46   46   46   47   49   50   51 
LCS_GDT     N    29_C     N    29_C     21   44   50      3   27   34   35   37   40   41   42   43   44   44   45   46   46   46   46   47   49   50   51 
LCS_GDT     V    30_C     V    30_C     21   44   50     19   32   34   35   37   40   41   42   43   44   44   45   46   46   46   46   47   49   50   51 
LCS_GDT     N    31_C     N    31_C     21   44   50     19   32   34   35   37   40   41   42   43   44   44   45   46   46   46   46   47   49   50   51 
LCS_GDT     Q    32_C     Q    32_C     21   44   50      6   32   34   35   37   40   41   42   43   44   44   45   46   46   46   46   47   49   50   51 
LCS_GDT     P    33_C     P    33_C     21   44   50     14   32   34   35   37   40   41   42   43   44   44   45   46   46   46   46   47   49   50   51 
LCS_GDT     R    34_C     R    34_C     21   44   50     19   32   34   35   37   40   41   42   43   44   44   45   46   46   46   46   47   49   50   51 
LCS_GDT     H    35_C     H    35_C     21   44   50     19   32   34   35   37   40   41   42   43   44   44   45   46   46   46   46   47   49   50   51 
LCS_GDT     F    36_C     F    36_C     21   44   50     19   32   34   35   37   40   41   42   43   44   44   45   46   46   46   46   47   49   50   51 
LCS_GDT     C    37_C     C    37_C     21   44   50     19   32   34   35   37   40   41   42   43   44   44   45   46   46   46   46   47   49   50   51 
LCS_GDT     K    38_C     K    38_C     21   44   50     19   32   34   35   37   40   41   42   43   44   44   45   46   46   46   46   47   49   50   51 
LCS_GDT     A    39_C     A    39_C     21   44   50     19   32   34   35   37   40   41   42   43   44   44   45   46   46   46   46   47   49   50   51 
LCS_GDT     C    40_C     C    40_C     21   44   50     15   32   34   35   37   40   41   42   43   44   44   45   46   46   46   46   47   49   50   51 
LCS_GDT     Q    41_C     Q    41_C     21   44   50     15   32   34   35   37   40   41   42   43   44   44   45   46   46   46   46   47   49   50   51 
LCS_GDT     R    42_C     R    42_C     21   44   50     17   32   34   35   37   40   41   42   43   44   44   45   46   46   46   46   47   49   50   51 
LCS_GDT     Y    43_C     Y    43_C     21   44   50     19   32   34   35   37   40   41   42   43   44   44   45   46   46   46   46   47   49   50   51 
LCS_GDT     W    44_C     W    44_C     21   44   50     19   32   34   35   37   40   41   42   43   44   44   45   46   46   46   46   47   49   50   51 
LCS_GDT     T    45_C     T    45_C     21   44   50      8   32   34   35   37   40   41   42   43   44   44   45   46   46   46   46   47   49   50   51 
LCS_GDT     S    46_C     S    46_C     21   44   50      9   32   34   35   37   40   41   42   43   44   44   45   46   46   46   46   47   49   50   51 
LCS_GDT     G    47_C     G    47_C     21   44   50      7   24   34   35   37   40   41   42   43   44   44   45   46   46   46   46   47   49   50   51 
LCS_GDT     G    48_C     G    48_C     21   44   50      3    4   19   33   37   40   41   42   43   44   44   45   46   46   46   46   47   49   50   51 
LCS_GDT     T    49_C     T    49_C      4   44   50      4   17   32   35   37   40   41   42   43   44   44   45   46   46   46   46   47   49   50   51 
LCS_GDT     M    50_C     M    50_C      4    6   50      3    4    4    6    8   11   14   26   35   43   44   45   46   46   46   46   47   49   50   51 
LCS_GDT     R    51_C     R    51_C      4    6   50      3    3    4    6    8   11   17   26   32   41   44   45   46   46   46   46   47   49   50   51 
LCS_GDT     S    52_C     S    52_C      4    6   50      3    3    4    5    6   10   13   16   17   18   20   24   33   37   41   43   47   49   50   51 
LCS_GDT     V    53_C     V    53_C      4    5   50      3    4    4    6    8   10   13   16   17   18   21   24   29   34   41   43   47   49   50   51 
LCS_GDT     P    54_C     P    54_C      4    5   50      3    4    4    5    5    5   10   16   17   18   21   24   31   37   41   44   47   49   50   51 
LCS_GDT     I    55_C     I    55_C      4    5   50      3    4    4    6    7   10   13   16   17   18   21   23   31   34   38   42   47   49   50   51 
LCS_GDT     G    56_C     G    56_C      4    5   16      3    4    4    5    5    7   13   16   17   18   20   22   23   33   34   34   44   48   49   51 
LCS_AVERAGE  LCS_A:  67.22  (  29.03   75.89   96.73 )

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     19     32     34     35     37     40     41     42     43     44     44     45     46     46     46     46     47     49     50     51 
GDT PERCENT_AT  37.25  62.75  66.67  68.63  72.55  78.43  80.39  82.35  84.31  86.27  86.27  88.24  90.20  90.20  90.20  90.20  92.16  96.08  98.04 100.00
GDT RMS_LOCAL    0.30   0.58   0.65   0.72   0.96   1.44   1.47   1.57   1.75   1.93   1.93   2.31   2.65   2.65   2.65   2.65   4.29   4.35   4.70   5.10
GDT RMS_ALL_AT   6.19   6.21   6.22   6.19   6.09   5.97   6.02   6.03   6.08   6.03   6.03   5.88   5.72   5.72   5.72   5.72   5.16   5.20   5.13   5.10

# Checking swapping
#   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     5.843     2    0.097   0.125     7.567   18.333   11.905
LGA    T     7_C      T     7_C     3.792     0    0.607   0.996     6.884   48.452   43.061
LGA    K     8_C      K     8_C     3.225     4    0.331   0.448     3.917   48.452   27.090
LGA    I     9_C      I     9_C     2.252     0    0.070   0.891     4.172   66.786   56.071
LGA    L    10_C      L    10_C     0.737     0    0.290   0.384     1.899   86.071   86.131
LGA    P    11_C      P    11_C     0.698     0    0.031   0.077     0.999   92.857   93.197
LGA    C    12_C      C    12_C     0.702     0    0.078   0.103     0.943   90.476   90.476
LGA    P    13_C      P    13_C     0.805     0    0.019   0.255     1.929   90.476   86.667
LGA    R    14_C      R    14_C     1.103     0    0.187   0.986     2.923   81.548   75.411
LGA    C    15_C      C    15_C     1.116     0    0.021   0.157     1.227   83.690   84.444
LGA    N    16_C      N    16_C     0.792     0    0.166   0.267     0.973   90.476   90.476
LGA    S    17_C      S    17_C     0.714     0    0.048   0.125     0.808   90.476   90.476
LGA    M    18_C      M    18_C     0.634     0    0.051   0.585     2.199   90.476   86.131
LGA    E    19_C      E    19_C     0.370     4    0.032   0.030     0.378  100.000   55.556
LGA    T    20_C      T    20_C     0.458     0    0.019   0.096     0.795   95.238   95.918
LGA    K    21_C      K    21_C     0.901     0    0.047   0.468     1.604   90.476   86.508
LGA    F    22_C      F    22_C     0.726     0    0.094   0.639     2.773   90.476   81.861
LGA    C    23_C      C    23_C     0.792     0    0.172   0.821     3.052   88.214   82.222
LGA    Y    24_C      Y    24_C     0.228     0    0.715   1.260    12.571   78.690   37.976
LGA    Y    25_C      Y    25_C     5.519     0    0.038   1.325    17.047   34.762   11.984
LGA    N    26_C      N    26_C     3.757     0    0.558   0.615     4.896   45.476   38.452
LGA    N    27_C      N    27_C     3.537     0    0.148   1.116     8.523   52.143   34.048
LGA    Y    28_C      Y    28_C     2.345     0    0.417   0.266     5.132   55.595   65.437
LGA    N    29_C      N    29_C     1.295     0    0.086   0.842     6.454   67.262   49.226
LGA    V    30_C      V    30_C     1.155     0    0.151   0.132     1.342   81.429   81.429
LGA    N    31_C      N    31_C     0.485     0    0.024   0.319     2.344   95.238   85.238
LGA    Q    32_C      Q    32_C     1.039     0    0.044   0.226     2.524   81.548   77.831
LGA    P    33_C      P    33_C     1.356     0    0.063   0.095     1.429   81.429   82.721
LGA    R    34_C      R    34_C     0.884     0    0.029   1.248     4.747   88.214   74.329
LGA    H    35_C      H    35_C     0.707     0    0.069   1.068     3.022   90.476   82.952
LGA    F    36_C      F    36_C     0.528     0    0.035   0.100     0.725   90.476   93.939
LGA    C    37_C      C    37_C     0.705     0    0.010   0.807     3.084   90.476   82.222
LGA    K    38_C      K    38_C     0.437     0    0.043   0.460     1.071   92.857   93.704
LGA    A    39_C      A    39_C     0.422     0    0.170   0.177     1.394   92.976   92.476
LGA    C    40_C      C    40_C     0.800     0    0.080   0.737     1.500   90.476   86.032
LGA    Q    41_C      Q    41_C     0.856     0    0.081   0.110     1.156   90.476   87.460
LGA    R    42_C      R    42_C     0.610     0    0.081   1.496     6.958   88.214   63.593
LGA    Y    43_C      Y    43_C     0.661     0    0.028   0.085     1.126   90.476   89.722
LGA    W    44_C      W    44_C     0.449     0    0.079   0.195     0.700   95.238   97.279
LGA    T    45_C      T    45_C     0.969     0    0.027   0.073     2.219   86.071   78.095
LGA    S    46_C      S    46_C     0.703     0    0.648   0.796     2.999   82.262   80.714
LGA    G    47_C      G    47_C     1.774     0    0.706   0.706     2.143   72.976   72.976
LGA    G    48_C      G    48_C     3.240     0    0.111   0.111     4.180   50.357   50.357
LGA    T    49_C      T    49_C     2.546     0    0.423   0.992     4.555   47.619   52.177
LGA    M    50_C      M    50_C     8.984     0    0.579   1.132    13.350    4.524    2.262
LGA    R    51_C      R    51_C    10.023     0    0.486   0.616    12.169    0.357   10.823
LGA    S    52_C      S    52_C    16.784     0    0.568   0.762    20.945    0.000    0.000
LGA    V    53_C      V    53_C    16.618     0    0.534   1.477    19.278    0.000    0.000
LGA    P    54_C      P    54_C    16.520     0    0.530   0.503    16.520    0.000    0.000
LGA    I    55_C      I    55_C    17.113     0    0.559   1.205    20.044    0.000    0.000
LGA    G    56_C      G    56_C    19.513     0    0.660   0.660    19.705    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):     5.103          5.200                  5.511           67.864   62.334

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   65   51    4.0     42    1.57    75.980    77.763     2.520

LGA_LOCAL      RMSD:   1.566  Number of atoms:   42  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   6.028  Number of assigned atoms:   51 
Std_ASGN_ATOMS RMSD:   5.103  Standard rmsd on all 51 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.434243 * X  +  -0.636973 * Y  +   0.636944 * Z  + -15.926663
  Y_new =   0.216154 * X  +   0.612749 * Y  +   0.760142 * Z  + -35.490036
  Z_new =  -0.874477 * X  +   0.467764 * Y  +  -0.128398 * Z  +  -2.448491 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.679729  1.064357  1.838690   [DEG:  153.5371   60.9832  105.3492 ]
ZXZ:  2.444149  1.699549 -1.079614   [DEG:  140.0394   97.3770  -61.8573 ]
 
# END of job
