
#######################################################
#                                                     #
#                        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   55 (  468),  selected   47 , name one
# Molecule2: number of CA atoms  127 ( 1099),  selected   47 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:B  -ch2:C  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    46       4_C - 57_C        4.55     5.19
  LCS_AVERAGE:     36.07

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    24       4_C - 27_C        0.92     9.27
  LCS_AVERAGE:     16.54

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    24       4_C - 27_C        0.92     9.27
  LCS_AVERAGE:     15.90

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   47
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     Q     4_B     Q     4_C     24   24   46      9   19   23   24   24   27   29   40   42   43   43   43   43   44   44   44   45   45   46   46 
LCS_GDT     E     5_B     E     5_C     24   24   46     11   20   23   24   24   27   29   40   42   43   43   43   43   44   44   44   45   45   46   46 
LCS_GDT     E     6_B     E     6_C     24   24   46     11   20   23   24   24   27   29   39   42   43   43   43   43   44   44   44   45   45   46   46 
LCS_GDT     I     7_B     I     7_C     24   24   46     11   20   23   24   24   27   29   40   42   43   43   43   43   44   44   44   45   45   46   46 
LCS_GDT     Q     8_B     Q     8_C     24   24   46     10   20   23   24   24   27   29   40   42   43   43   43   43   44   44   44   45   45   46   46 
LCS_GDT     K     9_B     K     9_C     24   24   46      9   20   23   24   24   27   29   40   42   43   43   43   43   44   44   44   45   45   46   46 
LCS_GDT     K    10_B     K    10_C     24   24   46     11   20   23   24   24   27   29   40   42   43   43   43   43   44   44   44   45   45   46   46 
LCS_GDT     V    11_B     V    11_C     24   24   46     11   20   23   24   24   27   29   40   42   43   43   43   43   44   44   44   45   45   46   46 
LCS_GDT     R    12_B     R    12_C     24   24   46     10   20   23   24   24   27   29   40   42   43   43   43   43   44   44   44   45   45   46   46 
LCS_GDT     E    13_B     E    13_C     24   24   46     10   20   23   24   24   27   29   40   42   43   43   43   43   44   44   44   45   45   46   46 
LCS_GDT     L    14_B     L    14_C     24   24   46      8   20   23   24   24   27   29   40   42   43   43   43   43   44   44   44   45   45   46   46 
LCS_GDT     L    15_B     L    15_C     24   24   46     11   20   23   24   24   27   29   40   42   43   43   43   43   44   44   44   45   45   46   46 
LCS_GDT     E    16_B     E    16_C     24   24   46     11   20   23   24   24   27   29   40   42   43   43   43   43   44   44   44   45   45   46   46 
LCS_GDT     K    17_B     K    17_C     24   24   46     11   20   23   24   24   27   29   40   42   43   43   43   43   44   44   44   45   45   46   46 
LCS_GDT     L    18_B     L    18_C     24   24   46      7   20   23   24   24   27   29   40   42   43   43   43   43   44   44   44   45   45   46   46 
LCS_GDT     I    19_B     I    19_C     24   24   46     11   20   23   24   24   27   29   40   42   43   43   43   43   44   44   44   45   45   46   46 
LCS_GDT     E    20_B     E    20_C     24   24   46     11   20   23   24   24   27   29   40   42   43   43   43   43   44   44   44   45   45   46   46 
LCS_GDT     Y    21_B     Y    21_C     24   24   46      7   20   23   24   24   27   29   40   42   43   43   43   43   44   44   44   45   45   46   46 
LCS_GDT     L    22_B     L    22_C     24   24   46     11   20   23   24   24   27   29   40   42   43   43   43   43   44   44   44   45   45   46   46 
LCS_GDT     E    23_B     E    23_C     24   24   46      7   20   23   24   24   27   29   40   42   43   43   43   43   44   44   44   45   45   46   46 
LCS_GDT     E    24_B     E    24_C     24   24   46      7   18   23   24   24   27   29   40   42   43   43   43   43   44   44   44   45   45   46   46 
LCS_GDT     L    25_B     L    25_C     24   24   46      7   18   23   24   24   27   29   40   42   43   43   43   43   44   44   44   45   45   46   46 
LCS_GDT     K    26_B     K    26_C     24   24   46      7   20   23   24   24   27   29   40   42   43   43   43   43   44   44   44   45   45   46   46 
LCS_GDT     E    27_B     E    27_C     24   24   46      3    3    7   24   24   27   29   40   42   43   43   43   43   44   44   44   45   45   46   46 
LCS_GDT     K    34_B     K    34_C     19   20   46     14   16   18   18   19   23   29   40   42   43   43   43   43   44   44   44   45   45   46   46 
LCS_GDT     E    35_B     E    35_C     19   20   46     14   16   18   18   19   19   25   40   42   43   43   43   43   44   44   44   45   45   46   46 
LCS_GDT     K    36_B     K    36_C     19   20   46     14   16   18   18   19   19   25   40   42   43   43   43   43   44   44   44   45   45   46   46 
LCS_GDT     L    37_B     L    37_C     19   20   46     14   16   18   18   24   27   29   40   42   43   43   43   43   44   44   44   45   45   46   46 
LCS_GDT     E    38_B     E    38_C     19   20   46     14   16   18   18   19   19   25   40   42   43   43   43   43   44   44   44   45   45   46   46 
LCS_GDT     E    39_B     E    39_C     19   20   46     14   16   18   18   19   19   25   40   42   43   43   43   43   44   44   44   45   45   46   46 
LCS_GDT     V    40_B     V    40_C     19   20   46     14   16   18   18   19   26   29   40   42   43   43   43   43   44   44   44   45   45   46   46 
LCS_GDT     I    41_B     I    41_C     19   20   46     14   16   18   18   19   21   28   40   42   43   43   43   43   44   44   44   45   45   46   46 
LCS_GDT     E    42_B     E    42_C     19   20   46     14   16   18   18   19   19   25   40   42   43   43   43   43   44   44   44   45   45   46   46 
LCS_GDT     G    43_B     G    43_C     19   20   46     14   16   18   18   19   19   25   40   42   43   43   43   43   44   44   44   45   45   46   46 
LCS_GDT     L    44_B     L    44_C     19   20   46     14   16   18   18   24   27   29   40   42   43   43   43   43   44   44   44   45   45   46   46 
LCS_GDT     E    45_B     E    45_C     19   20   46     14   16   18   18   19   19   25   40   42   43   43   43   43   44   44   44   45   45   46   46 
LCS_GDT     R    46_B     R    46_C     19   20   46     14   16   18   18   19   19   25   39   42   43   43   43   43   44   44   44   45   45   46   46 
LCS_GDT     L    47_B     L    47_C     19   20   46      3   16   18   18   19   25   29   40   42   43   43   43   43   44   44   44   45   45   46   46 
LCS_GDT     K    48_B     K    48_C     19   20   46     14   16   18   18   19   19   27   40   42   43   43   43   43   44   44   44   45   45   46   46 
LCS_GDT     E    49_B     E    49_C     19   20   46     13   16   18   18   19   19   25   40   42   43   43   43   43   44   44   44   45   45   46   46 
LCS_GDT     E    50_B     E    50_C     19   20   46      4   13   18   18   19   19   28   40   42   43   43   43   43   44   44   44   45   45   46   46 
LCS_GDT     V    51_B     V    51_C     19   20   46      4   13   18   18   21   27   29   40   42   43   43   43   43   44   44   44   45   45   46   46 
LCS_GDT     D    52_B     D    52_C     19   20   46      3    3    4   13   19   19   25   27   37   43   43   43   43   44   44   44   45   45   46   46 
LCS_GDT     Q    55_B     Q    55_C      3   20   46      0    3    3    5   11   15   21   29   30   32   36   39   42   44   44   44   45   45   46   46 
LCS_GDT     L    56_B     L    56_C      3    5   46      1    3    3    3    5    6    9   18   20   27   29   33   37   38   41   44   45   45   46   46 
LCS_GDT     N    57_B     N    57_C      3    3   46      1    3    3    3    5   10   24   25   26   26   28   31   37   38   41   43   44   45   46   46 
LCS_GDT     M    58_B     M    58_C      3    3   37      0    3    3   13   21   23   24   25   26   26   26   26   27   29   30   31   34   35   37   38 
LCS_AVERAGE  LCS_A:  22.83  (  15.90   16.54   36.07 )

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     14     20     23     24     24     27     29     40     42     43     43     43     43     44     44     44     45     45     46     46 
GDT PERCENT_AT  11.02  15.75  18.11  18.90  18.90  21.26  22.83  31.50  33.07  33.86  33.86  33.86  33.86  34.65  34.65  34.65  35.43  35.43  36.22  36.22
GDT RMS_LOCAL    0.25   0.58   0.75   0.92   0.92   2.06   2.29   3.39   3.44   3.49   3.49   3.49   3.49   3.81   3.81   3.81   4.19   4.19   4.55   4.55
GDT RMS_ALL_AT  12.63   9.22   9.31   9.27   9.27   6.46   6.05   5.71   5.81   5.78   5.78   5.78   5.78   5.53   5.53   5.53   5.33   5.33   5.19   5.19

# Checking swapping
#   possible swapping detected:  E     6_B      E     6_C
#   possible swapping detected:  E    13_B      E    13_C
#   possible swapping detected:  E    16_B      E    16_C
#   possible swapping detected:  Y    21_B      Y    21_C
#   possible swapping detected:  E    24_B      E    24_C
#   possible swapping detected:  E    35_B      E    35_C
#   possible swapping detected:  E    39_B      E    39_C
#   possible swapping detected:  E    42_B      E    42_C

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    Q     4_B      Q     4_C     2.992     0    0.032   0.865     4.453   62.976   52.116
LGA    E     5_B      E     5_C     2.369     0    0.023   0.087     6.861   67.024   42.275
LGA    E     6_B      E     6_C     4.313     0    0.030   1.311     9.821   41.905   22.487
LGA    I     7_B      I     7_C     3.663     0    0.039   0.077     7.397   53.810   36.369
LGA    Q     8_B      Q     8_C     2.261     0    0.052   1.456     7.502   68.810   48.042
LGA    K     9_B      K     9_C     3.523     0    0.020   1.304    13.665   52.024   26.984
LGA    K    10_B      K    10_C     3.752     0    0.081   0.688     9.757   50.119   29.259
LGA    V    11_B      V    11_C     2.649     0    0.068   0.115     5.124   64.881   51.497
LGA    R    12_B      R    12_C     2.841     0    0.119   1.214    11.408   62.976   26.926
LGA    E    13_B      E    13_C     3.108     0    0.080   0.988     9.258   59.167   32.540
LGA    L    14_B      L    14_C     3.231     0    0.064   0.099     7.704   61.071   39.167
LGA    L    15_B      L    15_C     2.649     0    0.049   1.404     8.419   62.976   40.417
LGA    E    16_B      E    16_C     3.124     0    0.093   0.947     8.642   59.167   35.873
LGA    K    17_B      K    17_C     2.773     0    0.043   0.202     7.994   62.976   39.524
LGA    L    18_B      L    18_C     2.935     0    0.047   0.258     7.482   62.976   40.595
LGA    I    19_B      I    19_C     3.162     0    0.021   0.679     7.643   59.167   41.071
LGA    E    20_B      E    20_C     2.676     0    0.042   0.198     6.936   64.881   43.386
LGA    Y    21_B      Y    21_C     2.718     0    0.078   0.664     9.906   62.976   30.714
LGA    L    22_B      L    22_C     3.682     0    0.017   1.163     8.930   48.452   32.202
LGA    E    23_B      E    23_C     3.824     0    0.076   0.207     9.523   51.905   28.571
LGA    E    24_B      E    24_C     3.004     0    0.059   1.192    11.139   59.167   31.005
LGA    L    25_B      L    25_C     3.383     0    0.109   1.396    10.030   55.833   32.440
LGA    K    26_B      K    26_C     3.797     0    0.633   0.694     8.492   55.595   33.651
LGA    E    27_B      E    27_C     3.329     0    0.590   0.438     4.131   46.667   44.868
LGA    K    34_B      K    34_C     3.252     0    0.238   0.820    11.532   61.190   32.593
LGA    E    35_B      E    35_C     4.064     0    0.079   1.022    10.595   46.905   23.862
LGA    K    36_B      K    36_C     4.175     0    0.008   1.397     8.333   48.571   27.884
LGA    L    37_B      L    37_C     3.289     0    0.024   0.348     8.356   59.167   37.500
LGA    E    38_B      E    38_C     3.671     0    0.065   0.852     8.054   50.357   28.360
LGA    E    39_B      E    39_C     4.188     0    0.036   1.269    11.727   45.119   23.228
LGA    V    40_B      V    40_C     3.452     0    0.023   0.052     6.544   57.262   40.816
LGA    I    41_B      I    41_C     3.501     0    0.031   0.061     7.664   53.810   34.464
LGA    E    42_B      E    42_C     4.203     0    0.049   1.381    11.648   46.905   23.757
LGA    G    43_B      G    43_C     3.908     0    0.034   0.034     3.908   51.905   51.905
LGA    L    44_B      L    44_C     2.940     0    0.081   1.131     6.295   62.976   45.476
LGA    E    45_B      E    45_C     4.360     0    0.119   0.954    10.731   43.690   21.746
LGA    R    46_B      R    46_C     4.443     0    0.024   1.291    10.645   43.571   18.052
LGA    L    47_B      L    47_C     3.073     0    0.058   0.931     8.113   63.095   42.024
LGA    K    48_B      K    48_C     3.633     0    0.085   0.789    11.537   52.381   27.513
LGA    E    49_B      E    49_C     4.585     0    0.208   1.148     9.115   40.476   24.021
LGA    E    50_B      E    50_C     2.871     0    0.186   0.210     8.682   67.024   36.825
LGA    V    51_B      V    51_C     3.225     0    0.093   0.109     6.688   52.976   41.156
LGA    D    52_B      D    52_C     5.390     0    0.149   0.250    10.355   35.952   19.464
LGA    Q    55_B      Q    55_C    11.065     0    0.618   1.184    14.297    0.714    0.317
LGA    L    56_B      L    56_C    13.988     0    0.612   0.490    17.939    0.000    0.000
LGA    N    57_B      N    57_C    15.429     0    0.660   0.725    18.080    0.000    0.000
LGA    M    58_B      M    58_C    21.149     0    0.643   1.088    24.396    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       47     188    188  100.00     404    404  100.00               127
SUMMARY(RMSD_GDC):     5.134          5.000                  6.890           18.752   11.677

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   55  127    4.0     40    3.39    25.197    23.422     1.146

LGA_LOCAL      RMSD:   3.391  Number of atoms:   40  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   5.707  Number of assigned atoms:   47 
Std_ASGN_ATOMS RMSD:   5.134  Standard rmsd on all 47 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.051281 * X  +   0.152662 * Y  +   0.986947 * Z  + -45.199886
  Y_new =   0.984284 * X  +   0.174946 * Y  +   0.024082 * Z  + -40.094437
  Z_new =  -0.168986 * X  +   0.972671 * Y  +  -0.159234 * Z  +  62.631710 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.622849  0.169801  1.733065   [DEG:   92.9824    9.7289   99.2973 ]
ZXZ:  1.595192  1.730711 -0.172017   [DEG:   91.3977   99.1624   -9.8559 ]
 
# END of job
