
#######################################################
#                                                     #
#                        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:    30       8_C - 37_C        4.94     7.72
  LONGEST_CONTINUOUS_SEGMENT:    30       9_C - 38_C        4.87     7.58
  LCS_AVERAGE:     52.25

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15       9_C - 23_C        1.91     9.68
  LCS_AVERAGE:     19.15

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11       9_C - 19_C        0.65    10.61
  LCS_AVERAGE:     11.61

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    4   23      3    3    3    6    8    8    9   14   16   18   20   21   24   27   28   31   33   35   39   42 
LCS_GDT     T     7_C     T     7_C      3    4   28      3    3    4    6   10   15   19   21   23   24   26   29   32   36   37   40   41   43   45   46 
LCS_GDT     K     8_C     K     8_C      3   14   30      3    3    3    4    6   10   10   19   23   24   26   29   30   36   37   40   41   43   45   46 
LCS_GDT     I     9_C     I     9_C     11   15   30      6   11   13   15   16   17   19   21   23   24   29   33   35   36   38   40   41   43   45   46 
LCS_GDT     L    10_C     L    10_C     11   15   30      7   11   13   15   16   17   19   21   23   24   29   33   35   36   38   40   41   43   45   46 
LCS_GDT     P    11_C     P    11_C     11   15   30      7   11   13   15   16   17   19   21   23   24   29   33   35   36   38   40   41   43   45   46 
LCS_GDT     C    12_C     C    12_C     11   15   30      7   11   13   15   16   17   19   21   23   24   29   33   35   36   38   40   41   43   45   46 
LCS_GDT     P    13_C     P    13_C     11   15   30      7   11   13   15   16   17   19   21   23   24   29   33   35   36   38   40   41   43   45   46 
LCS_GDT     R    14_C     R    14_C     11   15   30      7   11   13   15   16   17   19   21   23   24   29   33   35   36   38   40   41   43   45   46 
LCS_GDT     C    15_C     C    15_C     11   15   30      4   11   13   15   16   17   19   21   23   24   29   33   35   36   38   40   41   43   45   46 
LCS_GDT     N    16_C     N    16_C     11   15   30      7   11   13   15   16   17   19   21   23   24   29   33   35   36   38   40   41   43   45   46 
LCS_GDT     S    17_C     S    17_C     11   15   30      7   11   13   15   16   17   19   21   23   24   29   33   35   36   38   40   41   43   45   46 
LCS_GDT     M    18_C     M    18_C     11   15   30      6   11   13   15   16   17   19   21   23   24   29   33   35   36   38   40   41   43   45   46 
LCS_GDT     E    19_C     E    19_C     11   15   30      5   10   12   12   13   17   19   21   23   24   29   33   35   36   38   40   41   43   45   46 
LCS_GDT     T    20_C     T    20_C      8   15   30      3    6    9   12   13   17   19   21   23   24   29   33   35   36   38   40   41   43   45   46 
LCS_GDT     K    21_C     K    21_C      8   15   30      3    6    9   12   13   15   19   21   23   24   29   33   35   36   38   40   41   43   45   46 
LCS_GDT     F    22_C     F    22_C      4   15   30      3    3    4    9   13   15   16   21   23   24   29   33   35   36   38   40   41   43   45   46 
LCS_GDT     C    23_C     C    23_C      5   15   30      3    5    5    6    8   10   18   21   23   24   29   33   35   36   38   40   41   43   45   46 
LCS_GDT     Y    24_C     Y    24_C      5    8   30      3    3    5    6    9   10   12   15   19   24   29   33   35   36   38   40   41   43   45   46 
LCS_GDT     Y    25_C     Y    25_C      5    8   30      3    3    5    6    8   10   12   15   19   23   29   33   35   36   38   40   41   43   45   46 
LCS_GDT     N    26_C     N    26_C      5    8   30      3    4    5    6    8   10   12   15   18   23   27   32   33   36   38   40   41   43   45   46 
LCS_GDT     N    27_C     N    27_C      5    8   30      3    4    5    5    8   10   12   15   16   20   24   29   32   36   38   40   41   43   45   46 
LCS_GDT     Y    28_C     Y    28_C      4    8   30      3    4    4    6    7   10   12   13   14   16   20   24   29   32   36   40   40   43   45   46 
LCS_GDT     N    29_C     N    29_C      4    8   30      3    4    5    6    8   10   12   15   18   24   29   33   35   36   38   40   41   43   45   46 
LCS_GDT     V    30_C     V    30_C      4    8   30      3    4    4    6    8   10   12   13   20   24   28   33   35   36   38   40   41   43   45   46 
LCS_GDT     N    31_C     N    31_C      4    8   30      3    4    5    9   10   12   15   17   20   24   29   33   35   36   38   40   41   43   45   46 
LCS_GDT     Q    32_C     Q    32_C      3    8   30      3    4    5    8    9   12   14   17   19   24   29   33   35   36   38   40   41   43   45   46 
LCS_GDT     P    33_C     P    33_C      3    8   30      3    3    5    6    7   10   14   17   20   24   29   33   35   36   38   40   41   43   45   46 
LCS_GDT     R    34_C     R    34_C      5    8   30      3    4    6    7   12   17   18   19   20   23   27   32   33   36   38   40   41   43   45   46 
LCS_GDT     H    35_C     H    35_C      5    8   30      4    4    6    7   16   17   18   20   22   24   28   33   35   36   38   40   41   43   45   46 
LCS_GDT     F    36_C     F    36_C      5    8   30      4    4    6    7   12   17   18   20   23   24   29   33   35   36   38   40   41   43   45   46 
LCS_GDT     C    37_C     C    37_C      5    8   30      6   11   13   15   16   17   19   21   23   24   29   33   35   36   38   40   41   43   45   46 
LCS_GDT     K    38_C     K    38_C      5    8   30      4    9   13   15   16   17   19   21   23   24   27   32   35   36   38   40   41   43   45   46 
LCS_GDT     A    39_C     A    39_C      5    8   21      4    5    6   15   16   17   19   21   23   24   26   29   30   33   38   39   41   43   45   46 
LCS_GDT     C    40_C     C    40_C      5    8   21      4    9   13   15   16   17   19   21   23   24   26   29   30   32   34   38   41   43   45   46 
LCS_GDT     Q    41_C     Q    41_C      5    8   21      3    5   13   15   16   17   19   21   23   24   26   27   30   32   33   36   41   43   45   46 
LCS_GDT     R    42_C     R    42_C      3    4   21      3    3    3    3    6    8   15   18   23   24   26   30   35   35   38   40   41   43   45   46 
LCS_GDT     Y    43_C     Y    43_C      3    4   21      1    3    5    8   12   14   14   16   20   24   29   33   35   36   38   40   41   43   45   46 
LCS_GDT     W    44_C     W    44_C      3    3   21      3    4    6   11   12   14   14   16   20   24   29   33   35   36   38   40   41   43   45   46 
LCS_GDT     T    45_C     T    45_C      4    5   21      4    5    7   11   12   14   14   16   20   24   26   30   35   36   38   40   41   43   45   46 
LCS_GDT     S    46_C     S    46_C      4    5   21      4    4    6    6    8   11   14   16   16   17   18   18   21   21   24   25   31   32   35   37 
LCS_GDT     G    47_C     G    47_C      4    5   21      4    4    4    5    6    6    7    9   14   17   18   18   21   21   24   25   29   32   35   37 
LCS_GDT     G    48_C     G    48_C      4    9   21      4    4    7   11   12   14   14   16   16   18   21   27   30   34   38   40   41   42   45   46 
LCS_GDT     T    49_C     T    49_C      5    9   21      3    5    7   11   12   14   14   16   16   19   25   30   35   36   38   40   41   43   45   46 
LCS_GDT     M    50_C     M    50_C      5    9   21      3    4    6    9   12   14   14   16   20   24   29   33   35   36   38   40   41   43   45   46 
LCS_GDT     R    51_C     R    51_C      5    9   21      3    5    7   11   12   14   15   17   20   24   29   33   35   36   38   40   41   43   45   46 
LCS_GDT     S    52_C     S    52_C      5    9   21      3    5    7   11   12   14   15   17   20   24   29   33   35   36   38   40   41   43   45   46 
LCS_GDT     V    53_C     V    53_C      5    9   21      3    5    7   11   12   14   15   17   20   24   29   33   35   36   38   40   41   43   45   46 
LCS_GDT     P    54_C     P    54_C      5    9   21      3    5    7   11   12   14   14   16   18   24   28   33   35   36   38   40   41   43   45   46 
LCS_GDT     I    55_C     I    55_C      5    9   21      3    5    6   11   12   14   14   16   18   24   27   33   35   36   38   40   41   43   45   46 
LCS_GDT     G    56_C     G    56_C      5    9   21      0    3    5    6    9   13   13   16   16   18   20   24   29   31   36   37   39   40   43   45 
LCS_AVERAGE  LCS_A:  27.67  (  11.61   19.15   52.25 )

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     11     13     15     16     17     19     21     23     24     29     33     35     36     38     40     41     43     45     46 
GDT PERCENT_AT  13.73  21.57  25.49  29.41  31.37  33.33  37.25  41.18  45.10  47.06  56.86  64.71  68.63  70.59  74.51  78.43  80.39  84.31  88.24  90.20
GDT RMS_LOCAL    0.29   0.59   0.95   1.17   1.45   1.63   2.25   2.61   2.85   2.96   4.11   4.39   4.60   4.70   4.91   5.15   5.29   5.55   5.83   5.96
GDT RMS_ALL_AT  10.45  10.91  11.77  12.19  11.99  11.86  12.48  12.08  12.13  11.83   7.12   7.13   7.11   7.19   7.16   7.14   7.17   7.20   7.25   7.18

# Checking swapping
#   possible swapping detected:  F    22_C      F    22_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     9.297     2    0.105   0.104    10.808   11.548    6.599
LGA    T     7_C      T     7_C     3.842     0    0.299   1.016     7.482   42.143   32.313
LGA    K     8_C      K     8_C     4.933     4    0.557   0.543     6.409   39.524   19.471
LGA    I     9_C      I     9_C     2.716     0    0.623   1.417     7.367   62.976   40.298
LGA    L    10_C      L    10_C     1.914     0    0.023   0.096     3.218   72.976   67.083
LGA    P    11_C      P    11_C     1.478     0    0.056   0.196     1.792   79.286   78.980
LGA    C    12_C      C    12_C     0.650     0    0.063   0.140     0.895   95.238   95.238
LGA    P    13_C      P    13_C     1.136     0    0.062   0.155     1.647   81.548   79.048
LGA    R    14_C      R    14_C     1.652     0    0.018   1.685    12.476   72.976   38.918
LGA    C    15_C      C    15_C     1.999     0    0.163   0.645     2.683   75.000   70.317
LGA    N    16_C      N    16_C     0.786     0    0.203   0.720     3.200   88.214   76.905
LGA    S    17_C      S    17_C     1.413     0    0.112   0.188     1.757   81.429   78.571
LGA    M    18_C      M    18_C     1.893     0    0.191   0.920     2.902   70.833   67.857
LGA    E    19_C      E    19_C     2.979     4    0.290   0.296     4.182   57.143   29.524
LGA    T    20_C      T    20_C     2.761     0    0.117   0.978     4.888   69.286   60.476
LGA    K    21_C      K    21_C     3.266     0    0.179   0.751     7.901   40.714   30.688
LGA    F    22_C      F    22_C     4.804     0    0.188   0.815     9.403   43.810   19.870
LGA    C    23_C      C    23_C     4.315     0    0.575   0.979     6.454   27.143   34.841
LGA    Y    24_C      Y    24_C     8.987     0    0.040   1.411    10.373    4.762    3.571
LGA    Y    25_C      Y    25_C    11.091     0    0.209   0.220    13.613    0.000    0.040
LGA    N    26_C      N    26_C    12.217     0    0.074   0.464    14.129    0.000    0.000
LGA    N    27_C      N    27_C    17.557     0    0.620   1.310    19.521    0.000    0.000
LGA    Y    28_C      Y    28_C    22.654     0    0.056   1.445    28.315    0.000    0.000
LGA    N    29_C      N    29_C    20.060     0    0.192   0.309    20.352    0.000    0.000
LGA    V    30_C      V    30_C    21.302     0    0.171   1.070    22.959    0.000    0.000
LGA    N    31_C      N    31_C    16.848     0    0.498   1.044    18.327    0.000    0.000
LGA    Q    32_C      Q    32_C    11.935     0    0.468   0.575    14.407    0.119    0.053
LGA    P    33_C      P    33_C    10.090     0    0.081   0.482    11.693    0.476    0.272
LGA    R    34_C      R    34_C     7.963     0    0.159   1.169    12.167    6.667    2.597
LGA    H    35_C      H    35_C     5.774     0    0.106   0.834     6.478   19.286   21.667
LGA    F    36_C      F    36_C     4.768     0    0.116   1.094    10.579   39.405   17.446
LGA    C    37_C      C    37_C     0.836     0    0.347   1.048     2.705   71.310   73.254
LGA    K    38_C      K    38_C     2.723     0    0.116   0.796     4.811   54.286   48.571
LGA    A    39_C      A    39_C     3.199     0    0.085   0.105     3.311   53.571   52.857
LGA    C    40_C      C    40_C     1.914     0    0.206   0.806     2.197   68.810   71.587
LGA    Q    41_C      Q    41_C     3.110     0    0.389   1.519     7.722   67.500   36.720
LGA    R    42_C      R    42_C     4.833     0    0.564   0.820    13.499   26.667   11.255
LGA    Y    43_C      Y    43_C    10.244     0    0.586   1.468    17.324    1.786    0.595
LGA    W    44_C      W    44_C    12.135     0    0.569   1.269    15.360    0.000    0.034
LGA    T    45_C      T    45_C    15.687     0    0.587   1.017    18.990    0.000    0.000
LGA    S    46_C      S    46_C    21.533     0    0.538   0.810    24.903    0.000    0.000
LGA    G    47_C      G    47_C    25.567     0    0.250   0.250    26.650    0.000    0.000
LGA    G    48_C      G    48_C    21.715     0    0.649   0.649    22.449    0.000    0.000
LGA    T    49_C      T    49_C    21.465     0    0.039   0.068    25.276    0.000    0.000
LGA    M    50_C      M    50_C    16.835     0    0.040   0.685    19.606    0.000    0.000
LGA    R    51_C      R    51_C    16.859     0    0.036   1.510    25.506    0.000    0.000
LGA    S    52_C      S    52_C    15.128     0    0.067   0.729    17.936    0.000    0.000
LGA    V    53_C      V    53_C    15.605     0    0.050   1.124    15.676    0.000    0.000
LGA    P    54_C      P    54_C    17.579     0    0.169   0.230    20.316    0.000    0.000
LGA    I    55_C      I    55_C    15.172     0    0.212   0.754    17.839    0.000    0.000
LGA    G    56_C      G    56_C    19.040     0    0.625   0.625    22.376    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):     7.059          7.047                  7.694           29.930   24.853

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   65   51    4.0     21    2.61    42.647    36.770     0.775

LGA_LOCAL      RMSD:   2.611  Number of atoms:   21  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  12.082  Number of assigned atoms:   51 
Std_ASGN_ATOMS RMSD:   7.059  Standard rmsd on all 51 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.155901 * X  +   0.202899 * Y  +   0.966709 * Z  + -61.570034
  Y_new =  -0.980419 * X  +   0.087415 * Y  +  -0.176459 * Z  +   2.970914
  Z_new =  -0.120308 * X  +  -0.975290 * Y  +   0.185298 * Z  +   4.881589 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.728491  0.120600 -1.383041   [DEG:  -99.0352    6.9099  -79.2424 ]
ZXZ:  1.390248  1.384421 -3.018857   [DEG:   79.6554   79.3215 -172.9677 ]
 
# END of job
