
#######################################################
#                                                     #
#                        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:    41       6_C - 46_C        4.77     7.12
  LCS_AVERAGE:     73.13

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    16       7_C - 22_C        1.81     8.11
  LCS_AVERAGE:     22.38

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10      10_C - 19_C        0.98     7.60
  LCS_AVERAGE:     11.15

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      5    9   41      3    5    5    7    9   12   16   19   21   22   29   31   35   36   40   41   42   43   45   45 
LCS_GDT     T     7_C     T     7_C      5   16   41      3    5    5    8   12   18   23   28   31   33   35   38   39   40   41   42   43   44   45   45 
LCS_GDT     K     8_C     K     8_C      5   16   41      3    5   11   17   22   24   27   31   32   33   35   38   39   40   41   42   43   44   45   45 
LCS_GDT     I     9_C     I     9_C      5   16   41      3    5   10   17   22   24   27   31   32   33   36   38   39   40   41   42   43   44   45   45 
LCS_GDT     L    10_C     L    10_C     10   16   41      3    7   13   17   22   24   27   31   32   33   36   38   39   40   41   42   43   44   45   45 
LCS_GDT     P    11_C     P    11_C     10   16   41      4    8   13   17   22   24   27   31   32   33   36   38   39   40   41   42   43   44   45   45 
LCS_GDT     C    12_C     C    12_C     10   16   41      3    8   13   17   22   24   27   31   32   33   36   38   39   40   41   42   43   44   45   45 
LCS_GDT     P    13_C     P    13_C     10   16   41      3    8   13   17   22   24   27   31   32   33   36   38   39   40   41   42   43   44   45   45 
LCS_GDT     R    14_C     R    14_C     10   16   41      4    8   13   17   22   24   27   31   32   33   36   38   39   40   41   42   43   44   45   45 
LCS_GDT     C    15_C     C    15_C     10   16   41      3    8   13   16   22   24   27   31   32   33   36   38   39   40   41   42   43   44   45   45 
LCS_GDT     N    16_C     N    16_C     10   16   41      4    8   13   17   22   24   27   31   32   33   36   38   39   40   41   42   43   44   45   45 
LCS_GDT     S    17_C     S    17_C     10   16   41      4    8   13   17   22   24   27   31   32   33   36   38   39   40   41   42   43   44   45   45 
LCS_GDT     M    18_C     M    18_C     10   16   41      3    7   13   17   22   24   27   31   32   33   36   38   39   40   41   42   43   44   45   45 
LCS_GDT     E    19_C     E    19_C     10   16   41      3    7   11   16   19   23   27   31   32   33   36   38   39   40   41   42   43   44   45   45 
LCS_GDT     T    20_C     T    20_C      6   16   41      3    6   11   14   17   21   26   31   32   33   36   38   39   40   41   42   43   44   45   45 
LCS_GDT     K    21_C     K    21_C      6   16   41      3    6   11   14   17   21   26   31   32   33   36   38   39   40   41   42   43   44   45   45 
LCS_GDT     F    22_C     F    22_C      5   16   41      3    4    5    5   16   20   23   31   32   33   36   38   39   40   41   42   43   44   45   45 
LCS_GDT     C    23_C     C    23_C      5    8   41      3    4    5    7    8   10   13   18   28   33   36   38   39   40   41   42   43   44   45   45 
LCS_GDT     Y    24_C     Y    24_C      5    8   41      3    4    5    7    8   10   15   19   28   33   36   38   39   40   41   42   43   44   45   45 
LCS_GDT     Y    25_C     Y    25_C      4    8   41      3    4    5    7    8   10   12   16   25   33   35   38   39   40   41   42   43   44   45   45 
LCS_GDT     N    26_C     N    26_C      4    8   41      3    4    5    7    9   12   16   28   30   33   35   38   39   40   41   42   43   44   45   45 
LCS_GDT     N    27_C     N    27_C      4    8   41      3    4    5    7    9   10   12   17   26   33   35   37   39   40   40   42   43   44   45   45 
LCS_GDT     Y    28_C     Y    28_C      4    8   41      3    4    5    6    9   10   12   15   18   27   34   37   39   40   40   42   43   44   45   45 
LCS_GDT     N    29_C     N    29_C      4    8   41      3    4    5    6   10   18   26   31   32   33   36   38   39   40   41   42   43   44   45   45 
LCS_GDT     V    30_C     V    30_C      4    5   41      3    4    4    5    9   20   26   29   32   33   36   38   39   40   41   42   43   44   45   45 
LCS_GDT     N    31_C     N    31_C      5   13   41      3    4   12   17   22   24   27   31   32   33   36   38   39   40   41   42   43   44   45   45 
LCS_GDT     Q    32_C     Q    32_C      5   13   41      3    8   13   17   22   24   27   31   32   33   36   38   39   40   41   42   43   44   45   45 
LCS_GDT     P    33_C     P    33_C      5   13   41      4    8   13   17   22   24   27   31   32   33   36   38   39   40   41   42   43   44   45   45 
LCS_GDT     R    34_C     R    34_C      5   13   41      4    8   11   17   22   24   27   31   32   33   36   38   39   40   41   42   43   44   45   45 
LCS_GDT     H    35_C     H    35_C      5   13   41      4    5   11   17   22   24   27   31   32   33   36   38   39   40   41   42   43   44   45   45 
LCS_GDT     F    36_C     F    36_C      6   13   41      4    5   10   17   22   24   27   31   32   33   36   38   39   40   41   42   43   44   45   45 
LCS_GDT     C    37_C     C    37_C      6   13   41      4    8   13   17   22   24   27   31   32   33   36   38   39   40   41   42   43   44   45   45 
LCS_GDT     K    38_C     K    38_C      6   13   41      3    6    8   15   20   24   27   31   32   33   36   38   39   40   41   42   43   44   45   45 
LCS_GDT     A    39_C     A    39_C      6   13   41      3    4    7   15   20   24   27   31   32   33   36   38   39   40   41   42   43   44   45   45 
LCS_GDT     C    40_C     C    40_C      6   13   41      3    4    7   15   22   24   27   31   32   33   36   38   39   40   41   42   43   44   45   45 
LCS_GDT     Q    41_C     Q    41_C      6   13   41      3    6    7   15   22   24   27   31   32   33   36   38   39   40   41   42   43   44   45   45 
LCS_GDT     R    42_C     R    42_C      5   13   41      3    6    8   16   22   24   27   31   32   33   36   38   39   40   41   42   43   44   45   45 
LCS_GDT     Y    43_C     Y    43_C      4   13   41      3    4    7   13   22   24   27   31   32   33   36   38   39   40   41   42   43   44   45   45 
LCS_GDT     W    44_C     W    44_C      4   12   41      3    4    6    8   19   24   27   31   32   33   36   38   39   40   41   42   43   44   45   45 
LCS_GDT     T    45_C     T    45_C      4    9   41      3    4    6    7    9   14   15   26   30   33   36   37   39   40   41   42   43   44   45   45 
LCS_GDT     S    46_C     S    46_C      4    9   41      3    4    4    7    9   10   11   14   15   17   22   25   32   33   36   38   39   41   42   44 
LCS_GDT     G    47_C     G    47_C      4    5   23      3    4    5    7    7   10   11   13   14   17   18   21   22   22   25   33   35   38   39   41 
LCS_GDT     G    48_C     G    48_C      4    5   23      3    4    5    5    9   10   11   14   15   21   22   25   32   35   39   39   41   41   43   44 
LCS_GDT     T    49_C     T    49_C      4    5   23      3    3    5    5    8   16   20   28   29   33   36   37   38   40   41   42   43   44   45   45 
LCS_GDT     M    50_C     M    50_C      3    6   23      2    3    5    5    9   16   20   28   29   33   36   37   39   40   41   42   43   44   45   45 
LCS_GDT     R    51_C     R    51_C      4    6   23      0    7   13   16   19   22   27   31   32   33   36   38   39   40   41   42   43   44   45   45 
LCS_GDT     S    52_C     S    52_C      4    6   22      3    4    5    5    8   10   17   23   26   29   32   36   39   40   41   42   43   44   45   45 
LCS_GDT     V    53_C     V    53_C      4    6   21      3    4    5    7   13   16   21   27   29   32   35   38   39   40   40   42   43   44   45   45 
LCS_GDT     P    54_C     P    54_C      4    6   21      3    4    5    5    7    8   10   13   14   15   17   20   21   25   33   34   40   41   43   44 
LCS_GDT     I    55_C     I    55_C      3    6   21      3    3    5    5    9   10   11   13   14   15   17   18   20   21   27   38   40   40   42   44 
LCS_GDT     G    56_C     G    56_C      3    6   21      3    3    4    5    9   10   11   13   14   15   16   17   19   20   20   21   24   25   26   27 
LCS_AVERAGE  LCS_A:  35.55  (  11.15   22.38   73.13 )

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      4      8     13     17     22     24     27     31     32     33     36     38     39     40     41     42     43     44     45     45 
GDT PERCENT_AT   7.84  15.69  25.49  33.33  43.14  47.06  52.94  60.78  62.75  64.71  70.59  74.51  76.47  78.43  80.39  82.35  84.31  86.27  88.24  88.24
GDT RMS_LOCAL    0.34   0.72   0.99   1.45   1.74   1.87   2.18   2.64   2.78   2.90   3.61   3.68   3.86   4.04   4.10   4.28   4.46   4.64   4.81   4.81
GDT RMS_ALL_AT   7.14   7.11   7.39   7.05   7.05   7.10   7.09   7.03   7.03   7.03   7.20   7.08   7.16   7.23   7.12   7.16   7.14   7.13   7.11   7.11

# Checking swapping
#   possible swapping detected:  F    36_C      F    36_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     9.003     2    0.638   0.607    10.827    5.119    2.925
LGA    T     7_C      T     7_C     5.427     0    0.066   0.095     7.653   34.167   28.095
LGA    K     8_C      K     8_C     1.773     4    0.086   0.093     3.031   69.286   37.989
LGA    I     9_C      I     9_C     1.533     0    0.089   1.476     6.373   77.143   59.226
LGA    L    10_C      L    10_C     1.203     0    0.244   0.349     2.414   75.119   80.536
LGA    P    11_C      P    11_C     0.806     0    0.358   0.364     2.518   82.143   84.422
LGA    C    12_C      C    12_C     1.435     0    0.265   0.479     3.506   65.595   72.381
LGA    P    13_C      P    13_C     1.163     0    0.054   0.122     1.734   79.286   81.497
LGA    R    14_C      R    14_C     1.290     0    0.246   2.156    10.036   75.119   45.108
LGA    C    15_C      C    15_C     2.363     0    0.570   0.482     4.111   59.881   58.968
LGA    N    16_C      N    16_C     0.728     0    0.377   0.405     1.398   85.952   85.952
LGA    S    17_C      S    17_C     1.329     0    0.147   0.515     1.508   81.429   80.000
LGA    M    18_C      M    18_C     2.202     0    0.249   0.666     3.040   66.786   64.940
LGA    E    19_C      E    19_C     2.981     4    0.504   0.469     4.430   50.357   27.196
LGA    T    20_C      T    20_C     3.381     0    0.183   1.154     6.470   57.262   44.966
LGA    K    21_C      K    21_C     3.885     0    0.355   0.693     6.083   33.690   47.566
LGA    F    22_C      F    22_C     4.577     0    0.102   1.021     6.860   31.786   26.580
LGA    C    23_C      C    23_C     7.163     0    0.613   0.660     9.474    8.929    7.937
LGA    Y    24_C      Y    24_C     7.777     0    0.203   1.285    14.290   14.167    5.794
LGA    Y    25_C      Y    25_C     8.579     0    0.052   1.421    15.075    1.429    0.476
LGA    N    26_C      N    26_C     8.107     0    0.140   1.023     8.987    5.119   11.667
LGA    N    27_C      N    27_C    11.131     0    0.293   0.432    13.856    0.000    0.000
LGA    Y    28_C      Y    28_C    11.179     0    0.630   1.235    20.017    0.357    0.119
LGA    N    29_C      N    29_C     5.480     0    0.060   1.147     6.893   20.595   40.357
LGA    V    30_C      V    30_C     6.072     0    0.123   0.134    10.681   32.619   21.088
LGA    N    31_C      N    31_C     1.886     0    0.092   0.442     7.051   55.238   42.976
LGA    Q    32_C      Q    32_C     2.215     0    0.055   0.744     6.110   67.024   44.921
LGA    P    33_C      P    33_C     0.617     0    0.086   0.778     3.632   83.810   77.415
LGA    R    34_C      R    34_C     0.963     0    0.234   1.452     7.743   75.952   50.173
LGA    H    35_C      H    35_C     1.884     0    0.155   0.846     8.211   77.381   41.048
LGA    F    36_C      F    36_C     2.110     0    0.107   1.367    10.971   69.048   30.996
LGA    C    37_C      C    37_C     1.799     0    0.300   0.282     2.205   70.833   68.810
LGA    K    38_C      K    38_C     3.532     0    0.148   0.924     9.258   45.714   29.735
LGA    A    39_C      A    39_C     3.495     0    0.291   0.306     4.094   57.381   53.333
LGA    C    40_C      C    40_C     2.770     0    0.252   0.829     3.561   60.952   56.190
LGA    Q    41_C      Q    41_C     2.958     0    0.069   0.882     4.681   55.357   48.836
LGA    R    42_C      R    42_C     2.768     0    0.207   1.726     3.751   53.690   58.355
LGA    Y    43_C      Y    43_C     2.510     0    0.669   1.379     5.142   57.262   51.310
LGA    W    44_C      W    44_C     3.644     0    0.289   0.929     9.614   30.714   18.605
LGA    T    45_C      T    45_C     6.175     0    0.184   0.247     8.280   14.524   20.544
LGA    S    46_C      S    46_C    12.397     0    0.496   0.694    13.669    0.000    0.000
LGA    G    47_C      G    47_C    16.293     0    0.070   0.070    17.745    0.000    0.000
LGA    G    48_C      G    48_C    12.387     0    0.160   0.160    14.012    0.000    0.000
LGA    T    49_C      T    49_C     8.622     0    0.490   0.476     9.460    3.452    4.490
LGA    M    50_C      M    50_C     8.020     0    0.227   1.139    14.812    7.024    3.690
LGA    R    51_C      R    51_C     3.759     0    0.455   1.269    15.661   47.262   20.519
LGA    S    52_C      S    52_C     6.175     0    0.586   0.909     9.557   18.095   12.937
LGA    V    53_C      V    53_C     7.216     0    0.657   1.007     9.671    7.024    9.252
LGA    P    54_C      P    54_C    14.070     0    0.123   0.860    16.379    0.000    0.000
LGA    I    55_C      I    55_C    14.781     0    0.105   1.226    17.548    0.000    0.000
LGA    G    56_C      G    56_C    20.057     0    0.601   0.601    20.720    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):     6.974          7.049                  7.463           40.609   34.508

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   65   51    4.0     31    2.64    48.039    44.156     1.133

LGA_LOCAL      RMSD:   2.635  Number of atoms:   31  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   7.031  Number of assigned atoms:   51 
Std_ASGN_ATOMS RMSD:   6.974  Standard rmsd on all 51 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.808368 * X  +   0.508611 * Y  +   0.296405 * Z  + -31.378223
  Y_new =  -0.579065 * X  +   0.777636 * Y  +   0.244880 * Z  +  -8.193866
  Z_new =  -0.105946 * X  +  -0.369591 * Y  +   0.923135 * Z  +   5.142850 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.621607  0.106145 -0.380821   [DEG:  -35.6155    6.0817  -21.8194 ]
ZXZ:  2.261291  0.394641 -2.862421   [DEG:  129.5624   22.6112 -164.0046 ]
 
# END of job
