
#######################################################
#                                                     #
#                        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:    33       7_C - 39_C        4.85     7.75
  LONGEST_CONTINUOUS_SEGMENT:    33       8_C - 40_C        4.92     7.65
  LONGEST_CONTINUOUS_SEGMENT:    33       9_C - 41_C        4.96     7.61
  LCS_AVERAGE:     57.75

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15       8_C - 22_C        1.89     9.48
  LONGEST_CONTINUOUS_SEGMENT:    15       9_C - 23_C        1.96     9.10
  LCS_AVERAGE:     19.18

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12       9_C - 20_C        0.80     9.72
  LCS_AVERAGE:     12.50

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   32      3    3    3    6    8    8    9   13   16   17   20   21   22   25   28   30   34   36   39   42 
LCS_GDT     T     7_C     T     7_C      3    4   33      3    3    4    6   12   15   19   21   22   23   26   28   31   36   39   42   43   46   47   48 
LCS_GDT     K     8_C     K     8_C      3   15   33      3    3    3    4    4    4    9   21   22   23   26   28   31   36   39   42   43   46   47   48 
LCS_GDT     I     9_C     I     9_C     12   15   33      7   11   12   14   15   17   19   21   24   27   32   35   38   39   41   42   44   46   47   48 
LCS_GDT     L    10_C     L    10_C     12   15   33      7   11   12   14   15   17   19   21   24   27   32   35   38   39   41   42   44   46   47   48 
LCS_GDT     P    11_C     P    11_C     12   15   33      6   11   12   14   15   17   19   21   24   27   32   35   38   39   41   42   44   46   47   48 
LCS_GDT     C    12_C     C    12_C     12   15   33      6   11   12   14   15   17   19   21   24   27   32   35   38   39   41   42   44   46   47   48 
LCS_GDT     P    13_C     P    13_C     12   15   33      6   11   12   14   15   17   19   21   24   27   32   35   38   39   41   42   44   46   47   48 
LCS_GDT     R    14_C     R    14_C     12   15   33      6   11   12   14   15   17   19   21   22   27   32   35   38   39   41   42   44   46   47   48 
LCS_GDT     C    15_C     C    15_C     12   15   33      7   11   12   14   15   17   19   21   22   27   32   35   38   39   41   42   44   46   47   48 
LCS_GDT     N    16_C     N    16_C     12   15   33      7   11   12   14   15   17   19   21   24   27   32   35   38   39   41   42   44   46   47   48 
LCS_GDT     S    17_C     S    17_C     12   15   33      7   11   12   14   15   17   19   21   24   27   32   35   38   39   41   42   44   46   47   48 
LCS_GDT     M    18_C     M    18_C     12   15   33      7   11   12   14   15   17   19   21   24   27   32   35   38   39   41   42   44   46   47   48 
LCS_GDT     E    19_C     E    19_C     12   15   33      7   11   12   14   14   17   19   21   24   27   32   35   38   39   41   42   44   46   47   48 
LCS_GDT     T    20_C     T    20_C     12   15   33      3    7   12   14   15   17   19   21   24   27   32   35   38   39   41   42   44   46   47   48 
LCS_GDT     K    21_C     K    21_C      8   15   33      3    7   10   14   14   15   19   21   24   27   32   35   38   39   41   42   44   46   47   48 
LCS_GDT     F    22_C     F    22_C      7   15   33      3    3   10   14   14   15   19   21   24   27   32   35   38   39   41   42   44   46   47   48 
LCS_GDT     C    23_C     C    23_C      5   15   33      3    5    5    7   10   10   12   17   24   27   32   35   38   39   41   42   44   46   47   48 
LCS_GDT     Y    24_C     Y    24_C      5    8   33      3    5    5    7   10   10   12   17   24   27   32   35   38   39   41   42   44   46   47   48 
LCS_GDT     Y    25_C     Y    25_C      5    8   33      3    5    5    6   10   10   12   17   21   26   32   35   38   39   41   42   44   46   47   48 
LCS_GDT     N    26_C     N    26_C      5    8   33      3    5    5    7   10   10   12   16   21   25   31   35   38   39   41   42   44   46   47   48 
LCS_GDT     N    27_C     N    27_C      5    8   33      3    5    5    7   10   10   12   15   21   25   31   35   38   38   41   42   44   46   47   48 
LCS_GDT     Y    28_C     Y    28_C      4    8   33      3    4    5    6    6    9   11   14   18   21   26   31   38   38   40   42   44   46   47   48 
LCS_GDT     N    29_C     N    29_C      4    8   33      3    4    5    7   10   10   16   20   24   27   32   35   38   39   41   42   44   46   47   48 
LCS_GDT     V    30_C     V    30_C      4    8   33      3    4    5    7   10   13   19   20   24   27   32   35   38   39   41   42   44   46   47   48 
LCS_GDT     N    31_C     N    31_C      4    8   33      3    4    6    9   11   15   19   20   24   27   32   35   38   39   41   42   44   46   47   48 
LCS_GDT     Q    32_C     Q    32_C      3    8   33      3    4    5    7   10   11   15   20   24   27   32   35   38   39   41   42   44   46   47   48 
LCS_GDT     P    33_C     P    33_C      4    8   33      3    4    5    6    9    9   16   17   19   25   32   35   38   39   41   42   44   46   47   48 
LCS_GDT     R    34_C     R    34_C      5    8   33      3    5    5    8   10   11   16   17   19   21   25   31   33   38   40   42   44   46   47   48 
LCS_GDT     H    35_C     H    35_C      5    8   33      3    5    5    8   10   11   17   19   22   23   32   35   38   39   41   42   44   46   47   48 
LCS_GDT     F    36_C     F    36_C      5    8   33      3    5    5    8   10   11   16   19   22   23   31   35   38   39   41   42   44   46   47   48 
LCS_GDT     C    37_C     C    37_C      5    8   33      4    9   12   14   15   17   19   21   23   27   32   35   38   39   41   42   44   46   47   48 
LCS_GDT     K    38_C     K    38_C      5    8   33      4    8   12   14   15   17   19   21   22   23   29   34   38   39   41   42   44   46   47   48 
LCS_GDT     A    39_C     A    39_C      5    8   33      4    5    6   14   15   17   19   21   22   23   26   28   31   35   39   41   44   46   47   48 
LCS_GDT     C    40_C     C    40_C      5    8   33      4    8   12   14   15   17   19   21   22   23   26   28   30   32   39   41   44   45   47   48 
LCS_GDT     Q    41_C     Q    41_C      5    8   33      3    5   12   14   15   17   19   21   22   23   25   28   30   32   35   41   44   45   47   48 
LCS_GDT     R    42_C     R    42_C      3    4   21      3    3    3    3    6    8   17   19   20   22   26   32   37   39   41   42   44   46   47   48 
LCS_GDT     Y    43_C     Y    43_C      3    4   21      3    3    3    7    8   11   14   17   21   25   32   35   38   39   41   42   44   46   47   48 
LCS_GDT     W    44_C     W    44_C      3    3   21      3    3    3    9    9   12   14   16   21   24   31   34   38   39   41   42   44   46   47   48 
LCS_GDT     T    45_C     T    45_C      4    5   21      4    4    4    9    9   12   14   18   21   24   29   34   37   39   41   42   44   46   47   48 
LCS_GDT     S    46_C     S    46_C      4    5   21      4    4    4    6    9   10   13   16   17   18   19   20   21   22   24   25   30   36   36   42 
LCS_GDT     G    47_C     G    47_C      4    5   21      4    4    4    6    6    7    7    8   12   16   18   18   20   22   23   25   28   31   35   39 
LCS_GDT     G    48_C     G    48_C      6    9   21      4    5    6    9    9   12   14   16   17   22   23   28   34   36   41   42   44   46   47   48 
LCS_GDT     T    49_C     T    49_C      6    9   21      3    5    6    9    9   12   14   16   19   22   29   32   37   39   41   42   44   46   47   48 
LCS_GDT     M    50_C     M    50_C      6    9   21      4    5    6    9    9   12   14   18   21   25   32   35   38   39   41   42   44   46   47   48 
LCS_GDT     R    51_C     R    51_C      6    9   21      4    5    6    9   11   15   19   20   24   27   32   35   38   39   41   42   44   46   47   48 
LCS_GDT     S    52_C     S    52_C      6    9   21      4    5    6    9   11   15   19   20   24   27   32   35   38   39   41   42   44   46   47   48 
LCS_GDT     V    53_C     V    53_C      6    9   21      4    5    6    9   10   14   19   20   24   27   32   35   38   39   41   42   44   46   47   48 
LCS_GDT     P    54_C     P    54_C      4    9   21      3    4    5    9   10   15   19   20   24   27   32   35   38   39   41   42   44   46   47   48 
LCS_GDT     I    55_C     I    55_C      4    9   21      3    4    5    9   10   15   19   20   24   27   32   35   38   39   41   42   44   46   47   48 
LCS_GDT     G    56_C     G    56_C      4    9   21      0    4    5    9   10   15   19   20   24   27   32   35   38   39   41   42   44   46   47   48 
LCS_AVERAGE  LCS_A:  29.81  (  12.50   19.18   57.75 )

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     12     14     15     17     19     21     24     27     32     35     38     39     41     42     44     46     47     48 
GDT PERCENT_AT  13.73  21.57  23.53  27.45  29.41  33.33  37.25  41.18  47.06  52.94  62.75  68.63  74.51  76.47  80.39  82.35  86.27  90.20  92.16  94.12
GDT RMS_LOCAL    0.24   0.55   0.80   1.14   1.26   1.65   2.20   2.53   3.37   3.63   4.11   4.33   4.59   4.77   4.99   5.02   5.32   5.62   5.74   5.88
GDT RMS_ALL_AT  10.10   9.95   9.72  11.90  11.88  11.86  11.77  11.99   7.05   6.96   6.88   6.95   6.94   6.80   6.81   6.87   6.83   6.77   6.76   6.78

# Checking swapping
#   possible swapping detected:  F    22_C      F    22_C
#   possible swapping detected:  Y    24_C      Y    24_C
#   possible swapping detected:  Y    25_C      Y    25_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     9.567     2    0.023   0.044    10.986   10.000    5.714
LGA    T     7_C      T     7_C     3.793     0    0.242   1.091     7.483   45.833   35.102
LGA    K     8_C      K     8_C     4.626     4    0.522   0.516     6.132   44.405   21.640
LGA    I     9_C      I     9_C     2.899     0    0.591   0.530     7.610   61.071   38.393
LGA    L    10_C      L    10_C     2.015     0    0.094   0.903     4.698   70.952   66.964
LGA    P    11_C      P    11_C     1.741     0    0.071   0.440     2.044   75.119   74.218
LGA    C    12_C      C    12_C     0.463     0    0.059   0.062     0.916   97.619   96.825
LGA    P    13_C      P    13_C     1.535     0    0.035   0.131     2.195   72.976   72.993
LGA    R    14_C      R    14_C     2.188     0    0.036   1.119     9.075   64.881   39.827
LGA    C    15_C      C    15_C     2.330     0    0.166   0.585     2.987   70.833   66.270
LGA    N    16_C      N    16_C     0.867     0    0.255   0.774     3.220   88.214   76.905
LGA    S    17_C      S    17_C     1.826     0    0.076   0.161     2.567   75.000   70.317
LGA    M    18_C      M    18_C     2.457     0    0.233   0.922     3.765   60.952   58.274
LGA    E    19_C      E    19_C     3.283     4    0.312   0.319     4.417   51.786   27.143
LGA    T    20_C      T    20_C     1.617     0    0.117   1.064     3.365   77.262   71.088
LGA    K    21_C      K    21_C     3.007     0    0.482   1.218     6.473   50.119   40.053
LGA    F    22_C      F    22_C     3.443     0    0.122   1.474     5.512   37.976   40.260
LGA    C    23_C      C    23_C     6.133     0    0.558   0.557     7.121   20.238   17.381
LGA    Y    24_C      Y    24_C     9.000     0    0.071   1.501     9.852    2.976    3.373
LGA    Y    25_C      Y    25_C    11.391     0    0.184   0.286    13.312    0.000    0.040
LGA    N    26_C      N    26_C    12.763     0    0.043   0.369    14.053    0.000    0.000
LGA    N    27_C      N    27_C    17.184     0    0.578   0.892    19.200    0.000    0.000
LGA    Y    28_C      Y    28_C    21.571     0    0.083   1.044    25.473    0.000    0.000
LGA    N    29_C      N    29_C    18.671     0    0.241   0.665    19.160    0.000    0.000
LGA    V    30_C      V    30_C    19.159     0    0.149   1.036    20.144    0.000    0.000
LGA    N    31_C      N    31_C    15.536     0    0.560   0.673    18.732    0.000    0.000
LGA    Q    32_C      Q    32_C    11.473     0    0.529   0.733    14.855    0.119    0.053
LGA    P    33_C      P    33_C    11.314     0    0.140   0.528    12.739    0.000    0.000
LGA    R    34_C      R    34_C     9.317     0    0.048   0.744    12.773    1.548    0.563
LGA    H    35_C      H    35_C     6.302     0    0.076   0.945     7.176   14.405   19.667
LGA    F    36_C      F    36_C     5.307     0    0.142   1.178    11.425   33.571   14.589
LGA    C    37_C      C    37_C     1.201     0    0.343   0.771     2.527   69.048   74.841
LGA    K    38_C      K    38_C     2.315     0    0.124   1.049     6.248   61.667   55.926
LGA    A    39_C      A    39_C     2.870     0    0.095   0.116     3.135   57.262   55.810
LGA    C    40_C      C    40_C     1.690     0    0.258   0.833     1.908   75.000   74.286
LGA    Q    41_C      Q    41_C     2.829     0    0.408   1.493     7.037   71.190   42.011
LGA    R    42_C      R    42_C     4.910     0    0.578   0.698    15.753   26.667   10.866
LGA    Y    43_C      Y    43_C    10.067     0    0.568   1.271    14.554    1.786    0.595
LGA    W    44_C      W    44_C    12.104     0    0.626   1.005    14.959    0.000    0.748
LGA    T    45_C      T    45_C    15.274     0    0.570   1.015    18.620    0.000    0.000
LGA    S    46_C      S    46_C    21.406     0    0.570   0.771    24.833    0.000    0.000
LGA    G    47_C      G    47_C    25.522     0    0.237   0.237    26.908    0.000    0.000
LGA    G    48_C      G    48_C    22.012     0    0.650   0.650    22.597    0.000    0.000
LGA    T    49_C      T    49_C    21.661     0    0.089   1.154    25.175    0.000    0.000
LGA    M    50_C      M    50_C    17.290     0    0.060   1.201    19.227    0.000    0.000
LGA    R    51_C      R    51_C    17.811     0    0.069   1.324    28.449    0.000    0.000
LGA    S    52_C      S    52_C    16.484     0    0.190   0.463    18.186    0.000    0.000
LGA    V    53_C      V    53_C    15.567     0    0.104   1.053    16.782    0.000    0.000
LGA    P    54_C      P    54_C    17.004     0    0.197   0.277    17.934    0.000    0.000
LGA    I    55_C      I    55_C    16.094     0    0.233   0.734    17.662    0.000    0.000
LGA    G    56_C      G    56_C    17.785     0    0.205   0.205    18.008    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):     6.720          6.684                  7.372           29.225   24.956

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   65   51    4.0     21    2.53    43.137    37.768     0.799

LGA_LOCAL      RMSD:   2.530  Number of atoms:   21  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  11.991  Number of assigned atoms:   51 
Std_ASGN_ATOMS RMSD:   6.720  Standard rmsd on all 51 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.191772 * X  +   0.234939 * Y  +   0.952905 * Z  + -61.583363
  Y_new =  -0.961016 * X  +   0.152092 * Y  +  -0.230903 * Z  +   4.016716
  Z_new =  -0.199178 * X  +  -0.960037 * Y  +   0.196613 * Z  +   4.271029 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.767761  0.200519 -1.368793   [DEG: -101.2852   11.4889  -78.4260 ]
ZXZ:  1.333064  1.372894 -2.937026   [DEG:   76.3789   78.6611 -168.2792 ]
 
# END of job
