
#######################################################
#                                                     #
#                        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   52 (  422),  selected   52 , name one
# Molecule2: number of CA atoms  207 ( 1714),  selected   52 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:A  -ch2:A  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    32     109_A - 140_A       4.98    15.98
  LONGEST_CONTINUOUS_SEGMENT:    32     110_A - 141_A       4.98    16.23
  LCS_AVERAGE:     14.21

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    20     112_A - 131_A       2.00    17.48
  LONGEST_CONTINUOUS_SEGMENT:    20     113_A - 132_A       1.74    17.94
  LCS_AVERAGE:      7.92

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    16     115_A - 130_A       0.92    17.97
  LONGEST_CONTINUOUS_SEGMENT:    16     116_A - 131_A       0.95    18.33
  LCS_AVERAGE:      5.50

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   52
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     I    96_A     I    96_A      4   12   24      4    4    4    7   10   13   14   17   18   18   20   21   21   23   24   25   25   26   27   28 
LCS_GDT     D    97_A     D    97_A      8   13   24      4    4    7    9   12   14   16   17   18   18   20   21   21   23   24   25   25   26   27   28 
LCS_GDT     L    98_A     L    98_A      9   13   24      4    6    8   10   13   15   16   17   18   18   20   21   21   23   24   25   25   26   27   28 
LCS_GDT     I    99_A     I    99_A      9   13   24      6    8    9   10   13   15   16   17   18   18   20   21   21   23   24   25   25   26   27   28 
LCS_GDT     Q   100_A     Q   100_A      9   13   24      6    8    9   10   13   15   16   17   18   18   20   21   21   23   24   25   25   26   27   28 
LCS_GDT     Q   101_A     Q   101_A      9   13   24      6    8    9   10   13   15   16   17   18   18   20   21   21   23   24   25   25   26   27   28 
LCS_GDT     K   102_A     K   102_A      9   13   24      6    8    9   10   13   15   16   17   18   18   20   21   21   23   24   25   25   26   27   28 
LCS_GDT     L   103_A     L   103_A      9   13   24      6    8    9   10   13   15   16   17   18   18   20   21   21   23   24   25   25   26   27   28 
LCS_GDT     S   104_A     S   104_A      9   13   24      6    8    9   10   13   15   16   17   18   18   20   21   21   23   24   25   25   26   27   28 
LCS_GDT     Y   105_A     Y   105_A      9   13   24      5    8    8   10   13   15   16   17   18   18   20   21   21   23   24   25   25   26   27   28 
LCS_GDT     Y   106_A     Y   106_A      9   13   27      4    5    9   10   13   15   16   17   18   18   20   21   21   23   24   25   26   29   31   34 
LCS_GDT     V   107_A     V   107_A      6   13   29      4    5    7   10   13   15   16   17   18   18   20   21   21   23   25   25   27   28   31   34 
LCS_GDT     R   108_A     R   108_A      6   13   30      4    5    7   10   13   15   16   17   18   18   20   21   21   23   25   25   26   28   29   34 
LCS_GDT     N   109_A     N   109_A      6   13   32      4    5    7   10   13   15   16   17   20   21   24   24   25   26   29   30   32   34   35   37 
LCS_GDT     D   110_A     D   110_A      6   13   32      3    5    9   10   13   17   19   22   24   26   27   27   29   30   32   33   35   36   36   37 
LCS_GDT     I   111_A     I   111_A      3   11   32      3    3    7    8   12   15   19   22   24   26   27   27   29   30   32   33   35   36   36   37 
LCS_GDT     D   112_A     D   112_A      3   20   32      3    3    4    5   12   14   18   22   24   26   27   27   29   30   32   33   35   36   36   37 
LCS_GDT     N   113_A     N   113_A      5   20   32      3    6   16   17   19   19   19   22   24   26   27   27   29   30   32   33   35   36   36   37 
LCS_GDT     K   114_A     K   114_A      8   20   32      3    6    8   16   19   19   19   22   24   26   27   27   29   30   32   33   35   36   36   37 
LCS_GDT     T   115_A     T   115_A     16   20   32      3    7   16   17   19   19   19   22   24   26   27   27   29   30   32   33   35   36   36   37 
LCS_GDT     I   116_A     I   116_A     16   20   32      6   13   16   17   19   19   19   22   24   26   27   27   29   30   32   33   35   36   36   37 
LCS_GDT     K   117_A     K   117_A     16   20   32      3    8   16   17   19   19   19   22   24   26   27   27   28   30   32   33   35   36   36   37 
LCS_GDT     T   118_A     T   118_A     16   20   32      9   13   16   17   19   19   19   22   24   26   27   27   29   30   32   33   35   36   36   37 
LCS_GDT     F   119_A     F   119_A     16   20   32      9   13   16   17   19   19   19   22   24   26   27   27   29   30   32   33   35   36   36   37 
LCS_GDT     Y   120_A     Y   120_A     16   20   32      9   13   16   17   19   19   19   22   24   26   27   27   29   30   32   33   35   36   36   37 
LCS_GDT     S   121_A     S   121_A     16   20   32      7   13   16   17   19   19   19   22   24   26   27   27   29   30   32   33   35   36   36   37 
LCS_GDT     D   122_A     D   122_A     16   20   32      9   13   16   17   19   19   19   22   24   26   27   27   29   30   32   33   35   36   36   37 
LCS_GDT     Y   123_A     Y   123_A     16   20   32      9   13   16   17   19   19   19   22   24   26   27   27   29   30   32   33   35   36   36   37 
LCS_GDT     A   124_A     A   124_A     16   20   32      9   13   16   17   19   19   19   22   24   26   27   27   29   30   32   33   35   36   36   37 
LCS_GDT     K   125_A     K   125_A     16   20   32      9   13   16   17   19   19   19   22   24   26   27   27   29   30   32   33   35   36   36   37 
LCS_GDT     A   126_A     A   126_A     16   20   32      9   13   16   17   19   19   19   22   24   26   27   27   29   30   32   33   35   36   36   37 
LCS_GDT     L   127_A     L   127_A     16   20   32      9   13   16   17   19   19   19   22   24   26   27   27   29   30   32   33   35   36   36   37 
LCS_GDT     S   128_A     S   128_A     16   20   32      9   13   16   17   19   19   19   22   24   26   27   27   29   30   32   33   35   36   36   37 
LCS_GDT     E   129_A     E   129_A     16   20   32      9   13   16   17   19   19   19   22   24   26   27   27   29   30   32   33   35   36   36   37 
LCS_GDT     S   130_A     S   130_A     16   20   32      9   13   16   17   19   19   19   22   24   24   26   27   28   29   30   33   35   36   36   37 
LCS_GDT     K   131_A     K   131_A     16   20   32      9   13   13   15   19   19   19   22   23   23   26   26   26   29   30   32   35   36   36   37 
LCS_GDT     A   132_A     A   132_A     14   20   32     10   13   13   14   16   16   16   21   22   23   26   26   28   29   32   33   35   36   36   37 
LCS_GDT     D   133_A     D   133_A     14   17   32     10   13   13   14   16   18   19   21   24   26   27   27   29   30   32   33   35   36   36   37 
LCS_GDT     V   134_A     V   134_A     14   17   32     10   13   13   14   16   16   16   20   24   26   27   27   29   30   32   33   35   36   36   37 
LCS_GDT     K   135_A     K   135_A     14   17   32     10   13   13   14   17   19   19   22   24   26   27   27   29   30   32   33   35   36   36   37 
LCS_GDT     M   136_A     M   136_A     14   17   32     10   13   13   14   16   16   16   17   21   26   27   27   29   30   32   33   35   36   36   37 
LCS_GDT     L   137_A     L   137_A     14   17   32     10   13   13   14   16   16   16   17   18   21   27   27   29   30   32   33   35   36   36   37 
LCS_GDT     E   138_A     E   138_A     14   17   32     10   13   13   14   16   16   16   17   18   26   27   27   29   30   32   33   35   36   36   37 
LCS_GDT     Y   139_A     Y   139_A     14   17   32     10   13   13   14   16   16   16   17   21   26   27   27   29   30   32   33   35   36   36   37 
LCS_GDT     G   140_A     G   140_A     14   17   32     10   13   13   14   16   16   16   17   18   19   22   25   29   30   32   33   35   36   36   37 
LCS_GDT     C   141_A     C   141_A     14   17   32     10   13   13   14   16   16   16   17   18   19   22   25   28   30   32   33   35   36   36   37 
LCS_GDT     N   142_A     N   142_A     14   17   25      4   13   13   14   16   16   16   17   18   19   22   26   29   30   32   33   35   36   36   37 
LCS_GDT     E   143_A     E   143_A     14   17   25      4    5    8   14   16   16   16   17   18   19   22   25   29   30   32   33   35   36   36   37 
LCS_GDT     L   144_A     L   144_A      5   17   25      4    5    5   12   16   16   16   17   18   19   22   25   26   30   32   33   35   36   36   37 
LCS_GDT     K   145_A     K   145_A      5   17   25      4    5    9   14   16   16   16   17   18   19   22   25   25   27   32   33   35   36   36   37 
LCS_GDT     S   146_A     S   146_A      3    3   25      3    3    3    4    4    4    5    6    9   13   17   17   18   18   21   21   21   22   27   28 
LCS_GDT     A   147_A     A   147_A      3    3   23      3    3    3    4    4    4    5    6    6   10   11   14   18   18   18   19   19   20   22   22 
LCS_AVERAGE  LCS_A:   9.21  (   5.50    7.92   14.21 )

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     10     13     16     17     19     19     19     22     24     26     27     27     29     30     32     33     35     36     36     37 
GDT PERCENT_AT   4.83   6.28   7.73   8.21   9.18   9.18   9.18  10.63  11.59  12.56  13.04  13.04  14.01  14.49  15.46  15.94  16.91  17.39  17.39  17.87
GDT RMS_LOCAL    0.30   0.48   0.88   0.96   1.23   1.23   1.23   2.51   2.86   3.61   3.83   3.69   4.65   4.66   4.98   5.08   5.42   5.59   5.59   5.90
GDT RMS_ALL_AT  23.71  23.51  17.98  17.87  17.96  17.96  17.96  16.63  16.48  16.16  16.16  16.22  16.18  16.16  16.19  16.21  16.25  16.30  16.30  16.03

# Checking swapping
#   possible swapping detected:  D    97_A      D    97_A
#   possible swapping detected:  Y   106_A      Y   106_A
#   possible swapping detected:  D   110_A      D   110_A
#   possible swapping detected:  D   112_A      D   112_A
#   possible swapping detected:  F   119_A      F   119_A
#   possible swapping detected:  Y   120_A      Y   120_A
#   possible swapping detected:  Y   123_A      Y   123_A
#   possible swapping detected:  E   129_A      E   129_A
#   possible swapping detected:  E   138_A      E   138_A
#   possible swapping detected:  Y   139_A      Y   139_A
#   possible swapping detected:  E   143_A      E   143_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    I    96_A      I    96_A    35.649     0    0.062   0.073    37.791    0.000    0.000
LGA    D    97_A      D    97_A    37.999     0    0.091   1.083    42.055    0.000    0.000
LGA    L    98_A      L    98_A    37.808     0    0.158   1.443    42.678    0.000    0.000
LGA    I    99_A      I    99_A    31.923     0    0.075   0.176    35.337    0.000    0.000
LGA    Q   100_A      Q   100_A    27.118     0    0.019   1.079    29.187    0.000    0.000
LGA    Q   101_A      Q   101_A    29.256     0    0.080   1.192    34.479    0.000    0.000
LGA    K   102_A      K   102_A    27.858     0    0.087   0.176    33.447    0.000    0.000
LGA    L   103_A      L   103_A    21.108     0    0.032   1.093    23.868    0.000    0.000
LGA    S   104_A      S   104_A    19.976     0    0.129   0.659    23.360    0.000    0.000
LGA    Y   105_A      Y   105_A    20.668     0    0.261   1.219    29.413    0.000    0.000
LGA    Y   106_A      Y   106_A    14.811     0    0.042   1.512    18.532    0.000    0.000
LGA    V   107_A      V   107_A    12.800     0    0.218   0.928    14.928    0.000    0.000
LGA    R   108_A      R   108_A    13.582     0    0.100   0.789    22.972    0.000    0.000
LGA    N   109_A      N   109_A     9.789     0    0.191   0.901    15.062    5.238    2.619
LGA    D   110_A      D   110_A     4.358     0    0.441   1.178     6.508   27.024   31.369
LGA    I   111_A      I   111_A     4.696     0    0.027   0.087     5.247   34.286   31.548
LGA    D   112_A      D   112_A     4.777     0    0.407   1.112    10.738   42.500   24.345
LGA    N   113_A      N   113_A     2.175     0    0.145   0.241     5.081   68.214   50.595
LGA    K   114_A      K   114_A     2.545     0    0.545   0.986    11.701   68.929   40.053
LGA    T   115_A      T   115_A     1.348     0    0.096   0.112     1.963   77.143   77.755
LGA    I   116_A      I   116_A     1.475     0    0.079   1.241     2.746   75.119   71.131
LGA    K   117_A      K   117_A     2.011     0    0.020   1.067     3.100   64.881   65.026
LGA    T   118_A      T   118_A     2.570     0    0.173   1.157     4.566   60.952   56.735
LGA    F   119_A      F   119_A     2.358     0    0.053   0.113     2.621   64.881   64.113
LGA    Y   120_A      Y   120_A     1.828     0    0.030   1.533     7.406   72.976   56.825
LGA    S   121_A      S   121_A     1.569     0    0.069   0.661     2.763   84.048   76.349
LGA    D   122_A      D   122_A     1.452     0    0.076   0.168     4.263   81.429   66.845
LGA    Y   123_A      Y   123_A     0.627     0    0.022   0.456     1.421   92.976   89.048
LGA    A   124_A      A   124_A     0.188     0    0.020   0.025     0.880   95.238   96.190
LGA    K   125_A      K   125_A     1.116     0    0.042   0.802     6.055   81.548   59.947
LGA    A   126_A      A   126_A     1.653     0    0.016   0.025     2.000   72.976   72.952
LGA    L   127_A      L   127_A     1.701     0    0.024   1.042     3.967   72.976   70.298
LGA    S   128_A      S   128_A     1.534     0    0.046   0.687     3.660   70.833   68.016
LGA    E   129_A      E   129_A     2.240     0    0.181   0.843     4.946   59.524   48.254
LGA    S   130_A      S   130_A     2.674     0    0.540   0.804     3.562   59.048   57.381
LGA    K   131_A      K   131_A     4.574     0    0.042   0.929    13.925   37.262   18.571
LGA    A   132_A      A   132_A     6.752     0    0.073   0.072     8.933   16.310   13.619
LGA    D   133_A      D   133_A     6.609     0    0.014   0.254     9.990   14.762   10.595
LGA    V   134_A      V   134_A     5.169     0    0.060   0.072     6.676   27.976   24.082
LGA    K   135_A      K   135_A     3.725     0    0.063   1.067     6.814   30.952   34.444
LGA    M   136_A      M   136_A    10.351     0    0.041   0.785    15.036    1.786    0.893
LGA    L   137_A      L   137_A    12.489     0    0.041   0.220    15.793    0.000    0.000
LGA    E   138_A      E   138_A     9.980     0    0.022   1.040    11.715    0.119    3.598
LGA    Y   139_A      Y   139_A    11.241     0    0.027   1.466    15.166    0.119    0.040
LGA    G   140_A      G   140_A    17.923     0    0.019   0.019    20.863    0.000    0.000
LGA    C   141_A      C   141_A    18.738     0    0.088   0.711    20.062    0.000    0.000
LGA    N   142_A      N   142_A    16.135     0    0.069   0.151    17.503    0.000    0.000
LGA    E   143_A      E   143_A    18.157     0    0.025   1.129    21.275    0.000    0.000
LGA    L   144_A      L   144_A    22.480     0    0.101   0.223    25.235    0.000    0.000
LGA    K   145_A      K   145_A    23.623     0    0.269   0.841    26.120    0.000    0.000
LGA    S   146_A      S   146_A    26.843     0    0.593   0.806    29.684    0.000    0.000
LGA    A   147_A      A   147_A    33.322     0    0.586   0.593    35.001    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       52     208    208  100.00     422    422  100.00               207
SUMMARY(RMSD_GDC):    13.611         13.420                 14.157            7.546    6.682

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   52  207    4.0     22    2.51    10.266     9.842     0.842

LGA_LOCAL      RMSD:   2.513  Number of atoms:   22  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  16.634  Number of assigned atoms:   52 
Std_ASGN_ATOMS RMSD:  13.611  Standard rmsd on all 52 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.665044 * X  +  -0.542600 * Y  +  -0.513130 * Z  +   3.235033
  Y_new =   0.661823 * X  +   0.746538 * Y  +   0.068344 * Z  + -29.962223
  Z_new =   0.345988 * X  +  -0.385053 * Y  +   0.855586 * Z  + -65.622650 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.782971 -0.353292 -0.422892   [DEG:   44.8609  -20.2421  -24.2299 ]
ZXZ: -1.703207  0.544115  2.409581   [DEG:  -97.5866   31.1755  138.0588 ]
 
# END of job
