
#######################################################
#                                                     #
#                        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 (  445),  selected   55 , name one
# Molecule2: number of CA atoms  207 ( 1714),  selected   55 , 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:    34      92_A - 125_A       4.98    13.02
  LCS_AVERAGE:     15.87

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15     117_A - 131_A       1.77    11.05
  LONGEST_CONTINUOUS_SEGMENT:    15     118_A - 132_A       1.88    11.63
  LCS_AVERAGE:      5.22

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14     118_A - 131_A       0.76    11.38
  LCS_AVERAGE:      3.86

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   55
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     N    92_A     N    92_A      3    3   34      3    3    3    4    5    5    6    8   17   22   25   30   32   34   36   38   39   40   42   43 
LCS_GDT     I    93_A     I    93_A      3    3   34      3    3    3    4    5    5    7    8   15   22   25   30   32   34   36   38   44   46   48   48 
LCS_GDT     P    94_A     P    94_A      3    7   34      3    3    3    6    9   12   14   17   20   23   25   31   32   36   39   42   44   46   48   48 
LCS_GDT     A    95_A     A    95_A      5   11   34      4    5    5    6   11   11   13   14   17   21   25   30   32   34   38   41   44   46   48   48 
LCS_GDT     I    96_A     I    96_A      5   11   34      4    5    5    9   11   12   13   14   15   20   25   29   31   34   38   42   44   45   48   48 
LCS_GDT     D    97_A     D    97_A      8   11   34      4    5    7    9   11   12   13   14   19   26   29   32   33   36   39   42   44   46   48   48 
LCS_GDT     L    98_A     L    98_A      8   11   34      4    5    7   10   14   17   19   21   24   26   29   32   33   36   39   42   44   46   48   48 
LCS_GDT     I    99_A     I    99_A      8   11   34      6    6    7    9   11   12   13   16   22   26   29   32   33   36   39   42   44   46   48   48 
LCS_GDT     Q   100_A     Q   100_A      8   11   34      6    6    7    9   11   12   13   14   15   20   25   29   31   35   39   42   44   46   48   48 
LCS_GDT     Q   101_A     Q   101_A      8   11   34      6    6    7    9   11   12   13   17   19   23   29   32   33   36   39   42   44   46   48   48 
LCS_GDT     K   102_A     K   102_A      8   11   34      6    6    7    9   12   17   19   21   24   26   29   32   33   36   39   42   44   46   48   48 
LCS_GDT     L   103_A     L   103_A      8   11   34      6    6    7    9   11   12   13   15   22   26   29   32   33   36   39   42   44   46   48   48 
LCS_GDT     S   104_A     S   104_A      8   11   34      6    6    7    9   11   12   13   14   17   22   25   30   32   36   39   42   44   46   48   48 
LCS_GDT     Y   105_A     Y   105_A      7   11   34      3    5    6    7   11   11   14   17   20   23   25   30   33   36   39   42   44   46   48   48 
LCS_GDT     Y   106_A     Y   106_A      5   10   34      4    5    5    7    9   12   14   17   20   23   25   30   32   36   39   42   44   46   48   48 
LCS_GDT     V   107_A     V   107_A      5    7   34      4    5    5    6    9   12   14   17   20   23   25   30   32   36   39   42   44   46   48   48 
LCS_GDT     R   108_A     R   108_A      5    9   34      4    5    6    7    9   12   14   17   20   23   25   30   32   34   36   38   41   46   48   48 
LCS_GDT     N   109_A     N   109_A      5    9   34      4    5    6    7   10   12   14   17   20   23   25   30   32   34   36   38   39   40   42   45 
LCS_GDT     D   110_A     D   110_A      5    9   34      3    5    6    6    9   12   14   17   20   23   25   30   32   34   36   38   39   40   42   43 
LCS_GDT     I   111_A     I   111_A      5    9   34      3    5    6    7    9   12   14   17   20   23   25   30   32   34   36   38   39   40   42   43 
LCS_GDT     D   112_A     D   112_A      5    9   34      3    5    6    7    9   12   14   17   20   23   25   30   32   34   36   38   39   40   42   43 
LCS_GDT     N   113_A     N   113_A      5    9   34      4    4    5    7    9   12   14   17   20   23   25   30   32   34   36   38   39   40   42   43 
LCS_GDT     K   114_A     K   114_A      5    9   34      4    4    6    6    7    9    9   13   17   23   25   30   32   34   36   39   41   46   48   48 
LCS_GDT     T   115_A     T   115_A      5    9   34      4    4    5    6    8    9   11   15   20   23   25   30   32   34   36   39   41   46   48   48 
LCS_GDT     I   116_A     I   116_A      5    9   34      4    4    5    6    8    9   10   13   19   23   25   27   32   34   36   41   41   46   48   48 
LCS_GDT     K   117_A     K   117_A      5   15   34      1    4    5    6    9   12   14   17   20   24   29   32   33   36   39   42   44   46   48   48 
LCS_GDT     T   118_A     T   118_A     14   15   34      7   10   14   15   16   17   19   21   24   25   29   32   33   36   39   42   44   46   48   48 
LCS_GDT     F   119_A     F   119_A     14   15   34      8   13   14   15   16   17   19   21   24   25   29   32   33   36   39   42   44   46   48   48 
LCS_GDT     Y   120_A     Y   120_A     14   15   34     11   13   14   15   16   17   19   21   24   26   29   32   33   36   39   42   44   46   48   48 
LCS_GDT     S   121_A     S   121_A     14   15   34     11   13   14   15   16   17   19   21   24   26   29   32   33   36   39   42   44   46   48   48 
LCS_GDT     D   122_A     D   122_A     14   15   34     11   13   14   15   16   17   19   21   24   26   29   32   33   36   39   42   44   46   48   48 
LCS_GDT     Y   123_A     Y   123_A     14   15   34     11   13   14   15   16   17   19   21   24   26   29   32   33   36   39   42   44   46   48   48 
LCS_GDT     A   124_A     A   124_A     14   15   34     11   13   14   15   16   17   19   21   24   26   29   32   33   36   39   42   44   46   48   48 
LCS_GDT     K   125_A     K   125_A     14   15   34     11   13   14   15   16   17   19   21   24   26   29   32   33   36   39   42   44   46   48   48 
LCS_GDT     A   126_A     A   126_A     14   15   31     11   13   14   15   16   17   19   21   24   26   29   32   33   36   39   42   44   46   48   48 
LCS_GDT     L   127_A     L   127_A     14   15   31     11   13   14   15   16   17   19   21   24   26   29   32   33   36   39   42   44   46   48   48 
LCS_GDT     S   128_A     S   128_A     14   15   31     11   13   14   15   16   17   19   21   24   26   29   32   33   36   39   42   44   46   48   48 
LCS_GDT     E   129_A     E   129_A     14   15   31     11   13   14   15   16   17   19   21   24   26   29   32   33   36   39   42   44   46   48   48 
LCS_GDT     S   130_A     S   130_A     14   15   31     11   13   14   15   16   17   19   21   24   26   29   32   33   36   39   42   44   46   48   48 
LCS_GDT     K   131_A     K   131_A     14   15   31      5    6   13   15   16   17   19   21   24   26   29   32   33   36   39   42   44   46   48   48 
LCS_GDT     A   132_A     A   132_A      6   15   31      5    6    7    7   10   13   17   21   24   26   29   32   33   36   39   42   44   46   48   48 
LCS_GDT     D   133_A     D   133_A      6    6   31      5    6    7    7    7    8   11   13   19   26   29   32   33   36   39   42   44   46   48   48 
LCS_GDT     V   134_A     V   134_A      6    6   31      5    6    7    7    7    7   11   13   17   19   24   27   33   36   39   42   44   46   48   48 
LCS_GDT     K   135_A     K   135_A      6    7   31      5    6    7   13   15   16   17   19   24   26   29   32   33   36   39   42   44   46   48   48 
LCS_GDT     M   136_A     M   136_A      7   10   31      3    4    7   13   15   16   17   19   24   26   29   32   33   36   39   42   44   46   48   48 
LCS_GDT     L   137_A     L   137_A      7   10   31      3    6    8   13   15   16   17   19   24   26   29   32   33   36   39   42   44   46   48   48 
LCS_GDT     E   138_A     E   138_A      7   10   31      4   13   14   15   16   17   19   21   24   26   29   32   33   36   39   42   44   46   48   48 
LCS_GDT     Y   139_A     Y   139_A      7   10   31      4    6    7    8   10   16   19   21   24   26   29   32   33   36   39   42   44   46   48   48 
LCS_GDT     G   140_A     G   140_A      7   10   31      4    6    7    8   10   10   10   15   21   26   28   32   33   36   39   42   44   46   48   48 
LCS_GDT     C   141_A     C   141_A      7   10   31      4    6    7    8   10   10   18   21   24   26   29   32   33   36   39   42   44   46   48   48 
LCS_GDT     N   142_A     N   142_A      7   10   31      4    6    7    8   10   13   18   21   24   26   29   32   33   36   39   42   44   46   48   48 
LCS_GDT     E   143_A     E   143_A      7   10   31      4    5    7    8   10   10   10   11   12   13   19   25   30   35   39   42   44   46   48   48 
LCS_GDT     L   144_A     L   144_A      5   10   31      4    4    6    8   10   10   10   11   12   13   17   23   28   32   37   38   40   42   45   46 
LCS_GDT     K   145_A     K   145_A      5   10   31      4    4    5    7   10   10   13   21   23   26   29   32   33   36   39   42   44   45   48   48 
LCS_GDT     S   146_A     S   146_A      3    3   31      3    3    3   15   16   17   19   21   24   26   29   32   33   36   39   42   44   46   48   48 
LCS_AVERAGE  LCS_A:   8.32  (   3.86    5.22   15.87 )

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     11     13     14     15     16     17     19     21     24     26     29     32     33     36     39     42     44     46     48     48 
GDT PERCENT_AT   5.31   6.28   6.76   7.25   7.73   8.21   9.18  10.14  11.59  12.56  14.01  15.46  15.94  17.39  18.84  20.29  21.26  22.22  23.19  23.19
GDT RMS_LOCAL    0.32   0.49   0.65   0.80   1.20   1.70   2.13   2.57   2.97   3.59   3.75   4.18   4.26   4.78   5.21   5.50   5.70   6.48   6.56   6.56
GDT RMS_ALL_AT  11.69  11.84  11.76  11.78  11.04  10.59  10.25  10.34  10.55  10.26  10.13   9.58   9.66   9.21   8.86   8.87   8.88   8.11   8.14   8.14

# Checking swapping
#   possible swapping detected:  D    97_A      D    97_A
#   possible swapping detected:  D   110_A      D   110_A
#   possible swapping detected:  F   119_A      F   119_A
#   possible swapping detected:  Y   120_A      Y   120_A
#   possible swapping detected:  D   133_A      D   133_A
#   possible swapping detected:  E   143_A      E   143_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    N    92_A      N    92_A    13.285     0    0.694   0.604    14.014    0.000    0.060
LGA    I    93_A      I    93_A     9.853     0    0.637   0.765    11.505    4.643    2.738
LGA    P    94_A      P    94_A     6.415     0    0.623   0.666    10.191    9.762    7.075
LGA    A    95_A      A    95_A     9.125     0    0.584   0.580     9.724    3.214    2.667
LGA    I    96_A      I    96_A    12.026     0    0.076   0.096    17.905    0.000    0.000
LGA    D    97_A      D    97_A     9.396     0    0.096   1.134    13.104    4.762    2.560
LGA    L    98_A      L    98_A     2.962     0    0.162   0.156     5.466   51.548   51.786
LGA    I    99_A      I    99_A     6.802     0    0.063   0.150    11.797   12.857    6.786
LGA    Q   100_A      Q   100_A    11.892     0    0.000   1.114    20.637    0.119    0.053
LGA    Q   101_A      Q   101_A    10.393     0    0.071   0.399    17.125    0.833    0.370
LGA    K   102_A      K   102_A     4.166     0    0.106   0.809     9.115   29.286   32.063
LGA    L   103_A      L   103_A     8.134     0    0.053   1.117    11.513    4.643    2.321
LGA    S   104_A      S   104_A    13.209     0    0.589   0.705    16.434    0.000    0.000
LGA    Y   105_A      Y   105_A    12.969     0    0.435   1.284    14.681    0.000    0.000
LGA    Y   106_A      Y   106_A    12.081     0    0.053   1.256    14.686    0.000    2.143
LGA    V   107_A      V   107_A    12.797     0    0.102   0.102    16.407    0.000    0.204
LGA    R   108_A      R   108_A    19.005     0    0.206   1.322    22.450    0.000    0.000
LGA    N   109_A      N   109_A    21.170     0    0.653   0.939    22.059    0.000    0.000
LGA    D   110_A      D   110_A    23.007     0    0.425   1.157    27.634    0.000    0.000
LGA    I   111_A      I   111_A    21.518     0    0.130   1.000    21.742    0.000    0.000
LGA    D   112_A      D   112_A    22.690     0    0.377   0.380    24.290    0.000    0.000
LGA    N   113_A      N   113_A    21.475     0    0.540   0.465    25.945    0.000    0.000
LGA    K   114_A      K   114_A    17.516     0    0.128   1.253    19.640    0.000    0.000
LGA    T   115_A      T   115_A    16.012     0    0.035   0.123    17.829    0.000    0.000
LGA    I   116_A      I   116_A    13.591     0    0.636   0.995    17.206    0.119    0.060
LGA    K   117_A      K   117_A     7.732     0    0.597   1.120    10.281   17.738    9.683
LGA    T   118_A      T   118_A     2.650     0    0.724   1.369     6.848   62.143   43.061
LGA    F   119_A      F   119_A     1.883     0    0.030   0.154     2.584   75.119   69.307
LGA    Y   120_A      Y   120_A     1.453     0    0.000   1.536    10.799   81.548   43.452
LGA    S   121_A      S   121_A     1.237     0    0.073   0.475     1.853   81.429   81.508
LGA    D   122_A      D   122_A     1.134     0    0.000   0.172     1.604   81.548   83.750
LGA    Y   123_A      Y   123_A     1.431     0    0.000   0.229     2.245   81.429   73.690
LGA    A   124_A      A   124_A     0.912     0    0.000   0.000     1.181   83.690   85.048
LGA    K   125_A      K   125_A     1.749     0    0.054   0.542     2.919   72.976   69.365
LGA    A   126_A      A   126_A     2.468     0    0.000   0.000     2.815   62.857   61.714
LGA    L   127_A      L   127_A     1.588     0    0.056   1.376     3.706   77.143   70.357
LGA    S   128_A      S   128_A     1.291     0    0.076   0.165     2.156   75.119   75.794
LGA    E   129_A      E   129_A     2.311     0    0.188   0.900     3.141   66.786   61.481
LGA    S   130_A      S   130_A     2.445     0    0.561   0.771     3.119   62.857   61.032
LGA    K   131_A      K   131_A     2.564     0    0.000   0.847    13.974   69.286   35.926
LGA    A   132_A      A   132_A     4.954     0    0.031   0.047     7.090   30.000   26.000
LGA    D   133_A      D   133_A     7.009     0    0.086   1.074     9.842   10.952   11.726
LGA    V   134_A      V   134_A     7.783     0    0.180   1.185     9.815    9.286    7.823
LGA    K   135_A      K   135_A     5.919     0    0.212   1.017    10.596   19.405   14.021
LGA    M   136_A      M   136_A     5.655     0    0.627   1.044     7.978   21.548   18.690
LGA    L   137_A      L   137_A     5.529     0    0.000   1.415     9.620   30.476   22.381
LGA    E   138_A      E   138_A     1.462     0    0.071   0.180     5.455   73.214   57.513
LGA    Y   139_A      Y   139_A     3.141     0    0.000   0.163     8.393   46.548   30.040
LGA    G   140_A      G   140_A     6.266     0    0.071   0.071     6.912   19.762   19.762
LGA    C   141_A      C   141_A     4.480     0    0.108   0.819     5.441   34.286   34.444
LGA    N   142_A      N   142_A     4.690     0    0.000   0.116     7.981   23.810   29.167
LGA    E   143_A      E   143_A     9.794     0    0.000   1.216    15.321    1.905    0.847
LGA    L   144_A      L   144_A    10.757     0    0.071   0.223    15.444    0.476    0.238
LGA    K   145_A      K   145_A     5.905     0    0.319   0.836     7.302   25.000   22.487
LGA    S   146_A      S   146_A     2.467     0    0.238   0.816     3.903   50.357   59.286

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       55     220    220  100.00     445    445  100.00               207
SUMMARY(RMSD_GDC):     7.827          7.691                  8.574            7.587    6.717

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   55  207    4.0     21    2.57    10.990     9.381     0.787

LGA_LOCAL      RMSD:   2.567  Number of atoms:   21  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  10.343  Number of assigned atoms:   55 
Std_ASGN_ATOMS RMSD:   7.827  Standard rmsd on all 55 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.945640 * X  +   0.315492 * Y  +   0.078929 * Z  + -470.944244
  Y_new =  -0.264273 * X  +   0.604014 * Y  +   0.751882 * Z  + -271.459015
  Z_new =   0.189539 * X  +  -0.731869 * Y  +   0.654556 * Z  + -148.957977 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.272512 -0.190692 -0.841105   [DEG:  -15.6138  -10.9259  -48.1917 ]
ZXZ:  3.037001  0.857201  2.888181   [DEG:  174.0073   49.1140  165.4806 ]
 
# END of job
