
#######################################################
#                                                     #
#                        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   61 (  460),  selected   60 , name one
# Molecule2: number of CA atoms   60 (  451),  selected   60 , 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:    60       1_A - 60_A        3.00     3.00
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    36       4_A - 39_A        1.99     3.80
  LCS_AVERAGE:     50.03

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17       4_A - 20_A        0.97     3.15
  LONGEST_CONTINUOUS_SEGMENT:    17      43_A - 59_A        0.92     4.24
  LCS_AVERAGE:     23.83

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   60
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     D     1_A     D     1_A      7   20   60      3    4    7    7   10   19   26   37   41   47   54   59   60   60   60   60   60   60   60   60 
LCS_GDT     D     2_A     D     2_A      7   22   60      5   13   16   25   31   41   48   52   57   57   58   59   60   60   60   60   60   60   60   60 
LCS_GDT     K     3_A     K     3_A      7   22   60      5    6   11   19   30   41   45   52   57   57   58   59   60   60   60   60   60   60   60   60 
LCS_GDT     A     4_A     A     4_A     17   36   60      5   13   25   29   39   43   48   52   57   57   58   59   60   60   60   60   60   60   60   60 
LCS_GDT     A     5_A     A     5_A     17   36   60      5   10   25   35   39   43   48   52   57   57   58   59   60   60   60   60   60   60   60   60 
LCS_GDT     C     6_A     C     6_A     17   36   60     11   19   31   35   39   43   48   52   57   57   58   59   60   60   60   60   60   60   60   60 
LCS_GDT     A     7_A     A     7_A     17   36   60     11   19   31   35   39   43   48   52   57   57   58   59   60   60   60   60   60   60   60   60 
LCS_GDT     D     8_A     D     8_A     17   36   60     11   20   31   35   39   43   48   52   57   57   58   59   60   60   60   60   60   60   60   60 
LCS_GDT     G     9_A     G     9_A     17   36   60     11   20   31   35   39   43   48   52   57   57   58   59   60   60   60   60   60   60   60   60 
LCS_GDT     I    10_A     I    10_A     17   36   60     11   21   31   35   39   43   48   52   57   57   58   59   60   60   60   60   60   60   60   60 
LCS_GDT     A    11_A     A    11_A     17   36   60     11   21   31   35   39   43   48   52   57   57   58   59   60   60   60   60   60   60   60   60 
LCS_GDT     A    12_A     A    12_A     17   36   60     11   21   31   35   39   43   48   52   57   57   58   59   60   60   60   60   60   60   60   60 
LCS_GDT     V    13_A     V    13_A     17   36   60     11   21   31   35   39   43   48   52   57   57   58   59   60   60   60   60   60   60   60   60 
LCS_GDT     K    14_A     K    14_A     17   36   60     11   21   31   35   39   43   48   52   57   57   58   59   60   60   60   60   60   60   60   60 
LCS_GDT     A    15_A     A    15_A     17   36   60     11   21   31   35   39   43   48   52   57   57   58   59   60   60   60   60   60   60   60   60 
LCS_GDT     R    16_A     R    16_A     17   36   60     11   21   31   35   39   43   48   52   57   57   58   59   60   60   60   60   60   60   60   60 
LCS_GDT     V    17_A     V    17_A     17   36   60      8   21   31   35   39   43   48   52   57   57   58   59   60   60   60   60   60   60   60   60 
LCS_GDT     E    18_A     E    18_A     17   36   60      8   19   31   35   39   43   48   52   57   57   58   59   60   60   60   60   60   60   60   60 
LCS_GDT     K    19_A     K    19_A     17   36   60      9   21   31   35   39   43   48   52   57   57   58   59   60   60   60   60   60   60   60   60 
LCS_GDT     L    20_A     L    20_A     17   36   60      8   21   31   35   39   43   48   52   57   57   58   59   60   60   60   60   60   60   60   60 
LCS_GDT     A    21_A     A    21_A      4   36   60      3    4    4   15   31   37   45   52   57   57   58   59   60   60   60   60   60   60   60   60 
LCS_GDT     P    22_A     P    22_A      5   36   60      4    4    5   11   17   33   39   48   51   56   58   59   60   60   60   60   60   60   60   60 
LCS_GDT     E    23_A     E    23_A      5   36   60      4    4   20   28   36   42   48   52   57   57   58   59   60   60   60   60   60   60   60   60 
LCS_GDT     A    24_A     A    24_A      5   36   60      4    4    5    5    8   14   25   40   49   53   57   59   60   60   60   60   60   60   60   60 
LCS_GDT     V    25_A     V    25_A      5   36   60      4    4   18   26   36   42   48   52   57   57   58   59   60   60   60   60   60   60   60   60 
LCS_GDT     P    26_A     P    26_A     14   36   60      4   10   15   26   33   43   48   52   57   57   58   59   60   60   60   60   60   60   60   60 
LCS_GDT     Q    27_A     Q    27_A     14   36   60      9   13   18   34   39   43   48   52   57   57   58   59   60   60   60   60   60   60   60   60 
LCS_GDT     K    28_A     K    28_A     14   36   60     12   13   31   35   39   43   48   52   57   57   58   59   60   60   60   60   60   60   60   60 
LCS_GDT     L    29_A     L    29_A     14   36   60     12   21   31   35   39   43   48   52   57   57   58   59   60   60   60   60   60   60   60   60 
LCS_GDT     K    30_A     K    30_A     14   36   60     12   21   31   35   39   43   48   52   57   57   58   59   60   60   60   60   60   60   60   60 
LCS_GDT     R    31_A     R    31_A     14   36   60     12   21   31   35   39   43   48   52   57   57   58   59   60   60   60   60   60   60   60   60 
LCS_GDT     A    32_A     A    32_A     14   36   60     12   21   31   35   39   43   48   52   57   57   58   59   60   60   60   60   60   60   60   60 
LCS_GDT     L    33_A     L    33_A     14   36   60     12   21   31   35   39   43   48   52   57   57   58   59   60   60   60   60   60   60   60   60 
LCS_GDT     K    34_A     K    34_A     14   36   60     12   21   31   35   39   43   48   52   57   57   58   59   60   60   60   60   60   60   60   60 
LCS_GDT     I    35_A     I    35_A     14   36   60     12   21   31   35   39   43   48   52   57   57   58   59   60   60   60   60   60   60   60   60 
LCS_GDT     A    36_A     A    36_A     14   36   60     12   21   31   35   39   43   48   52   57   57   58   59   60   60   60   60   60   60   60   60 
LCS_GDT     E    37_A     E    37_A     14   36   60     12   21   31   35   39   43   48   52   57   57   58   59   60   60   60   60   60   60   60   60 
LCS_GDT     R    38_A     R    38_A     14   36   60     12   21   31   34   39   43   48   52   57   57   58   59   60   60   60   60   60   60   60   60 
LCS_GDT     E    39_A     E    39_A     14   36   60     12   21   31   35   39   43   48   52   57   57   58   59   60   60   60   60   60   60   60   60 
LCS_GDT     Q    40_A     Q    40_A      5   21   60      3    4    5    7   14   23   43   52   57   57   58   59   60   60   60   60   60   60   60   60 
LCS_GDT     G    41_A     G    41_A      9   21   60      3    4    7   12   18   30   42   52   57   57   58   59   60   60   60   60   60   60   60   60 
LCS_GDT     E    42_A     E    42_A     12   21   60      3    9   14   20   32   43   48   52   57   57   58   59   60   60   60   60   60   60   60   60 
LCS_GDT     G    43_A     G    43_A     17   21   60      5   12   18   23   27   39   46   52   57   57   58   59   60   60   60   60   60   60   60   60 
LCS_GDT     E    44_A     E    44_A     17   21   60      7   14   18   23   32   40   48   52   57   57   58   59   60   60   60   60   60   60   60   60 
LCS_GDT     F    45_A     F    45_A     17   21   60      7   14   18   23   32   42   48   52   57   57   58   59   60   60   60   60   60   60   60   60 
LCS_GDT     D    46_A     D    46_A     17   21   60      5   12   18   23   31   42   48   52   57   57   58   59   60   60   60   60   60   60   60   60 
LCS_GDT     E    47_A     E    47_A     17   21   60      5   12   18   25   33   43   48   52   57   57   58   59   60   60   60   60   60   60   60   60 
LCS_GDT     C    48_A     C    48_A     17   21   60      8   14   25   29   39   43   48   52   57   57   58   59   60   60   60   60   60   60   60   60 
LCS_GDT     L    49_A     L    49_A     17   21   60      7   14   25   35   39   43   48   52   57   57   58   59   60   60   60   60   60   60   60   60 
LCS_GDT     E    50_A     E    50_A     17   21   60      7   19   25   35   39   43   48   52   57   57   58   59   60   60   60   60   60   60   60   60 
LCS_GDT     A    51_A     A    51_A     17   21   60      7   14   25   30   39   43   48   52   57   57   58   59   60   60   60   60   60   60   60   60 
LCS_GDT     L    52_A     L    52_A     17   21   60      8   19   31   35   39   43   48   52   57   57   58   59   60   60   60   60   60   60   60   60 
LCS_GDT     D    53_A     D    53_A     17   21   60      8   17   31   35   39   43   48   52   57   57   58   59   60   60   60   60   60   60   60   60 
LCS_GDT     D    54_A     D    54_A     17   21   60      6   14   23   29   39   43   48   52   57   57   58   59   60   60   60   60   60   60   60   60 
LCS_GDT     A    55_A     A    55_A     17   21   60      8   14   25   35   39   43   48   52   57   57   58   59   60   60   60   60   60   60   60   60 
LCS_GDT     K    56_A     K    56_A     17   21   60      8   20   31   35   39   43   48   52   57   57   58   59   60   60   60   60   60   60   60   60 
LCS_GDT     R    57_A     R    57_A     17   21   60      8   14   25   29   39   43   48   52   57   57   58   59   60   60   60   60   60   60   60   60 
LCS_GDT     A    58_A     A    58_A     17   21   60      8   17   25   35   39   43   48   52   57   57   58   59   60   60   60   60   60   60   60   60 
LCS_GDT     L    59_A     L    59_A     17   21   60      8   19   31   35   39   43   48   52   57   57   58   59   60   60   60   60   60   60   60   60 
LCS_GDT     P    60_A     P    60_A     13   21   60      5    9   19   25   36   42   48   52   57   57   58   59   60   60   60   60   60   60   60   60 
LCS_AVERAGE  LCS_A:  57.95  (  23.83   50.03  100.00 )

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     12     21     31     35     39     43     48     52     57     57     58     59     60     60     60     60     60     60     60     60 
GDT PERCENT_AT  20.00  35.00  51.67  58.33  65.00  71.67  80.00  86.67  95.00  95.00  96.67  98.33 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.31   0.69   0.98   1.29   1.43   1.67   2.13   2.34   2.65   2.65   2.74   2.86   3.00   3.00   3.00   3.00   3.00   3.00   3.00   3.00
GDT RMS_ALL_AT   3.90   3.83   3.68   3.47   3.49   3.38   3.14   3.09   3.03   3.03   3.01   3.01   3.00   3.00   3.00   3.00   3.00   3.00   3.00   3.00

# Checking swapping
#   possible swapping detected:  D     1_A      D     1_A
#   possible swapping detected:  E    18_A      E    18_A
#   possible swapping detected:  E    23_A      E    23_A
#   possible swapping detected:  E    39_A      E    39_A
#   possible swapping detected:  E    42_A      E    42_A
#   possible swapping detected:  E    47_A      E    47_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    D     1_A      D     1_A     8.347     0    0.157   1.350    10.465    4.881   13.214
LGA    D     2_A      D     2_A     3.813     0    0.043   0.208     5.225   46.071   38.929
LGA    K     3_A      K     3_A     4.028     0    0.055   0.966     5.318   45.357   37.354
LGA    A     4_A      A     4_A     2.434     0    0.052   0.049     3.119   69.524   65.619
LGA    A     5_A      A     5_A     1.384     0    0.073   0.073     1.860   81.548   79.810
LGA    C     6_A      C     6_A     1.265     0    0.128   0.745     3.042   81.786   73.651
LGA    A     7_A      A     7_A     1.461     0    0.048   0.059     1.512   79.286   78.000
LGA    D     8_A      D     8_A     1.473     0    0.083   0.090     2.296   81.429   75.119
LGA    G     9_A      G     9_A     1.152     0    0.029   0.029     1.278   85.952   85.952
LGA    I    10_A      I    10_A     0.610     0    0.034   0.136     1.782   92.857   88.333
LGA    A    11_A      A    11_A     0.817     0    0.048   0.048     1.106   90.476   88.667
LGA    A    12_A      A    12_A     0.942     0    0.043   0.051     1.138   90.476   88.667
LGA    V    13_A      V    13_A     0.647     0    0.038   1.039     3.108   90.476   81.020
LGA    K    14_A      K    14_A     0.536     0    0.072   0.314     1.932   90.476   86.508
LGA    A    15_A      A    15_A     1.075     0    0.054   0.050     1.354   83.690   83.238
LGA    R    16_A      R    16_A     0.673     0    0.045   1.099     3.111   90.476   75.844
LGA    V    17_A      V    17_A     0.960     0    0.054   0.976     2.065   85.952   80.408
LGA    E    18_A      E    18_A     1.532     0    0.086   1.004     5.886   77.143   57.513
LGA    K    19_A      K    19_A     0.877     0    0.170   0.749     4.455   88.214   69.312
LGA    L    20_A      L    20_A     0.743     0    0.074   0.962     5.082   67.381   52.679
LGA    A    21_A      A    21_A     4.972     0    0.041   0.054     6.706   45.833   39.333
LGA    P    22_A      P    22_A     6.291     0    0.637   0.620    10.429   27.262   16.190
LGA    E    23_A      E    23_A     4.274     0    0.154   1.103    10.013   30.238   19.153
LGA    A    24_A      A    24_A     7.016     0    0.211   0.209     8.853   15.476   12.952
LGA    V    25_A      V    25_A     4.070     0    0.595   0.647     7.085   39.286   32.109
LGA    P    26_A      P    26_A     3.394     0    0.158   0.320     5.397   69.524   56.463
LGA    Q    27_A      Q    27_A     2.876     0    0.185   0.812     3.833   57.500   63.492
LGA    K    28_A      K    28_A     1.941     0    0.077   0.584     3.683   70.833   62.646
LGA    L    29_A      L    29_A     1.874     0    0.045   1.168     3.885   72.857   68.214
LGA    K    30_A      K    30_A     2.018     0    0.042   0.820     5.342   66.786   58.254
LGA    R    31_A      R    31_A     2.258     0    0.000   0.805     3.849   64.762   54.892
LGA    A    32_A      A    32_A     2.269     0    0.035   0.050     2.412   64.762   64.762
LGA    L    33_A      L    33_A     1.988     0    0.045   1.066     3.169   66.786   65.000
LGA    K    34_A      K    34_A     2.124     0    0.056   0.504     2.451   64.762   72.328
LGA    I    35_A      I    35_A     2.476     0    0.033   1.312     4.730   62.857   55.238
LGA    A    36_A      A    36_A     2.471     0    0.058   0.078     2.554   62.857   61.714
LGA    E    37_A      E    37_A     2.305     0    0.090   0.420     3.397   60.952   60.582
LGA    R    38_A      R    38_A     3.073     0    0.444   1.108    11.245   65.595   34.848
LGA    E    39_A      E    39_A     2.372     0    0.066   1.016     4.586   63.095   49.418
LGA    Q    40_A      Q    40_A     4.817     0    0.041   1.244     6.416   33.095   27.831
LGA    G    41_A      G    41_A     5.160     0    0.156   0.156     5.684   27.619   27.619
LGA    E    42_A      E    42_A     4.118     0    0.725   0.692     5.624   40.357   33.757
LGA    G    43_A      G    43_A     5.555     0    0.278   0.278     6.294   20.357   20.357
LGA    E    44_A      E    44_A     4.880     0    0.094   0.785     6.437   34.286   28.307
LGA    F    45_A      F    45_A     4.209     0    0.062   1.427     8.872   37.262   23.810
LGA    D    46_A      D    46_A     4.061     0    0.033   1.078     4.686   41.905   41.131
LGA    E    47_A      E    47_A     3.607     0    0.042   0.743     6.030   48.452   37.460
LGA    C    48_A      C    48_A     2.437     0    0.047   0.128     2.927   66.905   64.921
LGA    L    49_A      L    49_A     1.282     0    0.074   1.400     4.023   81.548   69.881
LGA    E    50_A      E    50_A     1.852     0    0.035   1.037     6.681   72.857   53.545
LGA    A    51_A      A    51_A     2.040     0    0.050   0.055     2.275   70.833   69.619
LGA    L    52_A      L    52_A     0.917     0    0.067   0.996     3.808   88.214   77.917
LGA    D    53_A      D    53_A     1.466     0    0.046   0.939     4.185   77.381   64.107
LGA    D    54_A      D    54_A     2.607     0    0.013   0.949     5.694   62.857   49.643
LGA    A    55_A      A    55_A     1.830     0    0.044   0.069     2.169   77.143   74.667
LGA    K    56_A      K    56_A     0.840     0    0.065   0.938     5.579   85.952   65.714
LGA    R    57_A      R    57_A     2.466     0    0.073   1.562     4.932   64.881   55.108
LGA    A    58_A      A    58_A     1.789     0    0.142   0.139     2.040   70.833   71.238
LGA    L    59_A      L    59_A     0.532     0    0.566   0.960     3.392   86.071   81.012
LGA    P    60_A      P    60_A     3.026     0    0.672   0.641     6.891   53.810   40.204

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       60     240    240  100.00     451    451  100.00                60
SUMMARY(RMSD_GDC):     2.997          2.907                  3.626           63.968   57.088

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   61   60    4.0     52    2.34    70.000    69.312     2.134

LGA_LOCAL      RMSD:   2.336  Number of atoms:   52  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   3.086  Number of assigned atoms:   60 
Std_ASGN_ATOMS RMSD:   2.997  Standard rmsd on all 60 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.952437 * X  +  -0.288627 * Y  +   0.097762 * Z  + -178.729980
  Y_new =  -0.247751 * X  +  -0.546612 * Y  +   0.799897 * Z  + -44.962368
  Z_new =  -0.177434 * X  +  -0.786072 * Y  +  -0.592121 * Z  + 119.025383 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.254483  0.178378 -2.216384   [DEG:  -14.5808   10.2203 -126.9895 ]
ZXZ:  3.019977  2.204485 -2.919591   [DEG:  173.0319  126.3077 -167.2803 ]
 
# END of job
