
#######################################################
#                                                     #
#                        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   46 (  341),  selected   46 , name one
# Molecule2: number of CA atoms  207 ( 1517),  selected   46 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:B  -ch2:B  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    20     153_B - 172_B       4.79    35.46
  LCS_AVERAGE:      8.75

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    16     153_B - 168_B       1.68    38.49
  LCS_AVERAGE:      4.76

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14     153_B - 166_B       0.95    36.48
  LCS_AVERAGE:      3.54

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   46
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     T   153_B     T   153_B     14   16   20      8   10   13   14   15   16   17   17   18   18   18   18   18   19   19   19   19   19   20   20 
LCS_GDT     L   154_B     L   154_B     14   16   20      8   10   13   14   15   16   17   17   18   18   18   18   18   19   19   19   19   19   20   20 
LCS_GDT     D   155_B     D   155_B     14   16   20      8   10   13   14   15   16   17   17   18   18   18   18   18   19   19   19   19   19   20   20 
LCS_GDT     Q   156_B     Q   156_B     14   16   20      8   10   13   14   15   16   17   17   18   18   18   18   18   19   19   19   19   19   20   20 
LCS_GDT     L   157_B     L   157_B     14   16   20      8   10   13   14   15   16   17   17   18   18   18   18   18   19   19   19   19   19   20   20 
LCS_GDT     L   158_B     L   158_B     14   16   20      8   10   13   14   15   16   17   17   18   18   18   18   18   19   19   19   19   19   20   20 
LCS_GDT     A   159_B     A   159_B     14   16   20      8   10   13   14   15   16   17   17   18   18   18   18   18   19   19   19   19   19   20   20 
LCS_GDT     V   160_B     V   160_B     14   16   20      8   10   13   14   15   16   17   17   18   18   18   18   18   19   19   19   19   19   20   20 
LCS_GDT     L   161_B     L   161_B     14   16   20      5   10   13   14   15   16   17   17   18   18   18   18   18   19   19   19   19   19   20   20 
LCS_GDT     Q   162_B     Q   162_B     14   16   20      4    8   13   14   15   16   17   17   18   18   18   18   18   19   19   19   20   23   24   24 
LCS_GDT     E   163_B     E   163_B     14   16   20      4    8   12   14   15   16   17   17   18   18   18   18   18   19   19   20   22   23   24   24 
LCS_GDT     K   164_B     K   164_B     14   16   20      8   10   13   14   15   16   17   17   18   18   18   18   18   19   19   19   20   23   24   24 
LCS_GDT     H   165_B     H   165_B     14   16   20      4   10   13   14   15   16   17   17   18   18   18   18   20   21   23   23   24   26   27   27 
LCS_GDT     K   166_B     K   166_B     14   16   20      5   10   13   14   15   16   17   17   18   18   18   18   20   21   23   23   24   26   27   27 
LCS_GDT     G   167_B     G   167_B      6   16   20      5    5    6   11   11   16   17   17   18   18   18   18   20   21   23   23   24   26   27   27 
LCS_GDT     K   168_B     K   168_B      6   16   20      5    8   10   13   15   16   17   17   18   18   18   18   20   21   23   23   24   26   27   27 
LCS_GDT     P   169_B     P   169_B      6   10   20      5    5    6    7   10   16   17   17   18   18   18   18   20   21   23   23   24   26   27   27 
LCS_GDT     A   170_B     A   170_B      6    9   20      5    5    6    7    8    8   11   15   18   18   18   18   18   21   23   23   24   26   27   27 
LCS_GDT     T   171_B     T   171_B      3    7   20      3    3    3    6    7    8    8   10   11   12   13   16   18   21   23   23   24   26   27   27 
LCS_GDT     T   172_B     T   172_B      4    7   20      3    4    5    6    7    8    8   10   11   12   14   16   20   21   23   23   24   26   27   27 
LCS_GDT     V   173_B     V   173_B      4    7   16      3    4    4    5    7    7    8   10   12   13   14   18   20   21   23   23   24   26   27   27 
LCS_GDT     T   174_B     T   174_B      4    7   16      3    4    4    5    7    7    8   10   12   13   14   18   20   21   23   23   24   26   27   27 
LCS_GDT     Y   175_B     Y   175_B      4    7   16      3    4    4    5    7    7    8   10   12   13   14   18   20   21   23   23   24   26   27   27 
LCS_GDT     E   176_B     E   176_B      4    7   16      3    4    4    5    7    7    8   10   12   12   14   17   20   21   23   23   24   26   27   27 
LCS_GDT     I   177_B     I   177_B      4    7   16      3    4    4    5    7    7    8   10   12   13   14   18   20   21   23   23   24   26   27   27 
LCS_GDT     S   178_B     S   178_B      4    5   16      3    4    4    5    5    6    7    8   12   13   14   18   20   21   23   23   24   26   27   27 
LCS_GDT     A   179_B     A   179_B      4    5   16      3    4    4    5    5    6    7    8   12   13   14   18   20   21   23   23   24   26   27   27 
LCS_GDT     E   180_B     E   180_B      4    5   16      2    3    4    5    5    6    7    9   11   13   14   18   20   21   23   23   24   26   27   27 
LCS_GDT     T   181_B     T   181_B      5    6   16      3    4    5    6    6    6    8    9   11   13   14   18   20   21   23   23   24   26   27   27 
LCS_GDT     L   182_B     L   182_B      5    6   17      4    4    5    6    6    6    8    9   12   13   14   18   20   21   23   23   24   26   27   27 
LCS_GDT     R   183_B     R   183_B      5    6   17      4    4    5    6    6    6    8    9   11   13   14   16   20   21   23   23   24   26   27   27 
LCS_GDT     A   184_B     A   184_B      5    6   17      4    4    5    6    6    6    8    9   11   13   14   18   20   21   23   23   24   25   27   27 
LCS_GDT     A   185_B     A   185_B      5    6   17      4    4    5    6    7    8    8    9   11   12   14   18   20   21   23   23   24   26   27   27 
LCS_GDT     V   186_B     V   186_B      4    6   17      3    4    5    6    7    8    8    9   11   12   14   18   20   21   23   23   24   26   27   27 
LCS_GDT     A   187_B     A   187_B      3    4   17      3    4    5    6    7    8    8    9   11   12   14   18   20   21   23   23   24   26   27   27 
LCS_GDT     A   188_B     A   188_B      3    4   17      0    3    3    4    4    8    8    9   11   12   13   15   18   19   22   23   24   26   27   27 
LCS_GDT     L   189_B     L   189_B      3    3   17      1    3    3    3    5    6    8    9   11   12   13   15   18   19   21   21   23   26   27   27 
LCS_GDT     A   190_B     A   190_B      3    3   17      1    3    3    5    5    7    9    9   11   12   13   15   18   19   21   21   23   26   27   27 
LCS_GDT     R   191_B     R   191_B      4    8   17      3    5    5    7    8    8    9    9   11   12   13   15   18   19   21   21   23   26   27   27 
LCS_GDT     A   192_B     A   192_B      4    8   17      3    5    5    7    8    8    9    9   10   11   13   15   17   19   21   21   23   24   25   25 
LCS_GDT     A   193_B     A   193_B      4    8   17      3    5    5    7    8    8    9    9   10   11   13   15   17   18   21   21   23   24   25   25 
LCS_GDT     E   194_B     E   194_B      5    8   17      5    5    5    7    8    8    9    9   10   11   13   15   17   19   21   21   23   24   25   25 
LCS_GDT     A   195_B     A   195_B      5    8   17      5    5    5    7    8    8    9    9   10   11   13   15   17   19   21   21   23   24   25   25 
LCS_GDT     A   196_B     A   196_B      5    8   17      5    5    5    6    8    8    9    9   10   11   11   15   17   19   21   21   23   24   25   25 
LCS_GDT     L   197_B     L   197_B      5    8   17      5    5    5    7    8    8    9    9   10   11   13   15   17   19   21   21   23   24   25   25 
LCS_GDT     R   198_B     R   198_B      5    8   17      5    5    5    7    8    8    9    9   10   12   13   15   17   19   21   21   23   24   25   25 
LCS_AVERAGE  LCS_A:   5.68  (   3.54    4.76    8.75 )

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      8     10     13     14     15     16     17     17     18     18     18     18     20     21     23     23     24     26     27     27 
GDT PERCENT_AT   3.86   4.83   6.28   6.76   7.25   7.73   8.21   8.21   8.70   8.70   8.70   8.70   9.66  10.14  11.11  11.11  11.59  12.56  13.04  13.04
GDT RMS_LOCAL    0.25   0.56   0.85   0.95   1.38   1.68   2.00   2.00   2.47   2.47   2.47   2.47   4.86   5.01   5.39   5.39   5.63   6.70   6.83   6.83
GDT RMS_ALL_AT  33.80  35.37  36.17  36.48  38.36  38.49  39.88  39.88  39.43  39.43  39.43  39.43  19.78  19.73  19.84  19.84  19.47  17.28  17.30  17.30

# Checking swapping
#   possible swapping detected:  E   176_B      E   176_B
#   possible swapping detected:  E   194_B      E   194_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    T   153_B      T   153_B     1.469     0    0.059   1.118     4.351   86.190   74.218
LGA    L   154_B      L   154_B     0.762     0    0.062   0.426     2.837   88.333   79.702
LGA    D   155_B      D   155_B     1.800     0    0.027   0.105     3.371   77.143   67.202
LGA    Q   156_B      Q   156_B     1.320     0    0.028   1.222     7.301   85.952   57.937
LGA    L   157_B      L   157_B     0.752     0    0.000   1.413     3.912   90.595   81.250
LGA    L   158_B      L   158_B     1.884     0    0.000   0.978     5.239   75.000   60.417
LGA    A   159_B      A   159_B     1.699     0    0.000   0.000     2.198   77.143   74.667
LGA    V   160_B      V   160_B     0.663     0    0.236   1.380     2.832   86.071   79.524
LGA    L   161_B      L   161_B     0.871     0    0.000   0.277     2.063   86.190   82.857
LGA    Q   162_B      Q   162_B     2.164     0    0.255   0.869     5.379   59.524   51.005
LGA    E   163_B      E   163_B     2.474     3    0.089   0.572     4.313   64.881   39.312
LGA    K   164_B      K   164_B     2.252     4    0.108   0.116     2.433   64.762   36.878
LGA    H   165_B      H   165_B     2.392     0    0.198   1.365     9.079   66.786   39.333
LGA    K   166_B      K   166_B     1.826     2    0.592   0.885     5.334   73.214   48.995
LGA    G   167_B      G   167_B     3.087     0    0.132   0.132     4.156   54.286   54.286
LGA    K   168_B      K   168_B     1.117     0    0.137   0.885     8.798   67.262   48.095
LGA    P   169_B      P   169_B     4.095     0    0.000   0.096     4.486   43.690   44.626
LGA    A   170_B      A   170_B     6.881     0    0.286   0.352     9.443    9.762    9.810
LGA    T   171_B      T   171_B    12.515     0    0.344   0.341    16.063    0.000    0.000
LGA    T   172_B      T   172_B    18.580     0    0.552   0.633    21.896    0.000    0.000
LGA    V   173_B      V   173_B    24.089     0    0.052   1.227    25.485    0.000    0.000
LGA    T   174_B      T   174_B    27.449     0    0.548   0.774    29.703    0.000    0.000
LGA    Y   175_B      Y   175_B    34.367     0    0.054   0.205    37.202    0.000    0.000
LGA    E   176_B      E   176_B    40.551     0    0.601   0.766    43.583    0.000    0.000
LGA    I   177_B      I   177_B    45.738     0    0.112   0.205    49.204    0.000    0.000
LGA    S   178_B      S   178_B    47.838     0    0.168   0.583    49.837    0.000    0.000
LGA    A   179_B      A   179_B    52.998     0    0.570   0.577    54.891    0.000    0.000
LGA    E   180_B      E   180_B    51.453     0    0.579   1.044    52.435    0.000    0.000
LGA    T   181_B      T   181_B    45.062     0    0.576   1.034    47.295    0.000    0.000
LGA    L   182_B      L   182_B    47.141     0    0.123   0.300    48.403    0.000    0.000
LGA    R   183_B      R   183_B    47.932     0    0.149   1.332    48.906    0.000    0.000
LGA    A   184_B      A   184_B    48.810     0    0.171   0.164    50.539    0.000    0.000
LGA    A   185_B      A   185_B    49.394     0    0.573   0.544    50.488    0.000    0.000
LGA    V   186_B      V   186_B    53.633     0    0.140   1.129    55.962    0.000    0.000
LGA    A   187_B      A   187_B    57.371     0    0.531   0.536    58.462    0.000    0.000
LGA    A   188_B      A   188_B    54.141     0    0.576   0.586    56.111    0.000    0.000
LGA    L   189_B      L   189_B    54.622     0    0.476   0.868    55.723    0.000    0.000
LGA    A   190_B      A   190_B    58.888     0    0.587   0.589    60.821    0.000    0.000
LGA    R   191_B      R   191_B    58.588     0    0.574   0.790    60.388    0.000    0.000
LGA    A   192_B      A   192_B    60.438     0    0.120   0.114    62.945    0.000    0.000
LGA    A   193_B      A   193_B    63.489     0    0.269   0.277    64.039    0.000    0.000
LGA    E   194_B      E   194_B    63.255     0    0.171   0.993    64.271    0.000    0.000
LGA    A   195_B      A   195_B    63.777     0    0.135   0.139    64.637    0.000    0.000
LGA    A   196_B      A   196_B    63.269     0    0.106   0.100    63.836    0.000    0.000
LGA    L   197_B      L   197_B    63.948     0    0.090   1.341    65.014    0.000    0.000
LGA    R   198_B      R   198_B    65.929     0    0.557   1.202    67.709    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       46     184    184  100.00     332    332  100.00               207
SUMMARY(RMSD_GDC):    13.506         13.266                 13.873            6.071    4.976

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   46  207    4.0     17    2.00     7.729     7.137     0.808

LGA_LOCAL      RMSD:   2.004  Number of atoms:   17  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  39.880  Number of assigned atoms:   46 
Std_ASGN_ATOMS RMSD:  13.506  Standard rmsd on all 46 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.592537 * X  +   0.804840 * Y  +  -0.033653 * Z  + -747.098145
  Y_new =   0.338401 * X  +  -0.286614 * Y  +  -0.896291 * Z  + 249.391312
  Z_new =  -0.731016 * X  +   0.519697 * Y  +  -0.442188 * Z  + 433.665863 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.518903  0.819810  2.275788   [DEG:   29.7309   46.9717  130.3930 ]
ZXZ: -0.037529  2.028833 -0.952776   [DEG:   -2.1503  116.2436  -54.5901 ]
 
# END of job
