
#######################################################
#                                                     #
#                        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   32 (  275),  selected   32 , name one
# Molecule2: number of CA atoms  192 ( 1575),  selected   32 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:D  -ch2:D  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    19     162_D - 180_D       4.97    10.41
  LONGEST_CONTINUOUS_SEGMENT:    19     163_D - 181_D       4.96    10.47
  LONGEST_CONTINUOUS_SEGMENT:    19     172_D - 190_D       4.37    14.77
  LCS_AVERAGE:      9.75

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15     175_D - 189_D       1.48    18.55
  LCS_AVERAGE:      5.32

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13     176_D - 188_D       0.81    19.47
  LONGEST_CONTINUOUS_SEGMENT:    13     177_D - 189_D       0.89    19.61
  LCS_AVERAGE:      4.17

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   32
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   159_D     D   159_D      3    3   15      0    3    3    3    6    9   10   11   13   15   17   19   21   22   23   23   24   25   26   27 
LCS_GDT     E   160_D     E   160_D      3    3   15      0    3    3    3    3    9   10   11   13   14   16   19   21   22   23   23   24   25   26   27 
LCS_GDT     N   161_D     N   161_D      3    4   18      3    5    5    6    8    9   10   10   13   15   17   19   21   22   23   23   24   25   26   27 
LCS_GDT     N   162_D     N   162_D      3    4   19      3    3    4    4    4    4    6    8   13   15   17   19   21   22   23   23   24   25   26   27 
LCS_GDT     L   163_D     L   163_D      5    6   19      3    3    6    6    6    6    7    7    9   12   13   19   21   22   23   23   24   25   26   27 
LCS_GDT     C   164_D     C   164_D      5    6   19      3    4    6    6    6    6    7    7    9   12   13   13   15   21   23   23   24   25   26   27 
LCS_GDT     S   165_D     S   165_D      5    6   19      3    4    6    6    6    6    9   10   13   15   17   19   21   22   23   23   24   25   26   27 
LCS_GDT     G   166_D     G   166_D      5    6   19      3    4    6    6    6    6    9   10   13   15   17   19   21   22   23   23   24   25   26   27 
LCS_GDT     D   167_D     D   167_D      5    6   19      3    4    6    6    7    8    9   11   13   15   17   19   21   22   23   23   24   25   26   27 
LCS_GDT     D   168_D     D   168_D      4    6   19      3    4    6    6    6    8    9   11   13   15   17   19   21   22   23   23   24   25   26   27 
LCS_GDT     G   169_D     G   169_D      4    8   19      3    4    5    6    7    9   10   11   13   15   17   19   21   22   23   23   24   25   26   27 
LCS_GDT     E   170_D     E   170_D      4    8   19      3    3    5    6    7    9   10   11   13   15   17   19   21   22   23   23   24   25   26   27 
LCS_GDT     Y   171_D     Y   171_D      4    8   19      3    3    4    6    7    8   10   11   13   15   17   19   21   22   23   23   24   25   26   27 
LCS_GDT     T   172_D     T   172_D      4    8   19      3    5    5    6    8    9   10   11   13   15   17   19   21   22   23   23   24   25   26   27 
LCS_GDT     Y   173_D     Y   173_D      4    8   19      3    5    5    6    8    9   10   11   13   15   17   19   21   22   23   23   24   25   26   27 
LCS_GDT     R   174_D     R   174_D      5    9   19      3    5    5    6    8   10   12   14   16   16   17   19   21   22   23   23   24   25   26   27 
LCS_GDT     I   175_D     I   175_D      5   15   19      3    5    5    9   15   15   15   15   16   16   17   19   21   22   23   23   24   25   26   27 
LCS_GDT     K   176_D     K   176_D     13   15   19      3    5   13   13   15   15   15   15   16   16   17   19   21   22   22   23   24   25   26   27 
LCS_GDT     Y   177_D     Y   177_D     13   15   19      5   12   13   13   15   15   15   15   16   16   17   19   21   22   23   23   24   25   26   27 
LCS_GDT     P   178_D     P   178_D     13   15   19      4   12   13   13   15   15   15   15   16   16   17   19   21   22   23   23   24   25   26   27 
LCS_GDT     E   179_D     E   179_D     13   15   19      9   12   13   13   15   15   15   15   16   16   17   19   21   22   23   23   24   25   26   27 
LCS_GDT     Q   180_D     Q   180_D     13   15   19      9   12   13   13   15   15   15   15   16   16   17   19   21   22   23   23   24   25   26   27 
LCS_GDT     L   181_D     L   181_D     13   15   19      9   12   13   13   15   15   15   15   16   16   17   19   21   22   23   23   24   25   26   27 
LCS_GDT     E   182_D     E   182_D     13   15   19      9   12   13   13   15   15   15   15   16   16   17   17   18   20   23   23   24   25   26   27 
LCS_GDT     E   183_D     E   183_D     13   15   19      9   12   13   13   15   15   15   15   16   16   17   17   17   18   19   21   24   25   26   27 
LCS_GDT     V   184_D     V   184_D     13   15   19      8   12   13   13   15   15   15   15   16   16   17   17   17   18   18   19   20   23   26   27 
LCS_GDT     F   185_D     F   185_D     13   15   19      9   12   13   13   15   15   15   15   16   16   17   17   17   18   18   19   20   22   26   27 
LCS_GDT     N   186_D     N   186_D     13   15   19      9   12   13   13   15   15   15   15   16   16   17   17   17   18   18   19   20   21   22   24 
LCS_GDT     Y   187_D     Y   187_D     13   15   19      9   12   13   13   15   15   15   15   16   16   17   17   17   18   18   19   20   21   22   22 
LCS_GDT     Y   188_D     Y   188_D     13   15   19      9   12   13   13   15   15   15   15   16   16   17   17   17   18   18   19   20   21   22   22 
LCS_GDT     D   189_D     D   189_D     13   15   19      1    4   10   13   15   15   15   15   16   16   17   17   17   18   18   19   20   21   22   24 
LCS_GDT     K   190_D     K   190_D      3    3   19      0    3    3    3    3    4   10   11   13   15   17   17   17   18   18   19   20   22   22   24 
LCS_AVERAGE  LCS_A:   6.41  (   4.17    5.32    9.75 )

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      9     12     13     13     15     15     15     15     16     16     17     19     21     22     23     23     24     25     26     27 
GDT PERCENT_AT   4.69   6.25   6.77   6.77   7.81   7.81   7.81   7.81   8.33   8.33   8.85   9.90  10.94  11.46  11.98  11.98  12.50  13.02  13.54  14.06
GDT RMS_LOCAL    0.35   0.54   0.81   0.81   1.48   1.48   1.48   1.48   2.23   2.23   2.92   4.54   4.79   4.94   5.27   5.15   5.40   5.78   6.14   6.50
GDT RMS_ALL_AT  20.07  19.98  19.47  19.47  18.55  18.55  18.55  18.55  17.60  17.60  16.75  10.45  10.37  10.25   9.74  10.15   9.80   9.48   9.27   9.04

# Checking swapping
#   possible swapping detected:  D   159_D      D   159_D
#   possible swapping detected:  E   160_D      E   160_D
#   possible swapping detected:  D   167_D      D   167_D
#   possible swapping detected:  D   168_D      D   168_D
#   possible swapping detected:  Y   171_D      Y   171_D
#   possible swapping detected:  E   179_D      E   179_D
#   possible swapping detected:  E   183_D      E   183_D
#   possible swapping detected:  D   189_D      D   189_D

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    D   159_D      D   159_D    17.953     0    0.078   1.096    18.619    0.000    0.000
LGA    E   160_D      E   160_D    21.943     0    0.652   1.345    26.107    0.000    0.000
LGA    N   161_D      N   161_D    20.114     0    0.673   0.737    21.936    0.000    0.000
LGA    N   162_D      N   162_D    22.220     0    0.204   1.270    24.277    0.000    0.000
LGA    L   163_D      L   163_D    27.593     0    0.075   1.358    31.717    0.000    0.000
LGA    C   164_D      C   164_D    31.232     0    0.522   0.516    33.571    0.000    0.000
LGA    S   165_D      S   165_D    31.755     0    0.148   0.771    32.666    0.000    0.000
LGA    G   166_D      G   166_D    35.302     0    0.251   0.251    35.815    0.000    0.000
LGA    D   167_D      D   167_D    36.821     0    0.422   0.800    37.721    0.000    0.000
LGA    D   168_D      D   168_D    34.083     0    0.529   1.175    34.705    0.000    0.000
LGA    G   169_D      G   169_D    31.484     0    0.532   0.532    32.178    0.000    0.000
LGA    E   170_D      E   170_D    26.011     0    0.575   0.959    28.462    0.000    0.000
LGA    Y   171_D      Y   171_D    23.278     0    0.562   1.219    27.289    0.000    0.000
LGA    T   172_D      T   172_D    16.326     0    0.085   1.294    19.105    0.000    0.000
LGA    Y   173_D      Y   173_D    11.967     0    0.037   0.337    18.797    0.119    0.040
LGA    R   174_D      R   174_D     7.764     0    0.136   1.454    11.880   10.714    4.502
LGA    I   175_D      I   175_D     3.679     0    0.044   0.124     5.387   45.476   41.845
LGA    K   176_D      K   176_D     1.263     0    0.190   0.757     5.051   81.548   64.603
LGA    Y   177_D      Y   177_D     1.260     0    0.179   0.198     3.304   88.214   70.119
LGA    P   178_D      P   178_D     1.211     0    0.084   0.371     2.148   79.286   76.599
LGA    E   179_D      E   179_D     0.986     0    0.096   1.225     6.636   90.476   63.492
LGA    Q   180_D      Q   180_D     0.438     0    0.021   0.829     3.628   95.238   79.259
LGA    L   181_D      L   181_D     0.983     0    0.042   1.425     5.009   90.476   75.893
LGA    E   182_D      E   182_D     0.342     0    0.059   0.918     4.881   95.238   74.868
LGA    E   183_D      E   183_D     0.809     0    0.028   0.761     2.885   88.333   83.915
LGA    V   184_D      V   184_D     1.438     0    0.069   0.067     2.010   81.429   76.599
LGA    F   185_D      F   185_D     1.006     0    0.240   0.226     3.008   79.286   71.905
LGA    N   186_D      N   186_D     1.017     0    0.129   0.145     1.546   83.690   82.619
LGA    Y   187_D      Y   187_D     0.989     0    0.063   0.956     5.719   85.952   64.484
LGA    Y   188_D      Y   188_D     0.984     0    0.593   1.553    11.471   80.357   41.468
LGA    D   189_D      D   189_D     2.361     0    0.674   1.243     6.014   47.381   46.250
LGA    K   190_D      K   190_D     9.511     0    0.121   0.182    20.301    3.810    1.693

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       32     128    128  100.00     275    275  100.00               192
SUMMARY(RMSD_GDC):     8.377          8.471                  9.193            6.391    5.313

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   32  192    4.0     15    1.48     8.203     7.567     0.951

LGA_LOCAL      RMSD:   1.477  Number of atoms:   15  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  18.552  Number of assigned atoms:   32 
Std_ASGN_ATOMS RMSD:   8.377  Standard rmsd on all 32 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.840343 * X  +   0.266339 * Y  +   0.472110 * Z  + -10.827984
  Y_new =  -0.147817 * X  +   0.725355 * Y  +  -0.672317 * Z  + -30.250750
  Z_new =  -0.521511 * X  +  -0.634763 * Y  +  -0.570177 * Z  + -68.744583 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.967473  0.548621 -2.302645   [DEG: -170.0237   31.4337 -131.9318 ]
ZXZ:  0.612210  2.177518 -2.453828   [DEG:   35.0770  124.7626 -140.5940 ]
 
# END of job
