
#######################################################
#                                                     #
#                        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   33 (  231),  selected   33 , name one
# Molecule2: number of CA atoms   33 (  231),  selected   33 , 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:    21      12_A - 32_A        4.85    14.28
  LONGEST_CONTINUOUS_SEGMENT:    21      13_A - 33_A        4.97    14.65
  LCS_AVERAGE:     55.74

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11      18_A - 28_A        1.65    14.91
  LCS_AVERAGE:     25.16

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7      18_A - 24_A        0.74    14.88
  LCS_AVERAGE:     15.34

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   33
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     Y     1_A     Y     1_A      5    7   10      4    4    5    5    6    6    8    8    9    9    9    9    9    9   10   11   12   12   12   12 
LCS_GDT     R     2_A     R     2_A      5    7   10      4    4    5    5    6    6    8    8    9    9    9    9    9    9   11   11   12   12   12   12 
LCS_GDT     Q     3_A     Q     3_A      5    7   10      4    4    5    5    6    6    8    8    9    9    9    9    9   10   11   11   12   12   12   12 
LCS_GDT     S     4_A     S     4_A      5    7   11      4    4    5    5    6    6    8    8    9    9    9    9   10   10   11   11   12   12   12   12 
LCS_GDT     S     5_A     S     5_A      5    7   11      3    4    5    5    6    6    8    9    9    9   10   10   10   11   11   11   12   13   13   14 
LCS_GDT     A     6_A     A     6_A      4    7   13      3    4    4    5    6    6    8    9    9    9   10   10   10   11   13   14   16   16   16   16 
LCS_GDT     T     7_A     T     7_A      4    7   14      3    4    4    5    6    8    8    9    9    9   10   12   12   13   14   15   16   16   20   20 
LCS_GDT     S     8_A     S     8_A      4    6   16      3    4    4    4    6    8    8    9   11   11   12   12   14   15   16   17   18   18   20   20 
LCS_GDT     S     9_A     S     9_A      3    5   16      3    3    3    4    5    8    8    9   11   11   11   12   13   13   14   15   18   18   20   20 
LCS_GDT     F    10_A     F    10_A      3    5   16      3    3    3    4    6    8    8    9   11   12   13   14   14   18   18   20   20   20   20   21 
LCS_GDT     G    11_A     G    11_A      3    5   18      3    3    3    4    6    8    9   11   12   13   15   17   19   19   19   20   20   21   22   22 
LCS_GDT     G    12_A     G    12_A      3    5   21      3    3    3    4    6   10   11   12   14   15   17   17   19   19   19   20   20   21   22   22 
LCS_GDT     L    13_A     L    13_A      4    5   21      3    3    4    5    6    8    8    9   12   15   17   17   19   19   19   20   20   21   22   22 
LCS_GDT     G    14_A     G    14_A      4    5   21      3    3    4    6    9    9   12   12   13   15   16   17   18   18   19   20   20   21   22   22 
LCS_GDT     G    15_A     G    15_A      4    7   21      3    3    5    8    9   11   11   12   13   15   16   17   18   18   19   20   20   21   22   22 
LCS_GDT     G    16_A     G    16_A      4    7   21      3    3    4    6    8    8    9   10   11   13   13   15   15   18   18   19   20   21   22   22 
LCS_GDT     S    17_A     S    17_A      4   10   21      3    3    5    8   10   11   12   12   13   15   16   17   18   18   19   20   20   21   22   22 
LCS_GDT     V    18_A     V    18_A      7   11   21      3    7    7    9   11   11   13   14   15   15   17   17   19   19   19   20   20   21   22   22 
LCS_GDT     R    19_A     R    19_A      7   11   21      3    7    7    9   11   11   13   14   15   15   17   17   19   19   19   20   20   21   22   22 
LCS_GDT     F    20_A     F    20_A      7   11   21      3    7    7    9   11   11   13   14   15   15   17   17   19   19   19   20   20   21   22   22 
LCS_GDT     G    21_A     G    21_A      7   11   21      3    7    7    9   11   11   13   14   15   15   17   17   19   19   19   20   20   21   22   22 
LCS_GDT     P    22_A     P    22_A      7   11   21      3    7    7    9   11   11   13   14   15   15   17   17   19   19   19   20   20   21   22   22 
LCS_GDT     G    23_A     G    23_A      7   11   21      4    7    7    9   11   11   13   14   15   15   17   17   19   19   19   20   20   21   22   22 
LCS_GDT     V    24_A     V    24_A      7   11   21      4    7    7    9   11   11   13   14   15   15   17   17   19   19   19   20   20   21   22   22 
LCS_GDT     A    25_A     A    25_A      4   11   21      4    4    7    9   11   11   13   14   15   15   17   17   19   19   19   20   20   21   22   22 
LCS_GDT     F    26_A     F    26_A      6   11   21      4    6    7    9   11   11   12   14   15   15   17   17   19   19   19   20   20   21   22   22 
LCS_GDT     R    27_A     R    27_A      6   11   21      4    6    6    8   11   11   13   14   15   15   17   17   19   19   19   20   20   21   22   22 
LCS_GDT     A    28_A     A    28_A      6   11   21      4    6    7    8   11   11   13   14   15   15   17   17   19   19   19   20   20   21   22   22 
LCS_GDT     P    29_A     P    29_A      6    9   21      4    6    6    8    9   11   13   14   15   15   17   17   19   19   19   20   20   21   22   22 
LCS_GDT     S    30_A     S    30_A      6    9   21      3    6    6    7    9   11   13   14   15   15   17   17   19   19   19   20   20   21   22   22 
LCS_GDT     I    31_A     I    31_A      6    9   21      3    6    6    8    9   11   13   14   15   15   17   17   19   19   19   20   20   21   22   22 
LCS_GDT     H    32_A     H    32_A      6    9   21      3    5    6    7    8    9   11   14   15   15   17   17   19   19   19   20   20   21   22   22 
LCS_GDT     G    33_A     G    33_A      3    8   21      3    3    3    4    4    7    8    9   10   11   13   16   19   19   19   20   20   21   22   22 
LCS_AVERAGE  LCS_A:  32.08  (  15.34   25.16   55.74 )

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      4      7      7      9     11     11     13     14     15     15     17     17     19     19     19     20     20     21     22     22 
GDT PERCENT_AT  12.12  21.21  21.21  27.27  33.33  33.33  39.39  42.42  45.45  45.45  51.52  51.52  57.58  57.58  57.58  60.61  60.61  63.64  66.67  66.67
GDT RMS_LOCAL    0.27   0.74   0.74   1.26   1.65   1.65   2.34   2.55   2.81   2.81   3.58   3.58   4.15   4.15   4.15   4.52   4.52   4.85   5.17   5.17
GDT RMS_ALL_AT  17.53  14.88  14.88  15.03  14.91  14.91  15.29  15.25  15.17  15.17  13.51  13.51  13.27  13.27  13.27  14.09  14.09  14.28  13.75  13.75

# Checking swapping
#   possible swapping detected:  Y     1_A      Y     1_A
#   possible swapping detected:  F    10_A      F    10_A
#   possible swapping detected:  F    20_A      F    20_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    Y     1_A      Y     1_A    27.143     0    0.032   0.301    27.478    0.000    0.000
LGA    R     2_A      R     2_A    27.502     0    0.138   1.227    33.231    0.000    0.000
LGA    Q     3_A      Q     3_A    27.439     0    0.054   0.912    27.663    0.000    0.000
LGA    S     4_A      S     4_A    28.275     0    0.086   0.691    28.488    0.000    0.000
LGA    S     5_A      S     5_A    28.996     0    0.553   0.842    29.926    0.000    0.000
LGA    A     6_A      A     6_A    28.094     0    0.233   0.264    28.249    0.000    0.000
LGA    T     7_A      T     7_A    26.887     0    0.150   1.300    30.653    0.000    0.000
LGA    S     8_A      S     8_A    23.645     0    0.405   0.692    24.757    0.000    0.000
LGA    S     9_A      S     9_A    21.343     0    0.504   0.674    23.168    0.000    0.000
LGA    F    10_A      F    10_A    14.667     0    0.519   1.360    17.220    0.000    0.000
LGA    G    11_A      G    11_A    13.539     0    0.500   0.500    14.218    0.000    0.000
LGA    G    12_A      G    12_A    12.362     0    0.109   0.109    12.572    0.357    0.357
LGA    L    13_A      L    13_A    11.279     0    0.256   0.318    14.848    0.000    0.000
LGA    G    14_A      G    14_A    10.507     0    0.206   0.206    11.879    0.119    0.119
LGA    G    15_A      G    15_A     8.166     0    0.148   0.148     8.405    6.071    6.071
LGA    G    16_A      G    16_A    11.190     0    0.591   0.591    11.190    2.143    2.143
LGA    S    17_A      S    17_A     7.217     0    0.020   0.650     8.892   12.857   10.238
LGA    V    18_A      V    18_A     2.331     0    0.248   0.529     4.080   57.857   62.245
LGA    R    19_A      R    19_A     1.863     0    0.231   1.194     7.630   70.952   46.234
LGA    F    20_A      F    20_A     0.626     0    0.155   0.348     1.846   88.214   85.628
LGA    G    21_A      G    21_A     1.179     0    0.087   0.087     2.211   75.119   75.119
LGA    P    22_A      P    22_A     1.869     0    0.312   0.491     3.449   65.119   70.884
LGA    G    23_A      G    23_A     2.606     0    0.563   0.563     2.606   62.976   62.976
LGA    V    24_A      V    24_A     0.958     0    0.204   0.906     2.366   77.381   75.510
LGA    A    25_A      A    25_A     3.366     0    0.036   0.059     4.252   50.357   47.714
LGA    F    26_A      F    26_A     4.255     0    0.251   1.145     5.159   40.238   38.528
LGA    R    27_A      R    27_A     3.020     0    0.097   1.063     5.572   65.833   47.532
LGA    A    28_A      A    28_A     2.121     0    0.045   0.053     3.177   73.452   68.762
LGA    P    29_A      P    29_A     2.710     0    0.077   0.377     4.452   68.929   57.143
LGA    S    30_A      S    30_A     3.029     0    0.164   0.721     5.434   44.048   38.095
LGA    I    31_A      I    31_A     3.045     0    0.605   0.486     7.660   50.833   39.167
LGA    H    32_A      H    32_A     6.094     0    0.062   0.310     8.683   16.071   13.524
LGA    G    33_A      G    33_A     9.975     0    0.563   0.563    10.012    1.429    1.429

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       33     132    132  100.00     231    231  100.00                33
SUMMARY(RMSD_GDC):    11.725         11.587                 12.020           28.193   25.740

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   33   33    4.0     14    2.55    37.879    35.463     0.529

LGA_LOCAL      RMSD:   2.546  Number of atoms:   14  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  15.249  Number of assigned atoms:   33 
Std_ASGN_ATOMS RMSD:  11.725  Standard rmsd on all 33 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.377199 * X  +   0.771752 * Y  +  -0.511977 * Z  +  -0.591639
  Y_new =  -0.246353 * X  +   0.449286 * Y  +   0.858751 * Z  +   1.758886
  Z_new =   0.892766 * X  +   0.450047 * Y  +   0.020653 * Z  +  -6.204937 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.563034 -1.103448  1.524938   [DEG: -146.8510  -63.2229   87.3725 ]
ZXZ: -2.603981  1.550142  1.103871   [DEG: -149.1971   88.8166   63.2472 ]
 
# END of job
