
#######################################################
#                                                     #
#                        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:    19       6_A - 24_A        4.90    14.13
  LONGEST_CONTINUOUS_SEGMENT:    19       8_A - 26_A        4.87    13.99
  LCS_AVERAGE:     53.54

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9      20_A - 28_A        1.86    17.34
  LONGEST_CONTINUOUS_SEGMENT:     9      24_A - 32_A        1.76    19.20
  LONGEST_CONTINUOUS_SEGMENT:     9      25_A - 33_A        1.97    20.24
  LCS_AVERAGE:     23.05

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7      26_A - 32_A        0.85    19.54
  LCS_AVERAGE:     15.52

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   11      3    4    5    6    6    6    7    8    8   10   12   14   15   15   16   17   18   18   19   20 
LCS_GDT     R     2_A     R     2_A      5    7   11      3    4    5    6    6    6    7    8    8    9   12   14   15   15   15   17   18   18   19   20 
LCS_GDT     Q     3_A     Q     3_A      5    7   11      3    4    5    6    6    6    7    8    8   10   12   14   15   15   16   17   18   18   19   20 
LCS_GDT     S     4_A     S     4_A      5    7   11      3    4    5    6    6    6    7    8    8   10   12   14   15   15   16   17   18   18   19   22 
LCS_GDT     S     5_A     S     5_A      5    7   14      3    4    5    5    6    6    7    8    8   10   12   14   15   15   19   19   20   20   22   22 
LCS_GDT     A     6_A     A     6_A      4    7   19      3    4    4    6    6    6    8   10   11   13   15   16   19   19   20   21   23   24   25   28 
LCS_GDT     T     7_A     T     7_A      4    7   19      3    4    4    6    6    7    8   10   11   13   15   16   19   19   20   21   23   24   25   28 
LCS_GDT     S     8_A     S     8_A      4    4   19      3    4    4    4    5    6    8   10   12   13   15   16   19   19   20   22   23   24   25   28 
LCS_GDT     S     9_A     S     9_A      5    6   19      3    3    5    5    6    7    7   10   12   13   15   16   19   19   20   22   23   24   25   28 
LCS_GDT     F    10_A     F    10_A      5    6   19      4    4    5    5    6    6    8    9   12   13   15   16   19   19   20   22   23   24   25   28 
LCS_GDT     G    11_A     G    11_A      5    6   19      4    4    5    5    6    7    8   10   12   13   15   16   19   19   20   22   23   24   25   28 
LCS_GDT     G    12_A     G    12_A      5    6   19      4    4    5    5    6    7    8   10   12   13   15   16   19   19   20   22   23   24   25   28 
LCS_GDT     L    13_A     L    13_A      5    6   19      4    4    5    5    6    7    8    9   12   13   15   16   19   19   20   22   23   24   24   28 
LCS_GDT     G    14_A     G    14_A      4    6   19      3    3    4    5    7   10   11   11   12   13   15   16   19   19   20   22   23   24   25   28 
LCS_GDT     G    15_A     G    15_A      4    6   19      3    3    4    5    7   10   11   11   12   13   15   16   19   19   20   22   23   24   25   28 
LCS_GDT     G    16_A     G    16_A      4    6   19      3    3    4    6    8   10   11   11   11   13   15   16   19   19   20   22   23   24   25   28 
LCS_GDT     S    17_A     S    17_A      4    8   19      3    4    4    5    8   10   11   11   11   13   15   16   19   19   20   22   23   24   25   28 
LCS_GDT     V    18_A     V    18_A      4    8   19      3    4    4    6    8   10   11   11   11   13   16   16   19   19   20   22   23   24   25   28 
LCS_GDT     R    19_A     R    19_A      4    8   19      3    4    4    6    8   10   11   11   12   15   16   16   19   19   20   22   23   24   25   28 
LCS_GDT     F    20_A     F    20_A      5    9   19      3    5    7    7    8   10   12   13   13   15   16   16   19   19   20   22   23   24   25   28 
LCS_GDT     G    21_A     G    21_A      5    9   19      3    5    7    7    8   10   12   13   13   15   16   16   19   19   20   22   23   24   25   28 
LCS_GDT     P    22_A     P    22_A      5    9   19      3    5    7    7    8   10   12   13   13   15   16   16   19   19   20   22   23   24   25   28 
LCS_GDT     G    23_A     G    23_A      5    9   19      3    5    7    7    8   10   12   13   13   15   16   16   19   19   20   22   23   24   25   28 
LCS_GDT     V    24_A     V    24_A      5    9   19      3    5    7    7    8   10   12   13   13   15   16   16   19   19   20   22   23   24   25   28 
LCS_GDT     A    25_A     A    25_A      6    9   19      3    4    6    8    8    9   12   13   13   15   16   16   18   19   20   22   23   24   25   28 
LCS_GDT     F    26_A     F    26_A      7    9   19      5    6    7    8    8   10   12   13   13   15   16   16   18   19   20   22   23   24   25   28 
LCS_GDT     R    27_A     R    27_A      7    9   18      5    6    7    8    8    9   12   13   13   15   16   16   17   18   20   22   23   24   24   28 
LCS_GDT     A    28_A     A    28_A      7    9   18      5    6    7    8    8   10   12   13   13   15   16   16   17   18   20   22   23   24   25   28 
LCS_GDT     P    29_A     P    29_A      7    9   18      5    6    7    8    8   10   12   13   13   15   16   16   17   18   20   22   23   24   25   28 
LCS_GDT     S    30_A     S    30_A      7    9   18      5    6    7    8    8   10   12   13   13   15   16   16   17   18   18   21   21   24   25   28 
LCS_GDT     I    31_A     I    31_A      7    9   18      3    6    7    8    8    8   12   13   13   15   16   16   17   18   18   21   21   22   24   28 
LCS_GDT     H    32_A     H    32_A      7    9   18      3    5    7    8    8   10   11   13   13   15   16   16   17   18   18   21   21   22   25   28 
LCS_GDT     G    33_A     G    33_A      3    9   18      3    3    3    4    4    7    8    9   12   15   16   16   17   18   18   21   21   22   25   28 
LCS_AVERAGE  LCS_A:  30.70  (  15.52   23.05   53.54 )

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      5      6      7      8      8     10     12     13     13     15     16     16     19     19     20     22     23     24     25     28 
GDT PERCENT_AT  15.15  18.18  21.21  24.24  24.24  30.30  36.36  39.39  39.39  45.45  48.48  48.48  57.58  57.58  60.61  66.67  69.70  72.73  75.76  84.85
GDT RMS_LOCAL    0.41   0.70   0.85   1.22   1.22   1.97   2.46   2.58   2.58   3.23   3.54   3.54   4.90   4.90   5.09   5.77   5.93   6.09   7.21   7.52
GDT RMS_ALL_AT  20.02  19.60  19.54  19.72  19.72  16.70  17.75  17.31  17.31  16.38  15.73  15.73  14.13  14.13  13.66  13.40  13.06  13.07  12.20  12.23

# Checking swapping

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    Y     1_A      Y     1_A    35.278     0    0.025   1.323    36.572    0.000    0.000
LGA    R     2_A      R     2_A    31.250     0    0.063   0.826    40.607    0.000    0.000
LGA    Q     3_A      Q     3_A    25.712     0    0.101   0.683    27.617    0.000    0.000
LGA    S     4_A      S     4_A    22.250     0    0.191   0.652    23.553    0.000    0.000
LGA    S     5_A      S     5_A    21.580     0    0.545   0.574    21.694    0.000    0.000
LGA    A     6_A      A     6_A    18.237     0    0.258   0.285    20.342    0.000    0.000
LGA    T     7_A      T     7_A    22.647     0    0.155   0.980    25.002    0.000    0.000
LGA    S     8_A      S     8_A    22.945     0    0.454   0.752    25.152    0.000    0.000
LGA    S     9_A      S     9_A    22.700     0    0.594   0.845    22.875    0.000    0.000
LGA    F    10_A      F    10_A    21.634     0    0.402   1.046    24.313    0.000    0.000
LGA    G    11_A      G    11_A    28.381     0    0.402   0.402    28.381    0.000    0.000
LGA    G    12_A      G    12_A    29.022     0    0.124   0.124    29.022    0.000    0.000
LGA    L    13_A      L    13_A    24.059     0    0.198   0.269    25.770    0.000    0.000
LGA    G    14_A      G    14_A    23.011     0    0.490   0.490    23.116    0.000    0.000
LGA    G    15_A      G    15_A    18.537     0    0.434   0.434    19.863    0.000    0.000
LGA    G    16_A      G    16_A    14.498     0    0.584   0.584    15.512    0.000    0.000
LGA    S    17_A      S    17_A    11.290     0    0.103   0.611    13.202    0.000    0.000
LGA    V    18_A      V    18_A     8.568     0    0.116   1.061     9.067    6.190    6.599
LGA    R    19_A      R    19_A     7.005     0    0.125   1.585    11.998   21.429    8.052
LGA    F    20_A      F    20_A     0.839     0    0.671   1.171     3.387   71.667   67.662
LGA    G    21_A      G    21_A     0.441     0    0.023   0.023     1.799   86.190   86.190
LGA    P    22_A      P    22_A     2.369     0    0.615   0.606     5.458   55.595   64.286
LGA    G    23_A      G    23_A     2.406     0    0.630   0.630     2.418   68.810   68.810
LGA    V    24_A      V    24_A     1.556     0    0.124   0.117     3.953   63.095   59.660
LGA    A    25_A      A    25_A     3.553     0    0.145   0.197     5.538   53.810   47.333
LGA    F    26_A      F    26_A     2.151     0    0.135   1.292     6.571   55.595   48.918
LGA    R    27_A      R    27_A     3.643     0    0.049   1.227    12.192   64.167   28.442
LGA    A    28_A      A    28_A     2.892     0    0.044   0.045     5.257   67.143   58.952
LGA    P    29_A      P    29_A     2.755     0    0.029   0.344     5.964   65.119   48.503
LGA    S    30_A      S    30_A     1.411     0    0.118   0.685     5.264   69.762   57.063
LGA    I    31_A      I    31_A     3.624     0    0.612   1.441    10.004   61.429   35.536
LGA    H    32_A      H    32_A     3.146     0    0.053   1.390     8.328   40.833   26.762
LGA    G    33_A      G    33_A     6.233     0    0.557   0.557     9.077   13.690   13.690

# 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):    11.600         11.411                 13.131           26.198   22.014

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   33   33    4.0     13    2.58    37.121    33.261     0.486

LGA_LOCAL      RMSD:   2.575  Number of atoms:   13  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  17.306  Number of assigned atoms:   33 
Std_ASGN_ATOMS RMSD:  11.600  Standard rmsd on all 33 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.475583 * X  +  -0.819743 * Y  +  -0.319127 * Z  +   4.923693
  Y_new =   0.868612 * X  +  -0.494956 * Y  +  -0.023066 * Z  +  -5.875783
  Z_new =  -0.139046 * X  +  -0.288168 * Y  +   0.947431 * Z  +  -2.241966 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.071734  0.139498 -0.295266   [DEG:  118.7016    7.9926  -16.9175 ]
ZXZ: -1.498644  0.325687 -2.692029   [DEG:  -85.8660   18.6605 -154.2419 ]
 
# END of job
