
#######################################################
#                                                     #
#                        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   42 (  348),  selected   41 , name one
# Molecule2: number of CA atoms   41 (  336),  selected   41 , 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:    36       2_B - 37_B        4.89     8.26
  LCS_AVERAGE:     84.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    23       6_B - 28_B        1.97    10.09
  LONGEST_CONTINUOUS_SEGMENT:    23       7_B - 29_B        1.93    10.20
  LCS_AVERAGE:     48.66

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    16       8_B - 23_B        0.93    10.77
  LONGEST_CONTINUOUS_SEGMENT:    16       9_B - 24_B        0.94    10.79
  LCS_AVERAGE:     30.76

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   41
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     A     2_B     A     2_B      4    5   36      0    3    5    5    5    6    6   11   12   14   16   18   29   31   32   33   34   34   35   35 
LCS_GDT     S     3_B     S     3_B      4    6   36      3    4    5    5    7   14   19   21   24   25   26   30   32   32   34   34   34   35   35   36 
LCS_GDT     Q     4_B     Q     4_B      4   13   36      3    4    5    5    8   15   19   21   24   27   29   30   32   32   34   34   34   35   35   36 
LCS_GDT     R     5_B     R     5_B      7   21   36      3    4   11   13   15   18   23   25   28   28   29   30   32   32   34   34   34   35   35   36 
LCS_GDT     L     6_B     L     6_B      7   23   36      3    6   11   16   20   21   23   25   28   28   29   30   32   32   34   34   34   35   35   36 
LCS_GDT     F     7_B     F     7_B      9   23   36      3    5   11   13   15   21   23   25   28   28   29   30   32   32   34   34   34   35   35   36 
LCS_GDT     V     8_B     V     8_B     16   23   36      4    6   11   17   20   21   23   25   28   28   29   30   32   32   34   34   34   35   35   36 
LCS_GDT     L     9_B     L     9_B     16   23   36      4   15   16   17   20   21   23   25   28   28   29   30   32   32   34   34   34   35   35   36 
LCS_GDT     D    10_B     D    10_B     16   23   36     11   15   16   17   20   21   23   25   28   28   29   30   32   32   34   34   34   35   35   36 
LCS_GDT     N    11_B     N    11_B     16   23   36     12   15   16   17   20   21   23   25   28   28   29   30   32   32   34   34   34   35   35   36 
LCS_GDT     E    12_B     E    12_B     16   23   36     12   15   16   17   20   21   23   25   28   28   29   30   32   32   34   34   34   35   35   36 
LCS_GDT     R    13_B     R    13_B     16   23   36     12   15   16   17   20   21   23   25   28   28   29   30   32   32   34   34   34   35   35   36 
LCS_GDT     Y    14_B     Y    14_B     16   23   36     12   15   16   17   20   21   23   25   28   28   29   30   32   32   34   34   34   35   35   36 
LCS_GDT     D    15_B     D    15_B     16   23   36     12   15   16   17   20   21   23   25   28   28   29   30   32   32   34   34   34   35   35   36 
LCS_GDT     S    16_B     S    16_B     16   23   36     12   15   16   17   20   21   23   25   28   28   29   30   32   32   34   34   34   35   35   36 
LCS_GDT     F    17_B     F    17_B     16   23   36     12   15   16   17   20   21   23   25   28   28   29   30   32   32   34   34   34   35   35   36 
LCS_GDT     I    18_B     I    18_B     16   23   36     11   15   16   17   20   21   23   25   28   28   29   30   32   32   34   34   34   35   35   36 
LCS_GDT     T    19_B     T    19_B     16   23   36     12   15   16   17   20   21   23   25   28   28   29   30   32   32   34   34   34   35   35   36 
LCS_GDT     Q    20_B     Q    20_B     16   23   36     12   15   16   17   20   21   23   25   28   28   29   30   32   32   34   34   34   35   35   36 
LCS_GDT     L    21_B     L    21_B     16   23   36     12   15   16   17   20   21   23   25   28   28   29   30   32   32   34   34   34   35   35   36 
LCS_GDT     E    22_B     E    22_B     16   23   36     12   15   16   17   20   21   23   25   28   28   29   30   32   32   34   34   34   35   35   36 
LCS_GDT     A    23_B     A    23_B     16   23   36     12   15   16   17   20   21   23   25   28   28   29   30   32   32   34   34   34   35   35   36 
LCS_GDT     P    24_B     P    24_B     16   23   36      3    4    9   17   20   21   23   25   28   28   29   30   32   32   34   34   34   35   35   36 
LCS_GDT     V    25_B     V    25_B      5   23   36      3    6   15   17   19   21   23   25   28   28   29   30   32   32   34   34   34   35   35   36 
LCS_GDT     Q    26_B     Q    26_B     14   23   36      3    7   15   17   19   21   21   24   28   28   29   30   32   32   34   34   34   35   35   36 
LCS_GDT     N    27_B     N    27_B     14   23   36      9   12   15   17   19   21   23   24   28   28   29   30   32   32   34   34   34   35   35   36 
LCS_GDT     A    28_B     A    28_B     14   23   36     11   15   16   17   20   21   23   25   28   28   29   30   32   32   34   34   34   35   35   36 
LCS_GDT     E    29_B     E    29_B     14   23   36     11   12   14   17   20   21   23   25   28   28   29   30   32   32   34   34   34   35   35   36 
LCS_GDT     G    30_B     G    30_B     14   17   36     11   12   14   15   15   16   17   17   28   28   29   30   32   32   34   34   34   35   35   36 
LCS_GDT     R    31_B     R    31_B     14   17   36     11   12   14   15   15   16   17   25   28   28   29   30   32   32   34   34   34   35   35   36 
LCS_GDT     E    32_B     E    32_B     14   17   36     11   12   14   15   15   16   21   25   28   28   29   30   32   32   34   34   34   35   35   36 
LCS_GDT     R    33_B     R    33_B     14   17   36     11   12   14   15   15   16   17   17   17   20   28   30   32   32   34   34   34   35   35   36 
LCS_GDT     L    34_B     L    34_B     14   17   36     11   12   14   15   15   16   17   17   17   18   18   20   28   32   34   34   34   35   35   36 
LCS_GDT     M    35_B     M    35_B     14   17   36     11   12   14   15   15   16   17   17   17   21   28   30   32   32   34   34   34   35   35   36 
LCS_GDT     A    36_B     A    36_B     14   17   36     11   12   14   15   15   16   17   17   17   18   18   23   29   32   34   34   34   35   35   36 
LCS_GDT     V    37_B     V    37_B     14   17   36     11   12   14   15   15   16   17   17   17   18   18   19   20   21   24   32   33   35   35   36 
LCS_GDT     K    38_B     K    38_B     14   17   24     11   12   14   15   15   16   17   17   17   18   18   19   20   21   22   24   28   34   35   36 
LCS_GDT     P    39_B     P    39_B     14   17   23      3    8   14   15   15   16   17   17   17   18   18   19   20   21   22   24   26   28   35   35 
LCS_GDT     E    40_B     E    40_B      3   17   23      3    3    4    5   12   16   16   16   17   18   18   18   18   20   20   20   22   23   24   24 
LCS_GDT     W    41_B     W    41_B      3   17   23      3   11   14   15   15   16   17   17   17   18   18   19   19   21   22   23   23   25   26   27 
LCS_GDT     K    42_B     K    42_B      3   17   23      3    3    3    3    6   16   17   17   17   18   18   19   19   21   22   23   23   25   26   26 
LCS_AVERAGE  LCS_A:  54.47  (  30.76   48.66   84.00 )

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     15     16     17     20     21     23     25     28     28     29     30     32     32     34     34     34     35     35     36 
GDT PERCENT_AT  29.27  36.59  39.02  41.46  48.78  51.22  56.10  60.98  68.29  68.29  70.73  73.17  78.05  78.05  82.93  82.93  82.93  85.37  85.37  87.80
GDT RMS_LOCAL    0.26   0.54   0.63   0.75   1.52   1.45   1.92   2.40   2.76   2.76   3.05   3.31   3.76   3.76   4.30   4.30   4.19   4.72   4.48   5.20
GDT RMS_ALL_AT  11.61  10.65  10.57  10.96   9.45  11.12   9.64   8.99   9.21   9.21   8.99   8.83   8.58   8.58   8.32   8.32   8.60   8.15   8.43   7.97

# Checking swapping
#   possible swapping detected:  F     7_B      F     7_B
#   possible swapping detected:  F    17_B      F    17_B
#   possible swapping detected:  E    22_B      E    22_B
#   possible swapping detected:  E    29_B      E    29_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A     2_B      A     2_B    11.878     0    0.257   0.362    14.420    0.833    0.667
LGA    S     3_B      S     3_B     9.121     0    0.277   0.350    10.132    4.048    8.730
LGA    Q     4_B      Q     4_B     7.672     0    0.063   0.264    13.775    7.024    3.280
LGA    R     5_B      R     5_B     4.150     0    0.670   1.197     8.921   43.571   25.671
LGA    L     6_B      L     6_B     2.131     0    0.620   1.427     4.363   64.881   60.417
LGA    F     7_B      F     7_B     3.008     0    0.211   0.299     4.269   50.119   46.494
LGA    V     8_B      V     8_B     2.128     0    0.053   1.187     4.434   68.810   63.197
LGA    L     9_B      L     9_B     1.324     0    0.097   1.411     2.585   81.429   77.560
LGA    D    10_B      D    10_B     1.410     0    0.075   0.908     2.950   77.143   75.179
LGA    N    11_B      N    11_B     1.975     0    0.021   0.947     4.772   72.857   65.774
LGA    E    12_B      E    12_B     1.444     0    0.017   1.164     5.899   79.286   61.164
LGA    R    13_B      R    13_B     1.366     0    0.013   1.119     3.845   81.429   78.918
LGA    Y    14_B      Y    14_B     1.763     0    0.037   0.189     2.902   72.857   65.595
LGA    D    15_B      D    15_B     1.516     0    0.010   0.460     2.087   77.143   73.988
LGA    S    16_B      S    16_B     0.980     0    0.005   0.170     1.264   83.690   84.444
LGA    F    17_B      F    17_B     1.704     0    0.041   0.265     2.137   75.000   72.164
LGA    I    18_B      I    18_B     1.803     0    0.017   0.115     2.625   77.143   70.000
LGA    T    19_B      T    19_B     1.086     0    0.024   0.246     1.599   81.429   80.204
LGA    Q    20_B      Q    20_B     1.666     0    0.023   1.168     8.423   72.976   50.635
LGA    L    21_B      L    21_B     2.265     0    0.020   1.323     5.038   66.786   64.405
LGA    E    22_B      E    22_B     1.604     0    0.117   0.757     2.546   72.857   66.825
LGA    A    23_B      A    23_B     1.600     0    0.612   0.603     4.006   63.929   65.714
LGA    P    24_B      P    24_B     1.737     0    0.404   0.475     3.162   77.262   68.707
LGA    V    25_B      V    25_B     3.409     0    0.063   0.178     4.906   55.476   49.660
LGA    Q    26_B      Q    26_B     5.246     0    0.666   1.160     9.374   21.548   16.243
LGA    N    27_B      N    27_B     4.624     0    0.368   0.433     7.492   38.810   29.286
LGA    A    28_B      A    28_B     1.744     0    0.011   0.011     2.848   71.071   71.429
LGA    E    29_B      E    29_B     2.000     0    0.108   0.750     4.473   62.619   55.185
LGA    G    30_B      G    30_B     5.633     0    0.106   0.106     6.746   24.881   24.881
LGA    R    31_B      R    31_B     4.864     0    0.044   0.625     5.479   30.119   38.658
LGA    E    32_B      E    32_B     4.973     0    0.064   0.839     7.686   22.262   31.481
LGA    R    33_B      R    33_B     8.243     0    0.060   1.193    10.471    4.881   10.563
LGA    L    34_B      L    34_B     9.684     0    0.015   1.394    13.022    0.952    0.655
LGA    M    35_B      M    35_B     8.393     0    0.021   0.101    10.089    2.738    7.976
LGA    A    36_B      A    36_B    11.016     0    0.037   0.038    13.576    0.119    0.095
LGA    V    37_B      V    37_B    13.984     0    0.055   0.094    15.615    0.000    0.000
LGA    K    38_B      K    38_B    16.202     4    0.631   0.568    18.861    0.000    0.000
LGA    P    39_B      P    39_B    18.028     0    0.428   0.568    22.211    0.000    0.000
LGA    E    40_B      E    40_B    23.750     0    0.452   0.360    27.284    0.000    0.000
LGA    W    41_B      W    41_B    22.522     0    0.023   0.348    23.484    0.000    0.000
LGA    K    42_B      K    42_B    24.389     0    0.535   1.260    27.037    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       41     164    164  100.00     336    336  100.00                41
SUMMARY(RMSD_GDC):     7.611          7.676                  8.154           43.609   40.630

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   42   41    4.0     25    2.40    55.488    55.223     1.001

LGA_LOCAL      RMSD:   2.398  Number of atoms:   25  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   8.985  Number of assigned atoms:   41 
Std_ASGN_ATOMS RMSD:   7.611  Standard rmsd on all 41 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.686602 * X  +   0.685625 * Y  +  -0.241861 * Z  +   2.825114
  Y_new =  -0.709728 * X  +   0.559932 * Y  +  -0.427506 * Z  + -25.285131
  Z_new =  -0.157683 * X  +   0.465182 * Y  +   0.871058 * Z  +  44.557339 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.801959  0.158344  0.490509   [DEG:  -45.9489    9.0725   28.1041 ]
ZXZ: -0.514853  0.513444 -0.326816   [DEG:  -29.4989   29.4182  -18.7252 ]
 
# END of job
