
#######################################################
#                                                     #
#                        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:    41       2_B - 42_B        3.67     3.67
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    33       3_B - 35_B        1.96     4.20
  LONGEST_CONTINUOUS_SEGMENT:    33       4_B - 36_B        1.91     4.28
  LONGEST_CONTINUOUS_SEGMENT:    33       5_B - 37_B        1.85     4.36
  LCS_AVERAGE:     75.19

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    21       5_B - 25_B        0.85     5.01
  LCS_AVERAGE:     41.23

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      3   24   41      3    3    4   17   19   23   25   33   35   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     S     3_B     S     3_B      4   33   41      3    4    4   18   19   29   31   33   35   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     Q     4_B     Q     4_B      4   33   41      3    4    4    4   19   26   31   33   35   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     R     5_B     R     5_B     21   33   41      6   11   21   24   28   31   31   32   35   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     L     6_B     L     6_B     21   33   41      6   18   22   26   28   31   31   33   35   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     F     7_B     F     7_B     21   33   41      6   18   22   26   28   31   31   33   35   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     V     8_B     V     8_B     21   33   41     11   18   22   26   28   31   31   33   35   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     L     9_B     L     9_B     21   33   41     16   18   22   26   28   31   31   33   35   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     D    10_B     D    10_B     21   33   41     16   18   22   26   28   31   31   33   35   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     N    11_B     N    11_B     21   33   41     16   18   22   26   28   31   31   33   35   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     E    12_B     E    12_B     21   33   41     16   18   22   26   28   31   31   33   35   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     R    13_B     R    13_B     21   33   41     16   18   22   26   28   31   31   33   35   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     Y    14_B     Y    14_B     21   33   41     16   18   22   26   28   31   31   33   35   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     D    15_B     D    15_B     21   33   41     16   18   22   26   28   31   31   33   35   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     S    16_B     S    16_B     21   33   41     16   18   22   26   28   31   31   33   35   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     F    17_B     F    17_B     21   33   41     16   18   22   26   28   31   31   33   35   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     I    18_B     I    18_B     21   33   41     16   18   22   26   28   31   31   33   35   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     T    19_B     T    19_B     21   33   41     16   18   22   26   28   31   31   33   35   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     Q    20_B     Q    20_B     21   33   41     16   18   22   26   28   31   31   33   35   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     L    21_B     L    21_B     21   33   41     16   18   22   26   28   31   31   33   35   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     E    22_B     E    22_B     21   33   41     16   18   22   26   28   31   31   33   35   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     A    23_B     A    23_B     21   33   41     16   18   22   26   28   31   31   33   35   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     P    24_B     P    24_B     21   33   41     16   18   22   26   28   31   31   33   35   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     V    25_B     V    25_B     21   33   41      4    5   21   26   28   31   31   33   35   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     Q    26_B     Q    26_B     20   33   41     11   14   14   15   22   28   31   32   34   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     N    27_B     N    27_B     20   33   41     11   18   22   26   28   31   31   33   35   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     A    28_B     A    28_B     15   33   41     11   14   19   26   28   31   31   33   35   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     E    29_B     E    29_B     15   33   41     11   18   22   26   28   31   31   33   35   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     G    30_B     G    30_B     15   33   41     11   14   14   25   28   31   31   33   35   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     R    31_B     R    31_B     15   33   41     11   14   22   26   28   31   31   33   35   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     E    32_B     E    32_B     15   33   41     11   18   22   26   28   31   31   33   35   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     R    33_B     R    33_B     15   33   41     11   14   14   23   28   31   31   33   35   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     L    34_B     L    34_B     15   33   41     11   14   14   21   27   31   31   33   35   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     M    35_B     M    35_B     15   33   41     11   14   22   26   28   31   31   33   35   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     A    36_B     A    36_B     15   33   41     11   14   14   20   27   31   31   33   35   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     V    37_B     V    37_B     15   33   41     11   14   14   15   18   27   31   32   35   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     K    38_B     K    38_B     15   17   41      7   14   14   15   15   21   28   32   34   36   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     P    39_B     P    39_B     15   17   41      5   14   14   15   15   16   19   24   31   33   37   38   38   39   40   40   41   41   41   41 
LCS_GDT     E    40_B     E    40_B     15   17   41      3    3    5   12   14   16   16   16   17   17   19   22   26   32   34   39   41   41   41   41 
LCS_GDT     W    41_B     W    41_B      3   17   41      3    3    3   14   15   16   16   16   17   17   25   37   38   39   40   40   41   41   41   41 
LCS_GDT     K    42_B     K    42_B      3   17   41      3    3    3    3    4    4   11   13   17   17   35   37   38   39   40   40   41   41   41   41 
LCS_AVERAGE  LCS_A:  72.14  (  41.23   75.19  100.00 )

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     16     18     22     26     28     31     31     33     35     36     37     38     38     39     40     40     41     41     41     41 
GDT PERCENT_AT  39.02  43.90  53.66  63.41  68.29  75.61  75.61  80.49  85.37  87.80  90.24  92.68  92.68  95.12  97.56  97.56 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.30   0.52   0.76   1.03   1.17   1.49   1.49   1.95   2.19   2.30   2.47   2.71   2.71   3.01   3.30   3.30   3.67   3.67   3.67   3.67
GDT RMS_ALL_AT   4.12   4.56   4.63   4.74   4.74   4.48   4.48   4.01   3.95   3.97   3.89   3.81   3.81   3.73   3.68   3.68   3.67   3.67   3.67   3.67

# 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
#   possible swapping detected:  E    40_B      E    40_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A     2_B      A     2_B     4.021     0    0.543   0.554     5.348   53.214   47.810
LGA    S     3_B      S     3_B     2.777     0    0.509   0.429     3.564   57.500   61.270
LGA    Q     4_B      Q     4_B     3.424     0    0.254   0.297    10.065   46.905   26.296
LGA    R     5_B      R     5_B     4.609     0    0.654   1.076    15.181   40.714   16.710
LGA    L     6_B      L     6_B     3.547     0    0.146   1.385     5.133   46.667   41.429
LGA    F     7_B      F     7_B     2.652     0    0.138   0.156     2.896   60.952   59.221
LGA    V     8_B      V     8_B     2.416     0    0.039   1.188     4.186   64.881   62.177
LGA    L     9_B      L     9_B     1.042     0    0.027   0.125     1.430   85.952   89.405
LGA    D    10_B      D    10_B     0.609     0    0.086   0.634     1.868   92.857   89.464
LGA    N    11_B      N    11_B     0.710     0    0.025   0.958     2.682   90.476   81.964
LGA    E    12_B      E    12_B     0.849     0    0.048   1.125     6.726   90.476   63.280
LGA    R    13_B      R    13_B     0.623     0    0.014   1.127     2.805   92.857   84.286
LGA    Y    14_B      Y    14_B     0.408     0    0.041   0.163     0.668   97.619   97.619
LGA    D    15_B      D    15_B     0.547     0    0.014   0.456     1.342   90.476   90.536
LGA    S    16_B      S    16_B     0.611     0    0.023   0.173     1.208   90.476   88.968
LGA    F    17_B      F    17_B     0.467     0    0.033   0.248     0.675   97.619   97.403
LGA    I    18_B      I    18_B     0.610     0    0.015   0.118     1.236   92.857   90.536
LGA    T    19_B      T    19_B     0.964     0    0.022   0.249     1.309   85.952   85.306
LGA    Q    20_B      Q    20_B     0.977     0    0.005   1.154     3.821   88.214   77.407
LGA    L    21_B      L    21_B     0.979     0    0.017   1.322     2.889   88.214   80.833
LGA    E    22_B      E    22_B     1.009     0    0.092   0.743     2.958   81.429   71.640
LGA    A    23_B      A    23_B     0.886     0    0.070   0.101     0.958   92.857   92.381
LGA    P    24_B      P    24_B     0.732     0    0.018   0.357     1.418   88.214   86.599
LGA    V    25_B      V    25_B     1.676     0    0.110   1.264     4.360   73.214   64.694
LGA    Q    26_B      Q    26_B     4.745     0    0.684   1.120    10.474   30.833   17.937
LGA    N    27_B      N    27_B     2.967     0    0.166   0.177     3.539   57.262   53.690
LGA    A    28_B      A    28_B     2.632     0    0.046   0.046     3.370   67.143   63.714
LGA    E    29_B      E    29_B     0.871     0    0.057   0.851     2.581   85.952   75.185
LGA    G    30_B      G    30_B     2.165     0    0.128   0.128     2.165   70.952   70.952
LGA    R    31_B      R    31_B     1.757     0    0.036   0.976     5.859   81.667   54.848
LGA    E    32_B      E    32_B     1.070     0    0.046   0.850     5.688   81.548   60.952
LGA    R    33_B      R    33_B     2.448     0    0.055   1.170     3.319   61.190   58.701
LGA    L    34_B      L    34_B     2.811     0    0.021   1.394     7.007   60.952   49.762
LGA    M    35_B      M    35_B     1.170     0    0.050   0.977     6.485   75.119   65.119
LGA    A    36_B      A    36_B     3.435     0    0.042   0.040     5.020   44.524   44.286
LGA    V    37_B      V    37_B     4.941     0    0.032   0.078     6.107   31.548   28.707
LGA    K    38_B      K    38_B     6.246     4    0.595   0.600     9.001   12.500    7.037
LGA    P    39_B      P    39_B     8.026     0    0.025   0.322    11.281    3.690    8.435
LGA    E    40_B      E    40_B    12.711     0    0.308   1.022    21.004    0.000    0.000
LGA    W    41_B      W    41_B    10.507     0    0.370   0.514    13.539    0.000    0.000
LGA    K    42_B      K    42_B     9.399     0    0.053   0.741    15.563    2.381    1.058

# 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):     3.667          3.694                  4.906           64.826   58.722

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   42   41    4.0     33    1.95    71.341    75.014     1.607

LGA_LOCAL      RMSD:   1.954  Number of atoms:   33  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   4.006  Number of assigned atoms:   41 
Std_ASGN_ATOMS RMSD:   3.667  Standard rmsd on all 41 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.972220 * X  +   0.046237 * Y  +   0.229457 * Z  +   7.884089
  Y_new =  -0.156455 * X  +  -0.600766 * Y  +   0.783965 * Z  + -25.181234
  Z_new =   0.174098 * X  +  -0.798086 * Y  +  -0.576843 * Z  +  41.669357 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.159558 -0.174990 -2.196650   [DEG:   -9.1420  -10.0262 -125.8587 ]
ZXZ:  2.856857  2.185655  2.926813   [DEG:  163.6859  125.2288  167.6940 ]
 
# END of job
