
#######################################################
#                                                     #
#                        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        1.43     1.43
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    41       2_B - 42_B        1.43     1.43
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    39       3_B - 41_B        0.98     1.47
  LCS_AVERAGE:     90.84

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   41   41      3    3    5    7   12   13   31   35   37   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     S     3_B     S     3_B     39   41   41      6   26   35   38   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     Q     4_B     Q     4_B     39   41   41      6   31   36   38   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     R     5_B     R     5_B     39   41   41     13   31   36   38   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     L     6_B     L     6_B     39   41   41      6   31   36   38   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     F     7_B     F     7_B     39   41   41      6   31   36   38   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     V     8_B     V     8_B     39   41   41      8   31   36   38   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     L     9_B     L     9_B     39   41   41     18   31   36   38   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     D    10_B     D    10_B     39   41   41     18   31   36   38   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     N    11_B     N    11_B     39   41   41     18   31   36   38   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     E    12_B     E    12_B     39   41   41     18   31   36   38   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     R    13_B     R    13_B     39   41   41     18   31   36   38   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     Y    14_B     Y    14_B     39   41   41     18   31   36   38   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     D    15_B     D    15_B     39   41   41     18   31   36   38   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     S    16_B     S    16_B     39   41   41     18   31   36   38   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     F    17_B     F    17_B     39   41   41     18   31   36   38   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     I    18_B     I    18_B     39   41   41     18   31   36   38   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     T    19_B     T    19_B     39   41   41     18   31   36   38   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     Q    20_B     Q    20_B     39   41   41     18   31   36   38   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     L    21_B     L    21_B     39   41   41     18   31   36   38   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     E    22_B     E    22_B     39   41   41     18   31   36   38   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     A    23_B     A    23_B     39   41   41     18   31   36   38   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     P    24_B     P    24_B     39   41   41     18   31   36   38   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     V    25_B     V    25_B     39   41   41     12   31   36   38   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     Q    26_B     Q    26_B     39   41   41     12   30   36   38   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     N    27_B     N    27_B     39   41   41     12   17   36   38   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     A    28_B     A    28_B     39   41   41     12   17   36   38   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     E    29_B     E    29_B     39   41   41     12   20   36   38   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     G    30_B     G    30_B     39   41   41     17   31   36   38   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     R    31_B     R    31_B     39   41   41     17   31   36   38   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     E    32_B     E    32_B     39   41   41     17   31   36   38   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     R    33_B     R    33_B     39   41   41     17   31   36   38   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     L    34_B     L    34_B     39   41   41     18   31   36   38   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     M    35_B     M    35_B     39   41   41     18   31   36   38   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     A    36_B     A    36_B     39   41   41     18   31   36   38   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     V    37_B     V    37_B     39   41   41     18   31   36   38   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     K    38_B     K    38_B     39   41   41     15   31   36   38   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     P    39_B     P    39_B     39   41   41      4   15   35   38   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     E    40_B     E    40_B     39   41   41      4    6   16   25   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     W    41_B     W    41_B     39   41   41      9   19   36   38   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     K    42_B     K    42_B      3   41   41      3    3    3    5   36   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_AVERAGE  LCS_A:  96.95  (  90.84  100.00  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     18     31     36     38     38     39     40     40     40     41     41     41     41     41     41     41     41     41     41     41 
GDT PERCENT_AT  43.90  75.61  87.80  92.68  92.68  95.12  97.56  97.56  97.56 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.27   0.57   0.76   0.85   0.85   0.98   1.13   1.13   1.13   1.43   1.43   1.43   1.43   1.43   1.43   1.43   1.43   1.43   1.43   1.43
GDT RMS_ALL_AT   1.54   1.46   1.45   1.44   1.44   1.47   1.44   1.44   1.44   1.43   1.43   1.43   1.43   1.43   1.43   1.43   1.43   1.43   1.43   1.43

# Checking swapping
#   possible swapping detected:  E    12_B      E    12_B
#   possible swapping detected:  Y    14_B      Y    14_B
#   possible swapping detected:  E    29_B      E    29_B
#   possible swapping detected:  E    32_B      E    32_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     5.820     0    0.703   0.693     6.466   28.333   26.095
LGA    S     3_B      S     3_B     1.559     0    0.479   0.698     2.614   77.143   73.095
LGA    Q     4_B      Q     4_B     0.909     0    0.018   0.238     1.899   85.952   80.582
LGA    R     5_B      R     5_B     0.861     0    0.087   0.384     2.737   88.214   80.216
LGA    L     6_B      L     6_B     0.957     0    0.055   0.175     1.709   88.214   83.750
LGA    F     7_B      F     7_B     0.816     0    0.024   0.141     0.928   90.476   90.476
LGA    V     8_B      V     8_B     0.815     0    0.045   1.145     2.613   92.857   84.558
LGA    L     9_B      L     9_B     0.431     0    0.020   0.140     0.772   92.857   91.667
LGA    D    10_B      D    10_B     0.607     0    0.046   0.488     1.576   90.476   87.143
LGA    N    11_B      N    11_B     0.257     0    0.076   0.850     2.453   97.619   87.679
LGA    E    12_B      E    12_B     0.359     0    0.036   1.167     6.363   97.619   71.481
LGA    R    13_B      R    13_B     0.667     0    0.048   1.089     3.810   92.857   74.199
LGA    Y    14_B      Y    14_B     0.366     0    0.049   0.108     0.854  100.000   96.032
LGA    D    15_B      D    15_B     0.065     0    0.025   0.449     1.023  100.000   96.488
LGA    S    16_B      S    16_B     0.388     0    0.048   0.819     2.422   97.619   92.540
LGA    F    17_B      F    17_B     0.294     0    0.023   0.238     0.751  100.000   95.671
LGA    I    18_B      I    18_B     0.261     0    0.026   0.113     0.376  100.000  100.000
LGA    T    19_B      T    19_B     0.232     0    0.017   0.236     0.923  100.000   98.639
LGA    Q    20_B      Q    20_B     0.377     0    0.032   1.006     3.442  100.000   86.455
LGA    L    21_B      L    21_B     0.419     0    0.019   0.251     1.636  100.000   91.964
LGA    E    22_B      E    22_B     0.345     0    0.024   0.734     2.306  100.000   84.339
LGA    A    23_B      A    23_B     0.390     0    0.082   0.096     0.570   97.619   96.190
LGA    P    24_B      P    24_B     0.491     0    0.048   0.060     0.843   95.238   95.918
LGA    V    25_B      V    25_B     0.916     0    0.113   1.272     2.780   85.952   78.163
LGA    Q    26_B      Q    26_B     1.184     0    0.060   1.121     5.266   81.429   65.503
LGA    N    27_B      N    27_B     1.725     0    0.062   0.082     2.041   75.000   72.917
LGA    A    28_B      A    28_B     1.530     0    0.083   0.093     1.690   79.405   78.095
LGA    E    29_B      E    29_B     1.419     0    0.076   0.552     2.509   81.548   75.926
LGA    G    30_B      G    30_B     0.892     0    0.108   0.108     1.115   88.214   88.214
LGA    R    31_B      R    31_B     0.693     0    0.033   1.130     6.117   90.476   67.143
LGA    E    32_B      E    32_B     0.629     0    0.096   0.753     3.408   92.857   81.534
LGA    R    33_B      R    33_B     0.670     0    0.057   1.041     2.691   90.476   84.978
LGA    L    34_B      L    34_B     0.614     0    0.017   0.067     1.014   92.857   90.536
LGA    M    35_B      M    35_B     0.447     0    0.023   0.926     3.367   95.238   91.369
LGA    A    36_B      A    36_B     0.584     0    0.025   0.030     0.783   92.857   92.381
LGA    V    37_B      V    37_B     0.633     0    0.047   0.076     0.927   90.476   90.476
LGA    K    38_B      K    38_B     1.115     4    0.126   0.148     2.473   77.381   42.487
LGA    P    39_B      P    39_B     1.724     0    0.091   0.331     2.166   75.000   75.442
LGA    E    40_B      E    40_B     3.268     0    0.382   0.314     8.502   61.190   35.132
LGA    W    41_B      W    41_B     1.436     0    0.244   0.672     3.660   63.571   59.116
LGA    K    42_B      K    42_B     3.521     0    0.625   1.092     6.850   53.810   34.603

# 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):     1.428          1.350                  2.035           87.337   79.736

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   42   41    4.0     40    1.13    91.463    95.486     3.250

LGA_LOCAL      RMSD:   1.131  Number of atoms:   40  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.440  Number of assigned atoms:   41 
Std_ASGN_ATOMS RMSD:   1.428  Standard rmsd on all 41 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.529164 * X  +  -0.614067 * Y  +   0.585583 * Z  +  17.498501
  Y_new =   0.817033 * X  +  -0.554997 * Y  +   0.156321 * Z  +  -7.124901
  Z_new =   0.229005 * X  +   0.561160 * Y  +   0.795397 * Z  +  35.972527 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.145529 -0.231056  0.614414   [DEG:  122.9297  -13.2385   35.2034 ]
ZXZ:  1.831663  0.651135  0.387463   [DEG:  104.9465   37.3073   22.2000 ]
 
# END of job
