
#######################################################
#                                                     #
#                        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   62 (  507),  selected   43 , name one
# Molecule2: number of CA atoms   43 (  346),  selected   43 , 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:    43       5_B - 47_B        1.63     1.63
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    43       5_B - 47_B        1.63     1.63
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    41       5_B - 45_B        0.90     1.74
  LCS_AVERAGE:     91.24

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   43
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     S     5_B     S     5_B     41   43   43      5   19   37   40   40   41   41   41   41   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     L     6_B     L     6_B     41   43   43     22   38   39   40   40   41   41   41   41   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     E     7_B     E     7_B     41   43   43     23   38   39   40   40   41   41   41   41   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     T     8_B     T     8_B     41   43   43     23   38   39   40   40   41   41   41   41   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     K     9_B     K     9_B     41   43   43     23   38   39   40   40   41   41   41   41   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     K    10_B     K    10_B     41   43   43     23   38   39   40   40   41   41   41   41   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     A    11_B     A    11_B     41   43   43     23   38   39   40   40   41   41   41   41   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     Y    12_B     Y    12_B     41   43   43     23   38   39   40   40   41   41   41   41   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     A    13_B     A    13_B     41   43   43     23   38   39   40   40   41   41   41   41   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     A    14_B     A    14_B     41   43   43     23   38   39   40   40   41   41   41   41   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     R    15_B     R    15_B     41   43   43     23   38   39   40   40   41   41   41   41   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     T    16_B     T    16_B     41   43   43     23   38   39   40   40   41   41   41   41   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     R    17_B     R    17_B     41   43   43     23   38   39   40   40   41   41   41   41   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     R    18_B     R    18_B     41   43   43     23   38   39   40   40   41   41   41   41   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     S    19_B     S    19_B     41   43   43     19   38   39   40   40   41   41   41   41   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     N    20_B     N    20_B     41   43   43     23   38   39   40   40   41   41   41   41   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     Y    21_B     Y    21_B     41   43   43     23   38   39   40   40   41   41   41   41   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     A    22_B     A    22_B     41   43   43     23   38   39   40   40   41   41   41   41   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     A    23_B     A    23_B     41   43   43     23   38   39   40   40   41   41   41   41   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     S    24_B     S    24_B     41   43   43     23   38   39   40   40   41   41   41   41   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     L    25_B     L    25_B     41   43   43     23   38   39   40   40   41   41   41   41   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     R    26_B     R    26_B     41   43   43     23   38   39   40   40   41   41   41   41   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     L    27_B     L    27_B     41   43   43     23   38   39   40   40   41   41   41   41   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     E    28_B     E    28_B     41   43   43     23   38   39   40   40   41   41   41   41   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     G    29_B     G    29_B     41   43   43     23   38   39   40   40   41   41   41   41   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     F    30_B     F    30_B     41   43   43     23   38   39   40   40   41   41   41   41   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     K    31_B     K    31_B     41   43   43     23   38   39   40   40   41   41   41   41   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     V    32_B     V    32_B     41   43   43     23   38   39   40   40   41   41   41   41   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     T    33_B     T    33_B     41   43   43     23   38   39   40   40   41   41   41   41   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     F    34_B     F    34_B     41   43   43     23   38   39   40   40   41   41   41   41   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     A    35_B     A    35_B     41   43   43     23   38   39   40   40   41   41   41   41   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     D    36_B     D    36_B     41   43   43     23   38   39   40   40   41   41   41   41   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     G    37_B     G    37_B     41   43   43     23   38   39   40   40   41   41   41   41   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     E    38_B     E    38_B     41   43   43     23   38   39   40   40   41   41   41   41   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     R    39_B     R    39_B     41   43   43     23   38   39   40   40   41   41   41   41   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     K    40_B     K    40_B     41   43   43     16   38   39   40   40   41   41   41   41   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     M    41_B     M    41_B     41   43   43     23   38   39   40   40   41   41   41   41   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     P    42_B     P    42_B     41   43   43     16   38   39   40   40   41   41   41   41   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     T    43_B     T    43_B     41   43   43     13   36   39   40   40   41   41   41   41   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     R    44_B     R    44_B     41   43   43     13   38   39   40   40   41   41   41   41   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     E    45_B     E    45_B     41   43   43      4    6   25   40   40   41   41   41   41   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     E    46_B     E    46_B      3   43   43      3    3    3    4    6    6    8   30   33   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     V    47_B     V    47_B      3   43   43      0    3    3    3    3    3    4   16   33   43   43   43   43   43   43   43   43   43   43   43 
LCS_AVERAGE  LCS_A:  97.08  (  91.24  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     23     38     39     40     40     41     41     41     41     43     43     43     43     43     43     43     43     43     43     43 
GDT PERCENT_AT  53.49  88.37  90.70  93.02  93.02  95.35  95.35  95.35  95.35 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.34   0.59   0.63   0.69   0.69   0.90   0.90   0.90   0.90   1.63   1.63   1.63   1.63   1.63   1.63   1.63   1.63   1.63   1.63   1.63
GDT RMS_ALL_AT   1.97   1.84   1.81   1.82   1.82   1.74   1.74   1.74   1.74   1.63   1.63   1.63   1.63   1.63   1.63   1.63   1.63   1.63   1.63   1.63

# Checking swapping
#   possible swapping detected:  E     7_B      E     7_B
#   possible swapping detected:  Y    12_B      Y    12_B
#   possible swapping detected:  Y    21_B      Y    21_B
#   possible swapping detected:  E    28_B      E    28_B
#   possible swapping detected:  F    30_B      F    30_B
#   possible swapping detected:  E    45_B      E    45_B
#   possible swapping detected:  E    46_B      E    46_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     5_B      S     5_B     1.884     0    0.618   0.695     6.467   79.286   60.952
LGA    L     6_B      L     6_B     0.679     0    0.045   0.856     2.811   92.857   82.083
LGA    E     7_B      E     7_B     0.830     0    0.055   0.798     3.327   90.476   79.683
LGA    T     8_B      T     8_B     0.731     0    0.041   1.169     3.079   90.476   79.932
LGA    K     9_B      K     9_B     0.434     0    0.019   0.118     1.060   97.619   93.704
LGA    K    10_B      K    10_B     0.241     0    0.048   0.940     3.118  100.000   91.429
LGA    A    11_B      A    11_B     0.779     0    0.026   0.038     0.926   90.476   90.476
LGA    Y    12_B      Y    12_B     0.538     0    0.033   0.069     0.636   95.238   96.032
LGA    A    13_B      A    13_B     0.308     0    0.022   0.021     0.720   95.238   96.190
LGA    A    14_B      A    14_B     0.685     0    0.079   0.092     1.161   88.214   88.667
LGA    R    15_B      R    15_B     0.801     0    0.060   0.803     2.723   88.214   85.801
LGA    T    16_B      T    16_B     0.544     0    0.024   0.055     0.627   92.857   91.837
LGA    R    17_B      R    17_B     0.505     0    0.048   0.816     4.642   95.238   73.853
LGA    R    18_B      R    18_B     0.876     0    0.037   0.927     3.264   88.214   81.905
LGA    S    19_B      S    19_B     0.879     0    0.034   0.636     2.241   90.476   86.190
LGA    N    20_B      N    20_B     0.703     0    0.060   0.476     1.145   90.476   90.536
LGA    Y    21_B      Y    21_B     0.489     0    0.049   0.161     1.900   92.857   86.865
LGA    A    22_B      A    22_B     0.714     0    0.011   0.019     0.772   90.476   90.476
LGA    A    23_B      A    23_B     0.720     0    0.031   0.036     0.752   90.476   90.476
LGA    S    24_B      S    24_B     0.807     0    0.087   0.714     1.634   88.214   86.032
LGA    L    25_B      L    25_B     0.760     0    0.021   0.075     1.022   90.476   89.345
LGA    R    26_B      R    26_B     0.649     0    0.013   0.968     2.931   90.476   86.840
LGA    L    27_B      L    27_B     0.730     0    0.054   0.167     1.227   90.476   89.345
LGA    E    28_B      E    28_B     0.640     0    0.057   0.511     1.299   90.476   89.524
LGA    G    29_B      G    29_B     0.780     0    0.040   0.040     0.780   90.476   90.476
LGA    F    30_B      F    30_B     0.742     0    0.034   0.046     1.300   90.476   87.186
LGA    K    31_B      K    31_B     0.738     0    0.032   0.614     3.994   90.476   76.085
LGA    V    32_B      V    32_B     0.443     0    0.050   1.239     3.208   97.619   85.102
LGA    T    33_B      T    33_B     0.509     0    0.061   1.074     3.086   97.619   86.258
LGA    F    34_B      F    34_B     0.279     0    0.025   1.400     6.156  100.000   70.909
LGA    A    35_B      A    35_B     0.450     0    0.025   0.025     0.450  100.000  100.000
LGA    D    36_B      D    36_B     0.413     0    0.017   0.165     0.677  100.000   97.619
LGA    G    37_B      G    37_B     0.390     0    0.056   0.056     0.473  100.000  100.000
LGA    E    38_B      E    38_B     0.541     0    0.082   0.869     2.898   92.857   82.169
LGA    R    39_B      R    39_B     0.374     0    0.094   1.094     4.471   97.619   81.558
LGA    K    40_B      K    40_B     0.552     0    0.113   1.207     8.075   90.595   61.958
LGA    M    41_B      M    41_B     0.206     0    0.023   0.863     3.152  100.000   93.750
LGA    P    42_B      P    42_B     0.646     0    0.049   0.055     0.880   95.238   93.197
LGA    T    43_B      T    43_B     1.188     0    0.004   0.050     1.677   81.429   78.980
LGA    R    44_B      R    44_B     1.032     0    0.603   0.936     4.114   81.429   73.810
LGA    E    45_B      E    45_B     3.523     0    0.477   1.421    10.477   41.905   25.132
LGA    E    46_B      E    46_B     7.480     0    0.592   1.418    12.288   13.452    6.032
LGA    V    47_B      V    47_B     6.429     0    0.406   1.361     8.495   16.190   14.422

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       43     172    172  100.00     346    346  100.00                43
SUMMARY(RMSD_GDC):     1.629          1.553                  2.495           87.597   80.996

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   62   43    4.0     41    0.90    94.186    96.420     4.119

LGA_LOCAL      RMSD:   0.896  Number of atoms:   41  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.740  Number of assigned atoms:   43 
Std_ASGN_ATOMS RMSD:   1.629  Standard rmsd on all 43 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.421749 * X  +   0.883462 * Y  +  -0.204019 * Z  +  20.495796
  Y_new =  -0.641280 * X  +  -0.131564 * Y  +   0.755943 * Z  + -32.090458
  Z_new =   0.641005 * X  +   0.449652 * Y  +   0.622034 * Z  +  19.207575 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.152542 -0.695807  0.625913   [DEG: -123.3316  -39.8668   35.8622 ]
ZXZ: -2.877986  0.899459  0.959079   [DEG: -164.8965   51.5352   54.9512 ]
 
# END of job
