
#######################################################
#                                                     #
#                        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   56 (  447),  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        3.40     3.40
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    36       5_B - 40_B        1.85     4.37
  LCS_AVERAGE:     76.37

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    29       5_B - 33_B        0.79     3.92
  LCS_AVERAGE:     54.08

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     29   36   43      4   24   28   28   32   32   36   36   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     L     6_B     L     6_B     29   36   43     25   27   28   29   32   32   36   36   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     E     7_B     E     7_B     29   36   43     25   27   28   29   32   32   36   36   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     T     8_B     T     8_B     29   36   43     25   27   28   29   32   32   36   36   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     K     9_B     K     9_B     29   36   43     25   27   28   29   32   32   36   36   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     K    10_B     K    10_B     29   36   43     25   27   28   29   32   32   36   36   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     A    11_B     A    11_B     29   36   43     25   27   28   29   32   32   36   36   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     Y    12_B     Y    12_B     29   36   43     25   27   28   29   32   32   36   36   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     A    13_B     A    13_B     29   36   43     25   27   28   29   32   32   36   36   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     A    14_B     A    14_B     29   36   43     25   27   28   29   32   32   36   36   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     R    15_B     R    15_B     29   36   43     25   27   28   29   32   32   36   36   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     T    16_B     T    16_B     29   36   43     25   27   28   29   32   32   36   36   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     R    17_B     R    17_B     29   36   43     25   27   28   29   32   32   36   36   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     R    18_B     R    18_B     29   36   43     25   27   28   29   32   32   36   36   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     S    19_B     S    19_B     29   36   43     25   27   28   28   32   32   36   36   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     N    20_B     N    20_B     29   36   43     25   27   28   29   32   32   36   36   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     Y    21_B     Y    21_B     29   36   43     25   27   28   29   32   32   36   36   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     A    22_B     A    22_B     29   36   43     25   27   28   29   32   32   36   36   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     A    23_B     A    23_B     29   36   43     25   27   28   29   32   32   36   36   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     S    24_B     S    24_B     29   36   43     25   27   28   29   32   32   36   36   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     L    25_B     L    25_B     29   36   43     25   27   28   29   32   32   36   36   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     R    26_B     R    26_B     29   36   43     25   27   28   29   32   32   36   36   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     L    27_B     L    27_B     29   36   43     25   27   28   29   32   32   36   36   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     E    28_B     E    28_B     29   36   43     25   27   28   29   32   32   36   36   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     G    29_B     G    29_B     29   36   43     25   27   28   29   32   32   36   36   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     F    30_B     F    30_B     29   36   43     25   27   28   29   32   32   36   36   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     K    31_B     K    31_B     29   36   43     24   27   28   29   32   32   36   36   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     V    32_B     V    32_B     29   36   43     13   27   28   29   32   32   36   36   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     T    33_B     T    33_B     29   36   43      6   11   26   29   32   32   36   36   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     F    34_B     F    34_B     15   36   43      6   11   14   29   32   32   36   36   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     A    35_B     A    35_B     14   36   43      6   11   22   29   32   32   36   36   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     D    36_B     D    36_B     14   36   43      6   11   18   29   32   32   36   36   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     G    37_B     G    37_B     14   36   43      6   11   14   17   21   32   36   36   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     E    38_B     E    38_B     14   36   43      6   11   14   17   20   29   36   36   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     R    39_B     R    39_B     14   36   43      6   11   14   17   22   31   36   36   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     K    40_B     K    40_B     14   36   43      5   11   14   17   20   26   36   36   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     M    41_B     M    41_B     14   24   43      4   11   14   16   18   22   26   36   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     P    42_B     P    42_B     14   23   43      4    7   11   15   18   22   24   33   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     T    43_B     T    43_B     11   22   43      4    7   11   12   16   19   23   27   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     R    44_B     R    44_B      8   20   43      4    6   10   12   13   16   18   23   28   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     E    45_B     E    45_B      7   15   43      4    6    7    9   12   13   15   17   26   41   42   42   42   43   43   43   43   43   43   43 
LCS_GDT     E    46_B     E    46_B      3    9   43      3    3    3    3    6    8    9   10   13   15   18   24   30   43   43   43   43   43   43   43 
LCS_GDT     V    47_B     V    47_B      3    3   43      3    3    3    3    6   29   33   36   40   41   42   42   42   43   43   43   43   43   43   43 
LCS_AVERAGE  LCS_A:  76.82  (  54.08   76.37  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     25     27     28     29     32     32     36     36     40     41     42     42     42     43     43     43     43     43     43     43 
GDT PERCENT_AT  58.14  62.79  65.12  67.44  74.42  74.42  83.72  83.72  93.02  95.35  97.67  97.67  97.67 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.31   0.44   0.50   1.13   1.29   1.29   1.85   1.85   2.72   2.94   3.13   3.13   3.13   3.40   3.40   3.40   3.40   3.40   3.40   3.40
GDT RMS_ALL_AT   4.17   4.05   4.07   4.12   4.14   4.14   4.37   4.37   3.58   3.50   3.43   3.43   3.43   3.40   3.40   3.40   3.40   3.40   3.40   3.40

# Checking swapping
#   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:  F    34_B      F    34_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     2.448     0    0.603   0.887     4.756   68.810   58.333
LGA    L     6_B      L     6_B     1.496     0    0.074   1.239     4.235   83.810   72.857
LGA    E     7_B      E     7_B     0.452     0    0.062   0.858     4.755   95.238   76.032
LGA    T     8_B      T     8_B     1.536     0    0.037   1.210     3.477   79.405   72.177
LGA    K     9_B      K     9_B     1.075     0    0.018   0.126     3.270   85.952   73.545
LGA    K    10_B      K    10_B     0.684     0    0.031   0.845     4.047   92.857   79.683
LGA    A    11_B      A    11_B     1.546     0    0.016   0.022     1.887   75.000   74.571
LGA    Y    12_B      Y    12_B     1.556     0    0.031   0.069     3.115   79.286   66.548
LGA    A    13_B      A    13_B     0.399     0    0.017   0.017     0.696   92.857   94.286
LGA    A    14_B      A    14_B     1.648     0    0.062   0.067     2.217   72.976   71.333
LGA    R    15_B      R    15_B     2.339     0    0.049   0.800     4.285   66.786   54.416
LGA    T    16_B      T    16_B     1.894     0    0.022   0.087     2.621   77.143   71.905
LGA    R    17_B      R    17_B     0.654     0    0.036   1.119     5.601   88.214   69.567
LGA    R    18_B      R    18_B     1.892     0    0.014   0.635     2.782   75.000   63.636
LGA    S    19_B      S    19_B     2.339     0    0.055   0.666     3.417   68.810   63.730
LGA    N    20_B      N    20_B     1.404     0    0.056   0.477     1.863   83.810   81.548
LGA    Y    21_B      Y    21_B     0.358     0    0.053   0.179     3.700   95.238   75.357
LGA    A    22_B      A    22_B     1.266     0    0.029   0.028     1.700   81.429   79.714
LGA    A    23_B      A    23_B     1.566     0    0.041   0.042     1.853   79.286   78.000
LGA    S    24_B      S    24_B     0.982     0    0.064   0.683     1.551   88.214   86.032
LGA    L    25_B      L    25_B     0.268     0    0.036   0.060     0.656   97.619   97.619
LGA    R    26_B      R    26_B     0.909     0    0.023   1.055     4.632   88.214   69.654
LGA    L    27_B      L    27_B     1.300     0    0.026   0.182     2.600   81.429   75.179
LGA    E    28_B      E    28_B     0.866     0    0.053   0.952     4.987   90.476   74.709
LGA    G    29_B      G    29_B     0.288     0    0.033   0.033     0.436  100.000  100.000
LGA    F    30_B      F    30_B     0.600     0    0.056   0.117     1.267   92.857   89.740
LGA    K    31_B      K    31_B     1.461     0    0.023   0.611     5.933   81.429   60.952
LGA    V    32_B      V    32_B     0.773     0    0.052   0.889     2.816   85.952   80.612
LGA    T    33_B      T    33_B     1.174     0    0.034   0.999     3.205   83.690   78.231
LGA    F    34_B      F    34_B     2.076     0    0.012   1.126     3.896   68.810   64.632
LGA    A    35_B      A    35_B     1.638     0    0.021   0.019     2.320   70.833   72.952
LGA    D    36_B      D    36_B     1.820     0    0.011   0.079     2.788   66.905   76.429
LGA    G    37_B      G    37_B     3.311     0    0.036   0.036     4.082   46.905   46.905
LGA    E    38_B      E    38_B     3.880     0    0.024   0.802     5.563   41.786   36.984
LGA    R    39_B      R    39_B     3.770     0    0.184   1.012     5.849   38.810   37.706
LGA    K    40_B      K    40_B     4.341     0    0.091   1.213     6.723   34.524   36.349
LGA    M    41_B      M    41_B     5.629     0    0.017   0.974     9.402   20.476   17.083
LGA    P    42_B      P    42_B     6.809     0    0.037   0.048     7.625   11.905   13.061
LGA    T    43_B      T    43_B     8.469     0    0.025   0.110     9.034    4.048    3.810
LGA    R    44_B      R    44_B    10.384     0    0.603   0.972    17.487    0.119    0.043
LGA    E    45_B      E    45_B    11.601     0    0.463   1.531    12.299    0.000    0.688
LGA    E    46_B      E    46_B    14.433     0    0.585   1.446    18.191    0.000    0.000
LGA    V    47_B      V    47_B     9.891     0    0.408   1.365    12.450    0.119    5.918

# 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):     3.399          3.424                  3.935           65.977   60.524

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   56   43    4.0     36    1.85    78.488    80.444     1.847

LGA_LOCAL      RMSD:   1.849  Number of atoms:   36  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   4.371  Number of assigned atoms:   43 
Std_ASGN_ATOMS RMSD:   3.399  Standard rmsd on all 43 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.544039 * X  +  -0.730814 * Y  +  -0.412229 * Z  +  23.589064
  Y_new =  -0.541103 * X  +  -0.069903 * Y  +   0.838046 * Z  + -31.014091
  Z_new =  -0.641272 * X  +   0.678988 * Y  +  -0.357415 * Z  +  19.878115 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.358900  0.696155  2.055336   [DEG: -135.1550   39.8867  117.7621 ]
ZXZ: -2.684452  1.936295 -0.756839   [DEG: -153.8077  110.9416  -43.3637 ]
 
# END of job
