
#######################################################
#                                                     #
#                        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   39 (  329),  selected   39 , name one
# Molecule2: number of CA atoms   41 (  336),  selected   39 , 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:    39       4_B - 42_B        1.20     1.20
  LCS_AVERAGE:     95.12

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    39       4_B - 42_B        1.20     1.20
  LCS_AVERAGE:     95.12

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    36       4_B - 39_B        0.98     1.22
  LCS_AVERAGE:     84.55

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   39
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     Q     4_B     Q     4_B     36   39   39      3   20   28   35   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     R     5_B     R     5_B     36   39   39     17   27   33   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     L     6_B     L     6_B     36   39   39      5   27   33   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     F     7_B     F     7_B     36   39   39     17   27   33   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     V     8_B     V     8_B     36   39   39      5   27   33   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     L     9_B     L     9_B     36   39   39     17   27   33   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     D    10_B     D    10_B     36   39   39     17   27   33   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     N    11_B     N    11_B     36   39   39     17   27   33   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     E    12_B     E    12_B     36   39   39     17   27   33   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     R    13_B     R    13_B     36   39   39     17   27   33   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     Y    14_B     Y    14_B     36   39   39     17   27   33   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     D    15_B     D    15_B     36   39   39     17   27   33   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     S    16_B     S    16_B     36   39   39     17   27   33   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     F    17_B     F    17_B     36   39   39     17   27   33   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     I    18_B     I    18_B     36   39   39     17   27   33   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     T    19_B     T    19_B     36   39   39     17   27   33   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     Q    20_B     Q    20_B     36   39   39     17   27   33   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     L    21_B     L    21_B     36   39   39     17   27   33   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     E    22_B     E    22_B     36   39   39     17   27   33   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     A    23_B     A    23_B     36   39   39     17   27   33   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     P    24_B     P    24_B     36   39   39     17   27   33   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     V    25_B     V    25_B     36   39   39     17   27   33   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     Q    26_B     Q    26_B     36   39   39      9   26   33   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     N    27_B     N    27_B     36   39   39      9   19   33   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     A    28_B     A    28_B     36   39   39     11   18   33   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     E    29_B     E    29_B     36   39   39     11   16   27   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     G    30_B     G    30_B     36   39   39     10   19   33   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     R    31_B     R    31_B     36   39   39     11   27   33   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     E    32_B     E    32_B     36   39   39     16   27   33   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     R    33_B     R    33_B     36   39   39     11   26   33   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     L    34_B     L    34_B     36   39   39     11   26   33   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     M    35_B     M    35_B     36   39   39     17   27   33   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     A    36_B     A    36_B     36   39   39     16   27   33   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     V    37_B     V    37_B     36   39   39     16   27   33   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     K    38_B     K    38_B     36   39   39     17   27   33   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     P    39_B     P    39_B     36   39   39      4   15   28   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     E    40_B     E    40_B     27   39   39      4    7   19   30   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     W    41_B     W    41_B     25   39   39      4   15   23   36   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_GDT     K    42_B     K    42_B      4   39   39      3    3    4   16   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39   39 
LCS_AVERAGE  LCS_A:  91.60  (  84.55   95.12   95.12 )

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     17     27     33     36     39     39     39     39     39     39     39     39     39     39     39     39     39     39     39     39 
GDT PERCENT_AT  41.46  65.85  80.49  87.80  95.12  95.12  95.12  95.12  95.12  95.12  95.12  95.12  95.12  95.12  95.12  95.12  95.12  95.12  95.12  95.12
GDT RMS_LOCAL    0.25   0.55   0.81   1.00   1.20   1.20   1.20   1.20   1.20   1.20   1.20   1.20   1.20   1.20   1.20   1.20   1.20   1.20   1.20   1.20
GDT RMS_ALL_AT   2.50   1.24   1.24   1.21   1.20   1.20   1.20   1.20   1.20   1.20   1.20   1.20   1.20   1.20   1.20   1.20   1.20   1.20   1.20   1.20

# 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    Q     4_B      Q     4_B     2.223     0    0.659   0.782    10.287   61.905   34.497
LGA    R     5_B      R     5_B     0.786     0    0.138   0.345     2.780   88.214   77.186
LGA    L     6_B      L     6_B     0.805     0    0.025   0.111     1.637   92.857   86.071
LGA    F     7_B      F     7_B     0.404     0    0.092   0.153     1.183   97.619   89.784
LGA    V     8_B      V     8_B     0.816     0    0.018   1.181     2.701   90.476   80.748
LGA    L     9_B      L     9_B     0.643     0    0.059   0.134     1.174   90.476   87.083
LGA    D    10_B      D    10_B     0.604     0    0.047   0.366     1.755   90.476   84.940
LGA    N    11_B      N    11_B     0.343     0    0.075   0.869     2.440   95.238   87.440
LGA    E    12_B      E    12_B     1.091     0    0.041   0.986     4.455   83.690   68.148
LGA    R    13_B      R    13_B     1.126     0    0.023   1.058     3.135   83.690   73.377
LGA    Y    14_B      Y    14_B     0.325     0    0.049   0.139     1.590  100.000   90.714
LGA    D    15_B      D    15_B     0.342     0    0.041   0.474     1.525  100.000   89.702
LGA    S    16_B      S    16_B     0.705     0    0.021   0.782     2.763   90.476   84.921
LGA    F    17_B      F    17_B     0.400     0    0.017   0.268     1.551  100.000   89.913
LGA    I    18_B      I    18_B     0.187     0    0.028   0.108     0.658  100.000   98.810
LGA    T    19_B      T    19_B     0.424     0    0.019   0.255     1.375  100.000   94.626
LGA    Q    20_B      Q    20_B     0.457     0    0.024   0.810     2.167  100.000   89.947
LGA    L    21_B      L    21_B     0.602     0    0.038   0.249     2.268   92.857   83.036
LGA    E    22_B      E    22_B     0.620     0    0.030   0.737     1.735   95.238   87.619
LGA    A    23_B      A    23_B     0.476     0    0.091   0.116     0.697   97.619   96.190
LGA    P    24_B      P    24_B     0.313     0    0.073   0.073     0.559   97.619   98.639
LGA    V    25_B      V    25_B     0.346     0    0.158   1.204     3.168   90.833   80.136
LGA    Q    26_B      Q    26_B     1.133     0    0.023   1.155     5.736   83.690   65.979
LGA    N    27_B      N    27_B     1.867     0    0.059   0.094     2.446   72.857   68.810
LGA    A    28_B      A    28_B     1.646     0    0.115   0.126     1.791   75.000   74.571
LGA    E    29_B      E    29_B     2.168     0    0.087   0.538     3.957   68.810   60.794
LGA    G    30_B      G    30_B     1.702     0    0.082   0.082     1.902   77.143   77.143
LGA    R    31_B      R    31_B     0.762     0    0.039   1.277     4.719   90.476   74.545
LGA    E    32_B      E    32_B     0.715     0    0.068   0.773     2.853   90.476   81.111
LGA    R    33_B      R    33_B     1.348     0    0.048   1.061     3.840   81.429   72.078
LGA    L    34_B      L    34_B     1.208     0    0.033   1.374     4.853   85.952   66.071
LGA    M    35_B      M    35_B     0.668     0    0.016   0.551     1.551   92.857   88.333
LGA    A    36_B      A    36_B     0.499     0    0.015   0.024     0.858  100.000   98.095
LGA    V    37_B      V    37_B     0.486     0    0.098   0.132     1.222   92.976   89.320
LGA    K    38_B      K    38_B     0.666     4    0.116   0.131     1.820   86.190   47.354
LGA    P    39_B      P    39_B     1.710     0    0.073   0.326     1.930   75.000   77.823
LGA    E    40_B      E    40_B     2.708     0    0.300   0.294     6.188   64.881   44.868
LGA    W    41_B      W    41_B     2.265     0    0.144   0.276     4.621   55.595   47.619
LGA    K    42_B      K    42_B     2.641     0    0.033   0.949     3.048   62.976   63.386

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       39     156    156  100.00     325    325  100.00                41
SUMMARY(RMSD_GDC):     1.199          1.201                  2.091           82.819   74.425

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   39   41    4.0     39    1.20    85.976    91.207     3.002

LGA_LOCAL      RMSD:   1.199  Number of atoms:   39  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.199  Number of assigned atoms:   39 
Std_ASGN_ATOMS RMSD:   1.199  Standard rmsd on all 39 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.905614 * X  +  -0.404774 * Y  +  -0.126570 * Z  +  19.186943
  Y_new =   0.407206 * X  +  -0.746510 * Y  +  -0.526219 * Z  + -11.858702
  Z_new =   0.118514 * X  +  -0.528092 * Y  +   0.840877 * Z  +  34.164841 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.719033 -0.118793 -0.560772   [DEG:  155.7891   -6.8064  -32.1299 ]
ZXZ: -0.236044  0.571895  2.920831   [DEG:  -13.5243   32.7672  167.3513 ]
 
# END of job
