
#######################################################
#                                                     #
#                        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   37 (  291),  selected   37 , name one
# Molecule2: number of CA atoms   37 (  291),  selected   37 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:C  -ch2:B  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    37       2_B - 38_B        1.22     1.22
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    37       2_B - 38_B        1.22     1.22
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    36       3_B - 38_B        0.59     1.30
  LCS_AVERAGE:     94.89

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   37
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_C     A     2_B      3   37   37      0    3    3    4    4    4    6    7   11   17   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     E     3_C     E     3_B     36   37   37      4   19   36   36   36   36   36   36   36   36   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     A     4_C     A     4_B     36   37   37      4   33   36   36   36   36   36   36   36   36   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     E     5_C     E     5_B     36   37   37      4   33   36   36   36   36   36   36   36   36   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     Q     6_C     Q     6_B     36   37   37     12   33   36   36   36   36   36   36   36   36   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     E     7_C     E     7_B     36   37   37     12   33   36   36   36   36   36   36   36   36   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     K     8_C     K     8_B     36   37   37     27   33   36   36   36   36   36   36   36   36   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     D     9_C     D     9_B     36   37   37     27   33   36   36   36   36   36   36   36   36   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     Q    10_C     Q    10_B     36   37   37     27   33   36   36   36   36   36   36   36   36   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     L    11_C     L    11_B     36   37   37     27   33   36   36   36   36   36   36   36   36   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     R    12_C     R    12_B     36   37   37     27   33   36   36   36   36   36   36   36   36   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     T    13_C     T    13_B     36   37   37     27   33   36   36   36   36   36   36   36   36   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     Q    14_C     Q    14_B     36   37   37     27   33   36   36   36   36   36   36   36   36   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     V    15_C     V    15_B     36   37   37     27   33   36   36   36   36   36   36   36   36   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     V    16_C     V    16_B     36   37   37     27   33   36   36   36   36   36   36   36   36   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     R    17_C     R    17_B     36   37   37     27   33   36   36   36   36   36   36   36   36   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     L    18_C     L    18_B     36   37   37     21   33   36   36   36   36   36   36   36   36   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     Q    19_C     Q    19_B     36   37   37     21   33   36   36   36   36   36   36   36   36   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     A    20_C     A    20_B     36   37   37     27   33   36   36   36   36   36   36   36   36   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     E    21_C     E    21_B     36   37   37     27   33   36   36   36   36   36   36   36   36   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     K    22_C     K    22_B     36   37   37     27   33   36   36   36   36   36   36   36   36   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     A    23_C     A    23_B     36   37   37     27   33   36   36   36   36   36   36   36   36   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     D    24_C     D    24_B     36   37   37     27   33   36   36   36   36   36   36   36   36   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     L    25_C     L    25_B     36   37   37     27   33   36   36   36   36   36   36   36   36   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     L    26_C     L    26_B     36   37   37     27   33   36   36   36   36   36   36   36   36   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     G    27_C     G    27_B     36   37   37     27   33   36   36   36   36   36   36   36   36   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     I    28_C     I    28_B     36   37   37     27   33   36   36   36   36   36   36   36   36   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     V    29_C     V    29_B     36   37   37     27   33   36   36   36   36   36   36   36   36   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     S    30_C     S    30_B     36   37   37     27   33   36   36   36   36   36   36   36   36   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     E    31_C     E    31_B     36   37   37     27   33   36   36   36   36   36   36   36   36   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     L    32_C     L    32_B     36   37   37     27   33   36   36   36   36   36   36   36   36   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     Q    33_C     Q    33_B     36   37   37     27   33   36   36   36   36   36   36   36   36   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     L    34_C     L    34_B     36   37   37     27   33   36   36   36   36   36   36   36   36   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     K    35_C     K    35_B     36   37   37     27   33   36   36   36   36   36   36   36   36   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     L    36_C     L    36_B     36   37   37     27   33   36   36   36   36   36   36   36   36   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     N    37_C     N    37_B     36   37   37     19   33   36   36   36   36   36   36   36   36   37   37   37   37   37   37   37   37   37   37 
LCS_GDT     S    38_C     S    38_B     36   37   37      9   33   36   36   36   36   36   36   36   36   37   37   37   37   37   37   37   37   37   37 
LCS_AVERAGE  LCS_A:  98.30  (  94.89  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     27     33     36     36     36     36     36     36     36     36     37     37     37     37     37     37     37     37     37     37 
GDT PERCENT_AT  72.97  89.19  97.30  97.30  97.30  97.30  97.30  97.30  97.30  97.30 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.34   0.45   0.59   0.59   0.59   0.59   0.59   0.59   0.59   0.59   1.22   1.22   1.22   1.22   1.22   1.22   1.22   1.22   1.22   1.22
GDT RMS_ALL_AT   1.42   1.46   1.30   1.30   1.30   1.30   1.30   1.30   1.30   1.30   1.22   1.22   1.22   1.22   1.22   1.22   1.22   1.22   1.22   1.22

# Checking swapping
#   possible swapping detected:  D     9_C      D     9_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A     2_C      A     2_B     7.090     0    0.411   0.394     8.858   23.333   20.095
LGA    E     3_C      E     3_B     1.498     0    0.639   1.176     7.037   75.833   45.661
LGA    A     4_C      A     4_B     0.933     0    0.072   0.094     1.479   85.952   85.048
LGA    E     5_C      E     5_B     1.022     0    0.172   0.909     6.449   90.595   63.333
LGA    Q     6_C      Q     6_B     1.092     0    0.099   1.142     3.811   88.214   79.259
LGA    E     7_C      E     7_B     0.759     0    0.022   0.946     4.505   95.238   76.296
LGA    K     8_C      K     8_B     0.274     0    0.046   1.308     4.876  100.000   78.095
LGA    D     9_C      D     9_B     0.348     0    0.022   0.112     0.678  100.000   95.238
LGA    Q    10_C      Q    10_B     0.452     0    0.000   0.258     1.181  100.000   94.762
LGA    L    11_C      L    11_B     0.392     0    0.049   0.096     0.688  100.000   97.619
LGA    R    12_C      R    12_B     0.392     0    0.050   0.984     3.606  100.000   87.186
LGA    T    13_C      T    13_B     0.237     0    0.000   0.234     0.765  100.000   98.639
LGA    Q    14_C      Q    14_B     0.366     0    0.000   1.018     4.003  100.000   82.487
LGA    V    15_C      V    15_B     0.597     0    0.000   0.024     0.767   92.857   91.837
LGA    V    16_C      V    16_B     0.440     0    0.000   0.062     0.876  100.000   95.918
LGA    R    17_C      R    17_B     0.375     0    0.051   1.981     8.995   97.619   61.342
LGA    L    18_C      L    18_B     0.839     0    0.051   0.127     1.790   90.476   83.810
LGA    Q    19_C      Q    19_B     0.685     0    0.030   0.127     1.723   95.238   85.714
LGA    A    20_C      A    20_B     0.219     0    0.068   0.067     0.484  100.000  100.000
LGA    E    21_C      E    21_B     0.431     0    0.000   0.069     0.711  100.000   94.709
LGA    K    22_C      K    22_B     0.337     0    0.048   0.824     4.340  100.000   79.101
LGA    A    23_C      A    23_B     0.203     0    0.016   0.027     0.333  100.000  100.000
LGA    D    24_C      D    24_B     0.381     0    0.046   0.190     1.117   97.619   95.298
LGA    L    25_C      L    25_B     0.432     0    0.044   0.063     0.989  100.000   96.429
LGA    L    26_C      L    26_B     0.386     0    0.060   0.083     1.259  100.000   92.976
LGA    G    27_C      G    27_B     0.292     0    0.048   0.048     0.337  100.000  100.000
LGA    I    28_C      I    28_B     0.240     0    0.000   0.078     0.669  100.000   98.810
LGA    V    29_C      V    29_B     0.115     0    0.036   0.077     0.589  100.000   98.639
LGA    S    30_C      S    30_B     0.129     0    0.044   0.630     2.000  100.000   94.127
LGA    E    31_C      E    31_B     0.483     0    0.042   0.966     5.332  100.000   74.180
LGA    L    32_C      L    32_B     0.481     0    0.000   0.038     0.889  100.000   95.238
LGA    Q    33_C      Q    33_B     0.464     0    0.089   1.075     3.038  100.000   88.254
LGA    L    34_C      L    34_B     0.453     0    0.000   0.155     1.059  100.000   92.976
LGA    K    35_C      K    35_B     0.451     0    0.012   0.547     2.071   97.619   92.910
LGA    L    36_C      L    36_B     0.288     0    0.134   0.184     0.874   97.619   96.429
LGA    N    37_C      N    37_B     0.636     0    0.189   0.840     4.258   90.595   72.143
LGA    S    38_C      S    38_B     1.031     0    0.121   0.631     1.848   79.405   80.159

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       37     148    148  100.00     291    291  100.00                37
SUMMARY(RMSD_GDC):     1.217          1.134                  1.999           94.546   85.533

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   37   37    4.0     36    0.59    95.946    97.866     5.249

LGA_LOCAL      RMSD:   0.586  Number of atoms:   36  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.301  Number of assigned atoms:   37 
Std_ASGN_ATOMS RMSD:   1.217  Standard rmsd on all 37 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.117758 * X  +  -0.959994 * Y  +   0.254058 * Z  + -13.801023
  Y_new =   0.059000 * X  +  -0.248622 * Y  +  -0.966802 * Z  +  47.066982
  Z_new =   0.991288 * X  +   0.128838 * Y  +   0.027362 * Z  + -300.070343 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.464467 -1.438701  1.361530   [DEG:   26.6120  -82.4315   78.0099 ]
ZXZ:  0.256972  1.543431  1.441551   [DEG:   14.7234   88.4321   82.5948 ]
 
# END of job
