
#######################################################
#                                                     #
#                        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   38 (  302),  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        3.80     3.80
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    33       6_B - 38_B        1.86     4.54
  LCS_AVERAGE:     80.42

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    31       7_B - 37_B        0.45     4.74
  LCS_AVERAGE:     71.51

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    3   37      0    3    3    3    3    4    4    7    9   10   11   13   14   16   20   22   25   27   31   34 
LCS_GDT     E     3_C     E     3_B      3    3   37      0    3    3    3    3    4    5   16   21   25   29   32   35   35   35   35   36   36   36   36 
LCS_GDT     A     4_C     A     4_B      3    3   37      3    3    3    3    6    6    7   19   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     E     5_C     E     5_B      3    3   37      3    3    3    4    6    8   12   18   25   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     Q     6_C     Q     6_B      3   33   37      3    3    3    6   10   17   26   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     E     7_C     E     7_B     31   33   37     22   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     K     8_C     K     8_B     31   33   37     18   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     D     9_C     D     9_B     31   33   37     22   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     Q    10_C     Q    10_B     31   33   37     22   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     L    11_C     L    11_B     31   33   37     25   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     R    12_C     R    12_B     31   33   37     25   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     T    13_C     T    13_B     31   33   37     25   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     Q    14_C     Q    14_B     31   33   37     25   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     V    15_C     V    15_B     31   33   37     25   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     V    16_C     V    16_B     31   33   37     24   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     R    17_C     R    17_B     31   33   37     25   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     L    18_C     L    18_B     31   33   37     25   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     Q    19_C     Q    19_B     31   33   37     25   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     A    20_C     A    20_B     31   33   37     25   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     E    21_C     E    21_B     31   33   37     25   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     K    22_C     K    22_B     31   33   37     25   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     A    23_C     A    23_B     31   33   37     25   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     D    24_C     D    24_B     31   33   37     25   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     L    25_C     L    25_B     31   33   37     25   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     L    26_C     L    26_B     31   33   37     25   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     G    27_C     G    27_B     31   33   37     25   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     I    28_C     I    28_B     31   33   37     25   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     V    29_C     V    29_B     31   33   37     25   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     S    30_C     S    30_B     31   33   37     25   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     E    31_C     E    31_B     31   33   37     25   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     L    32_C     L    32_B     31   33   37     25   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     Q    33_C     Q    33_B     31   33   37     25   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     L    34_C     L    34_B     31   33   37     25   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     K    35_C     K    35_B     31   33   37     25   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     L    36_C     L    36_B     31   33   37     25   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     N    37_C     N    37_B     31   33   37     25   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     S    38_C     S    38_B      3   33   37      3    3    3    3    3    4    6    9    9   20   29   32   32   32   34   35   36   36   36   36 
LCS_AVERAGE  LCS_A:  83.98  (  71.51   80.42  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     31     31     31     31     31     31     31     33     34     34     34     35     35     35     35     36     36     36     36 
GDT PERCENT_AT  67.57  83.78  83.78  83.78  83.78  83.78  83.78  83.78  89.19  91.89  91.89  91.89  94.59  94.59  94.59  94.59  97.30  97.30  97.30  97.30
GDT RMS_LOCAL    0.37   0.45   0.45   0.45   0.45   0.45   0.45   0.45   1.97   2.39   2.39   2.39   2.84   2.84   2.84   2.70   3.12   3.12   3.12   3.12
GDT RMS_ALL_AT   4.91   4.74   4.74   4.74   4.74   4.74   4.74   4.74   4.19   4.01   4.01   4.01   3.87   3.87   3.87   4.04   3.88   3.88   3.88   3.88

# Checking swapping
#   possible swapping detected:  E     3_C      E     3_B
#   possible swapping detected:  E     7_C      E     7_B
#   possible swapping detected:  D     9_C      D     9_B
#   possible swapping detected:  E    31_C      E    31_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A     2_C      A     2_B    18.321     0    0.394   0.375    19.994    0.000    0.000
LGA    E     3_C      E     3_B    12.777     0    0.637   1.042    14.601    0.000    0.000
LGA    A     4_C      A     4_B     9.862     0    0.595   0.569    11.102    0.119    0.095
LGA    E     5_C      E     5_B    10.679     0    0.606   0.999    12.647    1.071    0.476
LGA    Q     6_C      Q     6_B     7.510     0    0.597   1.297    15.133   14.405    6.931
LGA    E     7_C      E     7_B     0.466     0    0.582   0.962     8.457   84.524   52.011
LGA    K     8_C      K     8_B     0.722     0    0.078   1.110     4.505   95.238   78.307
LGA    D     9_C      D     9_B     0.619     0    0.046   0.177     1.943   90.476   86.012
LGA    Q    10_C      Q    10_B     0.613     0    0.034   0.288     1.800   92.857   88.571
LGA    L    11_C      L    11_B     0.359     0    0.009   0.071     0.809  100.000   96.429
LGA    R    12_C      R    12_B     0.405     0    0.014   0.372     2.045  100.000   87.576
LGA    T    13_C      T    13_B     0.279     0    0.028   0.978     2.474  100.000   89.932
LGA    Q    14_C      Q    14_B     0.404     0    0.014   0.638     3.633  100.000   81.905
LGA    V    15_C      V    15_B     0.526     0    0.017   0.047     0.854   95.238   93.197
LGA    V    16_C      V    16_B     0.609     0    0.031   0.099     0.966   95.238   93.197
LGA    R    17_C      R    17_B     0.307     0    0.020   1.729     7.521  100.000   68.485
LGA    L    18_C      L    18_B     0.266     0    0.022   0.111     0.626  100.000   98.810
LGA    Q    19_C      Q    19_B     0.541     0    0.018   0.196     0.971   92.857   92.593
LGA    A    20_C      A    20_B     0.532     0    0.018   0.019     0.594   90.476   90.476
LGA    E    21_C      E    21_B     0.430     0    0.012   0.108     0.733   97.619   95.767
LGA    K    22_C      K    22_B     0.521     0    0.028   0.074     1.031   92.857   90.529
LGA    A    23_C      A    23_B     0.535     0    0.000   0.010     0.572   95.238   94.286
LGA    D    24_C      D    24_B     0.489     0    0.006   0.200     1.432   97.619   92.917
LGA    L    25_C      L    25_B     0.352     0    0.000   0.025     0.606  100.000   96.429
LGA    L    26_C      L    26_B     0.087     0    0.038   0.039     0.204  100.000  100.000
LGA    G    27_C      G    27_B     0.490     0    0.082   0.082     0.490  100.000  100.000
LGA    I    28_C      I    28_B     0.311     0    0.025   0.085     0.811  100.000   97.619
LGA    V    29_C      V    29_B     0.225     0    0.025   0.059     0.394  100.000  100.000
LGA    S    30_C      S    30_B     0.300     0    0.031   0.103     0.581  100.000   98.413
LGA    E    31_C      E    31_B     0.492     0    0.027   1.099     6.146  100.000   69.735
LGA    L    32_C      L    32_B     0.106     0    0.007   0.039     0.470  100.000  100.000
LGA    Q    33_C      Q    33_B     0.419     0    0.044   1.068     3.295  100.000   88.201
LGA    L    34_C      L    34_B     0.530     0    0.043   0.178     0.982   97.619   94.048
LGA    K    35_C      K    35_B     0.331     0    0.038   0.556     2.584   97.619   92.116
LGA    L    36_C      L    36_B     0.480     0    0.106   0.131     0.789   95.238   92.857
LGA    N    37_C      N    37_B     0.551     0    0.438   0.855     6.772   72.024   53.214
LGA    S    38_C      S    38_B     7.667     0    0.506   0.798    11.280   10.119    6.984

# 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):     3.803          3.733                  4.201           81.310   74.814

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   38   37    4.0     31    0.45    86.486    85.563     5.605

LGA_LOCAL      RMSD:   0.453  Number of atoms:   31  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   4.741  Number of assigned atoms:   37 
Std_ASGN_ATOMS RMSD:   3.803  Standard rmsd on all 37 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.910096 * X  +   0.289325 * Y  +   0.296674 * Z  + -35.928127
  Y_new =   0.405125 * X  +  -0.470602 * Y  +  -0.783841 * Z  +  47.107491
  Z_new =  -0.087169 * X  +   0.833561 * Y  +  -0.545506 * Z  + -37.958248 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.418809  0.087280  2.150278   [DEG:   23.9960    5.0008  123.2019 ]
ZXZ:  0.361825  2.147789 -0.104195   [DEG:   20.7310  123.0593   -5.9699 ]
 
# END of job
