
#######################################################
#                                                     #
#                        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        1.55     1.55
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    43       5_B - 47_B        1.55     1.55
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    41       5_B - 45_B        0.81     1.66
  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      4   14   38   40   41   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     21   39   39   40   41   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     21   39   39   40   41   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     21   39   39   40   41   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     21   39   39   40   41   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     21   39   39   40   41   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     21   39   39   40   41   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     21   39   39   40   41   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     25   39   39   40   41   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     25   39   39   40   41   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     17   39   39   40   41   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     25   39   39   40   41   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     25   39   39   40   41   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     21   39   39   40   41   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   39   39   40   41   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     25   39   39   40   41   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     25   39   39   40   41   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     25   39   39   40   41   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     25   39   39   40   41   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     25   39   39   40   41   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     25   39   39   40   41   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     25   39   39   40   41   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     25   39   39   40   41   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     25   39   39   40   41   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     25   39   39   40   41   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     25   39   39   40   41   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     25   39   39   40   41   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     25   39   39   40   41   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     14   39   39   40   41   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     25   39   39   40   41   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     25   39   39   40   41   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     25   39   39   40   41   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     25   39   39   40   41   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     25   39   39   40   41   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     25   39   39   40   41   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     25   39   39   40   41   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     25   39   39   40   41   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     25   39   39   40   41   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     18   39   39   40   41   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     11   39   39   40   41   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   10   32   40   41   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    4    4    4    6    6   10   13   34   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    5   20   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     25     39     39     40     41     41     41     41     41     43     43     43     43     43     43     43     43     43     43     43 
GDT PERCENT_AT  58.14  90.70  90.70  93.02  95.35  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    0.32   0.58   0.58   0.64   0.81   0.81   0.81   0.81   0.81   1.55   1.55   1.55   1.55   1.55   1.55   1.55   1.55   1.55   1.55   1.55
GDT RMS_ALL_AT   1.88   1.74   1.74   1.75   1.66   1.66   1.66   1.66   1.66   1.55   1.55   1.55   1.55   1.55   1.55   1.55   1.55   1.55   1.55   1.55

# 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:  E    38_B      E    38_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     1.919     0    0.617   0.680     6.356   77.143   59.524
LGA    L     6_B      L     6_B     0.578     0    0.063   0.849     3.155   95.238   83.571
LGA    E     7_B      E     7_B     0.627     0    0.068   0.906     3.674   90.476   78.095
LGA    T     8_B      T     8_B     0.682     0    0.047   1.160     3.107   90.476   79.932
LGA    K     9_B      K     9_B     0.506     0    0.013   0.134     1.376   95.238   88.571
LGA    K    10_B      K    10_B     0.127     0    0.045   0.870     2.778  100.000   91.323
LGA    A    11_B      A    11_B     0.633     0    0.029   0.042     0.801   92.857   92.381
LGA    Y    12_B      Y    12_B     0.382     0    0.042   0.082     0.808  100.000   96.032
LGA    A    13_B      A    13_B     0.427     0    0.028   0.026     0.807   95.238   94.286
LGA    A    14_B      A    14_B     0.739     0    0.082   0.094     1.284   88.214   88.667
LGA    R    15_B      R    15_B     0.801     0    0.069   0.829     2.882   88.214   84.978
LGA    T    16_B      T    16_B     0.598     0    0.017   0.083     0.765   90.476   90.476
LGA    R    17_B      R    17_B     0.386     0    0.041   0.765     4.096  100.000   76.753
LGA    R    18_B      R    18_B     0.760     0    0.052   0.673     2.073   90.476   81.688
LGA    S    19_B      S    19_B     0.858     0    0.041   0.773     1.614   90.476   87.540
LGA    N    20_B      N    20_B     0.702     0    0.058   0.469     1.077   90.476   90.536
LGA    Y    21_B      Y    21_B     0.389     0    0.047   0.173     2.159   97.619   86.310
LGA    A    22_B      A    22_B     0.586     0    0.011   0.018     0.639   90.476   90.476
LGA    A    23_B      A    23_B     0.640     0    0.035   0.041     0.647   90.476   90.476
LGA    S    24_B      S    24_B     0.705     0    0.086   0.714     1.588   90.476   87.540
LGA    L    25_B      L    25_B     0.580     0    0.032   0.091     0.900   90.476   91.667
LGA    R    26_B      R    26_B     0.494     0    0.018   0.969     2.679   92.857   89.437
LGA    L    27_B      L    27_B     0.550     0    0.059   0.206     1.128   90.476   90.536
LGA    E    28_B      E    28_B     0.407     0    0.045   0.535     1.462  100.000   95.820
LGA    G    29_B      G    29_B     0.600     0    0.045   0.045     0.600   90.476   90.476
LGA    F    30_B      F    30_B     0.598     0    0.031   0.062     1.266   92.857   88.874
LGA    K    31_B      K    31_B     0.552     0    0.021   0.615     3.742   95.238   78.201
LGA    V    32_B      V    32_B     0.365     0    0.043   1.235     3.208   95.238   83.742
LGA    T    33_B      T    33_B     0.744     0    0.069   1.052     3.353   97.619   84.966
LGA    F    34_B      F    34_B     0.300     0    0.029   1.424     6.282  100.000   69.524
LGA    A    35_B      A    35_B     0.595     0    0.015   0.019     0.651   90.476   90.476
LGA    D    36_B      D    36_B     0.514     0    0.014   0.353     1.299   90.476   90.536
LGA    G    37_B      G    37_B     0.426     0    0.064   0.064     0.567   95.238   95.238
LGA    E    38_B      E    38_B     0.662     0    0.035   1.028     3.629   90.476   82.275
LGA    R    39_B      R    39_B     0.709     0    0.061   1.161     3.399   90.476   80.519
LGA    K    40_B      K    40_B     0.975     0    0.106   1.217     7.878   90.476   61.587
LGA    M    41_B      M    41_B     0.790     0    0.035   0.619     1.827   90.476   86.012
LGA    P    42_B      P    42_B     0.243     0    0.051   0.056     0.357  100.000  100.000
LGA    T    43_B      T    43_B     0.544     0    0.006   0.065     1.017   90.476   89.184
LGA    R    44_B      R    44_B     0.863     0    0.602   0.827     5.519   86.071   66.623
LGA    E    45_B      E    45_B     2.970     0    0.477   1.228     8.870   48.690   31.905
LGA    E    46_B      E    46_B     7.400     0    0.594   1.408    12.425   14.524    6.508
LGA    V    47_B      V    47_B     6.073     0    0.400   1.358     8.106   18.214   16.735

# 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):     1.549          1.483                  2.437           88.032   80.930

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   62   43    4.0     41    0.81    94.767    96.756     4.509

LGA_LOCAL      RMSD:   0.809  Number of atoms:   41  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.660  Number of assigned atoms:   43 
Std_ASGN_ATOMS RMSD:   1.549  Standard rmsd on all 43 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.187855 * X  +  -0.975507 * Y  +   0.114443 * Z  +  28.067589
  Y_new =  -0.662035 * X  +  -0.039687 * Y  +   0.748421 * Z  + -34.516739
  Z_new =  -0.725548 * X  +  -0.216360 * Y  +  -0.653275 * Z  +  19.781090 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.294310  0.811830 -2.821770   [DEG:  -74.1585   46.5145 -161.6755 ]
ZXZ:  2.989856  2.282698 -1.860603   [DEG:  171.3061  130.7890 -106.6047 ]
 
# END of job
