
#######################################################
#                                                     #
#                        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        2.69     2.69
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    40       5_B - 44_B        1.58     3.03
  LCS_AVERAGE:     87.45

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    33       5_B - 37_B        0.95     3.29
  LCS_AVERAGE:     65.06

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     33   40   43      8   27   33   35   37   38   39   40   40   41   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     L     6_B     L     6_B     33   40   43     15   27   33   35   37   38   39   40   40   41   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     E     7_B     E     7_B     33   40   43     12   26   33   35   37   38   39   40   40   41   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     T     8_B     T     8_B     33   40   43     12   26   33   35   37   38   39   40   40   41   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     K     9_B     K     9_B     33   40   43     15   27   33   35   37   38   39   40   40   41   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     K    10_B     K    10_B     33   40   43     13   27   33   35   37   38   39   40   40   41   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     A    11_B     A    11_B     33   40   43     13   27   33   35   37   38   39   40   40   41   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     Y    12_B     Y    12_B     33   40   43     14   27   33   35   37   38   39   40   40   41   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     A    13_B     A    13_B     33   40   43     15   27   33   35   37   38   39   40   40   41   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     A    14_B     A    14_B     33   40   43     12   27   33   35   37   38   39   40   40   41   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     R    15_B     R    15_B     33   40   43     15   27   33   35   37   38   39   40   40   41   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     T    16_B     T    16_B     33   40   43     15   27   33   35   37   38   39   40   40   41   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     R    17_B     R    17_B     33   40   43     12   27   33   35   37   38   39   40   40   41   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     R    18_B     R    18_B     33   40   43     15   27   33   35   37   38   39   40   40   41   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     S    19_B     S    19_B     33   40   43     15   27   33   35   37   38   39   40   40   41   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     N    20_B     N    20_B     33   40   43     13   27   33   35   37   38   39   40   40   41   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     Y    21_B     Y    21_B     33   40   43     15   27   33   35   37   38   39   40   40   41   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     A    22_B     A    22_B     33   40   43     15   27   33   35   37   38   39   40   40   41   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     A    23_B     A    23_B     33   40   43     15   27   33   35   37   38   39   40   40   41   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     S    24_B     S    24_B     33   40   43     15   27   33   35   37   38   39   40   40   41   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     L    25_B     L    25_B     33   40   43     15   27   33   35   37   38   39   40   40   41   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     R    26_B     R    26_B     33   40   43     15   27   33   35   37   38   39   40   40   41   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     L    27_B     L    27_B     33   40   43     14   27   33   35   37   38   39   40   40   41   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     E    28_B     E    28_B     33   40   43     15   27   33   35   37   38   39   40   40   41   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     G    29_B     G    29_B     33   40   43     15   27   33   35   37   38   39   40   40   41   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     F    30_B     F    30_B     33   40   43      8   27   33   35   37   38   39   40   40   41   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     K    31_B     K    31_B     33   40   43      3   19   30   35   37   38   39   40   40   41   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     V    32_B     V    32_B     33   40   43      9   27   33   35   37   38   39   40   40   41   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     T    33_B     T    33_B     33   40   43      4   27   33   35   37   38   39   40   40   41   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     F    34_B     F    34_B     33   40   43      4   19   33   35   37   38   39   40   40   41   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     A    35_B     A    35_B     33   40   43      4    4   20   33   37   38   39   40   40   41   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     D    36_B     D    36_B     33   40   43      4   20   33   35   37   38   39   40   40   41   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     G    37_B     G    37_B     33   40   43      3   11   33   35   37   38   39   40   40   41   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     E    38_B     E    38_B     31   40   43      3   12   22   35   37   38   39   40   40   41   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     R    39_B     R    39_B     31   40   43      4   27   33   35   37   38   39   40   40   41   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     K    40_B     K    40_B     25   40   43      4    5   30   35   37   37   39   40   40   41   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     M    41_B     M    41_B      5   40   43      4    5    5   18   25   30   39   40   40   41   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     P    42_B     P    42_B      5   40   43      4   13   21   31   37   38   39   40   40   41   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     T    43_B     T    43_B      5   40   43      3   16   33   34   37   38   39   40   40   41   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     R    44_B     R    44_B      3   40   43      3   11   21   27   31   38   38   40   40   41   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     E    45_B     E    45_B      3    7   43      3    3    3    5    7    9   29   33   38   41   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     E    46_B     E    46_B      3    7   43      3    3    3    5    7    7    8   15   32   38   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     V    47_B     V    47_B      3    3   43      3    3    3    3    3    3   10   15   32   38   43   43   43   43   43   43   43   43   43   43 
LCS_AVERAGE  LCS_A:  84.17  (  65.06   87.45  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     15     27     33     35     37     38     39     40     40     41     43     43     43     43     43     43     43     43     43     43 
GDT PERCENT_AT  34.88  62.79  76.74  81.40  86.05  88.37  90.70  93.02  93.02  95.35 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.37   0.61   0.88   0.96   1.12   1.40   1.38   1.58   1.58   2.04   2.69   2.69   2.69   2.69   2.69   2.69   2.69   2.69   2.69   2.69
GDT RMS_ALL_AT   3.74   3.53   3.24   3.57   3.36   2.96   3.21   3.03   3.03   2.82   2.69   2.69   2.69   2.69   2.69   2.69   2.69   2.69   2.69   2.69

# Checking swapping
#   possible swapping detected:  E     7_B      E     7_B
#   possible swapping detected:  Y    12_B      Y    12_B
#   possible swapping detected:  Y    21_B      Y    21_B
#   possible swapping detected:  F    30_B      F    30_B
#   possible swapping detected:  F    34_B      F    34_B
#   possible swapping detected:  D    36_B      D    36_B
#   possible swapping detected:  E    38_B      E    38_B
#   possible swapping detected:  E    45_B      E    45_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     5_B      S     5_B     0.543     0    0.642   0.673     4.385   82.143   70.476
LGA    L     6_B      L     6_B     0.543     0    0.048   1.302     3.153   92.857   83.274
LGA    E     7_B      E     7_B     1.180     0    0.018   0.988     4.730   83.690   65.185
LGA    T     8_B      T     8_B     1.070     0    0.060   0.224     1.715   88.214   85.374
LGA    K     9_B      K     9_B     0.371     0    0.021   0.831     5.286   97.619   73.016
LGA    K    10_B      K    10_B     0.390     0    0.030   0.870     5.097  100.000   75.661
LGA    A    11_B      A    11_B     0.620     0    0.019   0.020     0.869   92.857   92.381
LGA    Y    12_B      Y    12_B     0.653     0    0.039   0.086     1.241   90.476   88.214
LGA    A    13_B      A    13_B     0.390     0    0.027   0.026     0.666   97.619   98.095
LGA    A    14_B      A    14_B     0.335     0    0.061   0.066     0.624   97.619   98.095
LGA    R    15_B      R    15_B     0.578     0    0.044   1.371     7.249   92.857   64.589
LGA    T    16_B      T    16_B     0.719     0    0.040   0.076     0.934   90.476   90.476
LGA    R    17_B      R    17_B     0.656     0    0.046   0.710     3.565   90.476   70.433
LGA    R    18_B      R    18_B     1.145     0    0.015   1.245     5.698   81.429   63.117
LGA    S    19_B      S    19_B     0.827     0    0.046   0.721     2.078   90.476   86.190
LGA    N    20_B      N    20_B     0.757     0    0.049   0.373     1.288   90.476   88.214
LGA    Y    21_B      Y    21_B     0.775     0    0.048   0.102     1.205   90.476   90.516
LGA    A    22_B      A    22_B     0.894     0    0.055   0.054     0.908   90.476   90.476
LGA    A    23_B      A    23_B     0.605     0    0.053   0.053     0.730   90.476   90.476
LGA    S    24_B      S    24_B     1.031     0    0.080   0.701     1.853   83.690   81.508
LGA    L    25_B      L    25_B     0.853     0    0.045   1.394     4.122   90.476   76.429
LGA    R    26_B      R    26_B     0.343     0    0.038   0.897     5.598   95.238   77.316
LGA    L    27_B      L    27_B     1.067     0    0.056   0.189     1.374   83.690   83.690
LGA    E    28_B      E    28_B     1.191     0    0.059   1.131     3.193   81.429   77.090
LGA    G    29_B      G    29_B     1.149     0    0.019   0.019     1.549   81.548   81.548
LGA    F    30_B      F    30_B     1.385     0    0.123   0.203     3.464   85.952   69.913
LGA    K    31_B      K    31_B     2.036     0    0.053   0.602     8.073   70.833   45.714
LGA    V    32_B      V    32_B     0.739     0    0.034   0.096     1.206   85.952   87.959
LGA    T    33_B      T    33_B     0.861     0    0.073   0.850     2.118   92.857   83.129
LGA    F    34_B      F    34_B     1.464     0    0.043   1.605     7.860   77.143   50.043
LGA    A    35_B      A    35_B     2.533     0    0.095   0.087     3.489   66.905   63.524
LGA    D    36_B      D    36_B     1.302     0    0.047   0.727     2.062   83.810   79.464
LGA    G    37_B      G    37_B     1.447     0    0.111   0.111     2.486   75.119   75.119
LGA    E    38_B      E    38_B     2.295     0    0.154   0.909     4.590   64.881   53.175
LGA    R    39_B      R    39_B     1.476     0    0.291   0.759     3.363   69.405   73.247
LGA    K    40_B      K    40_B     3.149     0    0.079   0.870    10.300   65.119   36.561
LGA    M    41_B      M    41_B     3.683     0    0.028   0.680    11.736   57.738   32.440
LGA    P    42_B      P    42_B     2.925     0    0.115   0.301     6.831   48.929   37.347
LGA    T    43_B      T    43_B     1.462     0    0.570   0.600     4.853   69.405   58.503
LGA    R    44_B      R    44_B     4.735     0    0.585   1.230    10.050   33.571   18.052
LGA    E    45_B      E    45_B     8.976     0    0.429   1.025    11.685    2.619    1.481
LGA    E    46_B      E    46_B    10.564     0    0.562   1.421    12.415    0.357    0.159
LGA    V    47_B      V    47_B    10.127     0    0.438   1.439    12.374    0.119    0.204

# 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):     2.690          2.726                  3.778           76.686   67.625

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   62   43    4.0     40    1.58    84.302    87.816     2.383

LGA_LOCAL      RMSD:   1.578  Number of atoms:   40  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   3.028  Number of assigned atoms:   43 
Std_ASGN_ATOMS RMSD:   2.690  Standard rmsd on all 43 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.964393 * X  +  -0.233820 * Y  +  -0.123589 * Z  +  56.306396
  Y_new =   0.256005 * X  +  -0.942623 * Y  +  -0.214297 * Z  +  -4.216811
  Z_new =  -0.066391 * X  +  -0.238306 * Y  +   0.968918 * Z  +  17.435392 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.882120  0.066439 -0.241164   [DEG:  165.1333    3.8067  -13.8177 ]
ZXZ: -0.523123  0.249977 -2.869889   [DEG:  -29.9728   14.3226 -164.4325 ]
 
# END of job
