
#######################################################
#                                                     #
#                        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        4.98     4.98
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    28       5_B - 32_B        1.79     5.21
  LONGEST_CONTINUOUS_SEGMENT:    28       6_B - 33_B        1.89     5.28
  LCS_AVERAGE:     50.08

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    22       9_B - 30_B        0.93     5.15
  LCS_AVERAGE:     34.45

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      3   28   43      3    3    3    3   15   20   23   29   32   33   35   35   36   36   37   38   39   39   42   42 
LCS_GDT     L     6_B     L     6_B     11   28   43     12   16   22   25   27   28   29   30   32   34   35   35   36   36   38   38   39   41   42   42 
LCS_GDT     E     7_B     E     7_B     11   28   43      6    9   18   22   27   28   29   30   32   34   35   35   36   36   38   38   39   41   42   42 
LCS_GDT     T     8_B     T     8_B     12   28   43      7    9   13   22   27   28   29   30   32   34   35   35   36   36   38   38   39   41   42   42 
LCS_GDT     K     9_B     K     9_B     22   28   43      7   10   22   25   27   28   29   30   32   34   35   35   36   36   38   38   39   41   42   42 
LCS_GDT     K    10_B     K    10_B     22   28   43     12   16   22   25   27   28   29   30   32   34   35   35   36   36   38   38   39   41   42   42 
LCS_GDT     A    11_B     A    11_B     22   28   43      7   15   22   25   27   28   29   30   32   34   35   35   36   36   38   38   39   41   42   42 
LCS_GDT     Y    12_B     Y    12_B     22   28   43      7    9   21   25   27   28   29   30   32   34   35   35   36   36   38   38   39   41   42   42 
LCS_GDT     A    13_B     A    13_B     22   28   43      5   15   22   25   27   28   29   30   32   34   35   35   36   36   38   38   39   41   42   42 
LCS_GDT     A    14_B     A    14_B     22   28   43     12   16   22   25   27   28   29   30   32   34   35   35   36   36   38   38   39   41   42   42 
LCS_GDT     R    15_B     R    15_B     22   28   43      6   16   22   25   27   28   29   30   32   34   35   35   36   36   38   38   39   41   42   42 
LCS_GDT     T    16_B     T    16_B     22   28   43     12   16   22   25   27   28   29   30   32   34   35   35   36   36   38   38   39   41   42   42 
LCS_GDT     R    17_B     R    17_B     22   28   43     12   16   22   25   27   28   29   30   32   34   35   35   36   36   38   38   39   41   42   42 
LCS_GDT     R    18_B     R    18_B     22   28   43     12   16   22   25   27   28   29   30   32   34   35   35   36   36   38   38   39   41   42   42 
LCS_GDT     S    19_B     S    19_B     22   28   43      7   16   22   24   27   28   29   30   32   34   35   35   36   36   38   38   39   41   42   42 
LCS_GDT     N    20_B     N    20_B     22   28   43      3   16   22   25   27   28   29   30   32   34   35   35   36   36   38   38   39   41   42   42 
LCS_GDT     Y    21_B     Y    21_B     22   28   43     12   16   22   25   27   28   29   30   32   34   35   35   36   36   38   38   39   41   42   42 
LCS_GDT     A    22_B     A    22_B     22   28   43     12   16   22   25   27   28   29   30   32   34   35   35   36   36   38   38   39   41   42   42 
LCS_GDT     A    23_B     A    23_B     22   28   43     11   16   22   25   27   28   29   30   32   34   35   35   36   36   38   38   39   41   42   42 
LCS_GDT     S    24_B     S    24_B     22   28   43     11   16   22   25   27   28   29   30   32   34   35   35   36   36   38   38   39   41   42   42 
LCS_GDT     L    25_B     L    25_B     22   28   43     12   16   22   25   27   28   29   30   32   34   35   35   36   36   38   38   39   41   42   42 
LCS_GDT     R    26_B     R    26_B     22   28   43     12   16   22   25   27   28   29   30   32   34   35   35   36   36   38   38   39   41   42   42 
LCS_GDT     L    27_B     L    27_B     22   28   43     12   16   22   25   27   28   29   30   32   34   35   35   36   36   38   38   39   41   42   42 
LCS_GDT     E    28_B     E    28_B     22   28   43     12   16   22   25   27   28   29   30   32   34   35   35   36   36   38   38   39   41   42   42 
LCS_GDT     G    29_B     G    29_B     22   28   43      4   16   22   25   27   28   29   30   32   34   35   35   36   36   38   38   39   41   42   42 
LCS_GDT     F    30_B     F    30_B     22   28   43      6   16   22   25   27   28   29   30   32   34   35   35   36   36   38   38   39   41   42   42 
LCS_GDT     K    31_B     K    31_B     20   28   43      4   12   21   25   27   28   29   30   32   34   35   35   36   36   38   38   39   41   42   42 
LCS_GDT     V    32_B     V    32_B     17   28   43      5    6   18   25   27   28   29   30   32   34   35   35   36   36   38   38   39   41   42   42 
LCS_GDT     T    33_B     T    33_B      6   28   43      5    6    6    8   16   24   27   29   31   31   32   32   35   36   38   38   39   41   42   42 
LCS_GDT     F    34_B     F    34_B      6   12   43      5    6    6    7   10   15   21   27   31   31   32   32   33   36   38   38   39   41   42   42 
LCS_GDT     A    35_B     A    35_B      6   12   43      5    6    9   15   21   25   29   29   31   31   32   32   35   36   38   38   39   41   42   42 
LCS_GDT     D    36_B     D    36_B      6    9   43      5    8   18   25   27   28   29   30   31   34   35   35   36   36   38   38   39   41   42   42 
LCS_GDT     G    37_B     G    37_B      5    9   43      3    4    4    5    7   10   17   30   32   34   35   35   36   36   38   38   39   41   42   42 
LCS_GDT     E    38_B     E    38_B      6    8   43      3    4    5    6    7   10   16   22   31   34   35   35   36   36   38   38   39   41   42   42 
LCS_GDT     R    39_B     R    39_B      6    8   43      3   10   19   24   26   27   28   30   32   34   35   35   36   36   38   38   39   41   42   42 
LCS_GDT     K    40_B     K    40_B      6    8   43      3    5    5    7    7   19   28   29   32   34   35   35   36   36   38   38   39   41   42   42 
LCS_GDT     M    41_B     M    41_B      6    8   43      3    5    5    7   16   24   28   29   32   34   35   35   36   36   38   38   39   41   42   42 
LCS_GDT     P    42_B     P    42_B      6    8   43      3    5    5    7    7   10   21   29   32   34   35   35   36   36   38   38   39   41   42   42 
LCS_GDT     T    43_B     T    43_B      6    8   43      3    5    5    7    7   10   13   16   23   28   31   35   36   36   38   38   39   41   42   42 
LCS_GDT     R    44_B     R    44_B      4    8   43      3    4    5    7    7    8    9   13   18   19   23   25   28   31   34   37   39   41   42   42 
LCS_GDT     E    45_B     E    45_B      4    8   43      3    4    5    7    7    8    9   10   13   19   23   25   26   31   34   36   39   41   42   42 
LCS_GDT     E    46_B     E    46_B      3    5   43      3    3    3    3    4    4    5    8    9   11   16   17   26   28   32   37   38   41   42   42 
LCS_GDT     V    47_B     V    47_B      3    3   43      0    3    3    3    3    3    4    5    6    6    9    9    9   10   11   19   24   27   30   39 
LCS_AVERAGE  LCS_A:  61.51  (  34.45   50.08  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     12     16     22     25     27     28     29     30     32     34     35     35     36     36     38     38     39     41     42     42 
GDT PERCENT_AT  27.91  37.21  51.16  58.14  62.79  65.12  67.44  69.77  74.42  79.07  81.40  81.40  83.72  83.72  88.37  88.37  90.70  95.35  97.67  97.67
GDT RMS_LOCAL    0.38   0.50   0.86   1.29   1.42   1.52   1.88   1.84   2.19   2.43   2.58   2.58   2.83   2.83   3.57   3.43   3.69   4.39   4.50   4.50
GDT RMS_ALL_AT   5.21   5.22   5.17   5.15   5.12   5.15   5.44   5.13   5.21   5.17   5.24   5.24   5.19   5.19   5.08   5.10   5.11   5.00   4.99   4.99

# Checking swapping
#   possible swapping detected:  E     7_B      E     7_B
#   possible swapping detected:  F    30_B      F    30_B
#   possible swapping detected:  E    38_B      E    38_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     5_B      S     5_B     6.513     0    0.155   0.695     7.804   20.952   21.905
LGA    L     6_B      L     6_B     0.393     0    0.586   1.149     6.801   82.262   57.798
LGA    E     7_B      E     7_B     2.663     0    0.072   1.035     4.241   62.857   50.635
LGA    T     8_B      T     8_B     2.657     0    0.050   1.042     4.583   64.881   57.959
LGA    K     9_B      K     9_B     1.572     0    0.052   0.757     3.661   77.143   67.196
LGA    K    10_B      K    10_B     0.770     0    0.031   0.932     5.862   95.238   65.714
LGA    A    11_B      A    11_B     0.978     0    0.039   0.043     1.640   90.476   86.952
LGA    Y    12_B      Y    12_B     1.609     0    0.044   1.447    11.920   79.286   39.246
LGA    A    13_B      A    13_B     1.574     0    0.057   0.069     1.576   77.143   76.286
LGA    A    14_B      A    14_B     1.026     0    0.061   0.060     1.268   81.429   81.429
LGA    R    15_B      R    15_B     0.951     0    0.076   0.576     1.806   90.476   82.381
LGA    T    16_B      T    16_B     1.155     0    0.112   1.024     2.847   85.952   78.163
LGA    R    17_B      R    17_B     0.741     0    0.034   1.190     2.331   90.476   79.524
LGA    R    18_B      R    18_B     1.132     0    0.040   0.803     3.504   83.690   64.502
LGA    S    19_B      S    19_B     1.726     0    0.653   1.010     3.258   69.286   70.556
LGA    N    20_B      N    20_B     1.501     0    0.039   0.283     1.945   81.667   81.548
LGA    Y    21_B      Y    21_B     0.474     0    0.057   0.992     6.995   95.238   61.627
LGA    A    22_B      A    22_B     0.901     0    0.051   0.056     1.342   90.476   88.667
LGA    A    23_B      A    23_B     0.779     0    0.048   0.053     1.184   95.238   92.476
LGA    S    24_B      S    24_B     0.390     0    0.073   0.066     1.096  100.000   95.317
LGA    L    25_B      L    25_B     0.527     0    0.041   1.032     2.303   95.238   86.429
LGA    R    26_B      R    26_B     0.653     0    0.070   0.993     4.845   97.619   77.532
LGA    L    27_B      L    27_B     0.488     0    0.075   1.011     2.891   92.976   85.298
LGA    E    28_B      E    28_B     0.821     0    0.140   0.650     2.196   85.952   79.683
LGA    G    29_B      G    29_B     1.293     0    0.115   0.115     1.293   85.952   85.952
LGA    F    30_B      F    30_B     0.594     0    0.051   0.580     3.330   86.190   78.225
LGA    K    31_B      K    31_B     2.388     0    0.289   0.908     3.625   59.524   63.492
LGA    V    32_B      V    32_B     3.264     0    0.045   1.202     5.568   40.000   50.612
LGA    T    33_B      T    33_B     7.744     0    0.070   1.105    11.353   13.929    8.367
LGA    F    34_B      F    34_B     9.165     0    0.036   1.215    17.277    4.405    1.602
LGA    A    35_B      A    35_B     8.451     0    0.097   0.095    10.226   12.738   10.190
LGA    D    36_B      D    36_B     3.759     0    0.530   1.227     5.673   54.762   42.500
LGA    G    37_B      G    37_B     3.982     0    0.634   0.634     4.332   43.690   43.690
LGA    E    38_B      E    38_B     5.402     0    0.152   1.277     5.858   27.619   26.349
LGA    R    39_B      R    39_B     3.938     0    0.097   1.204     4.774   38.810   39.567
LGA    K    40_B      K    40_B     5.814     0    0.044   0.850    10.386   26.310   13.598
LGA    M    41_B      M    41_B     5.355     0    0.055   1.091     6.428   22.619   21.548
LGA    P    42_B      P    42_B     5.418     0    0.482   0.596     5.857   23.810   25.578
LGA    T    43_B      T    43_B     7.840     0    0.113   0.096     9.433    5.000    6.190
LGA    R    44_B      R    44_B    10.867     0    0.579   1.615    15.578    0.119    0.043
LGA    E    45_B      E    45_B    11.505     0    0.447   1.284    11.692    0.000    0.000
LGA    E    46_B      E    46_B    10.038     0    0.573   1.556    12.417    0.000    1.005
LGA    V    47_B      V    47_B    15.476     0    0.463   1.360    17.121    0.000    0.000

# 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):     4.978          4.909                  5.740           58.870   52.264

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   62   43    4.0     30    1.84    63.372    62.847     1.550

LGA_LOCAL      RMSD:   1.835  Number of atoms:   30  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   5.131  Number of assigned atoms:   43 
Std_ASGN_ATOMS RMSD:   4.978  Standard rmsd on all 43 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.954844 * X  +   0.251457 * Y  +   0.158250 * Z  +  17.644749
  Y_new =  -0.250271 * X  +  -0.967779 * Y  +   0.027709 * Z  + -65.665504
  Z_new =   0.160119 * X  +  -0.013147 * Y  +   0.987010 * Z  +   6.566777 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.885252 -0.160811 -0.013320   [DEG: -165.3128   -9.2138   -0.7632 ]
ZXZ:  1.744137  0.161357  1.652723   [DEG:   99.9317    9.2451   94.6940 ]
 
# END of job
