
#######################################################
#                                                     #
#                        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   36 (  290),  selected   36 , name one
# Molecule2: number of CA atoms   61 (  491),  selected   36 , 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:    25      24_B - 48_B        4.82     8.97
  LCS_AVERAGE:     38.52

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    21      24_B - 44_B        1.61    11.35
  LCS_AVERAGE:     26.37

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    20      24_B - 43_B        0.43    11.55
  LCS_AVERAGE:     23.68

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   36
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     D    24_B     D    24_B     20   21   25     16   20   20   20   20   20   20   20   20   22   22   23   23   23   23   24   27   28   32   33 
LCS_GDT     A    25_B     A    25_B     20   21   25     16   20   20   20   20   20   20   20   20   22   22   23   23   23   23   23   27   28   32   33 
LCS_GDT     Q    26_B     Q    26_B     20   21   25     16   20   20   20   20   20   20   20   20   22   22   23   23   23   23   25   27   29   32   34 
LCS_GDT     R    27_B     R    27_B     20   21   25     16   20   20   20   20   20   20   20   20   22   22   23   23   23   23   25   27   29   32   34 
LCS_GDT     V    28_B     V    28_B     20   21   25     16   20   20   20   20   20   20   20   20   22   22   23   23   23   23   25   27   29   32   34 
LCS_GDT     A    29_B     A    29_B     20   21   25     16   20   20   20   20   20   20   20   20   22   22   23   23   23   23   25   27   29   32   34 
LCS_GDT     D    30_B     D    30_B     20   21   25     16   20   20   20   20   20   20   20   20   22   22   23   23   23   23   25   27   29   32   34 
LCS_GDT     E    31_B     E    31_B     20   21   25     16   20   20   20   20   20   20   20   20   22   22   23   23   23   23   25   27   29   32   34 
LCS_GDT     L    32_B     L    32_B     20   21   25     16   20   20   20   20   20   20   20   20   22   22   23   23   23   23   25   27   29   32   34 
LCS_GDT     M    33_B     M    33_B     20   21   25     16   20   20   20   20   20   20   20   20   22   22   23   23   23   23   25   27   29   32   34 
LCS_GDT     K    34_B     K    34_B     20   21   25     16   20   20   20   20   20   20   20   20   22   22   23   23   23   23   25   27   29   32   34 
LCS_GDT     K    35_B     K    35_B     20   21   25     16   20   20   20   20   20   20   20   20   22   22   23   23   23   23   25   27   29   32   34 
LCS_GDT     L    36_B     L    36_B     20   21   25     16   20   20   20   20   20   20   20   20   22   22   23   23   23   23   25   27   29   32   34 
LCS_GDT     F    37_B     F    37_B     20   21   25     16   20   20   20   20   20   20   20   20   22   22   23   23   23   23   25   27   29   32   34 
LCS_GDT     D    38_B     D    38_B     20   21   25     16   20   20   20   20   20   20   20   20   22   22   23   23   23   23   25   27   29   32   34 
LCS_GDT     A    39_B     A    39_B     20   21   25     14   20   20   20   20   20   20   20   20   22   22   23   23   23   23   25   27   29   32   34 
LCS_GDT     A    40_B     A    40_B     20   21   25     16   20   20   20   20   20   20   20   20   22   22   23   23   23   23   25   27   29   32   34 
LCS_GDT     H    41_B     H    41_B     20   21   25     16   20   20   20   20   20   20   20   20   22   22   23   23   23   23   25   27   29   32   34 
LCS_GDT     R    42_B     R    42_B     20   21   25     14   20   20   20   20   20   20   20   20   21   22   23   23   23   23   25   27   29   32   34 
LCS_GDT     N    43_B     N    43_B     20   21   25     16   20   20   20   20   20   20   20   20   22   22   23   23   23   23   25   27   29   32   34 
LCS_GDT     D    44_B     D    44_B      3   21   25      3    3    3    4    6    8   11   19   20   22   22   23   23   23   23   25   27   29   32   34 
LCS_GDT     K    45_B     K    45_B      3    4   25      3    3    3    4    5    7   11   13   16   22   22   23   23   23   23   25   27   29   32   34 
LCS_GDT     D    46_B     D    46_B      3    4   25      3    3    3    4    5    7   11   13   16   22   22   23   23   23   23   25   27   29   32   34 
LCS_GDT     K    47_B     K    47_B      3    4   25      3    3    3    5    8   10   11   13   13   14   15   17   18   21   23   25   27   29   32   34 
LCS_GDT     V    48_B     V    48_B      4    5   25      4    4    4    4    4    8   12   13   13   13   13   16   17   20   20   24   24   27   32   34 
LCS_GDT     K    49_B     K    49_B      4   11   21      4    4    4    5    9   11   12   13   13   13   15   16   18   20   22   24   26   29   32   34 
LCS_GDT     K    50_B     K    50_B     10   11   21     10   10   10   10   10   11   12   13   13   14   15   17   18   21   22   24   26   29   32   34 
LCS_GDT     V    51_B     V    51_B     10   11   21     10   10   10   10   10   11   12   13   13   14   15   17   18   20   22   24   26   29   32   34 
LCS_GDT     V    52_B     V    52_B     10   11   21     10   10   10   10   10   11   12   13   13   14   15   17   18   21   22   25   26   29   32   34 
LCS_GDT     E    53_B     E    53_B     10   11   21     10   10   10   10   10   11   12   13   13   14   15   17   18   21   23   25   27   29   32   34 
LCS_GDT     E    54_B     E    54_B     10   11   21     10   10   10   10   10   11   12   13   13   14   15   17   18   21   22   25   27   29   32   34 
LCS_GDT     A    55_B     A    55_B     10   11   21     10   10   10   10   10   11   12   13   13   13   15   17   18   21   22   25   27   29   32   34 
LCS_GDT     K    56_B     K    56_B     10   11   21     10   10   10   10   10   11   12   13   13   13   15   17   18   21   23   25   27   29   32   34 
LCS_GDT     K    57_B     K    57_B     10   11   21     10   10   10   10   10   11   12   13   13   13   13   17   18   21   23   25   27   29   32   34 
LCS_GDT     V    58_B     V    58_B     10   11   16     10   10   10   10   10   11   12   13   13   13   13   13   14   17   20   23   26   29   32   34 
LCS_GDT     V    59_B     V    59_B     10   11   16     10   10   10   10   10   11   12   13   13   13   13   13   16   19   20   25   27   29   32   34 
LCS_AVERAGE  LCS_A:  29.52  (  23.68   26.37   38.52 )

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     16     20     20     20     20     20     20     20     20     22     22     23     23     23     23     25     27     29     32     34 
GDT PERCENT_AT  26.23  32.79  32.79  32.79  32.79  32.79  32.79  32.79  32.79  36.07  36.07  37.70  37.70  37.70  37.70  40.98  44.26  47.54  52.46  55.74
GDT RMS_LOCAL    0.31   0.43   0.43   0.43   0.43   0.43   0.43   0.43   0.43   3.02   3.02   3.08   3.08   3.08   3.08   5.55   5.58   6.45   6.74   7.11
GDT RMS_ALL_AT  11.31  11.55  11.55  11.55  11.55  11.55  11.55  11.55  11.55   9.73   9.73   9.91   9.91   9.91   9.91   7.83   8.06   7.47   7.41   7.39

# Checking swapping
#   possible swapping detected:  D    46_B      D    46_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    D    24_B      D    24_B     0.308     0    0.085   0.457     1.678   97.619   91.905
LGA    A    25_B      A    25_B     0.695     0    0.005   0.007     0.929   90.476   90.476
LGA    Q    26_B      Q    26_B     0.479     0    0.022   1.324     4.677   97.619   74.709
LGA    R    27_B      R    27_B     0.152     0    0.024   0.997     3.208  100.000   91.255
LGA    V    28_B      V    28_B     0.306     0    0.037   0.052     0.491  100.000  100.000
LGA    A    29_B      A    29_B     0.184     0    0.030   0.037     0.308  100.000  100.000
LGA    D    30_B      D    30_B     0.248     0    0.034   0.695     2.798  100.000   84.881
LGA    E    31_B      E    31_B     0.462     0    0.022   0.042     0.598  100.000   94.709
LGA    L    32_B      L    32_B     0.414     0    0.011   0.152     0.880  100.000   96.429
LGA    M    33_B      M    33_B     0.393     0    0.012   0.114     0.920  100.000   98.810
LGA    K    34_B      K    34_B     0.369     0    0.017   0.289     1.570  100.000   94.868
LGA    K    35_B      K    35_B     0.280     0    0.013   0.291     1.466  100.000   95.873
LGA    L    36_B      L    36_B     0.212     0    0.064   0.111     1.083   97.619   94.107
LGA    F    37_B      F    37_B     0.348     0    0.047   1.217     6.209  100.000   67.662
LGA    D    38_B      D    38_B     0.523     0    0.014   0.189     1.434   95.238   91.726
LGA    A    39_B      A    39_B     0.688     0    0.007   0.010     0.881   90.476   90.476
LGA    A    40_B      A    40_B     0.445     0    0.089   0.094     0.795  100.000   98.095
LGA    H    41_B      H    41_B     0.398     0    0.094   0.928     3.139   97.619   80.810
LGA    R    42_B      R    42_B     0.716     0    0.231   1.054     6.482   92.857   70.260
LGA    N    43_B      N    43_B     0.375     0    0.391   0.818     5.465   73.333   59.702
LGA    D    44_B      D    44_B     7.749     0    0.539   0.920    12.240   10.000    5.179
LGA    K    45_B      K    45_B    10.714     0    0.630   0.835    17.378    0.714    0.317
LGA    D    46_B      D    46_B    11.845     0    0.579   1.308    14.382    0.000    0.714
LGA    K    47_B      K    47_B    15.904     0    0.512   0.716    20.770    0.000    0.000
LGA    V    48_B      V    48_B    17.342     0    0.582   1.479    19.437    0.000    0.000
LGA    K    49_B      K    49_B    19.982     0    0.083   0.947    21.957    0.000    0.000
LGA    K    50_B      K    50_B    18.784     0    0.403   0.836    18.847    0.000    0.000
LGA    V    51_B      V    51_B    18.996     0    0.006   0.974    20.962    0.000    0.000
LGA    V    52_B      V    52_B    18.182     0    0.028   0.083    18.373    0.000    0.000
LGA    E    53_B      E    53_B    18.264     0    0.039   0.891    18.729    0.000    0.000
LGA    E    54_B      E    54_B    19.377     0    0.027   0.758    20.388    0.000    0.000
LGA    A    55_B      A    55_B    18.680     0    0.030   0.034    18.823    0.000    0.000
LGA    K    56_B      K    56_B    18.294     0    0.005   0.393    18.617    0.000    0.000
LGA    K    57_B      K    57_B    19.413     0    0.018   0.034    20.876    0.000    0.000
LGA    V    58_B      V    58_B    19.370     0    0.092   0.182    19.549    0.000    0.000
LGA    V    59_B      V    59_B    18.470     0    0.048   0.221    18.701    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       36     144    144  100.00     290    290  100.00                61
SUMMARY(RMSD_GDC):     7.311          7.209                  7.727           31.862   29.065

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   36   61    4.0     20    0.43    34.836    32.526     3.775

LGA_LOCAL      RMSD:   0.430  Number of atoms:   20  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  11.549  Number of assigned atoms:   36 
Std_ASGN_ATOMS RMSD:   7.311  Standard rmsd on all 36 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.476074 * X  +  -0.274579 * Y  +   0.835440 * Z  +  28.152224
  Y_new =   0.871837 * X  +   0.023002 * Y  +  -0.489255 * Z  +  -8.890486
  Z_new =   0.115123 * X  +   0.961289 * Y  +   0.250339 * Z  +  -6.621025 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.070984 -0.115378  1.316035   [DEG:   61.3629   -6.6107   75.4033 ]
ZXZ:  1.041013  1.317766  0.119191   [DEG:   59.6457   75.5024    6.8291 ]
 
# END of job
