
#######################################################
#                                                     #
#                        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        4.75     4.75
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    30       7_B - 36_B        1.99     5.62
  LONGEST_CONTINUOUS_SEGMENT:    30       8_B - 37_B        1.97     5.59
  LCS_AVERAGE:     57.49

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    23       8_B - 30_B        0.98     4.93
  LONGEST_CONTINUOUS_SEGMENT:    23       9_B - 31_B        1.00     4.84
  LCS_AVERAGE:     36.94

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      5   29   43      3    4    6    9   24   27   29   30   32   34   35   35   38   38   39   39   42   42   42   42 
LCS_GDT     L     6_B     L     6_B     11   29   43      3    6   11   24   26   28   29   31   32   34   35   35   38   38   39   39   42   42   42   42 
LCS_GDT     E     7_B     E     7_B     14   30   43      4   16   21   25   28   28   29   31   32   34   35   35   38   38   39   39   42   42   42   42 
LCS_GDT     T     8_B     T     8_B     23   30   43      4   11   20   25   28   28   29   31   32   34   35   35   38   38   39   39   42   42   42   42 
LCS_GDT     K     9_B     K     9_B     23   30   43      5   12   22   25   28   28   29   31   32   34   35   35   38   38   39   39   42   42   42   42 
LCS_GDT     K    10_B     K    10_B     23   30   43      5   17   22   25   28   28   29   31   32   34   35   35   38   38   39   39   42   42   42   42 
LCS_GDT     A    11_B     A    11_B     23   30   43      5   16   22   25   28   28   29   31   32   34   35   35   38   38   39   39   42   42   42   42 
LCS_GDT     Y    12_B     Y    12_B     23   30   43      5   11   22   25   28   28   29   31   32   34   35   35   38   38   39   39   42   42   42   42 
LCS_GDT     A    13_B     A    13_B     23   30   43      5   16   22   25   28   28   29   31   32   34   35   35   38   38   39   39   42   42   42   42 
LCS_GDT     A    14_B     A    14_B     23   30   43      7   17   22   25   28   28   29   31   32   34   35   35   38   38   39   39   42   42   42   42 
LCS_GDT     R    15_B     R    15_B     23   30   43      5   17   22   25   28   28   29   31   32   34   35   35   38   38   39   39   42   42   42   42 
LCS_GDT     T    16_B     T    16_B     23   30   43      9   17   22   25   28   28   29   31   32   34   35   35   38   38   39   39   42   42   42   42 
LCS_GDT     R    17_B     R    17_B     23   30   43      9   17   22   25   28   28   29   31   32   34   35   35   38   38   39   39   42   42   42   42 
LCS_GDT     R    18_B     R    18_B     23   30   43     11   17   22   25   28   28   29   31   32   34   35   35   38   38   39   39   42   42   42   42 
LCS_GDT     S    19_B     S    19_B     23   30   43     11   17   22   25   28   28   29   31   32   34   35   35   38   38   39   39   42   42   42   42 
LCS_GDT     N    20_B     N    20_B     23   30   43     11   17   22   25   28   28   29   31   32   34   35   35   38   38   39   39   42   42   42   42 
LCS_GDT     Y    21_B     Y    21_B     23   30   43     11   17   22   25   28   28   29   31   32   34   35   35   38   38   39   39   42   42   42   42 
LCS_GDT     A    22_B     A    22_B     23   30   43     11   17   22   25   28   28   29   31   32   34   35   35   38   38   39   39   42   42   42   42 
LCS_GDT     A    23_B     A    23_B     23   30   43     11   17   22   25   28   28   29   31   32   34   35   35   38   38   39   39   42   42   42   42 
LCS_GDT     S    24_B     S    24_B     23   30   43     11   17   22   25   28   28   29   31   32   34   35   35   38   38   39   39   42   42   42   42 
LCS_GDT     L    25_B     L    25_B     23   30   43     11   17   22   25   28   28   29   31   32   34   35   35   38   38   39   39   42   42   42   42 
LCS_GDT     R    26_B     R    26_B     23   30   43     11   17   22   25   28   28   29   31   32   34   35   35   38   38   39   39   42   42   42   42 
LCS_GDT     L    27_B     L    27_B     23   30   43     11   17   22   25   28   28   29   31   32   34   35   35   38   38   39   39   42   42   42   42 
LCS_GDT     E    28_B     E    28_B     23   30   43     11   17   22   25   28   28   29   31   32   34   35   35   38   38   39   39   42   42   42   42 
LCS_GDT     G    29_B     G    29_B     23   30   43      6   17   22   25   28   28   29   31   32   34   35   35   38   38   39   39   42   42   42   42 
LCS_GDT     F    30_B     F    30_B     23   30   43      7   17   22   25   28   28   29   31   32   34   35   35   38   38   39   39   42   42   42   42 
LCS_GDT     K    31_B     K    31_B     23   30   43      4   15   20   25   28   28   29   31   32   34   35   35   38   38   39   39   42   42   42   42 
LCS_GDT     V    32_B     V    32_B     18   30   43      4    5   16   24   28   28   29   31   32   34   35   35   38   38   39   39   42   42   42   42 
LCS_GDT     T    33_B     T    33_B      7   30   43      3    5    7   11   16   24   29   31   32   33   33   34   38   38   39   39   42   42   42   42 
LCS_GDT     F    34_B     F    34_B      7   30   43      4    5    7   11   17   24   29   31   32   33   33   34   38   38   39   39   42   42   42   42 
LCS_GDT     A    35_B     A    35_B      7   30   43      4    5    8   17   23   28   29   31   32   33   33   34   38   38   39   39   42   42   42   42 
LCS_GDT     D    36_B     D    36_B      7   30   43      4    9   16   24   28   28   29   31   32   33   35   35   38   38   39   39   42   42   42   42 
LCS_GDT     G    37_B     G    37_B      5   30   43      3    4    5   14   28   28   29   31   32   34   35   35   38   38   39   39   42   42   42   42 
LCS_GDT     E    38_B     E    38_B      3    8   43      3    3    4    6    6    7   18   28   32   34   35   35   38   38   39   39   42   42   42   42 
LCS_GDT     R    39_B     R    39_B      5    8   43      3    5   10   17   26   27   29   30   32   34   35   35   38   38   39   39   42   42   42   42 
LCS_GDT     K    40_B     K    40_B      6    8   43      3    5    7    7    7   25   28   30   32   34   35   35   38   38   39   39   42   42   42   42 
LCS_GDT     M    41_B     M    41_B      6    8   43      3    5    7    7   18   26   28   30   32   34   35   35   38   38   39   39   42   42   42   42 
LCS_GDT     P    42_B     P    42_B      6    8   43      4    5    7    7    7   11   20   23   30   34   35   35   38   38   39   39   42   42   42   42 
LCS_GDT     T    43_B     T    43_B      6    8   43      4    5    7    7    7    9   13   21   24   26   29   33   35   38   39   39   42   42   42   42 
LCS_GDT     R    44_B     R    44_B      6    8   43      4    5    7    7    7    7    9   13   17   20   25   27   31   34   37   39   42   42   42   42 
LCS_GDT     E    45_B     E    45_B      6    8   43      4    5    7    7    7    7    9    9   17   19   24   27   31   34   37   39   42   42   42   42 
LCS_GDT     E    46_B     E    46_B      3    8   43      3    3    3    4    4    4    7    8   11   12   16   18   28   34   37   38   42   42   42   42 
LCS_GDT     V    47_B     V    47_B      3    3   43      3    3    3    3    3    3    4    5    6    7    9    9    9   14   18   21   25   29   30   31 
LCS_AVERAGE  LCS_A:  64.81  (  36.94   57.49  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     11     17     22     25     28     28     29     31     32     34     35     35     38     38     39     39     42     42     42     42 
GDT PERCENT_AT  25.58  39.53  51.16  58.14  65.12  65.12  67.44  72.09  74.42  79.07  81.40  81.40  88.37  88.37  90.70  90.70  97.67  97.67  97.67  97.67
GDT RMS_LOCAL    0.32   0.63   0.89   1.13   1.48   1.48   1.59   2.01   2.05   2.37   2.54   2.54   3.29   3.29   3.50   3.50   4.28   4.28   4.28   4.28
GDT RMS_ALL_AT   5.18   4.86   4.88   4.90   5.03   5.03   5.02   5.40   5.16   5.09   5.01   5.01   4.93   4.93   4.88   4.88   4.76   4.76   4.76   4.76

# Checking swapping
#   possible swapping detected:  E     7_B      E     7_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     5.371     0    0.622   0.704     7.004   30.833   31.111
LGA    L     6_B      L     6_B     3.944     0    0.043   1.330     5.082   50.595   43.393
LGA    E     7_B      E     7_B     2.077     0    0.150   1.135     3.252   69.048   65.026
LGA    T     8_B      T     8_B     1.977     0    0.051   1.050     3.164   72.857   66.190
LGA    K     9_B      K     9_B     1.142     0    0.054   0.133     1.297   83.690   83.439
LGA    K    10_B      K    10_B     0.919     0    0.040   1.058     6.483   88.214   60.265
LGA    A    11_B      A    11_B     0.760     0    0.044   0.049     0.917   90.476   90.476
LGA    Y    12_B      Y    12_B     1.151     0    0.039   0.209     3.587   81.548   68.135
LGA    A    13_B      A    13_B     1.442     0    0.035   0.055     1.894   77.143   78.000
LGA    A    14_B      A    14_B     1.820     0    0.055   0.054     2.516   66.905   66.476
LGA    R    15_B      R    15_B     2.309     0    0.091   1.474     6.927   64.881   55.065
LGA    T    16_B      T    16_B     2.486     0    0.108   1.058     4.022   64.762   59.728
LGA    R    17_B      R    17_B     1.494     0    0.035   1.135     4.269   75.000   69.697
LGA    R    18_B      R    18_B     2.138     0    0.045   0.794     5.840   66.786   48.788
LGA    S    19_B      S    19_B     2.779     0    0.042   0.073     3.583   60.952   56.190
LGA    N    20_B      N    20_B     1.742     0    0.069   0.340     2.415   77.143   73.988
LGA    Y    21_B      Y    21_B     0.266     0    0.044   1.006     7.228   95.238   60.198
LGA    A    22_B      A    22_B     1.717     0    0.035   0.042     2.559   77.143   73.143
LGA    A    23_B      A    23_B     1.932     0    0.045   0.050     2.578   75.000   71.429
LGA    S    24_B      S    24_B     1.077     0    0.075   0.074     2.022   85.952   81.667
LGA    L    25_B      L    25_B     0.644     0    0.047   0.115     2.227   92.857   82.917
LGA    R    26_B      R    26_B     1.208     0    0.082   1.174     5.777   88.214   65.455
LGA    L    27_B      L    27_B     1.163     0    0.078   0.147     2.987   85.952   74.464
LGA    E    28_B      E    28_B     0.634     0    0.117   0.715     3.601   92.857   79.577
LGA    G    29_B      G    29_B     0.768     0    0.113   0.113     0.768   92.857   92.857
LGA    F    30_B      F    30_B     0.375     0    0.068   0.547     2.359   95.238   90.043
LGA    K    31_B      K    31_B     1.313     0    0.315   1.156     4.000   81.548   67.778
LGA    V    32_B      V    32_B     1.819     0    0.081   0.891     3.526   61.548   66.667
LGA    T    33_B      T    33_B     4.694     0    0.070   0.985     7.869   40.476   31.701
LGA    F    34_B      F    34_B     4.761     0    0.088   1.530    10.277   37.500   18.442
LGA    A    35_B      A    35_B     3.873     0    0.069   0.071     4.751   50.595   46.762
LGA    D    36_B      D    36_B     1.537     0    0.406   1.154     5.653   71.310   55.000
LGA    G    37_B      G    37_B     2.391     0    0.613   0.613     7.000   44.762   44.762
LGA    E    38_B      E    38_B     6.737     0    0.310   0.409    10.816   13.333    8.571
LGA    R    39_B      R    39_B     8.683     0    0.258   1.296     9.957    5.119    7.403
LGA    K    40_B      K    40_B     9.449     0    0.072   1.243    17.274    2.143    1.005
LGA    M    41_B      M    41_B     8.252     0    0.128   1.075     9.009    2.976    9.405
LGA    P    42_B      P    42_B     8.463     0    0.099   0.410     9.198    3.452    4.694
LGA    T    43_B      T    43_B     9.722     0    0.082   1.097    11.446    0.476    1.361
LGA    R    44_B      R    44_B    11.018     0    0.584   1.009    11.931    0.000    0.043
LGA    E    45_B      E    45_B    10.758     0    0.462   1.014    10.914    0.000    0.265
LGA    E    46_B      E    46_B    11.838     0    0.585   1.325    15.959    0.000    0.000
LGA    V    47_B      V    47_B    16.071     0    0.501   1.166    17.364    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):     4.751          4.739                  5.357           56.218   50.037

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   62   43    4.0     31    2.01    65.116    65.627     1.472

LGA_LOCAL      RMSD:   2.006  Number of atoms:   31  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   5.405  Number of assigned atoms:   43 
Std_ASGN_ATOMS RMSD:   4.751  Standard rmsd on all 43 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.092667 * X  +  -0.117825 * Y  +   0.988701 * Z  +  29.570084
  Y_new =  -0.692910 * X  +  -0.705457 * Y  +  -0.149014 * Z  + -47.230160
  Z_new =   0.715044 * X  +  -0.698890 * Y  +  -0.016270 * Z  +   0.999634 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.703743 -0.796687 -1.594072   [DEG:  -97.6173  -45.6468  -91.3336 ]
ZXZ:  1.421205  1.587067  2.344770   [DEG:   81.4291   90.9322  134.3454 ]
 
# END of job
