
#######################################################
#                                                     #
#                        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   58 (  481),  selected   58 , name one
# Molecule2: number of CA atoms   58 (  481),  selected   58 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:A  -ch2:A  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    29      30_A - 58_A        4.50    14.96
  LCS_AVERAGE:     43.85

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    25      34_A - 58_A        1.45    15.20
  LCS_AVERAGE:     32.91

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    24      35_A - 58_A        0.54    15.19
  LCS_AVERAGE:     29.49

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   58
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     A     1_A     A     1_A      3   14   17      3    3    3    5   12   18   30   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     E     2_A     E     2_A     13   14   17     31   32   35   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     Y     3_A     Y     3_A     13   14   17     31   32   35   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     V     4_A     V     4_A     13   14   17     31   32   35   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     R     5_A     R     5_A     13   14   17     31   32   35   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     A     6_A     A     6_A     13   14   17     31   32   35   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     L     7_A     L     7_A     13   14   17     31   32   35   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     F     8_A     F     8_A     13   14   17     31   32   35   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     D     9_A     D     9_A     13   14   17     31   32   35   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     H    10_A     H    10_A     13   14   17     31   32   35   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     T    11_A     T    11_A     13   14   17     25   32   35   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     G    12_A     G    12_A     13   14   22      3   25   35   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     H    13_A     H    13_A     13   14   25      3    3   15   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     D    14_A     D    14_A     13   14   25      3   24   35   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     E    15_A     E    15_A      3   16   25      3    3    3   10   16   27   31   36   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     Q    16_A     Q    16_A     15   16   25     14   14   14   15   15   15   17   25   30   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     E    17_A     E    17_A     15   16   25     14   14   14   15   15   15   17   18   20   22   22   22   24   29   33   40   42   45   46   46 
LCS_GDT     L    18_A     L    18_A     15   16   25     14   14   14   15   15   15   17   18   20   22   22   22   22   23   24   25   25   30   35   37 
LCS_GDT     P    19_A     P    19_A     15   16   25     14   14   14   15   15   15   17   18   20   22   22   22   22   23   24   25   25   28   29   29 
LCS_GDT     F    20_A     F    20_A     15   16   25     14   14   14   15   15   15   17   18   20   22   22   22   22   23   24   25   25   28   29   29 
LCS_GDT     K    21_A     K    21_A     15   16   25     14   14   14   15   15   15   17   18   20   22   22   22   22   23   24   25   25   28   29   29 
LCS_GDT     K    22_A     K    22_A     15   16   25     14   14   14   15   15   15   17   18   20   22   22   22   22   23   24   25   25   28   29   29 
LCS_GDT     G    23_A     G    23_A     15   16   25     14   14   14   15   15   15   17   18   20   22   22   22   22   23   24   25   25   28   29   29 
LCS_GDT     E    24_A     E    24_A     15   16   25     14   14   14   15   15   15   17   18   20   22   22   22   22   23   24   25   25   28   29   29 
LCS_GDT     I    25_A     I    25_A     15   16   25     14   14   14   15   15   15   17   18   20   22   22   22   22   23   24   25   25   28   29   29 
LCS_GDT     L    26_A     L    26_A     15   16   25     14   14   14   15   15   15   17   18   20   22   22   22   22   23   24   25   25   28   29   29 
LCS_GDT     R    27_A     R    27_A     15   16   25     14   14   14   15   15   15   17   18   20   22   22   22   22   23   24   25   25   28   29   29 
LCS_GDT     I    28_A     I    28_A     15   16   25     14   14   14   15   15   15   17   18   20   22   22   22   22   23   24   25   27   30   35   36 
LCS_GDT     R    29_A     R    29_A     15   16   25     14   14   14   15   15   15   17   18   20   22   22   22   22   23   24   29   32   34   39   42 
LCS_GDT     D    30_A     D    30_A     15   16   29      3    5   12   15   15   15   17   18   20   22   22   23   26   29   38   41   43   44   46   46 
LCS_GDT     K    31_A     K    31_A      4   16   29      3    3    4    5    7   12   15   18   20   22   22   26   29   34   41   44   44   45   46   46 
LCS_GDT     P    32_A     P    32_A      4    7   29      3    3    4    6    7   14   17   18   20   22   22   22   22   34   43   44   44   45   46   46 
LCS_GDT     E    33_A     E    33_A      4    7   29      3    3    4    5    7    9   12   25   31   37   40   41   42   42   43   44   44   45   46   46 
LCS_GDT     E    34_A     E    34_A      4   25   29      3    4    5    5    6    9   19   36   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     Q    35_A     Q    35_A     24   25   29      3   32   35   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     L    36_A     L    36_A     24   25   29     31   32   35   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     W    37_A     W    37_A     24   25   29     31   32   35   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     N    38_A     N    38_A     24   25   29     31   32   35   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     A    39_A     A    39_A     24   25   29     31   32   35   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     E    40_A     E    40_A     24   25   29     31   32   35   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     N    41_A     N    41_A     24   25   29     31   32   35   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     V    42_A     V    42_A     24   25   29     31   32   35   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     E    43_A     E    43_A     24   25   29     31   32   35   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     G    44_A     G    44_A     24   25   29     31   32   35   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     K    45_A     K    45_A     24   25   29     31   32   35   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     R    46_A     R    46_A     24   25   29     31   32   35   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     G    47_A     G    47_A     24   25   29     31   32   35   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     L    48_A     L    48_A     24   25   29     31   32   35   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     I    49_A     I    49_A     24   25   29     31   32   35   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     H    50_A     H    50_A     24   25   29     31   32   35   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     V    51_A     V    51_A     24   25   29     31   32   35   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     V    52_A     V    52_A     24   25   29     31   32   35   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     L    53_A     L    53_A     24   25   29     31   32   35   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     V    54_A     V    54_A     24   25   29     31   32   35   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     E    55_A     E    55_A     24   25   29     31   32   35   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     K    56_A     K    56_A     24   25   29     31   32   35   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     Y    57_A     Y    57_A     24   25   29     31   32   35   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_GDT     G    58_A     G    58_A     24   25   29      3    5   15   36   37   37   37   37   39   39   41   41   42   42   43   44   44   45   46   46 
LCS_AVERAGE  LCS_A:  35.41  (  29.49   32.91   43.85 )

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     31     32     35     36     37     37     37     37     39     39     41     41     42     42     43     44     44     45     46     46 
GDT PERCENT_AT  53.45  55.17  60.34  62.07  63.79  63.79  63.79  63.79  67.24  67.24  70.69  70.69  72.41  72.41  74.14  75.86  75.86  77.59  79.31  79.31
GDT RMS_LOCAL    0.29   0.32   0.55   0.64   0.77   0.77   0.77   0.77   1.69   1.69   2.32   2.32   2.73   2.73   3.21   3.64   3.64   4.00   4.41   4.41
GDT RMS_ALL_AT  15.22  15.21  15.20  15.18  15.19  15.19  15.19  15.19  15.10  15.10  14.91  14.91  14.88  14.88  14.84  14.75  14.75  14.63  14.52  14.52

# Checking swapping
#   possible swapping detected:  E     2_A      E     2_A
#   possible swapping detected:  Y     3_A      Y     3_A
#   possible swapping detected:  F     8_A      F     8_A
#   possible swapping detected:  E    40_A      E    40_A
#   possible swapping detected:  E    43_A      E    43_A
#   possible swapping detected:  E    55_A      E    55_A
#   possible swapping detected:  Y    57_A      Y    57_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A     1_A      A     1_A     6.875     0    0.472   0.528     8.396   21.667   18.762
LGA    E     2_A      E     2_A     0.251     0    0.638   1.172     7.077   89.286   54.127
LGA    Y     3_A      Y     3_A     0.158     0    0.028   0.122     0.909  100.000   96.825
LGA    V     4_A      V     4_A     0.121     0    0.012   0.023     0.299  100.000  100.000
LGA    R     5_A      R     5_A     0.129     0    0.023   0.237     2.062  100.000   92.554
LGA    A     6_A      A     6_A     0.374     0    0.020   0.018     0.432  100.000  100.000
LGA    L     7_A      L     7_A     0.407     0    0.022   0.046     0.479  100.000  100.000
LGA    F     8_A      F     8_A     0.617     0    0.021   0.062     0.637   90.476   90.476
LGA    D     9_A      D     9_A     0.555     0    0.044   0.088     0.869   90.476   90.476
LGA    H    10_A      H    10_A     0.593     0    0.047   1.142     2.576   92.857   84.619
LGA    T    11_A      T    11_A     1.104     0    0.634   0.994     3.039   75.833   73.537
LGA    G    12_A      G    12_A     1.522     0    0.059   0.059     1.522   77.143   77.143
LGA    H    13_A      H    13_A     2.514     0    0.625   1.524     4.244   55.952   52.476
LGA    D    14_A      D    14_A     1.676     0    0.096   1.243     5.495   55.952   53.929
LGA    E    15_A      E    15_A     7.336     0    0.685   0.666    14.126   14.643    6.825
LGA    Q    16_A      Q    16_A     8.207     0    0.659   1.261    10.140    3.333    3.016
LGA    E    17_A      E    17_A    12.123     0    0.058   1.022    15.839    0.000    0.000
LGA    L    18_A      L    18_A    19.144     0    0.073   1.365    23.198    0.000    0.000
LGA    P    19_A      P    19_A    24.794     0    0.030   0.085    27.512    0.000    0.000
LGA    F    20_A      F    20_A    30.648     0    0.010   1.440    32.782    0.000    0.000
LGA    K    21_A      K    21_A    37.455     0    0.013   0.098    40.010    0.000    0.000
LGA    K    22_A      K    22_A    40.261     0    0.012   0.484    48.990    0.000    0.000
LGA    G    23_A      G    23_A    42.207     0    0.036   0.036    42.207    0.000    0.000
LGA    E    24_A      E    24_A    38.722     0    0.016   1.035    39.514    0.000    0.000
LGA    I    25_A      I    25_A    36.374     0    0.060   0.646    41.161    0.000    0.000
LGA    L    26_A      L    26_A    29.991     0    0.018   0.057    32.021    0.000    0.000
LGA    R    27_A      R    27_A    28.359     0    0.065   0.579    32.522    0.000    0.000
LGA    I    28_A      I    28_A    21.324     0    0.041   0.054    24.060    0.000    0.000
LGA    R    29_A      R    29_A    21.175     0    0.615   1.129    30.673    0.000    0.000
LGA    D    30_A      D    30_A    17.201     0    0.686   0.844    21.432    0.000    0.000
LGA    K    31_A      K    31_A    15.042     0    0.302   0.341    22.395    0.000    0.000
LGA    P    32_A      P    32_A    13.928     0    0.117   0.345    16.200    0.000    0.000
LGA    E    33_A      E    33_A    11.160     0    0.697   1.046    13.872    0.119    0.053
LGA    E    34_A      E    34_A     7.558     0    0.219   1.120    10.508   13.810    6.984
LGA    Q    35_A      Q    35_A     1.092     0    0.609   0.657     5.310   80.476   66.455
LGA    L    36_A      L    36_A     0.639     0    0.190   1.098     2.638   90.595   79.821
LGA    W    37_A      W    37_A     0.451     0    0.028   0.248     1.414   97.619   90.612
LGA    N    38_A      N    38_A     0.290     0    0.049   0.617     2.885  100.000   90.000
LGA    A    39_A      A    39_A     0.061     0    0.014   0.016     0.286  100.000  100.000
LGA    E    40_A      E    40_A     0.204     0    0.043   0.204     1.043  100.000   95.820
LGA    N    41_A      N    41_A     0.274     0    0.011   0.036     0.437  100.000  100.000
LGA    V    42_A      V    42_A     0.542     0    0.038   1.162     3.269   97.619   86.258
LGA    E    43_A      E    43_A     0.160     0    0.062   0.169     1.180  100.000   94.762
LGA    G    44_A      G    44_A     0.124     0    0.022   0.022     0.170  100.000  100.000
LGA    K    45_A      K    45_A     0.222     0    0.016   0.706     4.058  100.000   79.788
LGA    R    46_A      R    46_A     0.350     0    0.013   0.137     0.789  100.000   94.805
LGA    G    47_A      G    47_A     0.202     0    0.024   0.024     0.202  100.000  100.000
LGA    L    48_A      L    48_A     0.304     0    0.030   0.075     0.535   97.619   98.810
LGA    I    49_A      I    49_A     0.321     0    0.020   0.050     0.390  100.000  100.000
LGA    H    50_A      H    50_A     0.335     0    0.014   0.086     0.676  100.000   94.286
LGA    V    51_A      V    51_A     0.097     0    0.043   0.066     0.162  100.000  100.000
LGA    V    52_A      V    52_A     0.351     0    0.034   0.041     0.703  100.000   95.918
LGA    L    53_A      L    53_A     0.536     0    0.033   0.092     1.249   97.619   91.786
LGA    V    54_A      V    54_A     0.284     0    0.021   0.077     0.432  100.000  100.000
LGA    E    55_A      E    55_A     0.066     0    0.030   0.136     0.412  100.000  100.000
LGA    K    56_A      K    56_A     0.158     0    0.051   0.583     1.819  100.000   94.868
LGA    Y    57_A      Y    57_A     0.182     0    0.573   0.552     2.591   89.286   88.690
LGA    G    58_A      G    58_A     2.027     0    0.124   0.124     2.671   62.976   62.976

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       58     232    232  100.00     481    481  100.00                58
SUMMARY(RMSD_GDC):    13.032         12.967                 13.387           60.265   57.025

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   58   58    4.0     37    0.77    64.224    57.123     4.276

LGA_LOCAL      RMSD:   0.765  Number of atoms:   37  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  15.194  Number of assigned atoms:   58 
Std_ASGN_ATOMS RMSD:  13.032  Standard rmsd on all 58 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.209248 * X  +  -0.785082 * Y  +  -0.582976 * Z  + -22.294258
  Y_new =  -0.551537 * X  +  -0.587049 * Y  +   0.592604 * Z  +  19.412848
  Z_new =  -0.807479 * X  +   0.197532 * Y  +  -0.555841 * Z  + -17.814558 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.208182  0.939866  2.800138   [DEG:  -69.2237   53.8503  160.4361 ]
ZXZ: -2.364385  2.160170 -1.330880   [DEG: -135.4693  123.7686  -76.2538 ]
 
# END of job
