
#######################################################
#                                                     #
#                        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        4.52    14.92
  LCS_AVERAGE:     43.85

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    25      34_A - 58_A        1.48    15.15
  LCS_AVERAGE:     32.82

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    24      35_A - 58_A        0.71    15.16
  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    7   23   34   37   39   40   41   42   42   42   44   44   44   45   46   46 
LCS_GDT     E     2_A     E     2_A     13   14   17     30   34   35   36   36   37   37   37   39   40   41   42   42   42   44   44   44   45   46   46 
LCS_GDT     Y     3_A     Y     3_A     13   14   17     30   34   35   36   36   37   37   37   39   40   41   42   42   42   44   44   44   45   46   46 
LCS_GDT     V     4_A     V     4_A     13   14   17     30   34   35   36   36   37   37   37   39   40   41   42   42   42   44   44   44   45   46   46 
LCS_GDT     R     5_A     R     5_A     13   14   17     30   34   35   36   36   37   37   37   39   40   41   42   42   42   44   44   44   45   46   46 
LCS_GDT     A     6_A     A     6_A     13   14   17     30   34   35   36   36   37   37   37   39   40   41   42   42   42   44   44   44   45   46   46 
LCS_GDT     L     7_A     L     7_A     13   14   17     30   34   35   36   36   37   37   37   39   40   41   42   42   42   44   44   44   45   46   46 
LCS_GDT     F     8_A     F     8_A     13   14   17     30   34   35   36   36   37   37   37   39   40   41   42   42   42   44   44   44   45   46   46 
LCS_GDT     D     9_A     D     9_A     13   14   17     27   34   35   36   36   37   37   37   39   40   41   42   42   42   44   44   44   45   46   46 
LCS_GDT     H    10_A     H    10_A     13   14   17     24   34   35   36   36   37   37   37   39   40   41   42   42   42   44   44   44   45   46   46 
LCS_GDT     T    11_A     T    11_A     13   14   17     30   34   35   36   36   37   37   37   39   40   41   42   42   42   44   44   44   45   46   46 
LCS_GDT     G    12_A     G    12_A     13   14   22      3   16   35   36   36   37   37   37   39   40   41   42   42   42   44   44   44   45   46   46 
LCS_GDT     H    13_A     H    13_A     13   14   25      3    5   35   36   36   37   37   37   39   40   41   42   42   42   44   44   44   45   46   46 
LCS_GDT     D    14_A     D    14_A     13   14   25     25   34   34   36   36   37   37   37   39   40   41   42   42   42   44   44   44   45   46   46 
LCS_GDT     E    15_A     E    15_A      3   16   25      3    3    3   15   16   21   24   36   39   40   41   42   42   42   44   44   44   45   46   46 
LCS_GDT     Q    16_A     Q    16_A     15   16   25     12   14   14   14   15   15   24   25   30   38   41   42   42   42   44   44   44   45   46   46 
LCS_GDT     E    17_A     E    17_A     15   16   25      9   14   14   14   15   15   16   18   20   22   22   22   27   33   36   40   43   45   46   46 
LCS_GDT     L    18_A     L    18_A     15   16   25     12   14   14   14   15   15   16   18   20   22   22   22   22   23   24   24   29   32   36   38 
LCS_GDT     P    19_A     P    19_A     15   16   25     12   14   14   14   15   15   16   18   20   22   22   22   22   23   24   24   27   28   29   29 
LCS_GDT     F    20_A     F    20_A     15   16   25     12   14   14   14   15   15   16   18   20   22   22   22   22   23   24   24   27   28   29   29 
LCS_GDT     K    21_A     K    21_A     15   16   25     12   14   14   14   15   15   16   18   20   22   22   22   22   23   24   24   25   28   29   29 
LCS_GDT     K    22_A     K    22_A     15   16   25     12   14   14   14   15   15   16   18   20   22   22   22   22   23   24   24   25   28   29   29 
LCS_GDT     G    23_A     G    23_A     15   16   25      4   14   14   14   15   15   16   18   20   22   22   22   22   23   24   24   27   28   29   29 
LCS_GDT     E    24_A     E    24_A     15   16   25     12   14   14   14   15   15   16   18   20   22   22   22   22   23   24   24   27   28   29   29 
LCS_GDT     I    25_A     I    25_A     15   16   25     12   14   14   14   15   15   16   18   20   22   22   22   22   23   24   24   27   28   29   29 
LCS_GDT     L    26_A     L    26_A     15   16   25     12   14   14   14   15   15   16   18   20   22   22   22   22   23   24   24   27   28   29   29 
LCS_GDT     R    27_A     R    27_A     15   16   25     12   14   14   14   15   15   16   18   20   22   22   22   22   23   24   24   27   28   29   29 
LCS_GDT     I    28_A     I    28_A     15   16   25     12   14   14   14   15   15   16   18   20   22   22   22   22   23   24   25   29   31   35   36 
LCS_GDT     R    29_A     R    29_A     15   16   25     12   14   14   14   15   15   16   18   20   22   22   22   22   23   24   31   33   34   37   38 
LCS_GDT     D    30_A     D    30_A     15   16   29      3    4    8   14   15   15   16   18   20   22   22   22   29   32   33   38   41   45   46   46 
LCS_GDT     K    31_A     K    31_A      4   16   29      3    3    4    5    7   11   15   18   20   22   24   24   29   38   44   44   44   45   46   46 
LCS_GDT     P    32_A     P    32_A      4    6   29      3    3    4    5    7   12   16   18   20   22   33   38   39   42   44   44   44   45   46   46 
LCS_GDT     E    33_A     E    33_A      4    5   29      3    3    4    5    6   10   15   25   31   38   40   42   42   42   44   44   44   45   46   46 
LCS_GDT     E    34_A     E    34_A      4   25   29      3    3    4    4    5   17   25   37   39   40   41   42   42   42   44   44   44   45   46   46 
LCS_GDT     Q    35_A     Q    35_A     24   25   29     13   34   35   36   36   37   37   37   39   40   41   42   42   42   44   44   44   45   46   46 
LCS_GDT     L    36_A     L    36_A     24   25   29     30   34   35   36   36   37   37   37   39   40   41   42   42   42   44   44   44   45   46   46 
LCS_GDT     W    37_A     W    37_A     24   25   29     30   34   35   36   36   37   37   37   39   40   41   42   42   42   44   44   44   45   46   46 
LCS_GDT     N    38_A     N    38_A     24   25   29     30   34   35   36   36   37   37   37   39   40   41   42   42   42   44   44   44   45   46   46 
LCS_GDT     A    39_A     A    39_A     24   25   29     30   34   35   36   36   37   37   37   39   40   41   42   42   42   44   44   44   45   46   46 
LCS_GDT     E    40_A     E    40_A     24   25   29     30   34   35   36   36   37   37   37   39   40   41   42   42   42   44   44   44   45   46   46 
LCS_GDT     N    41_A     N    41_A     24   25   29     30   34   35   36   36   37   37   37   39   40   41   42   42   42   44   44   44   45   46   46 
LCS_GDT     V    42_A     V    42_A     24   25   29     30   34   35   36   36   37   37   37   39   40   41   42   42   42   44   44   44   45   46   46 
LCS_GDT     E    43_A     E    43_A     24   25   29     30   34   35   36   36   37   37   37   39   40   41   42   42   42   44   44   44   45   46   46 
LCS_GDT     G    44_A     G    44_A     24   25   29     30   34   35   36   36   37   37   37   39   40   41   42   42   42   44   44   44   45   46   46 
LCS_GDT     K    45_A     K    45_A     24   25   29     30   34   35   36   36   37   37   37   39   40   41   42   42   42   44   44   44   45   46   46 
LCS_GDT     R    46_A     R    46_A     24   25   29     30   34   35   36   36   37   37   37   39   40   41   42   42   42   44   44   44   45   46   46 
LCS_GDT     G    47_A     G    47_A     24   25   29     30   34   35   36   36   37   37   37   39   40   41   42   42   42   44   44   44   45   46   46 
LCS_GDT     L    48_A     L    48_A     24   25   29     30   34   35   36   36   37   37   37   39   40   41   42   42   42   44   44   44   45   46   46 
LCS_GDT     I    49_A     I    49_A     24   25   29     30   34   35   36   36   37   37   37   39   40   41   42   42   42   44   44   44   45   46   46 
LCS_GDT     H    50_A     H    50_A     24   25   29     30   34   35   36   36   37   37   37   39   40   41   42   42   42   44   44   44   45   46   46 
LCS_GDT     V    51_A     V    51_A     24   25   29     30   34   35   36   36   37   37   37   39   40   41   42   42   42   44   44   44   45   46   46 
LCS_GDT     V    52_A     V    52_A     24   25   29     30   34   35   36   36   37   37   37   39   40   41   42   42   42   44   44   44   45   46   46 
LCS_GDT     L    53_A     L    53_A     24   25   29     30   34   35   36   36   37   37   37   39   40   41   42   42   42   44   44   44   45   46   46 
LCS_GDT     V    54_A     V    54_A     24   25   29     30   34   35   36   36   37   37   37   39   40   41   42   42   42   44   44   44   45   46   46 
LCS_GDT     E    55_A     E    55_A     24   25   29     30   34   35   36   36   37   37   37   39   40   41   42   42   42   44   44   44   45   46   46 
LCS_GDT     K    56_A     K    56_A     24   25   29     30   34   35   36   36   37   37   37   39   40   41   42   42   42   44   44   44   45   46   46 
LCS_GDT     Y    57_A     Y    57_A     24   25   29     30   34   35   36   36   37   37   37   39   40   41   42   42   42   44   44   44   45   46   46 
LCS_GDT     G    58_A     G    58_A     24   25   29      3    3    7   19   35   37   37   37   39   40   41   42   42   42   44   44   44   45   46   46 
LCS_AVERAGE  LCS_A:  35.38  (  29.49   32.82   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     30     34     35     36     36     37     37     37     39     40     41     42     42     42     44     44     44     45     46     46 
GDT PERCENT_AT  51.72  58.62  60.34  62.07  62.07  63.79  63.79  63.79  67.24  68.97  70.69  72.41  72.41  72.41  75.86  75.86  75.86  77.59  79.31  79.31
GDT RMS_LOCAL    0.24   0.35   0.61   0.63   0.63   0.84   0.84   0.84   1.69   2.01   2.32   2.71   2.71   2.71   3.61   3.61   3.61   3.96   4.37   4.37
GDT RMS_ALL_AT  15.17  15.16  15.21  15.19  15.19  15.17  15.17  15.17  15.07  14.98  14.88  14.86  14.86  14.86  14.72  14.72  14.72  14.60  14.49  14.49

# Checking swapping
#   possible swapping detected:  F     8_A      F     8_A
#   possible swapping detected:  D    14_A      D    14_A
#   possible swapping detected:  E    15_A      E    15_A
#   possible swapping detected:  F    20_A      F    20_A
#   possible swapping detected:  D    30_A      D    30_A
#   possible swapping detected:  E    34_A      E    34_A
#   possible swapping detected:  E    55_A      E    55_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A     1_A      A     1_A     7.198     0    0.415   0.455     8.808   17.619   15.048
LGA    E     2_A      E     2_A     0.288     0    0.660   1.150     6.377   89.286   57.884
LGA    Y     3_A      Y     3_A     0.149     0    0.035   0.145     1.469  100.000   91.429
LGA    V     4_A      V     4_A     0.149     0    0.025   0.086     0.233  100.000  100.000
LGA    R     5_A      R     5_A     0.182     0    0.028   0.250     1.672  100.000   93.290
LGA    A     6_A      A     6_A     0.284     0    0.042   0.061     0.293  100.000  100.000
LGA    L     7_A      L     7_A     0.336     0    0.124   1.018     2.414   97.619   90.000
LGA    F     8_A      F     8_A     0.385     0    0.050   0.129     0.488  100.000  100.000
LGA    D     9_A      D     9_A     0.547     0    0.040   0.211     1.226   90.476   89.345
LGA    H    10_A      H    10_A     0.734     0    0.091   0.527     1.429   90.476   86.857
LGA    T    11_A      T    11_A     0.314     0    0.605   1.048     2.657   89.286   81.633
LGA    G    12_A      G    12_A     1.903     0    0.150   0.150     1.903   77.262   77.262
LGA    H    13_A      H    13_A     2.299     0    0.535   1.425     3.844   61.429   57.571
LGA    D    14_A      D    14_A     1.171     0    0.063   1.038     5.259   58.095   52.262
LGA    E    15_A      E    15_A     7.158     0    0.624   0.851    13.827   14.643    6.878
LGA    Q    16_A      Q    16_A     8.416     0    0.637   0.473    10.752    3.095    2.328
LGA    E    17_A      E    17_A    12.060     0    0.090   1.226    15.655    0.000    0.000
LGA    L    18_A      L    18_A    19.206     0    0.096   0.906    23.585    0.000    0.000
LGA    P    19_A      P    19_A    24.578     0    0.029   0.424    27.370    0.000    0.000
LGA    F    20_A      F    20_A    30.493     0    0.038   1.436    32.585    0.000    0.000
LGA    K    21_A      K    21_A    37.234     0    0.067   0.384    39.710    0.000    0.000
LGA    K    22_A      K    22_A    40.361     0    0.651   1.150    47.850    0.000    0.000
LGA    G    23_A      G    23_A    42.653     0    0.071   0.071    42.653    0.000    0.000
LGA    E    24_A      E    24_A    38.442     0    0.057   1.317    39.464    0.000    0.000
LGA    I    25_A      I    25_A    36.290     0    0.057   0.636    40.745    0.000    0.000
LGA    L    26_A      L    26_A    30.059     0    0.034   0.087    31.994    0.000    0.000
LGA    R    27_A      R    27_A    28.308     0    0.034   1.002    32.076    0.000    0.000
LGA    I    28_A      I    28_A    21.304     0    0.065   0.147    24.051    0.000    0.000
LGA    R    29_A      R    29_A    21.122     0    0.604   0.833    28.886    0.000    0.000
LGA    D    30_A      D    30_A    17.044     0    0.681   1.212    21.464    0.000    0.000
LGA    K    31_A      K    31_A    14.985     0    0.260   0.336    22.265    0.000    0.000
LGA    P    32_A      P    32_A    13.722     0    0.114   0.313    16.480    0.000    0.000
LGA    E    33_A      E    33_A    10.824     0    0.719   0.998    11.869    0.476    0.212
LGA    E    34_A      E    34_A     6.933     0    0.247   0.951     9.874   18.333    9.577
LGA    Q    35_A      Q    35_A     0.658     0    0.637   0.770     5.635   84.524   63.016
LGA    L    36_A      L    36_A     0.569     0    0.066   1.262     2.848   92.857   84.286
LGA    W    37_A      W    37_A     0.529     0    0.028   0.285     1.472   95.238   89.286
LGA    N    38_A      N    38_A     0.423     0    0.041   0.569     2.490   97.619   88.690
LGA    A    39_A      A    39_A     0.176     0    0.032   0.038     0.217  100.000  100.000
LGA    E    40_A      E    40_A     0.153     0    0.016   0.084     0.382  100.000  100.000
LGA    N    41_A      N    41_A     0.323     0    0.041   0.847     3.282   97.619   83.571
LGA    V    42_A      V    42_A     0.705     0    0.060   0.119     1.286   90.476   87.891
LGA    E    43_A      E    43_A     0.102     0    0.189   0.381     1.740   97.619   88.730
LGA    G    44_A      G    44_A     0.262     0    0.057   0.057     0.381  100.000  100.000
LGA    K    45_A      K    45_A     0.320     0    0.068   1.007     5.101   97.619   73.651
LGA    R    46_A      R    46_A     0.131     0    0.043   0.090     0.890  100.000   97.403
LGA    G    47_A      G    47_A     0.244     0    0.015   0.015     0.259  100.000  100.000
LGA    L    48_A      L    48_A     0.324     0    0.017   0.865     2.203   97.619   90.000
LGA    I    49_A      I    49_A     0.473     0    0.007   0.078     0.580  100.000   98.810
LGA    H    50_A      H    50_A     0.556     0    0.021   1.137     3.044   90.476   83.143
LGA    V    51_A      V    51_A     0.522     0    0.028   0.094     0.591   95.238   93.197
LGA    V    52_A      V    52_A     0.377     0    0.107   1.112     3.025   97.619   87.483
LGA    L    53_A      L    53_A     0.362     0    0.122   0.108     1.299   97.619   91.786
LGA    V    54_A      V    54_A     0.315     0    0.029   0.093     0.412  100.000  100.000
LGA    E    55_A      E    55_A     0.064     0    0.042   0.838     2.123  100.000   87.989
LGA    K    56_A      K    56_A     0.200     0    0.064   0.603     1.558  100.000   93.810
LGA    Y    57_A      Y    57_A     0.221     0    0.588   0.600     1.838   93.214   90.794
LGA    G    58_A      G    58_A     3.284     0    0.087   0.087     5.661   38.690   38.690

# 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):    13.011         12.941                 13.362           59.865   55.583

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   58   58    4.0     37    0.84    65.086    57.433     3.943

LGA_LOCAL      RMSD:   0.838  Number of atoms:   37  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  15.172  Number of assigned atoms:   58 
Std_ASGN_ATOMS RMSD:  13.011  Standard rmsd on all 58 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.319128 * X  +   0.212125 * Y  +  -0.923667 * Z  +  -0.033474
  Y_new =  -0.450044 * X  +  -0.891646 * Y  +  -0.049281 * Z  +  44.287777
  Z_new =  -0.834037 * X  +   0.399963 * Y  +   0.380014 * Z  +  11.272680 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.187606  0.986386  0.810969   [DEG: -125.3406   56.5157   46.4651 ]
ZXZ: -1.517493  1.180984 -1.123641   [DEG:  -86.9460   67.6654  -64.3799 ]
 
# END of job
