
#######################################################
#                                                     #
#                        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        4.54    14.95
  LCS_AVERAGE:     43.85

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    25      34_A - 58_A        1.43    15.20
  LCS_AVERAGE:     33.38

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    4   12   21   28   38   39   40   41   41   42   42   44   44   44   44   46   46 
LCS_GDT     E     2_A     E     2_A     13   14   17     31   33   34   36   37   37   37   38   39   40   41   41   42   42   44   44   44   44   46   46 
LCS_GDT     Y     3_A     Y     3_A     13   14   17     31   33   34   36   37   37   37   38   39   40   41   41   42   42   44   44   44   44   46   46 
LCS_GDT     V     4_A     V     4_A     13   14   17     31   33   34   36   37   37   37   38   39   40   41   41   42   42   44   44   44   44   46   46 
LCS_GDT     R     5_A     R     5_A     13   14   17     31   33   34   36   37   37   37   38   39   40   41   41   42   42   44   44   44   44   46   46 
LCS_GDT     A     6_A     A     6_A     13   14   17     31   33   34   36   37   37   37   38   39   40   41   41   42   42   44   44   44   44   46   46 
LCS_GDT     L     7_A     L     7_A     13   14   17     31   33   34   36   37   37   37   38   39   40   41   41   42   42   44   44   44   44   46   46 
LCS_GDT     F     8_A     F     8_A     13   14   17     31   33   34   36   37   37   37   38   39   40   41   41   42   42   44   44   44   44   46   46 
LCS_GDT     D     9_A     D     9_A     13   14   17     31   33   34   36   37   37   37   38   39   40   41   41   42   42   44   44   44   44   46   46 
LCS_GDT     H    10_A     H    10_A     13   14   17     31   33   34   36   37   37   37   38   39   40   41   41   42   42   44   44   44   44   46   46 
LCS_GDT     T    11_A     T    11_A     13   14   17     30   33   34   36   37   37   37   38   39   40   41   41   42   42   44   44   44   44   46   46 
LCS_GDT     G    12_A     G    12_A     13   14   22      3   31   34   36   37   37   37   38   39   40   41   41   42   42   44   44   44   44   46   46 
LCS_GDT     H    13_A     H    13_A     13   14   25      3    6   32   36   37   37   37   38   39   40   41   41   42   42   44   44   44   44   46   46 
LCS_GDT     D    14_A     D    14_A     13   17   25      3   28   34   36   37   37   37   38   39   40   41   41   42   42   44   44   44   44   46   46 
LCS_GDT     E    15_A     E    15_A      3   17   25      3    3   10   14   16   21   31   37   39   40   41   41   42   42   44   44   44   44   46   46 
LCS_GDT     Q    16_A     Q    16_A     15   17   25      5   14   14   14   15   15   16   28   30   38   41   41   42   42   44   44   44   44   46   46 
LCS_GDT     E    17_A     E    17_A     15   17   25     12   14   14   14   15   15   16   18   20   22   22   22   23   30   34   40   41   44   46   46 
LCS_GDT     L    18_A     L    18_A     15   17   25     12   14   14   14   15   15   16   18   20   22   22   22   22   23   24   25   27   31   35   37 
LCS_GDT     P    19_A     P    19_A     15   17   25     12   14   14   14   15   15   16   18   20   22   22   22   22   23   24   25   27   28   28   29 
LCS_GDT     F    20_A     F    20_A     15   17   25     12   14   14   14   15   15   16   18   20   22   22   22   22   23   24   25   27   28   28   29 
LCS_GDT     K    21_A     K    21_A     15   17   25     12   14   14   14   15   15   16   18   20   22   22   22   22   23   24   25   25   28   28   29 
LCS_GDT     K    22_A     K    22_A     15   17   25     12   14   14   14   15   15   16   18   20   22   22   22   22   23   24   25   25   28   28   29 
LCS_GDT     G    23_A     G    23_A     15   17   25     12   14   14   14   15   15   16   18   20   22   22   22   22   23   24   25   27   28   28   29 
LCS_GDT     E    24_A     E    24_A     15   17   25     12   14   14   14   15   15   16   18   20   22   22   22   22   23   24   25   27   28   28   29 
LCS_GDT     I    25_A     I    25_A     15   17   25     12   14   14   14   15   15   16   18   20   22   22   22   22   23   24   25   27   28   28   29 
LCS_GDT     L    26_A     L    26_A     15   17   25     12   14   14   14   15   15   16   18   20   22   22   22   22   23   24   25   27   28   28   29 
LCS_GDT     R    27_A     R    27_A     15   17   25     12   14   14   14   15   15   16   18   20   22   22   22   22   23   24   25   27   28   28   29 
LCS_GDT     I    28_A     I    28_A     15   17   25     12   14   14   14   15   15   16   18   20   22   22   22   22   23   24   25   27   31   35   36 
LCS_GDT     R    29_A     R    29_A     15   17   25     12   14   14   14   15   15   16   18   20   22   22   22   22   23   24   27   31   34   35   41 
LCS_GDT     D    30_A     D    30_A     15   17   29      3    4   12   14   15   15   16   18   20   22   22   22   26   30   35   41   42   43   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   28   32   44   44   44   44   46   46 
LCS_GDT     P    32_A     P    32_A      4    6   29      3    3    4    6    8   14   16   18   20   22   22   23   24   39   44   44   44   44   46   46 
LCS_GDT     E    33_A     E    33_A      4    5   29      3    3    4    5    7    9   12   21   30   37   40   41   42   42   44   44   44   44   46   46 
LCS_GDT     E    34_A     E    34_A      4   25   29      3    4    5    5    6   10   21   38   39   40   41   41   42   42   44   44   44   44   46   46 
LCS_GDT     Q    35_A     Q    35_A     24   25   29      4   33   34   36   37   37   37   38   39   40   41   41   42   42   44   44   44   44   46   46 
LCS_GDT     L    36_A     L    36_A     24   25   29     31   33   34   36   37   37   37   38   39   40   41   41   42   42   44   44   44   44   46   46 
LCS_GDT     W    37_A     W    37_A     24   25   29     31   33   34   36   37   37   37   38   39   40   41   41   42   42   44   44   44   44   46   46 
LCS_GDT     N    38_A     N    38_A     24   25   29     31   33   34   36   37   37   37   38   39   40   41   41   42   42   44   44   44   44   46   46 
LCS_GDT     A    39_A     A    39_A     24   25   29     31   33   34   36   37   37   37   38   39   40   41   41   42   42   44   44   44   44   46   46 
LCS_GDT     E    40_A     E    40_A     24   25   29     31   33   34   36   37   37   37   38   39   40   41   41   42   42   44   44   44   44   46   46 
LCS_GDT     N    41_A     N    41_A     24   25   29     31   33   34   36   37   37   37   38   39   40   41   41   42   42   44   44   44   44   46   46 
LCS_GDT     V    42_A     V    42_A     24   25   29     31   33   34   36   37   37   37   38   39   40   41   41   42   42   44   44   44   44   46   46 
LCS_GDT     E    43_A     E    43_A     24   25   29     31   33   34   36   37   37   37   38   39   40   41   41   42   42   44   44   44   44   46   46 
LCS_GDT     G    44_A     G    44_A     24   25   29     31   33   34   36   37   37   37   38   39   40   41   41   42   42   44   44   44   44   46   46 
LCS_GDT     K    45_A     K    45_A     24   25   29     31   33   34   36   37   37   37   38   39   40   41   41   42   42   44   44   44   44   46   46 
LCS_GDT     R    46_A     R    46_A     24   25   29     31   33   34   36   37   37   37   38   39   40   41   41   42   42   44   44   44   44   46   46 
LCS_GDT     G    47_A     G    47_A     24   25   29     31   33   34   36   37   37   37   38   39   40   41   41   42   42   44   44   44   44   46   46 
LCS_GDT     L    48_A     L    48_A     24   25   29     31   33   34   36   37   37   37   38   39   40   41   41   42   42   44   44   44   44   46   46 
LCS_GDT     I    49_A     I    49_A     24   25   29     31   33   34   36   37   37   37   38   39   40   41   41   42   42   44   44   44   44   46   46 
LCS_GDT     H    50_A     H    50_A     24   25   29     31   33   34   36   37   37   37   38   39   40   41   41   42   42   44   44   44   44   46   46 
LCS_GDT     V    51_A     V    51_A     24   25   29     31   33   34   36   37   37   37   38   39   40   41   41   42   42   44   44   44   44   46   46 
LCS_GDT     V    52_A     V    52_A     24   25   29     31   33   34   36   37   37   37   38   39   40   41   41   42   42   44   44   44   44   46   46 
LCS_GDT     L    53_A     L    53_A     24   25   29     31   33   34   36   37   37   37   38   39   40   41   41   42   42   44   44   44   44   46   46 
LCS_GDT     V    54_A     V    54_A     24   25   29     31   33   34   36   37   37   37   38   39   40   41   41   42   42   44   44   44   44   46   46 
LCS_GDT     E    55_A     E    55_A     24   25   29     31   33   34   36   37   37   37   38   39   40   41   41   42   42   44   44   44   44   46   46 
LCS_GDT     K    56_A     K    56_A     24   25   29     31   33   34   36   37   37   37   38   39   40   41   41   42   42   44   44   44   44   46   46 
LCS_GDT     Y    57_A     Y    57_A     24   25   29     31   33   34   36   37   37   37   38   39   40   41   41   42   42   44   44   44   44   46   46 
LCS_GDT     G    58_A     G    58_A     24   25   29      3    5    9   36   37   37   37   38   39   40   41   41   42   42   44   44   44   44   46   46 
LCS_AVERAGE  LCS_A:  35.57  (  29.49   33.38   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     33     34     36     37     37     37     38     39     40     41     41     42     42     44     44     44     44     46     46 
GDT PERCENT_AT  53.45  56.90  58.62  62.07  63.79  63.79  63.79  65.52  67.24  68.97  70.69  70.69  72.41  72.41  75.86  75.86  75.86  75.86  79.31  79.31
GDT RMS_LOCAL    0.23   0.30   0.39   0.59   0.70   0.70   0.70   1.26   1.64   1.98   2.28   2.28   2.70   2.70   3.64   3.64   3.64   3.64   4.41   4.41
GDT RMS_ALL_AT  15.22  15.21  15.22  15.21  15.20  15.20  15.20  15.14  15.10  15.01  14.92  14.92  14.89  14.89  14.75  14.75  14.75  14.75  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     6.187     0    0.524   0.574     7.655   24.762   21.810
LGA    E     2_A      E     2_A     0.733     0    0.651   1.125     7.516   84.048   48.836
LGA    Y     3_A      Y     3_A     0.480     0    0.007   0.142     0.676   97.619   96.032
LGA    V     4_A      V     4_A     0.376     0    0.033   0.042     0.457  100.000  100.000
LGA    R     5_A      R     5_A     0.265     0    0.024   0.157     1.698  100.000   93.290
LGA    A     6_A      A     6_A     0.229     0    0.051   0.053     0.310  100.000  100.000
LGA    L     7_A      L     7_A     0.253     0    0.048   0.074     0.431  100.000  100.000
LGA    F     8_A      F     8_A     0.369     0    0.025   0.110     0.447  100.000  100.000
LGA    D     9_A      D     9_A     0.459     0    0.045   0.125     1.014   95.238   92.917
LGA    H    10_A      H    10_A     0.556     0    0.015   1.141     2.503   92.857   85.571
LGA    T    11_A      T    11_A     1.107     0    0.656   0.965     3.345   75.833   73.537
LGA    G    12_A      G    12_A     1.269     0    0.055   0.055     1.269   83.690   83.690
LGA    H    13_A      H    13_A     1.916     0    0.657   1.232     4.997   61.905   56.857
LGA    D    14_A      D    14_A     1.766     0    0.108   1.223     5.526   55.476   54.821
LGA    E    15_A      E    15_A     7.422     0    0.711   0.672    14.436   15.357    7.143
LGA    Q    16_A      Q    16_A     8.200     0    0.653   1.254    10.148    3.333    2.857
LGA    E    17_A      E    17_A    12.046     0    0.038   0.996    15.698    0.000    0.000
LGA    L    18_A      L    18_A    19.119     0    0.103   1.361    23.279    0.000    0.000
LGA    P    19_A      P    19_A    24.732     0    0.047   0.340    27.516    0.000    0.000
LGA    F    20_A      F    20_A    30.584     0    0.035   1.451    32.745    0.000    0.000
LGA    K    21_A      K    21_A    37.451     0    0.025   0.141    39.905    0.000    0.000
LGA    K    22_A      K    22_A    40.307     0    0.026   0.517    48.756    0.000    0.000
LGA    G    23_A      G    23_A    42.250     0    0.020   0.020    42.250    0.000    0.000
LGA    E    24_A      E    24_A    38.588     0    0.023   1.007    39.463    0.000    0.000
LGA    I    25_A      I    25_A    36.277     0    0.083   0.640    41.088    0.000    0.000
LGA    L    26_A      L    26_A    29.833     0    0.036   0.072    31.906    0.000    0.000
LGA    R    27_A      R    27_A    28.229     0    0.089   1.340    32.966    0.000    0.000
LGA    I    28_A      I    28_A    21.116     0    0.011   0.078    23.847    0.000    0.000
LGA    R    29_A      R    29_A    20.981     0    0.598   1.209    30.820    0.000    0.000
LGA    D    30_A      D    30_A    16.920     0    0.689   0.832    21.306    0.000    0.000
LGA    K    31_A      K    31_A    14.743     0    0.268   0.268    21.596    0.000    0.000
LGA    P    32_A      P    32_A    13.721     0    0.069   0.370    15.965    0.000    0.000
LGA    E    33_A      E    33_A    10.910     0    0.689   1.058    13.968    0.476    0.212
LGA    E    34_A      E    34_A     7.066     0    0.224   1.107    10.030   17.500    9.259
LGA    Q    35_A      Q    35_A     0.633     0    0.649   0.676     5.337   86.905   67.196
LGA    L    36_A      L    36_A     0.510     0    0.158   0.601     1.433   92.857   88.274
LGA    W    37_A      W    37_A     0.197     0    0.070   0.277     1.449  100.000   92.585
LGA    N    38_A      N    38_A     0.170     0    0.056   0.549     1.981  100.000   90.893
LGA    A    39_A      A    39_A     0.348     0    0.018   0.031     0.431  100.000  100.000
LGA    E    40_A      E    40_A     0.396     0    0.048   0.474     1.721  100.000   94.868
LGA    N    41_A      N    41_A     0.309     0    0.023   0.125     0.702  100.000   98.810
LGA    V    42_A      V    42_A     0.493     0    0.044   1.156     3.315  100.000   87.619
LGA    E    43_A      E    43_A     0.210     0    0.052   0.136     1.197  100.000   94.762
LGA    G    44_A      G    44_A     0.480     0    0.015   0.015     0.544   97.619   97.619
LGA    K    45_A      K    45_A     0.364     0    0.025   0.749     4.467  100.000   79.101
LGA    R    46_A      R    46_A     0.406     0    0.015   0.136     1.487  100.000   89.827
LGA    G    47_A      G    47_A     0.386     0    0.011   0.011     0.386  100.000  100.000
LGA    L    48_A      L    48_A     0.408     0    0.037   0.044     0.591  100.000   97.619
LGA    I    49_A      I    49_A     0.268     0    0.033   0.054     0.328  100.000  100.000
LGA    H    50_A      H    50_A     0.389     0    0.021   0.116     0.655  100.000   97.143
LGA    V    51_A      V    51_A     0.420     0    0.035   0.046     0.438  100.000  100.000
LGA    V    52_A      V    52_A     0.654     0    0.014   0.055     0.950   92.857   91.837
LGA    L    53_A      L    53_A     0.407     0    0.025   0.079     0.922  100.000   96.429
LGA    V    54_A      V    54_A     0.203     0    0.075   0.089     0.468  100.000  100.000
LGA    E    55_A      E    55_A     0.375     0    0.022   0.117     0.461  100.000  100.000
LGA    K    56_A      K    56_A     0.384     0    0.028   0.581     1.340  100.000   93.757
LGA    Y    57_A      Y    57_A     0.419     0    0.576   0.571     2.100   91.190   91.587
LGA    G    58_A      G    58_A     2.556     0    0.235   0.235     3.279   57.262   57.262

# 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):    13.037         12.970                 13.435           60.807   57.483

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   58   58    4.0     38    1.26    65.086    57.438     2.803

LGA_LOCAL      RMSD:   1.256  Number of atoms:   38  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  15.138  Number of assigned atoms:   58 
Std_ASGN_ATOMS RMSD:  13.037  Standard rmsd on all 58 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.993494 * X  +  -0.097635 * Y  +   0.058618 * Z  + -21.352930
  Y_new =  -0.067160 * X  +  -0.086632 * Y  +   0.993974 * Z  +  16.119291
  Z_new =  -0.091969 * X  +  -0.991445 * Y  +  -0.092625 * Z  + -15.362170 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.067497  0.092099 -1.663951   [DEG:   -3.8673    5.2769  -95.3373 ]
ZXZ:  3.082688  1.663555 -3.049095   [DEG:  176.6250   95.3147 -174.7003 ]
 
# END of job
