
#######################################################
#                                                     #
#                        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    14.96
  LCS_AVERAGE:     43.85

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    25      34_A - 58_A        1.42    15.20
  LCS_AVERAGE:     32.82

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    24      35_A - 58_A        0.53    15.20
  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   13   22   35   37   39   39   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     E     2_A     E     2_A     13   14   17     31   33   34   36   37   37   37   38   39   39   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     Y     3_A     Y     3_A     13   14   17     31   33   34   36   37   37   37   38   39   39   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     V     4_A     V     4_A     13   14   17     31   33   34   36   37   37   37   38   39   39   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     R     5_A     R     5_A     13   14   17     31   33   34   36   37   37   37   38   39   39   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     A     6_A     A     6_A     13   14   17     31   33   34   36   37   37   37   38   39   39   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     L     7_A     L     7_A     13   14   17     31   33   34   36   37   37   37   38   39   39   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     F     8_A     F     8_A     13   14   17     31   33   34   36   37   37   37   38   39   39   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     D     9_A     D     9_A     13   14   17     31   33   34   36   37   37   37   38   39   39   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     H    10_A     H    10_A     13   14   17     31   33   34   36   37   37   37   38   39   39   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     T    11_A     T    11_A     13   14   17     28   33   34   36   37   37   37   38   39   39   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     G    12_A     G    12_A     13   14   22      3   24   34   36   37   37   37   38   39   39   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     H    13_A     H    13_A     13   14   25      3    5   29   36   37   37   37   38   39   39   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     D    14_A     D    14_A     13   14   25      3   33   34   36   37   37   37   38   39   39   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     E    15_A     E    15_A      3   16   25      3    5    9   11   15   27   31   36   39   39   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     Q    16_A     Q    16_A     15   16   25      5   14   14   14   15   15   18   26   30   38   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     E    17_A     E    17_A     15   16   25     13   14   14   14   15   15   16   19   20   22   22   22   24   31   34   39   41   45   46   46 
LCS_GDT     L    18_A     L    18_A     15   16   25     13   14   14   14   15   15   16   19   20   22   22   22   22   23   24   25   25   31   35   37 
LCS_GDT     P    19_A     P    19_A     15   16   25     13   14   14   14   15   15   16   19   20   22   22   22   22   23   24   25   25   28   28   29 
LCS_GDT     F    20_A     F    20_A     15   16   25     13   14   14   14   15   15   16   19   20   22   22   22   22   23   24   25   25   28   28   29 
LCS_GDT     K    21_A     K    21_A     15   16   25     13   14   14   14   15   15   16   19   20   22   22   22   22   23   24   25   25   28   28   29 
LCS_GDT     K    22_A     K    22_A     15   16   25     13   14   14   14   15   15   16   19   20   22   22   22   22   23   24   25   25   28   28   29 
LCS_GDT     G    23_A     G    23_A     15   16   25     13   14   14   14   15   15   16   19   20   22   22   22   22   23   24   25   25   28   28   29 
LCS_GDT     E    24_A     E    24_A     15   16   25     13   14   14   14   15   15   16   19   20   22   22   22   22   23   24   25   25   28   28   29 
LCS_GDT     I    25_A     I    25_A     15   16   25     13   14   14   14   15   15   16   19   20   22   22   22   22   23   24   25   25   28   28   29 
LCS_GDT     L    26_A     L    26_A     15   16   25     13   14   14   14   15   15   16   19   20   22   22   22   22   23   24   25   25   28   28   29 
LCS_GDT     R    27_A     R    27_A     15   16   25     13   14   14   14   15   15   16   19   20   22   22   22   22   23   24   25   25   28   28   29 
LCS_GDT     I    28_A     I    28_A     15   16   25     13   14   14   14   15   15   16   19   20   22   22   22   22   23   24   25   27   31   34   36 
LCS_GDT     R    29_A     R    29_A     15   16   25     13   14   14   14   15   15   16   19   20   22   22   22   22   23   24   29   33   34   37   42 
LCS_GDT     D    30_A     D    30_A     15   16   29      3    5   12   14   15   15   16   19   20   22   22   22   26   30   34   40   42   44   46   46 
LCS_GDT     K    31_A     K    31_A      4   16   29      3    3    4    5    7   12   15   19   20   22   22   26   28   32   44   44   44   45   46   46 
LCS_GDT     P    32_A     P    32_A      4    6   29      3    3    4    6    7   13   16   19   20   22   22   22   25   39   44   44   44   45   46   46 
LCS_GDT     E    33_A     E    33_A      4    5   29      3    3    4    5    7    9   12   21   32   37   40   41   42   42   44   44   44   45   46   46 
LCS_GDT     E    34_A     E    34_A      4   25   29      3    4    5    5    5   13   24   38   39   39   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     Q    35_A     Q    35_A     24   25   29      4   33   34   36   37   37   37   38   39   39   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     L    36_A     L    36_A     24   25   29     31   33   34   36   37   37   37   38   39   39   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     W    37_A     W    37_A     24   25   29     31   33   34   36   37   37   37   38   39   39   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     N    38_A     N    38_A     24   25   29     31   33   34   36   37   37   37   38   39   39   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     A    39_A     A    39_A     24   25   29     31   33   34   36   37   37   37   38   39   39   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     E    40_A     E    40_A     24   25   29     31   33   34   36   37   37   37   38   39   39   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     N    41_A     N    41_A     24   25   29     31   33   34   36   37   37   37   38   39   39   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     V    42_A     V    42_A     24   25   29     31   33   34   36   37   37   37   38   39   39   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     E    43_A     E    43_A     24   25   29     31   33   34   36   37   37   37   38   39   39   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     G    44_A     G    44_A     24   25   29     31   33   34   36   37   37   37   38   39   39   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     K    45_A     K    45_A     24   25   29     31   33   34   36   37   37   37   38   39   39   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     R    46_A     R    46_A     24   25   29     31   33   34   36   37   37   37   38   39   39   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     G    47_A     G    47_A     24   25   29     31   33   34   36   37   37   37   38   39   39   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     L    48_A     L    48_A     24   25   29     31   33   34   36   37   37   37   38   39   39   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     I    49_A     I    49_A     24   25   29     31   33   34   36   37   37   37   38   39   39   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     H    50_A     H    50_A     24   25   29     31   33   34   36   37   37   37   38   39   39   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     V    51_A     V    51_A     24   25   29     31   33   34   36   37   37   37   38   39   39   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     V    52_A     V    52_A     24   25   29     31   33   34   36   37   37   37   38   39   39   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     L    53_A     L    53_A     24   25   29     31   33   34   36   37   37   37   38   39   39   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     V    54_A     V    54_A     24   25   29     31   33   34   36   37   37   37   38   39   39   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     E    55_A     E    55_A     24   25   29     31   33   34   36   37   37   37   38   39   39   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     K    56_A     K    56_A     24   25   29     31   33   34   36   37   37   37   38   39   39   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     Y    57_A     Y    57_A     24   25   29     31   33   34   36   37   37   37   38   39   39   41   41   42   42   44   44   44   45   46   46 
LCS_GDT     G    58_A     G    58_A     24   25   29      3    5   15   36   37   37   37   38   39   39   41   41   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     31     33     34     36     37     37     37     38     39     39     41     41     42     42     44     44     44     45     46     46 
GDT PERCENT_AT  53.45  56.90  58.62  62.07  63.79  63.79  63.79  65.52  67.24  67.24  70.69  70.69  72.41  72.41  75.86  75.86  75.86  77.59  79.31  79.31
GDT RMS_LOCAL    0.23   0.31   0.39   0.62   0.72   0.72   0.72   1.33   1.65   1.65   2.30   2.30   2.71   2.71   3.64   3.64   3.64   3.99   4.41   4.41
GDT RMS_ALL_AT  15.23  15.21  15.19  15.22  15.21  15.21  15.21  15.16  15.12  15.12  14.93  14.93  14.90  14.90  14.76  14.76  14.76  14.64  14.54  14.54

# 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    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     6.452     0    0.514   0.564     7.948   26.190   22.381
LGA    E     2_A      E     2_A     0.709     0    0.650   1.158     7.546   86.429   49.894
LGA    Y     3_A      Y     3_A     0.440     0    0.010   0.143     0.721   95.238   96.032
LGA    V     4_A      V     4_A     0.321     0    0.036   0.042     0.427  100.000  100.000
LGA    R     5_A      R     5_A     0.133     0    0.021   0.171     1.569  100.000   93.290
LGA    A     6_A      A     6_A     0.347     0    0.058   0.060     0.498  100.000  100.000
LGA    L     7_A      L     7_A     0.313     0    0.053   0.078     0.607   97.619   98.810
LGA    F     8_A      F     8_A     0.471     0    0.028   0.107     0.627   97.619   96.537
LGA    D     9_A      D     9_A     0.524     0    0.055   0.393     2.283   92.857   87.321
LGA    H    10_A      H    10_A     0.622     0    0.023   1.143     2.625   90.476   84.571
LGA    T    11_A      T    11_A     1.229     0    0.646   0.953     3.393   73.571   71.224
LGA    G    12_A      G    12_A     1.203     0    0.059   0.059     1.254   83.690   83.690
LGA    H    13_A      H    13_A     2.225     0    0.654   1.482     4.524   58.452   55.000
LGA    D    14_A      D    14_A     2.084     0    0.101   1.233     5.555   51.190   53.095
LGA    E    15_A      E    15_A     7.619     0    0.711   0.634    14.667   11.905    5.450
LGA    Q    16_A      Q    16_A     8.297     0    0.654   0.966    10.214    3.095    3.016
LGA    E    17_A      E    17_A    12.249     0    0.040   0.996    15.901    0.000    0.000
LGA    L    18_A      L    18_A    19.294     0    0.097   1.362    23.437    0.000    0.000
LGA    P    19_A      P    19_A    24.988     0    0.052   0.346    27.751    0.000    0.000
LGA    F    20_A      F    20_A    30.795     0    0.042   1.451    32.953    0.000    0.000
LGA    K    21_A      K    21_A    37.658     0    0.032   0.129    40.244    0.000    0.000
LGA    K    22_A      K    22_A    40.461     0    0.024   0.511    48.917    0.000    0.000
LGA    G    23_A      G    23_A    42.345     0    0.021   0.021    42.345    0.000    0.000
LGA    E    24_A      E    24_A    38.715     0    0.020   1.019    39.591    0.000    0.000
LGA    I    25_A      I    25_A    36.276     0    0.090   0.637    41.038    0.000    0.000
LGA    L    26_A      L    26_A    29.835     0    0.034   0.084    31.899    0.000    0.000
LGA    R    27_A      R    27_A    28.154     0    0.104   0.982    33.255    0.000    0.000
LGA    I    28_A      I    28_A    21.008     0    0.011   0.069    23.753    0.000    0.000
LGA    R    29_A      R    29_A    20.726     0    0.593   1.188    30.333    0.000    0.000
LGA    D    30_A      D    30_A    16.733     0    0.692   0.937    21.399    0.000    0.000
LGA    K    31_A      K    31_A    14.540     0    0.269   0.266    21.406    0.000    0.000
LGA    P    32_A      P    32_A    13.542     0    0.067   0.362    15.907    0.000    0.000
LGA    E    33_A      E    33_A    10.569     0    0.688   1.052    13.648    1.071    0.476
LGA    E    34_A      E    34_A     6.593     0    0.230   1.111     9.271   20.476   11.693
LGA    Q    35_A      Q    35_A     0.713     0    0.651   0.665     5.636   86.429   64.815
LGA    L    36_A      L    36_A     0.767     0    0.165   0.588     1.529   90.595   86.071
LGA    W    37_A      W    37_A     0.559     0    0.061   0.271     1.776   95.238   88.027
LGA    N    38_A      N    38_A     0.512     0    0.048   0.555     2.114   95.238   86.310
LGA    A    39_A      A    39_A     0.253     0    0.017   0.029     0.347  100.000  100.000
LGA    E    40_A      E    40_A     0.161     0    0.050   0.680     1.656  100.000   94.921
LGA    N    41_A      N    41_A     0.124     0    0.029   0.154     0.889  100.000   98.810
LGA    V    42_A      V    42_A     0.549     0    0.036   1.159     3.144   97.619   86.258
LGA    E    43_A      E    43_A     0.241     0    0.067   0.464     1.778  100.000   91.799
LGA    G    44_A      G    44_A     0.318     0    0.014   0.014     0.357  100.000  100.000
LGA    K    45_A      K    45_A     0.150     0    0.031   0.762     4.720  100.000   77.566
LGA    R    46_A      R    46_A     0.330     0    0.017   0.150     0.984  100.000   94.805
LGA    G    47_A      G    47_A     0.353     0    0.013   0.013     0.397  100.000  100.000
LGA    L    48_A      L    48_A     0.445     0    0.037   0.066     0.687  100.000   98.810
LGA    I    49_A      I    49_A     0.375     0    0.030   0.059     0.438  100.000  100.000
LGA    H    50_A      H    50_A     0.506     0    0.017   0.108     0.880   90.476   90.476
LGA    V    51_A      V    51_A     0.550     0    0.022   0.036     0.591   92.857   91.837
LGA    V    52_A      V    52_A     0.856     0    0.015   0.047     1.181   90.476   86.599
LGA    L    53_A      L    53_A     0.651     0    0.029   0.082     1.190   95.238   91.726
LGA    V    54_A      V    54_A     0.194     0    0.069   0.081     0.448  100.000  100.000
LGA    E    55_A      E    55_A     0.288     0    0.024   0.293     0.733  100.000   97.884
LGA    K    56_A      K    56_A     0.428     0    0.009   0.939     4.610  100.000   83.439
LGA    Y    57_A      Y    57_A     0.439     0    0.574   0.576     2.479   88.810   87.063
LGA    G    58_A      G    58_A     2.161     0    0.636   0.636     3.190   59.167   59.167

# 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):    13.047         12.983                 13.440           59.862   56.360

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   58   58    4.0     38    1.33    65.086    57.237     2.655

LGA_LOCAL      RMSD:   1.331  Number of atoms:   38  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  15.162  Number of assigned atoms:   58 
Std_ASGN_ATOMS RMSD:  13.047  Standard rmsd on all 58 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.079971 * X  +   0.830005 * Y  +  -0.551992 * Z  + -23.395897
  Y_new =  -0.986986 * X  +   0.143437 * Y  +   0.072689 * Z  +  15.673302
  Z_new =   0.139508 * X  +   0.538996 * Y  +   0.830675 * Z  + -15.518232 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.489947 -0.139965  0.575577   [DEG:  -85.3677   -8.0194   32.9781 ]
ZXZ: -1.701727  0.590478  0.253272   [DEG:  -97.5018   33.8319   14.5114 ]
 
# END of job
