
#######################################################
#                                                     #
#                        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   61 (  460),  selected   60 , name one
# Molecule2: number of CA atoms   60 (  451),  selected   60 , 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:    60       1_A - 60_A        2.21     2.21
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    39       1_A - 39_A        2.00     2.69
  LONGEST_CONTINUOUS_SEGMENT:    39       2_A - 40_A        1.98     2.58
  LCS_AVERAGE:     63.33

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    29      26_A - 54_A        0.98     3.75
  LCS_AVERAGE:     40.36

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   60
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     D     1_A     D     1_A     22   39   60      4   10   22   34   43   49   54   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D     2_A     D     2_A     22   39   60     12   23   33   41   48   52   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K     3_A     K     3_A     22   39   60     18   27   33   41   48   52   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A     4_A     A     4_A     22   39   60     14   27   33   41   48   52   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A     5_A     A     5_A     22   39   60     14   27   33   41   48   52   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     C     6_A     C     6_A     22   39   60     19   27   33   41   48   52   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A     7_A     A     7_A     22   39   60     19   27   33   41   48   52   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D     8_A     D     8_A     22   39   60     19   27   33   41   48   52   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     G     9_A     G     9_A     22   39   60     19   27   33   41   48   52   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     I    10_A     I    10_A     22   39   60     19   27   33   41   48   52   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    11_A     A    11_A     22   39   60     19   27   33   41   48   52   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    12_A     A    12_A     22   39   60     19   27   33   41   48   52   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     V    13_A     V    13_A     22   39   60     19   27   33   41   48   52   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    14_A     K    14_A     22   39   60     19   27   33   41   48   52   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    15_A     A    15_A     22   39   60     19   27   33   41   48   52   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     R    16_A     R    16_A     22   39   60     19   27   33   41   48   52   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     V    17_A     V    17_A     22   39   60     14   27   33   41   48   52   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    18_A     E    18_A     22   39   60     14   27   33   41   48   52   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    19_A     K    19_A     22   39   60     19   27   33   41   48   52   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    20_A     L    20_A     22   39   60      3   19   30   41   48   52   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    21_A     A    21_A     22   39   60      3    3   12   40   48   52   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     P    22_A     P    22_A     22   39   60      4   16   25   34   42   49   53   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    23_A     E    23_A      4   39   60      4    4   24   40   48   52   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    24_A     A    24_A      4   39   60      4    4    4    7    8   11   34   45   56   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     V    25_A     V    25_A      4   39   60      8   22   33   41   48   52   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     P    26_A     P    26_A     29   39   60      6   21   27   32   38   46   53   56   57   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     Q    27_A     Q    27_A     29   39   60     12   21   27   35   45   51   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    28_A     K    28_A     29   39   60     12   21   27   37   45   52   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    29_A     L    29_A     29   39   60     12   21   27   39   47   52   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    30_A     K    30_A     29   39   60     12   21   27   39   48   52   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     R    31_A     R    31_A     29   39   60     12   21   27   41   48   52   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    32_A     A    32_A     29   39   60     12   21   28   41   48   52   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    33_A     L    33_A     29   39   60     12   21   27   41   48   52   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    34_A     K    34_A     29   39   60     12   21   28   41   48   52   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     I    35_A     I    35_A     29   39   60     12   22   33   41   48   52   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    36_A     A    36_A     29   39   60     12   21   33   41   48   52   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    37_A     E    37_A     29   39   60     12   21   30   41   48   52   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     R    38_A     R    38_A     29   39   60     12   21   33   41   48   52   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    39_A     E    39_A     29   39   60     12   27   33   41   48   52   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     Q    40_A     Q    40_A     29   39   60     12   18   33   41   48   52   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     G    41_A     G    41_A     29   36   60     12   21   27   39   48   52   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    42_A     E    42_A     29   36   60      6   21   27   40   48   52   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     G    43_A     G    43_A     29   36   60      6    9   27   36   44   52   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    44_A     E    44_A     29   36   60      6   19   27   36   47   52   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     F    45_A     F    45_A     29   36   60      8   21   27   39   48   52   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D    46_A     D    46_A     29   36   60      6   21   27   40   48   52   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    47_A     E    47_A     29   36   60     10   21   30   40   48   52   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     C    48_A     C    48_A     29   36   60     10   21   32   40   48   52   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    49_A     L    49_A     29   36   60     10   26   33   41   48   52   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    50_A     E    50_A     29   36   60     10   27   33   41   48   52   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    51_A     A    51_A     29   36   60     10   27   33   41   48   52   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    52_A     L    52_A     29   36   60     10   27   33   41   48   52   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D    53_A     D    53_A     29   36   60     19   27   33   41   48   52   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D    54_A     D    54_A     29   36   60     19   27   33   41   48   52   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    55_A     A    55_A     20   36   60     19   27   33   41   48   52   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    56_A     K    56_A     20   36   60     19   27   33   41   48   52   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     R    57_A     R    57_A     20   36   60     19   27   33   41   48   52   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    58_A     A    58_A     20   36   60     19   27   33   41   48   52   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    59_A     L    59_A     20   36   60     19   27   33   41   48   52   55   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     P    60_A     P    60_A     16   36   60      3    3    3   25   42   49   54   57   58   60   60   60   60   60   60   60   60   60   60   60 
LCS_AVERAGE  LCS_A:  67.90  (  40.36   63.33  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     19     27     33     41     48     52     55     57     58     60     60     60     60     60     60     60     60     60     60     60 
GDT PERCENT_AT  31.67  45.00  55.00  68.33  80.00  86.67  91.67  95.00  96.67 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.28   0.53   0.79   1.21   1.43   1.63   1.81   1.93   2.00   2.21   2.21   2.21   2.21   2.21   2.21   2.21   2.21   2.21   2.21   2.21
GDT RMS_ALL_AT   2.40   2.45   2.38   2.30   2.25   2.22   2.23   2.23   2.22   2.21   2.21   2.21   2.21   2.21   2.21   2.21   2.21   2.21   2.21   2.21

# Checking swapping
#   possible swapping detected:  D     1_A      D     1_A
#   possible swapping detected:  D     2_A      D     2_A
#   possible swapping detected:  D     8_A      D     8_A
#   possible swapping detected:  E    37_A      E    37_A
#   possible swapping detected:  E    39_A      E    39_A
#   possible swapping detected:  E    44_A      E    44_A
#   possible swapping detected:  F    45_A      F    45_A
#   possible swapping detected:  D    46_A      D    46_A
#   possible swapping detected:  E    47_A      E    47_A
#   possible swapping detected:  E    50_A      E    50_A
#   possible swapping detected:  D    54_A      D    54_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    D     1_A      D     1_A     3.539     0    0.564   1.363     4.891   49.167   53.214
LGA    D     2_A      D     2_A     1.611     0    0.070   0.214     3.070   77.381   67.440
LGA    K     3_A      K     3_A     1.154     0    0.063   0.564     3.601   81.429   69.841
LGA    A     4_A      A     4_A     1.399     0    0.039   0.042     1.714   81.429   79.714
LGA    A     5_A      A     5_A     1.206     0    0.063   0.058     1.409   81.429   81.429
LGA    C     6_A      C     6_A     0.851     0    0.054   0.126     1.545   90.476   87.540
LGA    A     7_A      A     7_A     0.761     0    0.042   0.044     0.764   90.476   90.476
LGA    D     8_A      D     8_A     0.832     0    0.050   0.164     1.457   90.476   87.083
LGA    G     9_A      G     9_A     0.702     0    0.026   0.026     0.784   90.476   90.476
LGA    I    10_A      I    10_A     0.636     0    0.042   0.047     0.708   90.476   90.476
LGA    A    11_A      A    11_A     0.722     0    0.036   0.040     0.840   90.476   90.476
LGA    A    12_A      A    12_A     0.786     0    0.019   0.023     0.801   90.476   90.476
LGA    V    13_A      V    13_A     0.432     0    0.014   0.032     0.617   92.857   95.918
LGA    K    14_A      K    14_A     0.688     0    0.033   0.695     4.400   90.476   71.217
LGA    A    15_A      A    15_A     0.884     0    0.055   0.067     1.089   88.214   88.667
LGA    R    16_A      R    16_A     0.660     0    0.030   0.847     2.665   90.476   83.420
LGA    V    17_A      V    17_A     1.262     0    0.038   1.009     2.248   81.548   77.891
LGA    E    18_A      E    18_A     1.711     0    0.109   0.911     3.849   72.976   62.011
LGA    K    19_A      K    19_A     0.964     0    0.122   1.053     3.402   85.952   81.111
LGA    L    20_A      L    20_A     2.186     0    0.605   0.559     4.504   56.548   58.750
LGA    A    21_A      A    21_A     2.140     0    0.397   0.495     2.436   66.786   68.000
LGA    P    22_A      P    22_A     4.030     0    0.627   0.858     8.405   47.143   31.429
LGA    E    23_A      E    23_A     2.269     0    0.133   1.082     6.258   51.071   40.106
LGA    A    24_A      A    24_A     5.859     0    0.235   0.248     7.678   26.786   22.857
LGA    V    25_A      V    25_A     1.796     0    0.615   0.688     5.368   63.214   54.150
LGA    P    26_A      P    26_A     5.519     0    0.569   0.604     7.853   33.571   26.122
LGA    Q    27_A      Q    27_A     4.615     0    0.061   1.536     6.685   34.286   31.164
LGA    K    28_A      K    28_A     3.989     0    0.037   0.856     4.594   43.452   40.000
LGA    L    29_A      L    29_A     3.107     0    0.039   1.075     3.478   51.786   58.571
LGA    K    30_A      K    30_A     3.411     0    0.049   0.064     5.262   50.000   41.058
LGA    R    31_A      R    31_A     2.971     0    0.028   1.568     6.868   57.262   44.026
LGA    A    32_A      A    32_A     2.444     0    0.016   0.017     2.660   62.857   61.714
LGA    L    33_A      L    33_A     2.396     0    0.046   1.408     2.709   64.762   65.119
LGA    K    34_A      K    34_A     2.373     0    0.022   1.048     3.657   68.810   60.053
LGA    I    35_A      I    35_A     1.538     0    0.020   0.088     1.837   77.143   76.071
LGA    A    36_A      A    36_A     1.511     0    0.034   0.034     1.767   75.000   74.571
LGA    E    37_A      E    37_A     1.772     0    0.054   0.205     3.120   72.857   65.873
LGA    R    38_A      R    38_A     1.315     0    0.039   0.965     3.409   79.286   76.753
LGA    E    39_A      E    39_A     0.563     0    0.038   1.087     3.923   90.476   79.524
LGA    Q    40_A      Q    40_A     1.456     0    0.065   1.110     4.347   77.143   66.032
LGA    G    41_A      G    41_A     2.480     0    0.116   0.116     3.007   61.190   61.190
LGA    E    42_A      E    42_A     2.307     0    0.578   1.153     3.672   57.500   63.333
LGA    G    43_A      G    43_A     3.670     0    0.101   0.101     3.976   43.333   43.333
LGA    E    44_A      E    44_A     3.124     0    0.126   0.172     6.398   57.738   42.910
LGA    F    45_A      F    45_A     2.354     0    0.061   0.554     2.661   64.762   61.299
LGA    D    46_A      D    46_A     2.318     0    0.027   1.082     6.180   66.786   49.286
LGA    E    47_A      E    47_A     1.898     0    0.041   1.298     5.370   70.833   55.556
LGA    C    48_A      C    48_A     1.470     0    0.044   0.119     1.711   79.286   77.143
LGA    L    49_A      L    49_A     0.901     0    0.015   0.089     1.138   88.214   89.345
LGA    E    50_A      E    50_A     1.149     0    0.032   0.806     4.806   81.429   65.450
LGA    A    51_A      A    51_A     1.108     0    0.047   0.052     1.162   83.690   83.238
LGA    L    52_A      L    52_A     0.726     0    0.032   0.109     1.503   90.476   86.012
LGA    D    53_A      D    53_A     0.666     0    0.036   0.790     2.517   90.476   86.310
LGA    D    54_A      D    54_A     0.970     0    0.026   0.168     1.910   90.476   83.810
LGA    A    55_A      A    55_A     0.865     0    0.050   0.053     0.920   90.476   90.476
LGA    K    56_A      K    56_A     0.376     0    0.054   0.663     2.045   95.238   88.995
LGA    R    57_A      R    57_A     0.946     0    0.098   1.066     3.200   88.214   80.346
LGA    A    58_A      A    58_A     0.780     0    0.166   0.190     1.441   88.214   88.667
LGA    L    59_A      L    59_A     0.301     0    0.581   0.593     1.896   90.833   90.714
LGA    P    60_A      P    60_A     3.497     0    0.668   0.954     7.509   50.119   35.170

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       60     240    240  100.00     451    451  100.00                60
SUMMARY(RMSD_GDC):     2.210          2.168                  2.699           73.103   68.390

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   61   60    4.0     57    1.93    77.083    77.880     2.811

LGA_LOCAL      RMSD:   1.928  Number of atoms:   57  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.228  Number of assigned atoms:   60 
Std_ASGN_ATOMS RMSD:   2.210  Standard rmsd on all 60 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.393249 * X  +  -0.720119 * Y  +  -0.571651 * Z  +  60.856514
  Y_new =   0.770599 * X  +  -0.597291 * Y  +   0.222309 * Z  +  10.241831
  Z_new =  -0.501531 * X  +  -0.353090 * Y  +   0.789806 * Z  +  -2.748953 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.042663  0.525367 -0.420406   [DEG:  117.0359   30.1013  -24.0875 ]
ZXZ: -1.941688  0.660303 -2.184219   [DEG: -111.2505   37.8326 -125.1465 ]
 
# END of job
