
#######################################################
#                                                     #
#                        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   70 (  573),  selected   61 , name one
# Molecule2: number of CA atoms   61 (  491),  selected   61 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:B  -ch2:B  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    61       1_B - 61_B        1.15     1.15
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    61       1_B - 61_B        1.15     1.15
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    45       4_B - 48_B        0.99     1.23
  LONGEST_CONTINUOUS_SEGMENT:    45       5_B - 49_B        0.98     1.21
  LCS_AVERAGE:     70.25

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   61
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_B     D     1_B     20   61   61      8   29   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Y     2_B     Y     2_B     20   61   61     10   37   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     I     3_B     I     3_B     20   61   61     10   18   21   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R     4_B     R     4_B     45   61   61     10   21   52   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E     5_B     E     5_B     45   61   61     15   34   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L     6_B     L     6_B     45   61   61     13   37   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R     7_B     R     7_B     45   61   61     12   33   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A     8_B     A     8_B     45   61   61     10   32   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A     9_B     A     9_B     45   61   61     11   34   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    10_B     L    10_B     45   61   61     17   37   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     I    11_B     I    11_B     45   61   61     10   33   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    12_B     L    12_B     45   61   61     10   30   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    13_B     L    13_B     45   61   61     10   37   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    14_B     A    14_B     45   61   61     17   37   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    15_B     L    15_B     45   61   61      9   34   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    16_B     K    16_B     45   61   61      9   37   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    17_B     K    17_B     45   61   61     17   37   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Q    18_B     Q    18_B     45   61   61      8   33   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     H    19_B     H    19_B     45   61   61      8   34   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    20_B     A    20_B     45   61   61      8   32   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    21_B     E    21_B     45   61   61      3    4    4   30   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    22_B     D    22_B     45   61   61     19   37   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     P    23_B     P    23_B     45   61   61     19   37   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    24_B     D    24_B     45   61   61     19   37   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    25_B     A    25_B     45   61   61     19   37   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Q    26_B     Q    26_B     45   61   61     19   37   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    27_B     R    27_B     45   61   61     19   37   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    28_B     V    28_B     45   61   61     19   37   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    29_B     A    29_B     45   61   61     19   37   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    30_B     D    30_B     45   61   61     19   37   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    31_B     E    31_B     45   61   61     19   37   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    32_B     L    32_B     45   61   61     19   37   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     M    33_B     M    33_B     45   61   61     19   37   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    34_B     K    34_B     45   61   61     19   37   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    35_B     K    35_B     45   61   61     19   37   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    36_B     L    36_B     45   61   61     19   37   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     F    37_B     F    37_B     45   61   61     19   37   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    38_B     D    38_B     45   61   61     19   37   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    39_B     A    39_B     45   61   61     19   37   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    40_B     A    40_B     45   61   61     19   37   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     H    41_B     H    41_B     45   61   61     19   37   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    42_B     R    42_B     45   61   61      4   26   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     N    43_B     N    43_B     45   61   61     17   37   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    44_B     D    44_B     45   61   61     17   37   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    45_B     K    45_B     45   61   61     10   37   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    46_B     D    46_B     45   61   61      7   37   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    47_B     K    47_B     45   61   61     11   37   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    48_B     V    48_B     45   61   61     17   37   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    49_B     K    49_B     45   61   61     11   37   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    50_B     K    50_B     41   61   61     11   21   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    51_B     V    51_B     41   61   61     11   33   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    52_B     V    52_B     41   61   61     17   37   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    53_B     E    53_B     41   61   61     11   36   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    54_B     E    54_B     40   61   61     11   21   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    55_B     A    55_B     40   61   61     11   33   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    56_B     K    56_B     40   61   61     11   37   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    57_B     K    57_B     40   61   61     10   21   53   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    58_B     V    58_B     40   61   61     10   21   48   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    59_B     V    59_B     40   61   61      9   32   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     S    60_B     S    60_B     40   61   61      9   37   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     T    61_B     T    61_B     40   61   61      6   21   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_AVERAGE  LCS_A:  90.08  (  70.25  100.00  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     37     54     60     61     61     61     61     61     61     61     61     61     61     61     61     61     61     61     61 
GDT PERCENT_AT  31.15  60.66  88.52  98.36 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.31   0.68   0.95   1.07   1.15   1.15   1.15   1.15   1.15   1.15   1.15   1.15   1.15   1.15   1.15   1.15   1.15   1.15   1.15   1.15
GDT RMS_ALL_AT   1.53   1.29   1.16   1.16   1.15   1.15   1.15   1.15   1.15   1.15   1.15   1.15   1.15   1.15   1.15   1.15   1.15   1.15   1.15   1.15

# Checking swapping
#   possible swapping detected:  D     1_B      D     1_B
#   possible swapping detected:  E     5_B      E     5_B
#   possible swapping detected:  D    30_B      D    30_B
#   possible swapping detected:  E    31_B      E    31_B
#   possible swapping detected:  F    37_B      F    37_B
#   possible swapping detected:  E    54_B      E    54_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    D     1_B      D     1_B     1.435     0    0.512   1.310     4.077   74.881   71.190
LGA    Y     2_B      Y     2_B     1.359     0    0.078   1.325    11.636   83.690   41.111
LGA    I     3_B      I     3_B     2.133     0    0.029   0.034     4.427   70.833   58.869
LGA    R     4_B      R     4_B     1.581     0    0.042   0.969     8.245   77.143   51.169
LGA    E     5_B      E     5_B     0.853     0    0.014   1.013     2.213   90.595   81.799
LGA    L     6_B      L     6_B     0.954     0    0.027   0.831     2.594   90.476   78.750
LGA    R     7_B      R     7_B     0.866     0    0.019   0.972     6.427   90.476   65.974
LGA    A     8_B      A     8_B     1.357     0    0.034   0.033     1.766   81.429   79.714
LGA    A     9_B      A     9_B     1.205     0    0.025   0.028     1.491   85.952   85.048
LGA    L    10_B      L    10_B     0.274     0    0.029   1.391     3.609  100.000   84.940
LGA    I    11_B      I    11_B     0.922     0    0.017   0.031     1.603   85.952   81.548
LGA    L    12_B      L    12_B     1.438     0    0.016   1.419     4.581   81.429   74.167
LGA    L    13_B      L    13_B     0.979     0    0.053   1.405     4.028   92.976   82.798
LGA    A    14_B      A    14_B     0.139     0    0.044   0.041     0.475  100.000  100.000
LGA    L    15_B      L    15_B     0.850     0    0.051   0.160     1.471   90.476   85.952
LGA    K    16_B      K    16_B     0.715     0    0.035   0.192     2.830   95.238   83.016
LGA    K    17_B      K    17_B     0.744     0    0.060   0.328     1.276   90.595   91.640
LGA    Q    18_B      Q    18_B     1.198     0    0.087   1.372     4.824   83.690   67.989
LGA    H    19_B      H    19_B     1.198     0    0.201   0.845     3.794   79.286   71.238
LGA    A    20_B      A    20_B     1.284     0    0.045   0.099     2.067   75.119   76.381
LGA    E    21_B      E    21_B     3.404     0    0.031   0.471     9.611   55.476   32.169
LGA    D    22_B      D    22_B     0.298     0    0.217   0.940     2.429   95.357   87.440
LGA    P    23_B      P    23_B     0.601     0    0.025   0.295     0.714   90.476   91.837
LGA    D    24_B      D    24_B     0.634     0    0.129   0.460     1.359   92.857   90.536
LGA    A    25_B      A    25_B     0.682     0    0.019   0.025     0.841   90.476   90.476
LGA    Q    26_B      Q    26_B     0.501     0    0.045   0.795     3.656   95.238   80.635
LGA    R    27_B      R    27_B     0.417     0    0.025   1.632     8.125  100.000   65.281
LGA    V    28_B      V    28_B     0.473     0    0.037   0.054     0.660  100.000   95.918
LGA    A    29_B      A    29_B     0.593     0    0.020   0.020     0.778   90.476   90.476
LGA    D    30_B      D    30_B     0.489     0    0.061   0.283     1.073   95.238   91.726
LGA    E    31_B      E    31_B     0.386     0    0.046   0.875     3.358   97.619   78.307
LGA    L    32_B      L    32_B     0.534     0    0.073   1.267     3.104   92.857   85.774
LGA    M    33_B      M    33_B     0.948     0    0.025   0.211     1.162   85.952   85.952
LGA    K    34_B      K    34_B     1.046     0    0.054   0.242     1.415   85.952   83.439
LGA    K    35_B      K    35_B     0.692     0    0.015   0.287     1.183   90.476   91.640
LGA    L    36_B      L    36_B     1.042     0    0.023   0.138     1.693   83.690   81.488
LGA    F    37_B      F    37_B     1.417     0    0.044   1.209     5.241   79.286   63.333
LGA    D    38_B      D    38_B     1.318     0    0.034   0.172     1.613   81.429   80.357
LGA    A    39_B      A    39_B     1.231     0    0.030   0.032     1.259   81.429   81.429
LGA    A    40_B      A    40_B     1.181     0    0.081   0.087     1.310   83.690   83.238
LGA    H    41_B      H    41_B     1.124     0    0.093   0.946     2.178   83.690   78.143
LGA    R    42_B      R    42_B     1.139     0    0.180   0.998     5.931   88.214   63.593
LGA    N    43_B      N    43_B     0.517     0    0.170   0.184     1.050   90.476   89.345
LGA    D    44_B      D    44_B     0.578     0    0.101   0.331     1.409   92.857   90.536
LGA    K    45_B      K    45_B     1.112     0    0.022   0.298     2.927   83.690   76.032
LGA    D    46_B      D    46_B     1.078     0    0.095   0.119     1.958   79.286   79.286
LGA    K    47_B      K    47_B     0.676     0    0.036   0.758     1.452   92.857   89.524
LGA    V    48_B      V    48_B     0.731     0    0.023   0.095     1.490   95.238   89.320
LGA    K    49_B      K    49_B     1.261     0    0.025   0.922     8.411   83.690   54.550
LGA    K    50_B      K    50_B     1.604     0    0.044   0.831     7.661   77.143   53.333
LGA    V    51_B      V    51_B     1.050     0    0.013   1.133     2.873   85.952   78.163
LGA    V    52_B      V    52_B     0.330     0    0.010   0.052     0.765  100.000   95.918
LGA    E    53_B      E    53_B     1.258     0    0.071   0.682     5.658   83.690   56.720
LGA    E    54_B      E    54_B     1.600     0    0.041   0.899     1.974   77.143   79.630
LGA    A    55_B      A    55_B     1.137     0    0.018   0.033     1.221   83.690   83.238
LGA    K    56_B      K    56_B     0.476     0    0.017   0.406     1.450   92.857   89.524
LGA    K    57_B      K    57_B     1.642     0    0.047   0.610     4.894   75.000   61.058
LGA    V    58_B      V    58_B     2.026     0    0.078   0.119     3.118   70.833   63.946
LGA    V    59_B      V    59_B     1.299     0    0.111   0.181     1.861   85.952   82.789
LGA    S    60_B      S    60_B     0.832     0    0.161   0.560     2.967   85.952   80.397
LGA    T    61_B      T    61_B     1.622     0    0.052   0.124     2.866   75.000   69.524

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       61     244    244  100.00     491    491  100.00                61
SUMMARY(RMSD_GDC):     1.153          1.109                  2.298           86.417   77.858

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   70   61    4.0     61    1.15    89.754    95.923     4.868

LGA_LOCAL      RMSD:   1.153  Number of atoms:   61  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.153  Number of assigned atoms:   61 
Std_ASGN_ATOMS RMSD:   1.153  Standard rmsd on all 61 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.916169 * X  +  -0.400626 * Y  +   0.011536 * Z  +  53.969505
  Y_new =  -0.395361 * X  +  -0.898657 * Y  +   0.190014 * Z  + -46.461582
  Z_new =  -0.065758 * X  +  -0.178645 * Y  +  -0.981714 * Z  +  54.781960 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.407395  0.065805 -2.961589   [DEG:  -23.3420    3.7704 -169.6866 ]
ZXZ:  3.080956  2.950060 -2.788894   [DEG:  176.5258  169.0260 -159.7918 ]
 
# END of job
