
#######################################################
#                                                     #
#                        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   65 (  516),  selected   51 , name one
# Molecule2: number of CA atoms   51 (  404),  selected   51 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:C  -ch2:C  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    51       6_C - 56_C        2.30     2.30
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    50       7_C - 56_C        1.66     2.33
  LCS_AVERAGE:     97.92

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    46       8_C - 53_C        0.96     2.41
  LCS_AVERAGE:     84.47

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   51
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     P     6_C     P     6_C      3   47   51      3    3    3    4    5    7    8    9   12   14   14   42   45   50   51   51   51   51   51   51 
LCS_GDT     T     7_C     T     7_C     42   50   51      3    5   10   17   32   40   45   46   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     K     8_C     K     8_C     46   50   51      3   13   40   44   46   47   47   49   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     I     9_C     I     9_C     46   50   51     20   41   43   45   46   48   48   49   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     L    10_C     L    10_C     46   50   51     20   41   43   45   46   48   48   49   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     P    11_C     P    11_C     46   50   51     31   41   43   45   46   48   48   49   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     C    12_C     C    12_C     46   50   51     31   41   43   45   46   48   48   49   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     P    13_C     P    13_C     46   50   51     31   41   43   45   46   48   48   49   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     R    14_C     R    14_C     46   50   51     31   41   43   45   46   48   48   49   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     C    15_C     C    15_C     46   50   51     31   41   43   45   46   48   48   49   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     N    16_C     N    16_C     46   50   51     31   41   43   45   46   48   48   49   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     S    17_C     S    17_C     46   50   51     31   41   43   45   46   48   48   49   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     M    18_C     M    18_C     46   50   51     31   41   43   45   46   48   48   49   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     E    19_C     E    19_C     46   50   51     14   41   43   45   46   48   48   49   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     T    20_C     T    20_C     46   50   51     11   41   43   45   46   48   48   49   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     K    21_C     K    21_C     46   50   51     31   41   43   45   46   48   48   49   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     F    22_C     F    22_C     46   50   51     31   41   43   45   46   48   48   49   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     C    23_C     C    23_C     46   50   51     31   41   43   45   46   48   48   49   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     Y    24_C     Y    24_C     46   50   51     31   41   43   45   46   48   48   49   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     Y    25_C     Y    25_C     46   50   51     31   41   43   45   46   48   48   49   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     N    26_C     N    26_C     46   50   51     14   41   43   45   46   48   48   49   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     N    27_C     N    27_C     46   50   51      4   41   43   45   46   48   48   49   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     Y    28_C     Y    28_C     46   50   51     21   41   43   45   46   48   48   49   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     N    29_C     N    29_C     46   50   51     31   41   43   45   46   48   48   49   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     V    30_C     V    30_C     46   50   51     31   41   43   45   46   48   48   49   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     N    31_C     N    31_C     46   50   51     31   41   43   45   46   48   48   49   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     Q    32_C     Q    32_C     46   50   51     31   41   43   45   46   48   48   49   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     P    33_C     P    33_C     46   50   51     31   41   43   45   46   48   48   49   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     R    34_C     R    34_C     46   50   51     31   41   43   45   46   48   48   49   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     H    35_C     H    35_C     46   50   51     31   41   43   45   46   48   48   49   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     F    36_C     F    36_C     46   50   51     31   41   43   45   46   48   48   49   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     C    37_C     C    37_C     46   50   51     31   41   43   45   46   48   48   49   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     K    38_C     K    38_C     46   50   51     31   41   43   45   46   48   48   49   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     A    39_C     A    39_C     46   50   51     31   41   43   45   46   48   48   49   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     C    40_C     C    40_C     46   50   51     31   41   43   45   46   48   48   49   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     Q    41_C     Q    41_C     46   50   51     31   41   43   45   46   48   48   49   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     R    42_C     R    42_C     46   50   51     31   41   43   45   46   48   48   49   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     Y    43_C     Y    43_C     46   50   51     31   41   43   45   46   48   48   49   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     W    44_C     W    44_C     46   50   51     31   41   43   45   46   48   48   49   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     T    45_C     T    45_C     46   50   51     31   41   43   45   46   48   48   49   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     S    46_C     S    46_C     46   50   51     31   41   43   45   46   48   48   49   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     G    47_C     G    47_C     46   50   51     16   41   43   45   46   48   48   49   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     G    48_C     G    48_C     46   50   51     31   41   43   45   46   48   48   49   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     T    49_C     T    49_C     46   50   51     16   41   43   45   46   48   48   49   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     M    50_C     M    50_C     46   50   51     14   39   43   45   46   48   48   49   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     R    51_C     R    51_C     46   50   51      3    8   43   45   46   48   48   49   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     S    52_C     S    52_C     46   50   51      3   11   32   45   46   48   48   49   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     V    53_C     V    53_C     46   50   51      3   24   41   45   46   48   48   49   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     P    54_C     P    54_C     12   50   51      3    4    6   22   41   48   48   49   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     I    55_C     I    55_C     12   50   51      3   11   18   34   45   48   48   49   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_GDT     G    56_C     G    56_C     12   50   51      3    4   13   25   41   48   48   49   50   50   50   50   50   50   51   51   51   51   51   51 
LCS_AVERAGE  LCS_A:  94.13  (  84.47   97.92  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     31     41     43     45     46     48     48     49     50     50     50     50     50     50     51     51     51     51     51     51 
GDT PERCENT_AT  60.78  80.39  84.31  88.24  90.20  94.12  94.12  96.08  98.04  98.04  98.04  98.04  98.04  98.04 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.33   0.52   0.63   0.86   0.96   1.37   1.37   1.45   1.66   1.66   1.66   1.66   1.66   1.66   2.30   2.30   2.30   2.30   2.30   2.30
GDT RMS_ALL_AT   2.59   2.54   2.49   2.42   2.41   2.43   2.43   2.38   2.33   2.33   2.33   2.33   2.33   2.33   2.30   2.30   2.30   2.30   2.30   2.30

# Checking swapping
#   possible swapping detected:  F    22_C      F    22_C
#   possible swapping detected:  F    36_C      F    36_C

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    P     6_C      P     6_C    12.222     2    0.177   0.205    14.394    0.000    0.000
LGA    T     7_C      T     7_C     6.092     0    0.653   0.501     8.118   21.190   21.973
LGA    K     8_C      K     8_C     3.503     4    0.267   0.293     4.430   50.595   29.683
LGA    I     9_C      I     9_C     1.705     0    0.048   0.724     3.553   70.833   70.357
LGA    L    10_C      L    10_C     1.187     0    0.038   0.205     2.706   85.952   79.583
LGA    P    11_C      P    11_C     0.563     0    0.017   0.058     1.109   90.476   87.891
LGA    C    12_C      C    12_C     0.712     0    0.016   0.093     1.181   90.476   88.968
LGA    P    13_C      P    13_C     1.245     0    0.023   0.258     2.099   79.286   77.823
LGA    R    14_C      R    14_C     1.596     0    0.054   0.702     2.695   72.976   70.087
LGA    C    15_C      C    15_C     1.317     0    0.035   0.148     1.373   81.429   81.429
LGA    N    16_C      N    16_C     0.854     0    0.117   0.203     1.783   90.476   86.012
LGA    S    17_C      S    17_C     0.704     0    0.033   0.123     0.796   90.476   90.476
LGA    M    18_C      M    18_C     0.265     0    0.022   0.628     1.791   95.238   91.845
LGA    E    19_C      E    19_C     0.634     4    0.026   0.036     0.722   90.476   50.265
LGA    T    20_C      T    20_C     0.689     0    0.065   0.135     1.035   88.214   89.184
LGA    K    21_C      K    21_C     0.552     0    0.014   0.406     3.716   95.238   79.894
LGA    F    22_C      F    22_C     0.447     0    0.031   0.046     0.670   97.619   97.403
LGA    C    23_C      C    23_C     0.462     0    0.053   0.072     0.673   95.238   93.651
LGA    Y    24_C      Y    24_C     0.408     0    0.022   0.028     1.275  100.000   91.389
LGA    Y    25_C      Y    25_C     0.193     0    0.090   0.093     0.983  100.000   95.238
LGA    N    26_C      N    26_C     0.677     0    0.059   0.321     2.005   90.476   85.000
LGA    N    27_C      N    27_C     1.256     0    0.018   0.136     2.241   81.429   76.190
LGA    Y    28_C      Y    28_C     1.036     0    0.016   0.064     3.163   85.952   70.754
LGA    N    29_C      N    29_C     0.401     0    0.058   0.205     1.284   97.619   94.107
LGA    V    30_C      V    30_C     0.709     0    0.015   1.152     3.380   90.476   82.177
LGA    N    31_C      N    31_C     0.714     0    0.036   0.374     1.166   90.476   89.345
LGA    Q    32_C      Q    32_C     0.454     0    0.037   0.402     1.939   97.619   94.868
LGA    P    33_C      P    33_C     0.580     0    0.046   0.067     0.735   90.476   91.837
LGA    R    34_C      R    34_C     0.664     0    0.047   0.864     3.579   95.238   78.485
LGA    H    35_C      H    35_C     0.417     0    0.057   0.177     0.938   92.857   93.333
LGA    F    36_C      F    36_C     1.100     0    0.026   0.114     1.943   85.952   79.957
LGA    C    37_C      C    37_C     1.073     0    0.051   0.135     1.541   79.286   81.508
LGA    K    38_C      K    38_C     1.154     0    0.010   0.476     1.676   83.690   81.481
LGA    A    39_C      A    39_C     1.110     0    0.085   0.087     1.226   81.429   83.238
LGA    C    40_C      C    40_C     1.613     0    0.023   0.037     1.782   72.857   74.286
LGA    Q    41_C      Q    41_C     1.894     0    0.035   0.741     3.038   72.857   68.519
LGA    R    42_C      R    42_C     1.587     0    0.042   1.048     5.160   75.000   65.152
LGA    Y    43_C      Y    43_C     1.116     0    0.039   0.080     1.272   81.429   81.429
LGA    W    44_C      W    44_C     1.032     0    0.024   0.209     1.239   85.952   82.721
LGA    T    45_C      T    45_C     0.756     0    0.056   0.150     1.074   88.214   87.891
LGA    S    46_C      S    46_C     0.396     0    0.031   0.038     0.564   97.619   98.413
LGA    G    47_C      G    47_C     0.633     0    0.060   0.060     0.979   90.476   90.476
LGA    G    48_C      G    48_C     0.831     0    0.036   0.036     0.831   92.857   92.857
LGA    T    49_C      T    49_C     0.403     0    0.061   0.995     2.637   97.619   87.483
LGA    M    50_C      M    50_C     0.343     0    0.056   0.730     4.202   97.619   78.274
LGA    R    51_C      R    51_C     1.372     0    0.028   0.246     4.917   83.690   60.476
LGA    S    52_C      S    52_C     1.834     0    0.080   0.168     2.968   77.143   71.746
LGA    V    53_C      V    53_C     1.420     0    0.091   1.118     3.071   70.952   67.483
LGA    P    54_C      P    54_C     4.127     0    0.130   0.330     5.151   43.452   41.020
LGA    I    55_C      I    55_C     3.298     0    0.078   1.323     4.849   43.452   42.083
LGA    G    56_C      G    56_C     4.253     0    0.694   0.694     4.720   35.833   35.833

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       51     204    204  100.00     404    404  100.00                51
SUMMARY(RMSD_GDC):     2.300          2.275                  2.202           81.102   76.109

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   65   51    4.0     49    1.45    91.176    93.951     3.161

LGA_LOCAL      RMSD:   1.450  Number of atoms:   49  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.383  Number of assigned atoms:   51 
Std_ASGN_ATOMS RMSD:   2.300  Standard rmsd on all 51 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.399073 * X  +   0.510625 * Y  +  -0.761579 * Z  + -28.135090
  Y_new =  -0.911872 * X  +   0.308048 * Y  +  -0.271286 * Z  +  -9.868155
  Z_new =   0.096078 * X  +   0.802726 * Y  +   0.588558 * Z  +   7.401429 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.158267 -0.096226  0.938134   [DEG:  -66.3638   -5.5134   53.7511 ]
ZXZ: -1.228595  0.941522  0.119123   [DEG:  -70.3933   53.9452    6.8252 ]
 
# END of job
