
#######################################################
#                                                     #
#                        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   63 (  471),  selected   63 , name one
# Molecule2: number of CA atoms   63 (  471),  selected   63 , 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:    63       1_A - 63_A        2.11     2.11
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    60       3_A - 62_A        1.98     2.13
  LCS_AVERAGE:     94.10

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    28       8_A - 35_A        0.99     3.74
  LCS_AVERAGE:     33.51

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   63
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     10   41   63      4    6   20   34   46   53   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H     2_A     H     2_A     10   49   63      4    6   14   30   40   52   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     I     3_A     I     3_A     12   60   63      7   18   28   44   53   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D     4_A     D     4_A     13   60   63      7   18   31   44   53   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     5_A     C     5_A     21   60   63      7   17   31   43   53   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D     6_A     D     6_A     21   60   63      7   17   28   38   53   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K     7_A     K     7_A     24   60   63      9   18   31   44   53   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E     8_A     E     8_A     28   60   63      9   18   31   44   53   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     9_A     C     9_A     28   60   63      9   18   31   44   53   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    10_A     N    10_A     28   60   63      9   18   31   44   53   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    11_A     R    11_A     28   60   63      5   17   31   39   53   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    12_A     R    12_A     28   60   63      6   17   31   43   53   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    13_A     C    13_A     28   60   63      3   18   31   44   53   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    14_A     S    14_A     28   60   63      6   18   31   44   53   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    15_A     K    15_A     28   60   63      4   17   31   44   53   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    16_A     A    16_A     28   60   63      6   17   31   44   53   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    17_A     S    17_A     28   60   63      6   17   31   40   53   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    18_A     A    18_A     28   60   63      4   17   31   40   53   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H    19_A     H    19_A     28   60   63      4   17   31   44   53   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    20_A     D    20_A     28   60   63      6   17   31   44   53   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    21_A     R    21_A     28   60   63      7   17   31   44   53   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    22_A     C    22_A     28   60   63      7   17   31   44   53   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    23_A     L    23_A     28   60   63      6   17   31   44   53   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    24_A     K    24_A     28   60   63      6   17   31   44   53   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    25_A     Y    25_A     28   60   63      7   17   31   44   53   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    26_A     C    26_A     28   60   63      3   17   31   44   53   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    27_A     G    27_A     28   60   63      4   17   31   44   53   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     I    28_A     I    28_A     28   60   63      7   17   31   44   53   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    29_A     C    29_A     28   60   63      7   17   31   44   53   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    30_A     C    30_A     28   60   63      6   17   31   44   53   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    31_A     E    31_A     28   60   63      6   12   27   44   53   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    32_A     K    32_A     28   60   63      6   17   31   44   53   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    33_A     C    33_A     28   60   63      7   18   31   44   53   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    34_A     N    34_A     28   60   63      9   18   31   44   53   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    35_A     C    35_A     28   60   63      7   18   31   44   53   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    36_A     V    36_A     24   60   63      9   18   29   44   53   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    37_A     P    37_A     22   60   63      9   18   28   44   53   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    38_A     P    38_A     21   60   63      9   18   28   44   53   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    39_A     G    39_A     21   60   63      9   18   28   44   53   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     T    40_A     T    40_A     16   60   63      3   15   28   36   47   54   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    41_A     Y    41_A     16   60   63      3   13   26   36   46   54   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    42_A     G    42_A     16   60   63      3    3   26   36   47   54   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    43_A     N    43_A     16   60   63      5   17   28   38   52   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    44_A     E    44_A     16   60   63      5   17   28   44   53   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    45_A     D    45_A     16   60   63      9   18   28   44   53   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    46_A     S    46_A     16   60   63      5   10   28   40   52   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    47_A     C    47_A     16   60   63      8   18   28   44   53   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    48_A     P    48_A     11   60   63      4   17   27   44   53   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    49_A     C    49_A     12   60   63      5   12   28   44   53   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    50_A     Y    50_A     14   60   63      5    9   22   44   53   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    51_A     A    51_A     14   60   63      5   12   18   31   48   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    52_A     N    52_A     14   60   63      5   12   25   41   53   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    53_A     L    53_A     14   60   63      3   12   25   44   53   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    54_A     K    54_A     14   60   63      5   12   25   44   53   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    55_A     N    55_A     14   60   63      4   13   28   44   53   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    56_A     S    56_A     14   60   63      3   10   28   35   50   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    57_A     K    57_A     14   60   63      6   18   27   44   53   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    58_A     G    58_A     14   60   63      6   12   25   44   53   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    59_A     G    59_A     14   60   63      6   12   26   44   53   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H    60_A     H    60_A     14   60   63      6   12   25   44   53   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    61_A     K    61_A     14   60   63      4   17   28   44   53   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    62_A     C    62_A     14   60   63      6   17   31   43   53   56   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    63_A     P    63_A     14   45   63      6   12   18   32   42   54   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_AVERAGE  LCS_A:  75.87  (  33.51   94.10  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      9     18     31     44     53     56     60     63     63     63     63     63     63     63     63     63     63     63     63     63 
GDT PERCENT_AT  14.29  28.57  49.21  69.84  84.13  88.89  95.24 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.32   0.73   1.03   1.51   1.67   1.77   2.00   2.11   2.11   2.11   2.11   2.11   2.11   2.11   2.11   2.11   2.11   2.11   2.11   2.11
GDT RMS_ALL_AT   2.59   2.40   3.52   2.14   2.19   2.16   2.13   2.11   2.11   2.11   2.11   2.11   2.11   2.11   2.11   2.11   2.11   2.11   2.11   2.11

# Checking swapping
#   possible swapping detected:  D    45_A      D    45_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A     1_A      A     1_A     3.533     0    0.043   0.064     4.673   59.524   53.905
LGA    H     2_A      H     2_A     3.616     0    0.019   0.851     8.594   48.452   27.143
LGA    I     3_A      I     3_A     0.895     0    0.087   0.942     2.236   79.405   79.583
LGA    D     4_A      D     4_A     1.640     0    0.069   1.072     4.434   72.976   63.631
LGA    C     5_A      C     5_A     2.317     0    0.070   0.202     2.681   64.762   64.841
LGA    D     6_A      D     6_A     2.278     0    0.018   1.044     5.545   68.810   56.845
LGA    K     7_A      K     7_A     1.234     0    0.085   0.543     1.893   79.286   81.587
LGA    E     8_A      E     8_A     1.364     0    0.063   0.348     1.530   79.286   80.476
LGA    C     9_A      C     9_A     1.795     0    0.051   0.061     2.064   72.857   71.508
LGA    N    10_A      N    10_A     1.439     0    0.102   0.248     1.910   77.143   75.000
LGA    R    11_A      R    11_A     2.454     0    0.018   1.534     5.796   64.762   51.688
LGA    R    12_A      R    12_A     2.121     0    0.053   1.296     4.528   66.786   64.372
LGA    C    13_A      C    13_A     1.550     0    0.224   0.251     3.412   81.667   73.571
LGA    S    14_A      S    14_A     0.697     0    0.024   0.659     1.257   88.214   85.952
LGA    K    15_A      K    15_A     2.007     0    0.098   0.994     3.354   67.024   60.794
LGA    A    16_A      A    16_A     2.095     0    0.022   0.028     2.490   66.786   69.714
LGA    S    17_A      S    17_A     3.477     0    0.029   0.467     5.945   48.333   41.984
LGA    A    18_A      A    18_A     3.122     0    0.064   0.062     3.252   55.476   54.381
LGA    H    19_A      H    19_A     2.130     0    0.145   0.319     2.575   62.857   64.000
LGA    D    20_A      D    20_A     2.361     0    0.164   0.174     3.313   66.786   59.286
LGA    R    21_A      R    21_A     2.505     0    0.057   1.230    10.473   65.000   34.416
LGA    C    22_A      C    22_A     1.539     0    0.108   0.163     1.926   77.143   77.143
LGA    L    23_A      L    23_A     0.893     0    0.087   1.280     4.125   88.214   78.214
LGA    K    24_A      K    24_A     2.137     0    0.060   0.492     6.236   70.833   53.280
LGA    Y    25_A      Y    25_A     2.003     0    0.050   0.577     2.543   66.786   64.841
LGA    C    26_A      C    26_A     1.587     0    0.054   0.186     1.731   72.857   74.286
LGA    G    27_A      G    27_A     1.466     0    0.126   0.126     2.113   75.119   75.119
LGA    I    28_A      I    28_A     1.505     0    0.048   0.683     4.660   79.286   68.869
LGA    C    29_A      C    29_A     1.446     0    0.043   0.712     1.528   81.429   80.000
LGA    C    30_A      C    30_A     1.411     0    0.033   0.071     1.986   81.429   78.571
LGA    E    31_A      E    31_A     1.610     0    0.032   0.730     1.793   75.000   76.720
LGA    K    32_A      K    32_A     1.320     0    0.030   1.269     7.251   79.286   58.254
LGA    C    33_A      C    33_A     0.845     0    0.606   0.521     3.376   75.833   73.651
LGA    N    34_A      N    34_A     0.977     0    0.164   0.724     3.242   85.952   75.595
LGA    C    35_A      C    35_A     1.290     0    0.037   0.497     2.128   83.690   78.730
LGA    V    36_A      V    36_A     0.883     0    0.088   1.343     2.877   88.214   78.367
LGA    P    37_A      P    37_A     0.930     0    0.029   0.224     1.105   90.476   89.184
LGA    P    38_A      P    38_A     1.200     0    0.009   0.117     1.210   81.429   81.429
LGA    G    39_A      G    39_A     1.288     0    0.167   0.167     1.944   77.143   77.143
LGA    T    40_A      T    40_A     3.575     0    0.601   0.558     5.249   42.500   44.762
LGA    Y    41_A      Y    41_A     4.010     0    0.175   0.785    11.866   40.238   18.135
LGA    G    42_A      G    42_A     3.905     0    0.174   0.174     4.028   43.452   43.452
LGA    N    43_A      N    43_A     2.597     0    0.254   0.500     3.080   57.262   62.024
LGA    E    44_A      E    44_A     1.406     0    0.105   1.010     3.547   79.286   67.354
LGA    D    45_A      D    45_A     1.427     0    0.161   1.103     6.236   77.143   58.393
LGA    S    46_A      S    46_A     2.311     0    0.125   0.726     2.645   66.786   64.841
LGA    C    47_A      C    47_A     1.092     0    0.024   0.392     2.276   85.952   80.238
LGA    P    48_A      P    48_A     0.748     0    0.057   0.328     1.362   90.595   87.959
LGA    C    49_A      C    49_A     1.346     0    0.067   0.261     2.850   77.381   73.254
LGA    Y    50_A      Y    50_A     2.040     0    0.019   1.088     4.307   66.786   65.714
LGA    A    51_A      A    51_A     3.066     0    0.194   0.210     3.509   51.905   51.524
LGA    N    52_A      N    52_A     2.500     0    0.087   0.396     3.110   62.857   61.012
LGA    L    53_A      L    53_A     1.867     0    0.021   0.988     3.011   70.833   70.060
LGA    K    54_A      K    54_A     1.969     0    0.136   1.301     3.697   75.000   69.894
LGA    N    55_A      N    55_A     1.560     0    0.030   0.197     2.360   70.952   75.119
LGA    S    56_A      S    56_A     3.287     0    0.140   0.670     6.319   51.905   44.683
LGA    K    57_A      K    57_A     1.372     0    0.143   0.797     3.920   79.286   74.339
LGA    G    58_A      G    58_A     1.699     0    0.126   0.126     2.109   72.976   72.976
LGA    G    59_A      G    59_A     1.279     0    0.083   0.083     1.651   77.143   77.143
LGA    H    60_A      H    60_A     2.018     0    0.081   1.295     9.122   70.833   41.714
LGA    K    61_A      K    61_A     1.629     0    0.022   0.748     1.989   72.857   79.735
LGA    C    62_A      C    62_A     2.307     0    0.063   0.109     3.249   59.167   63.810
LGA    P    63_A      P    63_A     3.745     0    0.239   0.396     4.001   46.667   46.327

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       63     252    252  100.00     471    471  100.00                63
SUMMARY(RMSD_GDC):     2.109          2.094                  2.913           70.731   65.850

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63   63    4.0     63    2.11    74.603    84.985     2.852

LGA_LOCAL      RMSD:   2.109  Number of atoms:   63  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.109  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:   2.109  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.459013 * X  +   0.393791 * Y  +   0.796389 * Z  + -12.446405
  Y_new =   0.511548 * X  +  -0.615748 * Y  +   0.599310 * Z  +  -1.558742
  Z_new =   0.726378 * X  +   0.682482 * Y  +   0.081193 * Z  + -10.823270 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.302119 -0.813038  1.452385   [DEG:  131.9017  -46.5836   83.2155 ]
ZXZ:  2.215917  1.489513  0.816545   [DEG:  126.9627   85.3428   46.7846 ]
 
# END of job
