
#######################################################
#                                                     #
#                        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 (  545),  selected   70 , name one
# Molecule2: number of CA atoms   92 (  680),  selected   70 , 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:    70       8_A - 77_A        4.48     4.48
  LCS_AVERAGE:     76.09

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    20      58_A - 77_A        1.84     6.31
  LCS_AVERAGE:     16.94

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    16      61_A - 76_A        0.95     7.48
  LCS_AVERAGE:     11.04

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   70
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     G     8_A     G     8_A      3    8   70      3    3    6    8   10   16   24   30   43   49   51   57   62   65   67   68   70   70   70   70 
LCS_GDT     G     9_A     G     9_A      4    8   70      3    4    6    8   10   14   25   32   43   49   51   57   60   65   67   68   70   70   70   70 
LCS_GDT     G    10_A     G    10_A      4    8   70      3    4    5    5   10   13   18   28   39   49   51   57   62   65   67   68   70   70   70   70 
LCS_GDT     E    11_A     E    11_A      6    8   70      5    8   15   22   32   40   43   46   50   54   57   59   62   65   67   68   70   70   70   70 
LCS_GDT     R    12_A     R    12_A      6    8   70      5    8   15   22   32   40   43   46   50   54   57   59   62   65   67   68   70   70   70   70 
LCS_GDT     R    13_A     R    13_A      6    8   70      5    6   13   24   32   40   43   46   50   54   57   59   62   65   67   68   70   70   70   70 
LCS_GDT     K    14_A     K    14_A      6    8   70      5    6   12   22   32   40   43   46   50   54   57   59   62   65   67   68   70   70   70   70 
LCS_GDT     G    15_A     G    15_A      6    8   70      5    8   14   16   25   37   43   46   50   54   57   59   62   65   67   68   70   70   70   70 
LCS_GDT     S    16_A     S    16_A      6   17   70      4    8   14   22   32   40   43   46   50   54   57   59   62   65   67   68   70   70   70   70 
LCS_GDT     V    17_A     V    17_A      6   17   70      4    8   14   16   31   40   43   46   50   54   57   59   62   65   67   68   70   70   70   70 
LCS_GDT     K    18_A     K    18_A      4   17   70      3    8   14   16   26   40   42   46   50   54   57   59   62   65   67   68   70   70   70   70 
LCS_GDT     W    19_A     W    19_A     14   17   70      4   14   17   26   32   40   43   46   50   54   57   59   62   65   67   68   70   70   70   70 
LCS_GDT     F    20_A     F    20_A     14   17   70      5   14   17   26   32   40   43   46   50   54   57   59   62   65   67   68   70   70   70   70 
LCS_GDT     D    21_A     D    21_A     14   17   70      6   14   17   26   32   40   43   46   50   54   57   59   62   65   67   68   70   70   70   70 
LCS_GDT     T    22_A     T    22_A     14   17   70      6   13   15   26   32   40   43   46   50   54   57   59   62   65   67   68   70   70   70   70 
LCS_GDT     Q    23_A     Q    23_A     14   17   70      6   13   16   26   32   40   43   46   50   54   57   59   62   65   67   68   70   70   70   70 
LCS_GDT     K    24_A     K    24_A     14   17   70      8   13   16   26   32   40   43   46   50   54   57   59   62   65   67   68   70   70   70   70 
LCS_GDT     G    25_A     G    25_A     14   17   70      6   13   15   26   32   40   43   46   50   54   57   59   62   65   67   68   70   70   70   70 
LCS_GDT     F    26_A     F    26_A     14   17   70      6   13   17   26   32   40   43   46   50   54   57   59   62   65   67   68   70   70   70   70 
LCS_GDT     G    27_A     G    27_A     14   17   70      6   14   17   26   32   40   43   46   50   54   57   59   62   65   67   68   70   70   70   70 
LCS_GDT     F    28_A     F    28_A     14   17   70      8   14   17   26   32   40   43   46   50   54   57   59   62   65   67   68   70   70   70   70 
LCS_GDT     I    29_A     I    29_A     14   17   70      8   14   17   26   32   40   43   46   50   54   57   59   62   65   67   68   70   70   70   70 
LCS_GDT     T    30_A     T    30_A     14   17   70      8   14   17   26   32   40   43   46   50   54   57   59   62   65   67   68   70   70   70   70 
LCS_GDT     P    31_A     P    31_A     14   17   70      3   13   17   26   32   40   43   46   50   54   57   59   62   65   67   68   70   70   70   70 
LCS_GDT     D    32_A     D    32_A     14   17   70      4   13   16   21   29   38   43   46   50   54   57   59   62   65   67   68   70   70   70   70 
LCS_GDT     D    33_A     D    33_A      4   15   70      3    6    9   10   18   27   32   43   49   53   56   59   62   65   67   68   70   70   70   70 
LCS_GDT     G    34_A     G    34_A      4   11   70      3    4    7    9   11   12   22   30   36   46   51   57   59   61   64   66   70   70   70   70 
LCS_GDT     G    35_A     G    35_A      8   11   70      4    8   13   21   30   40   42   46   50   53   56   59   62   65   67   68   70   70   70   70 
LCS_GDT     D    36_A     D    36_A      8   11   70      3   13   15   21   32   40   43   46   50   54   56   59   62   65   67   68   70   70   70   70 
LCS_GDT     D    37_A     D    37_A      8   11   70      8   13   16   24   32   40   43   46   50   54   57   59   62   65   67   68   70   70   70   70 
LCS_GDT     L    38_A     L    38_A      8   11   70      8   13   16   21   32   40   43   46   50   54   57   59   62   65   67   68   70   70   70   70 
LCS_GDT     F    39_A     F    39_A      8   11   70      8   13   16   24   32   40   43   46   50   54   57   59   62   65   67   68   70   70   70   70 
LCS_GDT     V    40_A     V    40_A      8   11   70      8   13   16   21   32   40   43   46   50   54   57   59   62   65   67   68   70   70   70   70 
LCS_GDT     H    41_A     H    41_A      8   11   70      3   13   14   18   27   34   43   46   50   54   57   59   62   65   67   68   70   70   70   70 
LCS_GDT     Q    42_A     Q    42_A      8   11   70      3    8   16   21   32   40   43   46   50   54   57   59   62   65   67   68   70   70   70   70 
LCS_GDT     S    43_A     S    43_A      6   11   70      4    6   16   24   32   40   43   46   50   54   57   59   62   65   67   68   70   70   70   70 
LCS_GDT     S    44_A     S    44_A      5    6   70      4    5    5   19   23   31   39   46   50   54   57   59   62   65   67   68   70   70   70   70 
LCS_GDT     I    45_A     I    45_A      5   15   70      4    8   15   26   32   40   43   46   50   54   57   59   62   65   67   68   70   70   70   70 
LCS_GDT     R    46_A     R    46_A      5   16   70      4    5    5   16   18   20   23   27   46   54   57   58   61   63   67   68   70   70   70   70 
LCS_GDT     S    47_A     S    47_A      5   16   70      4    4   14   18   26   34   42   46   50   54   57   59   62   65   67   68   70   70   70   70 
LCS_GDT     E    48_A     E    48_A      5   16   70      4    4    9   16   19   30   38   45   50   54   57   59   61   65   67   68   70   70   70   70 
LCS_GDT     G    49_A     G    49_A      5   16   70      4    8   14   16   24   32   40   46   50   54   57   59   61   65   67   68   70   70   70   70 
LCS_GDT     F    50_A     F    50_A      5   16   70      4    4   13   18   26   35   42   46   50   54   57   59   62   65   67   68   70   70   70   70 
LCS_GDT     R    51_A     R    51_A      4   16   70      3    6   14   16   19   27   35   43   50   54   57   59   62   65   67   68   70   70   70   70 
LCS_GDT     S    52_A     S    52_A      8   16   70      4    7   11   15   18   20   24   31   39   48   52   56   60   63   67   68   70   70   70   70 
LCS_GDT     L    53_A     L    53_A      8   16   70      4    7   12   16   19   24   31   43   49   54   57   59   62   65   67   68   70   70   70   70 
LCS_GDT     A    54_A     A    54_A      8   16   70      3    5   14   16   20   35   42   46   50   54   57   59   62   65   67   68   70   70   70   70 
LCS_GDT     A    55_A     A    55_A      8   16   70      4    8   14   16   27   40   43   46   50   54   57   59   62   65   67   68   70   70   70   70 
LCS_GDT     E    56_A     E    56_A      8   16   70      4    9   17   26   32   40   43   46   50   54   57   59   62   65   67   68   70   70   70   70 
LCS_GDT     E    57_A     E    57_A      8   16   70      4    9   17   26   32   40   43   46   50   54   57   59   62   65   67   68   70   70   70   70 
LCS_GDT     A    58_A     A    58_A      8   20   70      6   14   17   26   32   40   43   46   50   54   57   59   62   65   67   68   70   70   70   70 
LCS_GDT     V    59_A     V    59_A      8   20   70      4   14   17   26   32   40   43   46   50   54   57   59   62   65   67   68   70   70   70   70 
LCS_GDT     E    60_A     E    60_A     12   20   70      6   14   17   26   32   40   43   46   50   54   57   59   62   65   67   68   70   70   70   70 
LCS_GDT     F    61_A     F    61_A     16   20   70      6   14   17   26   32   40   43   46   50   54   57   59   62   65   67   68   70   70   70   70 
LCS_GDT     E    62_A     E    62_A     16   20   70      7   12   17   26   32   40   43   46   50   54   57   59   62   65   67   68   70   70   70   70 
LCS_GDT     V    63_A     V    63_A     16   20   70      7   11   16   26   30   38   43   46   50   54   57   59   62   65   67   68   70   70   70   70 
LCS_GDT     E    64_A     E    64_A     16   20   70      5   11   16   19   26   34   41   46   50   54   57   59   62   65   67   68   70   70   70   70 
LCS_GDT     I    65_A     I    65_A     16   20   70      5   11   16   19   23   30   39   45   50   54   57   59   62   65   67   68   70   70   70   70 
LCS_GDT     D    66_A     D    66_A     16   20   70      7   10   16   19   23   25   28   36   43   50   55   58   62   65   67   68   70   70   70   70 
LCS_GDT     N    67_A     N    67_A     16   20   70      7   10   16   19   23   25   28   33   36   48   53   57   60   65   67   68   70   70   70   70 
LCS_GDT     N    68_A     N    68_A     16   20   70      5   11   16   19   23   25   28   32   35   48   52   57   60   64   67   68   70   70   70   70 
LCS_GDT     N    69_A     N    69_A     16   20   70      7   11   16   19   23   25   32   39   46   51   56   58   62   65   67   68   70   70   70   70 
LCS_GDT     R    70_A     R    70_A     16   20   70      7   11   16   19   23   25   32   39   46   50   56   58   62   65   67   68   70   70   70   70 
LCS_GDT     P    71_A     P    71_A     16   20   70      7   11   16   19   23   30   36   43   50   54   57   59   62   65   67   68   70   70   70   70 
LCS_GDT     K    72_A     K    72_A     16   20   70      4   11   16   19   23   32   39   46   50   54   57   59   62   65   67   68   70   70   70   70 
LCS_GDT     A    73_A     A    73_A     16   20   70      5   11   16   19   25   37   43   46   50   54   57   59   62   65   67   68   70   70   70   70 
LCS_GDT     I    74_A     I    74_A     16   20   70      4   11   16   26   32   38   43   46   50   54   57   59   62   65   67   68   70   70   70   70 
LCS_GDT     D    75_A     D    75_A     16   20   70      4   14   17   26   32   40   43   46   50   54   57   59   62   65   67   68   70   70   70   70 
LCS_GDT     V    76_A     V    76_A     16   20   70      6   14   17   26   32   40   43   46   50   54   57   59   62   65   67   68   70   70   70   70 
LCS_GDT     S    77_A     S    77_A      9   20   70      4   14   17   26   32   40   43   46   50   54   57   59   62   65   67   68   70   70   70   70 
LCS_AVERAGE  LCS_A:  34.69  (  11.04   16.94   76.09 )

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      8     14     17     26     32     40     43     46     50     54     57     59     62     65     67     68     70     70     70     70 
GDT PERCENT_AT   8.70  15.22  18.48  28.26  34.78  43.48  46.74  50.00  54.35  58.70  61.96  64.13  67.39  70.65  72.83  73.91  76.09  76.09  76.09  76.09
GDT RMS_LOCAL    0.30   0.78   0.91   1.40   1.71   2.09   2.16   2.33   2.62   2.91   3.16   3.31   3.90   4.05   4.21   4.29   4.48   4.48   4.48   4.48
GDT RMS_ALL_AT   8.68   5.22   5.12   5.05   5.09   5.50   5.21   5.36   4.98   4.85   4.81   4.74   4.52   4.50   4.50   4.49   4.48   4.48   4.48   4.48

# Checking swapping
#   possible swapping detected:  E    11_A      E    11_A
#   possible swapping detected:  F    20_A      F    20_A
#   possible swapping detected:  D    21_A      D    21_A
#   possible swapping detected:  D    33_A      D    33_A
#   possible swapping detected:  D    36_A      D    36_A
#   possible swapping detected:  E    48_A      E    48_A
#   possible swapping detected:  F    50_A      F    50_A
#   possible swapping detected:  E    56_A      E    56_A
#   possible swapping detected:  E    57_A      E    57_A
#   possible swapping detected:  E    62_A      E    62_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    G     8_A      G     8_A    10.391     0    0.353   0.353    12.006    0.357    0.357
LGA    G     9_A      G     9_A     9.289     0    0.471   0.471     9.289    1.429    1.429
LGA    G    10_A      G    10_A     8.763     0    0.053   0.053     9.043    8.690    8.690
LGA    E    11_A      E    11_A     2.549     0    0.306   1.006     4.845   52.619   56.032
LGA    R    12_A      R    12_A     2.242     0    0.060   1.281     3.365   66.786   66.623
LGA    R    13_A      R    13_A     1.628     0    0.097   0.704     3.066   75.000   72.641
LGA    K    14_A      K    14_A     2.118     0    0.097   0.737     5.466   62.857   48.519
LGA    G    15_A      G    15_A     3.216     0    0.116   0.116     3.216   57.262   57.262
LGA    S    16_A      S    16_A     2.272     0    0.021   0.056     3.319   57.262   59.762
LGA    V    17_A      V    17_A     3.145     0    0.653   0.573     4.267   48.571   49.252
LGA    K    18_A      K    18_A     3.838     0    0.108   0.452     9.828   60.238   32.434
LGA    W    19_A      W    19_A     2.358     0    0.497   1.120     9.762   66.786   28.401
LGA    F    20_A      F    20_A     2.150     0    0.089   0.339     3.084   62.857   60.000
LGA    D    21_A      D    21_A     1.731     0    0.208   1.094     5.849   75.000   61.845
LGA    T    22_A      T    22_A     2.602     0    0.130   1.015     5.495   59.048   51.769
LGA    Q    23_A      Q    23_A     2.386     0    0.102   1.581     3.965   64.762   69.947
LGA    K    24_A      K    24_A     1.697     0    0.071   0.163     2.731   70.833   71.217
LGA    G    25_A      G    25_A     2.001     0    0.062   0.062     2.017   68.810   68.810
LGA    F    26_A      F    26_A     0.780     0    0.197   1.247     7.642   85.952   55.281
LGA    G    27_A      G    27_A     0.503     0    0.059   0.059     0.620   95.238   95.238
LGA    F    28_A      F    28_A     0.687     0    0.047   0.357     2.509   85.952   79.567
LGA    I    29_A      I    29_A     1.548     0    0.045   0.638     2.706   79.286   72.083
LGA    T    30_A      T    30_A     0.958     0    0.182   1.189     2.673   81.548   76.939
LGA    P    31_A      P    31_A     1.518     0    0.053   0.122     2.129   70.952   75.442
LGA    D    32_A      D    32_A     3.311     0    0.064   1.037     8.258   63.333   37.321
LGA    D    33_A      D    33_A     6.078     0    0.027   1.266     9.557   17.738   12.500
LGA    G    34_A      G    34_A     7.763     0    0.474   0.474     7.763   16.905   16.905
LGA    G    35_A      G    35_A     4.016     0    0.250   0.250     5.694   36.310   36.310
LGA    D    36_A      D    36_A     2.517     0    0.030   0.562     3.532   59.167   57.381
LGA    D    37_A      D    37_A     1.666     0    0.050   0.208     2.314   68.810   77.381
LGA    L    38_A      L    38_A     2.548     0    0.072   1.271     3.073   62.857   62.024
LGA    F    39_A      F    39_A     1.943     0    0.060   0.754     6.699   64.881   44.978
LGA    V    40_A      V    40_A     2.473     0    0.068   0.136     2.948   60.952   61.497
LGA    H    41_A      H    41_A     3.597     0    0.156   0.473     7.204   48.333   31.857
LGA    Q    42_A      Q    42_A     2.710     0    0.575   0.982     4.948   55.595   52.963
LGA    S    43_A      S    43_A     1.603     0    0.266   0.636     4.709   65.119   58.175
LGA    S    44_A      S    44_A     4.887     0    0.037   0.617     6.769   35.000   27.778
LGA    I    45_A      I    45_A     2.403     0    0.312   0.700     4.934   47.619   59.643
LGA    R    46_A      R    46_A     7.145     0    0.698   1.292    17.378   19.881    7.403
LGA    S    47_A      S    47_A     5.426     0    0.202   0.657     6.948   17.500   21.270
LGA    E    48_A      E    48_A     8.139     0    0.154   0.931    12.570    6.071    3.016
LGA    G    49_A      G    49_A     7.740     0    0.072   0.072     7.740   10.238   10.238
LGA    F    50_A      F    50_A     6.249     0    0.243   1.286     8.097   16.190   16.494
LGA    R    51_A      R    51_A     7.445     0    0.047   0.967     9.826    8.214    6.797
LGA    S    52_A      S    52_A     8.968     0    0.349   0.394     9.585    4.286    3.413
LGA    L    53_A      L    53_A     6.516     0    0.013   0.958     8.615   16.548   14.583
LGA    A    54_A      A    54_A     4.619     0    0.088   0.121     5.147   36.071   35.143
LGA    A    55_A      A    55_A     3.585     0    0.631   0.609     5.518   37.857   40.286
LGA    E    56_A      E    56_A     2.224     0    0.196   0.666     5.903   68.810   47.513
LGA    E    57_A      E    57_A     1.555     0    0.021   1.081     2.584   81.667   74.180
LGA    A    58_A      A    58_A     0.523     0    0.133   0.186     1.234   90.595   88.762
LGA    V    59_A      V    59_A     0.936     0    0.041   0.232     1.476   85.952   85.306
LGA    E    60_A      E    60_A     0.960     0    0.029   0.836     3.216   90.476   80.317
LGA    F    61_A      F    61_A     1.186     0    0.020   0.100     3.005   83.690   69.654
LGA    E    62_A      E    62_A     1.428     0    0.040   0.665     2.974   71.190   69.418
LGA    V    63_A      V    63_A     3.612     0    0.036   0.176     5.029   43.690   39.320
LGA    E    64_A      E    64_A     5.617     0    0.019   0.322     7.037   21.786   18.042
LGA    I    65_A      I    65_A     8.207     0    0.047   0.158     9.314    4.405    4.762
LGA    D    66_A      D    66_A    10.780     0    0.050   0.717    11.578    0.119    0.238
LGA    N    67_A      N    67_A    12.945     0    0.028   1.003    17.442    0.000    0.000
LGA    N    68_A      N    68_A    13.866     0    0.074   1.400    18.426    0.000    0.000
LGA    N    69_A      N    69_A    11.603     0    0.098   0.843    12.137    0.000    0.238
LGA    R    70_A      R    70_A    10.893     0    0.074   1.287    19.667    0.238    0.087
LGA    P    71_A      P    71_A     8.004     0    0.086   0.162     9.210    6.190    5.170
LGA    K    72_A      K    72_A     5.481     0    0.043   0.617     6.326   26.548   29.471
LGA    A    73_A      A    73_A     3.732     0    0.031   0.028     4.314   45.119   44.762
LGA    I    74_A      I    74_A     2.796     0    0.050   0.623     5.501   59.167   51.071
LGA    D    75_A      D    75_A     2.044     0    0.074   0.501     3.936   70.952   62.321
LGA    V    76_A      V    76_A     1.116     0    0.091   0.101     2.054   75.119   80.408
LGA    S    77_A      S    77_A     1.905     0    0.086   0.590     4.919   79.405   67.698

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       70     280    280  100.00     545    545  100.00                92
SUMMARY(RMSD_GDC):     4.483          4.448                  5.212           36.290   32.974

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   70   92    4.0     46    2.33    41.848    37.769     1.895

LGA_LOCAL      RMSD:   2.327  Number of atoms:   46  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   5.357  Number of assigned atoms:   70 
Std_ASGN_ATOMS RMSD:   4.483  Standard rmsd on all 70 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.197676 * X  +  -0.708087 * Y  +  -0.677892 * Z  + -14.573203
  Y_new =   0.281936 * X  +   0.703386 * Y  +  -0.652503 * Z  +  12.793859
  Z_new =   0.938848 * X  +  -0.062138 * Y  +   0.338678 * Z  +  -1.372617 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.959306 -1.219271 -0.181453   [DEG:   54.9642  -69.8591  -10.3965 ]
ZXZ: -0.804480  1.225285  1.636885   [DEG:  -46.0933   70.2037   93.7866 ]
 
# END of job
