
#######################################################
#                                                     #
#                        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 (  472),  selected   63 , name one
# Molecule2: number of CA atoms   63 (  472),  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        1.90     1.90
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    63       1_A - 63_A        1.90     1.90
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    33       4_A - 36_A        0.98     3.03
  LONGEST_CONTINUOUS_SEGMENT:    33       5_A - 37_A        0.96     2.97
  LCS_AVERAGE:     37.79

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     G     1_A     G     1_A      7   63   63      2   11   27   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     2_A     S     2_A     12   63   63      3   15   33   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     3_A     S     3_A     12   63   63      3   12   33   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     F     4_A     F     4_A     33   63   63      3    9   33   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     5_A     C     5_A     33   63   63      4   22   34   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D     6_A     D     6_A     33   63   63      4   25   34   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     7_A     S     7_A     33   63   63      5   25   34   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K     8_A     K     8_A     33   63   63     10   25   34   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     9_A     C     9_A     33   63   63      9   24   34   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    10_A     G    10_A     33   63   63     10   25   34   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    11_A     V    11_A     33   63   63     10   25   34   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    12_A     R    12_A     33   63   63     10   25   34   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    13_A     C    13_A     33   63   63      7   25   34   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    14_A     S    14_A     33   63   63      4   21   34   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    15_A     K    15_A     33   63   63      5   21   34   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    16_A     A    16_A     33   63   63      5   23   34   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    17_A     G    17_A     33   63   63      4   21   29   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    18_A     Y    18_A     33   63   63      8   25   34   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Q    19_A     Q    19_A     33   63   63      4   21   34   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    20_A     E    20_A     33   63   63     11   25   34   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    21_A     R    21_A     33   63   63     10   25   34   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    22_A     C    22_A     33   63   63      6   25   34   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    23_A     L    23_A     33   63   63     11   25   34   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    24_A     K    24_A     33   63   63     10   25   34   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    25_A     Y    25_A     33   63   63     10   25   34   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    26_A     C    26_A     33   63   63     10   25   34   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    27_A     G    27_A     33   63   63     11   25   34   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     I    28_A     I    28_A     33   63   63     10   25   34   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    29_A     C    29_A     33   63   63     11   25   34   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    30_A     C    30_A     33   63   63     11   25   34   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    31_A     E    31_A     33   63   63     11   25   34   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    32_A     K    32_A     33   63   63     11   25   34   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    33_A     C    33_A     33   63   63     11   25   34   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H    34_A     H    34_A     33   63   63     11   25   34   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    35_A     C    35_A     33   63   63     11   23   34   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    36_A     V    36_A     33   63   63     11   25   34   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    37_A     P    37_A     33   63   63     11   21   34   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    38_A     S    38_A     27   63   63      5   21   32   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    39_A     G    39_A     27   63   63      6   25   34   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     T    40_A     T    40_A     24   63   63      4   15   33   40   51   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    41_A     Y    41_A     13   63   63      3   18   27   39   48   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    42_A     G    42_A     13   63   63      3    6   18   36   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    43_A     N    43_A     12   63   63      6   20   33   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    44_A     K    44_A     12   63   63      6   19   33   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    45_A     D    45_A     12   63   63      5   13   29   45   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    46_A     E    46_A     12   63   63      5   19   32   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    47_A     C    47_A     12   63   63      5   20   33   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    48_A     P    48_A     12   63   63      5    8   23   37   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    49_A     C    49_A     12   63   63      5   10   29   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    50_A     Y    50_A     12   63   63      5   10   24   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    51_A     R    51_A     12   63   63      5    8   33   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    52_A     D    52_A     12   63   63      5   20   33   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    53_A     L    53_A     12   63   63      5   19   33   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    54_A     K    54_A     12   63   63      5   18   30   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    55_A     N    55_A     11   63   63      5   13   26   38   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    56_A     S    56_A     11   63   63      5   10   24   35   44   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    57_A     K    57_A     11   63   63      5   13   26   38   52   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    58_A     G    58_A     11   63   63      5   13   27   45   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    59_A     N    59_A     11   63   63     11   20   33   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    60_A     P    60_A     11   63   63     11   21   34   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    61_A     K    61_A     11   63   63      3   10   34   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    62_A     C    62_A     11   63   63      3   15   33   39   48   58   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    63_A     P    63_A     11   63   63      3   11   27   37   48   55   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_AVERAGE  LCS_A:  79.26  (  37.79  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     11     25     34     48     56     59     62     63     63     63     63     63     63     63     63     63     63     63     63     63 
GDT PERCENT_AT  17.46  39.68  53.97  76.19  88.89  93.65  98.41 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.36   0.65   0.92   1.41   1.60   1.71   1.86   1.90   1.90   1.90   1.90   1.90   1.90   1.90   1.90   1.90   1.90   1.90   1.90   1.90
GDT RMS_ALL_AT   2.25   3.11   2.79   2.02   1.93   1.92   1.90   1.90   1.90   1.90   1.90   1.90   1.90   1.90   1.90   1.90   1.90   1.90   1.90   1.90

# Checking swapping
#   possible swapping detected:  F     4_A      F     4_A
#   possible swapping detected:  Y    18_A      Y    18_A
#   possible swapping detected:  E    46_A      E    46_A
#   possible swapping detected:  D    52_A      D    52_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    G     1_A      G     1_A     2.071     0    0.060   0.060     3.127   71.667   71.667
LGA    S     2_A      S     2_A     2.144     0    0.212   0.797     3.760   70.952   62.857
LGA    S     3_A      S     3_A     2.168     0    0.168   0.504     3.828   68.810   62.619
LGA    F     4_A      F     4_A     1.720     0    0.076   0.211     3.789   72.857   60.390
LGA    C     5_A      C     5_A     1.841     0    0.112   0.796     2.643   72.857   70.238
LGA    D     6_A      D     6_A     1.818     0    0.120   1.102     5.921   72.857   55.774
LGA    S     7_A      S     7_A     2.174     0    0.114   0.561     4.220   62.857   58.889
LGA    K     8_A      K     8_A     1.446     0    0.107   0.741     5.671   79.286   67.831
LGA    C     9_A      C     9_A     1.499     0    0.052   0.065     1.791   77.143   78.571
LGA    G    10_A      G    10_A     1.563     0    0.122   0.122     1.585   75.000   75.000
LGA    V    11_A      V    11_A     1.999     0    0.052   0.066     2.333   70.833   68.231
LGA    R    12_A      R    12_A     1.734     0    0.058   1.360     8.146   72.857   52.554
LGA    C    13_A      C    13_A     1.012     0    0.636   0.714     2.522   77.619   80.397
LGA    S    14_A      S    14_A     1.376     0    0.103   0.621     1.973   79.286   77.143
LGA    K    15_A      K    15_A     1.243     0    0.105   0.650     4.201   81.429   68.571
LGA    A    16_A      A    16_A     1.206     0    0.622   0.559     2.703   75.357   76.571
LGA    G    17_A      G    17_A     2.407     0    0.034   0.034     2.789   62.857   62.857
LGA    Y    18_A      Y    18_A     2.039     0    0.269   1.385     7.481   68.929   50.278
LGA    Q    19_A      Q    19_A     1.210     0    0.110   1.204     4.012   85.952   75.767
LGA    E    20_A      E    20_A     1.610     0    0.025   0.673     4.054   72.976   62.222
LGA    R    21_A      R    21_A     2.228     0    0.058   1.287    12.153   66.786   35.195
LGA    C    22_A      C    22_A     1.494     0    0.070   0.092     1.732   77.143   77.143
LGA    L    23_A      L    23_A     1.110     0    0.056   0.305     2.230   81.429   78.274
LGA    K    24_A      K    24_A     1.935     0    0.065   1.110     9.802   70.833   45.291
LGA    Y    25_A      Y    25_A     2.159     0    0.117   0.540     3.313   68.810   65.000
LGA    C    26_A      C    26_A     1.081     0    0.042   0.102     1.291   83.690   84.444
LGA    G    27_A      G    27_A     0.907     0    0.052   0.052     1.464   85.952   85.952
LGA    I    28_A      I    28_A     1.806     0    0.044   0.751     4.883   75.000   63.036
LGA    C    29_A      C    29_A     1.429     0    0.099   0.129     1.858   83.690   80.079
LGA    C    30_A      C    30_A     0.869     0    0.139   0.151     1.193   88.214   90.556
LGA    E    31_A      E    31_A     0.753     0    0.019   0.857     4.011   90.476   76.138
LGA    K    32_A      K    32_A     1.080     0    0.070   0.883     2.000   85.952   79.630
LGA    C    33_A      C    33_A     1.101     0    0.225   0.231     2.041   77.262   80.159
LGA    H    34_A      H    34_A     1.354     0    0.097   1.271     3.322   79.286   70.238
LGA    C    35_A      C    35_A     1.308     0    0.074   0.610     2.379   81.429   77.222
LGA    V    36_A      V    36_A     1.140     0    0.070   0.293     2.278   81.429   77.823
LGA    P    37_A      P    37_A     0.980     0    0.045   0.322     1.297   88.214   87.891
LGA    S    38_A      S    38_A     1.369     0    0.233   0.657     5.099   81.548   69.524
LGA    G    39_A      G    39_A     1.768     0    0.068   0.068     2.548   66.905   66.905
LGA    T    40_A      T    40_A     3.128     0    0.493   0.399     4.256   50.476   51.429
LGA    Y    41_A      Y    41_A     3.265     0    0.147   0.298     4.051   55.476   47.976
LGA    G    42_A      G    42_A     2.609     0    0.630   0.630     4.691   50.714   50.714
LGA    N    43_A      N    43_A     1.191     0    0.202   0.853     4.242   83.690   67.560
LGA    K    44_A      K    44_A     1.250     0    0.056   1.014     8.058   77.143   57.407
LGA    D    45_A      D    45_A     2.121     0    0.089   1.033     3.823   70.833   62.262
LGA    E    46_A      E    46_A     1.534     0    0.133   0.168     2.715   79.405   70.476
LGA    C    47_A      C    47_A     0.914     0    0.103   0.232     2.384   79.524   77.381
LGA    P    48_A      P    48_A     2.268     0    0.246   0.436     2.805   68.810   69.524
LGA    C    49_A      C    49_A     1.846     0    0.101   0.221     2.184   72.976   73.016
LGA    Y    50_A      Y    50_A     1.862     0    0.087   0.824     5.408   72.857   53.611
LGA    R    51_A      R    51_A     1.156     0    0.036   1.206     5.713   83.690   64.372
LGA    D    52_A      D    52_A     0.289     0    0.091   0.765     3.330   92.857   80.179
LGA    L    53_A      L    53_A     1.078     0    0.027   0.737     4.136   83.690   73.869
LGA    K    54_A      K    54_A     1.491     0    0.034   1.288     6.204   73.095   61.217
LGA    N    55_A      N    55_A     2.701     0    0.088   0.239     3.082   55.476   60.119
LGA    S    56_A      S    56_A     3.977     0    0.139   0.566     6.087   42.024   36.111
LGA    K    57_A      K    57_A     3.398     0    0.037   0.770     5.985   50.000   38.942
LGA    G    58_A      G    58_A     2.228     0    0.039   0.039     2.498   68.810   68.810
LGA    N    59_A      N    59_A     0.782     0    0.024   0.871     3.007   90.595   84.405
LGA    P    60_A      P    60_A     1.662     0    0.073   0.324     2.834   75.000   69.524
LGA    K    61_A      K    61_A     2.350     0    0.034   0.970     3.200   59.167   60.794
LGA    C    62_A      C    62_A     3.248     0    0.104   0.526     4.213   48.452   46.825
LGA    P    63_A      P    63_A     3.707     0    0.308   0.295     4.244   41.786   43.401

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       63     252    252  100.00     472    472  100.00                63
SUMMARY(RMSD_GDC):     1.902          1.924                  2.812           73.222   66.648

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63   63    4.0     63    1.90    78.968    88.924     3.147

LGA_LOCAL      RMSD:   1.902  Number of atoms:   63  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.902  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:   1.902  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.479775 * X  +  -0.003581 * Y  +   0.877384 * Z  +  -6.851749
  Y_new =   0.613735 * X  +   0.713257 * Y  +   0.338516 * Z  +   2.239069
  Z_new =  -0.627013 * X  +   0.700893 * Y  +  -0.340005 * Z  +  -9.619199 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.234297  0.677713  2.022455   [DEG:  128.0158   38.8301  115.8782 ]
ZXZ:  1.939022  1.917719 -0.729819   [DEG:  111.0978  109.8772  -41.8156 ]
 
# END of job
