
#######################################################
#                                                     #
#                        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        1.86     1.86
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    63       1_A - 63_A        1.86     1.86
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    26      14_A - 39_A        1.00     2.43
  LCS_AVERAGE:     30.84

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   63   63      4   16   24   44   57   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H     2_A     H     2_A     13   63   63      4   11   28   46   57   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     I     3_A     I     3_A     15   63   63      7   24   46   53   57   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D     4_A     D     4_A     21   63   63      7   21   46   53   57   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     5_A     C     5_A     21   63   63      7   16   34   53   57   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D     6_A     D     6_A     21   63   63      7   11   33   53   57   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K     7_A     K     7_A     21   63   63      7   24   46   53   57   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E     8_A     E     8_A     21   63   63     10   24   46   53   57   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     9_A     C     9_A     21   63   63      7   22   46   53   57   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    10_A     N    10_A     21   63   63     10   24   46   53   57   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    11_A     R    11_A     21   63   63      4   22   46   53   57   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    12_A     R    12_A     21   63   63      4   22   46   53   57   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    13_A     C    13_A     23   63   63      3   22   46   53   57   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    14_A     S    14_A     26   63   63      5   24   46   53   57   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    15_A     K    15_A     26   63   63      3    5   24   47   57   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    16_A     A    16_A     26   63   63      5   24   46   53   57   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    17_A     S    17_A     26   63   63      6   24   46   53   57   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    18_A     A    18_A     26   63   63      4   11   46   53   57   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H    19_A     H    19_A     26   63   63      4   22   46   53   57   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    20_A     D    20_A     26   63   63     10   24   46   53   57   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    21_A     R    21_A     26   63   63     10   24   46   53   57   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    22_A     C    22_A     26   63   63     10   24   46   53   57   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    23_A     L    23_A     26   63   63     10   24   46   53   57   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    24_A     K    24_A     26   63   63      6   24   46   53   57   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    25_A     Y    25_A     26   63   63      6   24   46   53   57   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    26_A     C    26_A     26   63   63      5   24   46   53   57   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    27_A     G    27_A     26   63   63      4   24   46   53   57   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     I    28_A     I    28_A     26   63   63      6   24   46   53   57   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    29_A     C    29_A     26   63   63      6   24   46   53   57   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    30_A     C    30_A     26   63   63      5   19   46   53   57   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    31_A     E    31_A     26   63   63      4   16   38   53   57   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    32_A     K    32_A     26   63   63      4   22   46   53   57   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    33_A     C    33_A     26   63   63      7   24   46   53   57   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    34_A     N    34_A     26   63   63      5   24   46   53   57   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    35_A     C    35_A     26   63   63      7   24   46   53   57   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    36_A     V    36_A     26   63   63     10   24   46   53   57   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    37_A     P    37_A     26   63   63     10   24   46   53   57   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    38_A     P    38_A     26   63   63     10   24   46   53   57   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    39_A     G    39_A     26   63   63      5   21   43   53   57   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     T    40_A     T    40_A      8   63   63      3    6   13   32   44   54   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    41_A     Y    41_A      8   63   63      3    7   13   23   40   53   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    42_A     G    42_A     12   63   63      4    6   15   24   40   53   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    43_A     N    43_A     13   63   63      5   18   46   53   57   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    44_A     E    44_A     13   63   63      7   22   46   53   57   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    45_A     D    45_A     13   63   63      5   22   46   53   57   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    46_A     S    46_A     13   63   63      5   18   46   53   57   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    47_A     C    47_A     13   63   63      5   22   46   53   57   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    48_A     P    48_A     13   63   63     10   24   46   53   57   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    49_A     C    49_A     13   63   63      4   22   38   53   57   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    50_A     Y    50_A     13   63   63     10   22   46   53   57   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    51_A     A    51_A     13   63   63     10   22   46   53   57   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    52_A     N    52_A     13   63   63      5   22   46   53   57   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    53_A     L    53_A     13   63   63      5   18   46   53   57   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    54_A     K    54_A     13   63   63      3   16   38   53   57   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    55_A     N    55_A     13   63   63      5   16   30   53   57   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    56_A     S    56_A     13   63   63      5    8   20   34   56   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    57_A     K    57_A     13   63   63      5   16   29   46   57   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    58_A     G    58_A     13   63   63      5   16   29   46   57   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    59_A     G    59_A     13   63   63      5   16   38   53   57   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H    60_A     H    60_A     13   63   63      5   14   46   53   57   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    61_A     K    61_A     12   63   63      5   20   46   53   57   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    62_A     C    62_A     12   63   63      7   24   46   53   57   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    63_A     P    63_A     12   63   63      7   24   46   53   57   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_AVERAGE  LCS_A:  76.95  (  30.84  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     10     24     46     53     57     60     60     63     63     63     63     63     63     63     63     63     63     63     63     63 
GDT PERCENT_AT  15.87  38.10  73.02  84.13  90.48  95.24  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    0.37   0.77   1.12   1.27   1.43   1.59   1.59   1.86   1.86   1.86   1.86   1.86   1.86   1.86   1.86   1.86   1.86   1.86   1.86   1.86
GDT RMS_ALL_AT   2.31   2.42   2.03   1.96   1.91   1.89   1.89   1.86   1.86   1.86   1.86   1.86   1.86   1.86   1.86   1.86   1.86   1.86   1.86   1.86

# Checking swapping
#   possible swapping detected:  E     8_A      E     8_A
#   possible swapping detected:  Y    41_A      Y    41_A
#   possible swapping detected:  E    44_A      E    44_A
#   possible swapping detected:  D    45_A      D    45_A
#   possible swapping detected:  Y    50_A      Y    50_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A     1_A      A     1_A     2.936     0    0.102   0.150     4.315   73.333   66.095
LGA    H     2_A      H     2_A     2.353     0    0.040   0.755     6.796   64.881   42.905
LGA    I     3_A      I     3_A     0.298     0    0.080   0.923     2.788   88.333   84.107
LGA    D     4_A      D     4_A     1.281     0    0.073   1.067     3.875   81.548   70.714
LGA    C     5_A      C     5_A     2.071     0    0.086   0.246     2.616   70.833   67.540
LGA    D     6_A      D     6_A     1.692     0    0.014   0.572     3.724   79.405   72.500
LGA    K     7_A      K     7_A     0.394     0    0.088   0.535     2.724   92.857   82.116
LGA    E     8_A      E     8_A     1.005     0    0.059   0.449     1.541   81.548   84.497
LGA    C     9_A      C     9_A     1.431     0    0.080   0.085     1.836   81.429   78.571
LGA    N    10_A      N    10_A     0.658     0    0.121   0.346     1.502   88.214   86.012
LGA    R    11_A      R    11_A     1.454     0    0.025   1.500     5.564   79.286   62.771
LGA    R    12_A      R    12_A     1.435     0    0.016   1.443     6.573   81.429   62.251
LGA    C    13_A      C    13_A     1.179     0    0.249   0.259     3.037   81.548   76.270
LGA    S    14_A      S    14_A     1.100     0    0.080   0.665     3.251   73.452   72.381
LGA    K    15_A      K    15_A     3.141     0    0.146   1.018     4.604   57.262   52.169
LGA    A    16_A      A    16_A     1.912     0    0.046   0.056     2.287   70.833   72.952
LGA    S    17_A      S    17_A     2.220     0    0.039   0.694     4.126   64.762   60.159
LGA    A    18_A      A    18_A     2.121     0    0.076   0.081     2.268   64.762   64.762
LGA    H    19_A      H    19_A     1.815     0    0.204   1.195     3.630   68.929   65.238
LGA    D    20_A      D    20_A     1.454     0    0.198   0.226     2.084   79.286   74.048
LGA    R    21_A      R    21_A     1.573     0    0.079   0.974     4.589   79.405   59.957
LGA    C    22_A      C    22_A     1.055     0    0.078   0.121     1.373   83.690   85.952
LGA    L    23_A      L    23_A     1.051     0    0.068   0.158     1.822   85.952   81.548
LGA    K    24_A      K    24_A     2.176     0    0.092   0.431     5.015   66.786   54.339
LGA    Y    25_A      Y    25_A     2.009     0    0.020   0.669     3.030   70.833   65.595
LGA    C    26_A      C    26_A     1.542     0    0.104   0.207     1.777   72.857   74.286
LGA    G    27_A      G    27_A     1.638     0    0.172   0.172     2.585   68.929   68.929
LGA    I    28_A      I    28_A     1.681     0    0.104   0.697     4.525   75.000   65.714
LGA    C    29_A      C    29_A     1.546     0    0.053   0.677     1.562   77.143   77.143
LGA    C    30_A      C    30_A     1.402     0    0.048   0.079     1.988   81.429   78.571
LGA    E    31_A      E    31_A     1.462     0    0.041   0.425     3.575   79.286   68.148
LGA    K    32_A      K    32_A     1.105     0    0.064   1.175     7.133   83.690   62.169
LGA    C    33_A      C    33_A     0.765     0    0.607   0.524     3.510   74.286   72.619
LGA    N    34_A      N    34_A     1.032     0    0.213   0.439     3.365   86.071   74.702
LGA    C    35_A      C    35_A     1.083     0    0.020   0.389     1.713   85.952   81.587
LGA    V    36_A      V    36_A     0.664     0    0.147   0.171     1.565   90.476   85.374
LGA    P    37_A      P    37_A     0.427     0    0.071   0.321     0.727   95.238   95.918
LGA    P    38_A      P    38_A     1.469     0    0.046   0.100     1.742   79.286   78.980
LGA    G    39_A      G    39_A     2.128     0    0.148   0.148     2.935   62.976   62.976
LGA    T    40_A      T    40_A     4.451     0    0.564   0.556     5.596   36.190   31.973
LGA    Y    41_A      Y    41_A     4.542     0    0.154   1.047     6.174   34.286   30.119
LGA    G    42_A      G    42_A     4.299     0    0.596   0.596     5.449   34.524   34.524
LGA    N    43_A      N    43_A     1.127     0    0.288   0.328     1.850   77.143   80.417
LGA    E    44_A      E    44_A     0.487     0    0.120   0.679     3.142   95.238   78.042
LGA    D    45_A      D    45_A     0.923     0    0.101   1.084     5.557   88.214   68.929
LGA    S    46_A      S    46_A     1.400     0    0.150   0.157     1.861   79.286   80.000
LGA    C    47_A      C    47_A     0.855     0    0.074   0.343     1.709   90.476   86.032
LGA    P    48_A      P    48_A     0.475     0    0.071   0.334     1.210   92.976   93.265
LGA    C    49_A      C    49_A     1.713     0    0.055   0.236     3.146   72.976   67.778
LGA    Y    50_A      Y    50_A     0.927     0    0.113   0.319     2.219   90.476   83.889
LGA    A    51_A      A    51_A     0.969     0    0.129   0.132     1.483   85.952   86.857
LGA    N    52_A      N    52_A     1.085     0    0.089   0.176     2.244   88.214   80.595
LGA    L    53_A      L    53_A     1.106     0    0.080   0.707     2.349   79.286   79.405
LGA    K    54_A      K    54_A     1.445     0    0.109   1.268     4.930   81.429   69.735
LGA    N    55_A      N    55_A     1.817     0    0.053   0.100     2.665   67.143   71.071
LGA    S    56_A      S    56_A     3.803     0    0.158   0.676     6.403   42.024   37.063
LGA    K    57_A      K    57_A     2.728     0    0.180   0.563     5.068   57.143   52.222
LGA    G    58_A      G    58_A     2.526     0    0.143   0.143     2.526   62.857   62.857
LGA    G    59_A      G    59_A     1.497     0    0.032   0.032     1.775   79.286   79.286
LGA    H    60_A      H    60_A     1.419     0    0.176   1.035     5.959   81.429   58.476
LGA    K    61_A      K    61_A     1.377     0    0.037   0.750     1.887   79.286   82.540
LGA    C    62_A      C    62_A     1.716     0    0.047   0.095     2.155   77.143   74.365
LGA    P    63_A      P    63_A     1.469     0    0.321   0.453     2.011   72.976   74.150

# 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):     1.857          1.878                  2.413           75.701   70.415

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63   63    4.0     63    1.86    80.556    90.796     3.219

LGA_LOCAL      RMSD:   1.857  Number of atoms:   63  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.857  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:   1.857  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.350212 * X  +   0.808946 * Y  +  -0.472184 * Z  + -15.411135
  Y_new =  -0.918564 * X  +  -0.395250 * Y  +   0.004143 * Z  +  -0.065359
  Z_new =  -0.183280 * X  +   0.435182 * Y  +   0.881490 * Z  + -12.619246 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.935044  0.184322  0.458586   [DEG: -110.8699   10.5609   26.2751 ]
ZXZ: -1.579570  0.491787 -0.398610   [DEG:  -90.5027   28.1773  -22.8387 ]
 
# END of job
