
#######################################################
#                                                     #
#                        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        1.93     1.93
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    63       1_A - 63_A        1.93     1.93
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    25      14_A - 38_A        0.98     2.44
  LCS_AVERAGE:     30.44

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     11   63   63      4   11   26   43   57   59   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   13   23   49   57   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     I     3_A     I     3_A     21   63   63      5   24   43   52   57   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D     4_A     D     4_A     22   63   63      7   22   43   52   57   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     5_A     C     5_A     22   63   63      7   16   35   52   57   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D     6_A     D     6_A     22   63   63      7   13   34   52   57   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K     7_A     K     7_A     22   63   63      7   24   43   52   57   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E     8_A     E     8_A     22   63   63     10   24   43   52   57   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     9_A     C     9_A     22   63   63      7   20   43   52   57   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    10_A     N    10_A     22   63   63     10   24   43   52   57   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    11_A     R    11_A     22   63   63      4   21   43   52   57   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    12_A     R    12_A     22   63   63      4   21   43   52   57   59   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      4   20   43   52   57   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    14_A     S    14_A     25   63   63      7   24   43   52   57   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    15_A     K    15_A     25   63   63      3    7   23   47   57   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    16_A     A    16_A     25   63   63      5   24   43   52   57   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    17_A     S    17_A     25   63   63      7   24   43   52   57   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    18_A     A    18_A     25   63   63      4   11   43   52   57   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H    19_A     H    19_A     25   63   63      5   24   43   52   57   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    20_A     D    20_A     25   63   63     10   24   43   52   57   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    21_A     R    21_A     25   63   63     10   24   43   52   57   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    22_A     C    22_A     25   63   63     10   24   43   52   57   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    23_A     L    23_A     25   63   63     10   24   43   52   57   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    24_A     K    24_A     25   63   63      6   24   43   52   57   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    25_A     Y    25_A     25   63   63      6   24   43   52   57   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    26_A     C    26_A     25   63   63      5   24   43   52   57   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    27_A     G    27_A     25   63   63      6   22   43   52   57   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     I    28_A     I    28_A     25   63   63      6   24   43   52   57   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    29_A     C    29_A     25   63   63      6   24   43   52   57   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    30_A     C    30_A     25   63   63      5   18   42   52   57   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    31_A     E    31_A     25   63   63      4   14   37   52   57   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    32_A     K    32_A     25   63   63      5   21   42   52   57   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    33_A     C    33_A     25   63   63      7   24   43   52   57   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    34_A     N    34_A     25   63   63      6   24   43   52   57   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    35_A     C    35_A     25   63   63      7   24   43   52   57   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    36_A     V    36_A     25   63   63     10   24   43   52   57   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    37_A     P    37_A     25   63   63     10   22   43   52   57   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    38_A     P    38_A     25   63   63      9   24   43   52   57   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    39_A     G    39_A     24   63   63      4   24   43   52   57   59   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   31   43   54   59   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    6   13   23   37   48   59   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    5   15   23   37   48   59   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   17   41   52   57   59   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      6   20   43   52   57   59   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      6   20   43   52   57   59   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   17   43   52   57   59   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   20   43   52   57   59   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   22   43   52   57   59   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   20   37   52   57   59   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   20   43   52   57   59   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   20   43   52   57   59   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   20   43   52   57   59   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      6   20   43   52   57   59   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      4   14   37   52   57   59   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      6   16   29   51   57   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    56_A     S    56_A     12   63   63      5    8   17   29   50   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    57_A     K    57_A     12   63   63      6   11   28   42   57   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    58_A     G    58_A     12   63   63      6    8   22   42   57   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    59_A     G    59_A     12   63   63      6   14   33   51   57   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H    60_A     H    60_A     12   63   63      6   14   42   52   57   59   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      4   18   43   52   57   59   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   43   52   57   59   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   43   52   57   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_AVERAGE  LCS_A:  76.81  (  30.44  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     43     52     57     59     60     63     63     63     63     63     63     63     63     63     63     63     63     63 
GDT PERCENT_AT  15.87  38.10  68.25  82.54  90.48  93.65  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    0.35   0.74   1.07   1.26   1.45   1.58   1.66   1.93   1.93   1.93   1.93   1.93   1.93   1.93   1.93   1.93   1.93   1.93   1.93   1.93
GDT RMS_ALL_AT   2.46   2.64   2.24   2.09   2.00   1.96   1.96   1.93   1.93   1.93   1.93   1.93   1.93   1.93   1.93   1.93   1.93   1.93   1.93   1.93

# 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     2.536     0    0.134   0.191     3.573   75.476   69.048
LGA    H     2_A      H     2_A     2.049     0    0.049   0.760     5.712   73.095   50.810
LGA    I     3_A      I     3_A     0.227     0    0.090   0.904     2.962   90.595   85.238
LGA    D     4_A      D     4_A     1.319     0    0.064   1.065     3.954   79.405   69.643
LGA    C     5_A      C     5_A     2.015     0    0.083   0.251     2.490   70.833   70.159
LGA    D     6_A      D     6_A     1.587     0    0.020   0.581     3.458   79.405   73.333
LGA    K     7_A      K     7_A     0.453     0    0.086   0.537     2.612   92.857   84.974
LGA    E     8_A      E     8_A     1.151     0    0.059   0.402     1.617   81.548   84.497
LGA    C     9_A      C     9_A     1.448     0    0.071   0.084     1.675   81.429   78.571
LGA    N    10_A      N    10_A     0.734     0    0.124   0.300     1.381   85.952   84.821
LGA    R    11_A      R    11_A     1.569     0    0.026   1.507     5.733   75.000   59.870
LGA    R    12_A      R    12_A     1.467     0    0.016   1.480     6.648   81.429   62.251
LGA    C    13_A      C    13_A     1.161     0    0.248   0.266     2.999   81.548   77.460
LGA    S    14_A      S    14_A     1.000     0    0.072   0.667     3.191   77.381   75.000
LGA    K    15_A      K    15_A     3.033     0    0.153   1.016     4.551   57.262   52.963
LGA    A    16_A      A    16_A     1.824     0    0.061   0.074     2.215   70.833   72.952
LGA    S    17_A      S    17_A     2.081     0    0.028   0.690     3.892   66.786   62.540
LGA    A    18_A      A    18_A     2.129     0    0.046   0.052     2.318   68.810   68.000
LGA    H    19_A      H    19_A     1.772     0    0.206   1.172     3.436   68.929   65.905
LGA    D    20_A      D    20_A     1.474     0    0.193   0.220     2.039   79.286   74.048
LGA    R    21_A      R    21_A     1.702     0    0.073   1.293     8.300   77.143   50.087
LGA    C    22_A      C    22_A     1.175     0    0.082   0.128     1.487   81.429   82.937
LGA    L    23_A      L    23_A     1.063     0    0.067   0.165     1.793   85.952   81.548
LGA    K    24_A      K    24_A     2.318     0    0.086   0.433     5.227   66.786   53.016
LGA    Y    25_A      Y    25_A     2.219     0    0.025   0.681     3.255   64.762   63.651
LGA    C    26_A      C    26_A     1.772     0    0.098   0.201     2.013   70.833   72.937
LGA    G    27_A      G    27_A     1.866     0    0.173   0.173     2.803   66.905   66.905
LGA    I    28_A      I    28_A     1.875     0    0.109   0.726     4.734   72.857   64.643
LGA    C    29_A      C    29_A     1.723     0    0.056   0.692     1.734   75.000   75.714
LGA    C    30_A      C    30_A     1.541     0    0.050   0.077     2.072   77.143   74.365
LGA    E    31_A      E    31_A     1.484     0    0.033   0.408     3.605   81.429   69.101
LGA    K    32_A      K    32_A     1.053     0    0.059   1.048     6.314   83.690   62.698
LGA    C    33_A      C    33_A     0.835     0    0.600   0.520     3.542   74.286   72.619
LGA    N    34_A      N    34_A     1.014     0    0.233   0.394     3.388   88.333   72.917
LGA    C    35_A      C    35_A     1.028     0    0.023   0.390     1.777   88.214   83.095
LGA    V    36_A      V    36_A     0.623     0    0.146   0.170     1.586   90.476   87.959
LGA    P    37_A      P    37_A     0.349     0    0.071   0.318     0.675   95.238   95.918
LGA    P    38_A      P    38_A     1.456     0    0.046   0.103     1.709   79.286   78.980
LGA    G    39_A      G    39_A     2.192     0    0.144   0.144     2.951   62.976   62.976
LGA    T    40_A      T    40_A     4.563     0    0.573   0.545     5.748   34.762   31.156
LGA    Y    41_A      Y    41_A     4.713     0    0.151   1.027     6.524   31.429   26.746
LGA    G    42_A      G    42_A     4.466     0    0.590   0.590     5.636   31.786   31.786
LGA    N    43_A      N    43_A     1.295     0    0.285   0.336     2.040   75.119   78.274
LGA    E    44_A      E    44_A     0.545     0    0.128   0.595     3.285   92.857   73.545
LGA    D    45_A      D    45_A     1.050     0    0.096   1.067     5.839   83.690   64.762
LGA    S    46_A      S    46_A     1.334     0    0.155   0.166     1.771   79.286   80.000
LGA    C    47_A      C    47_A     0.727     0    0.083   0.340     1.645   92.857   87.619
LGA    P    48_A      P    48_A     0.476     0    0.067   0.334     1.345   92.976   93.265
LGA    C    49_A      C    49_A     1.781     0    0.032   0.240     3.134   72.976   67.778
LGA    Y    50_A      Y    50_A     0.969     0    0.113   0.343     2.344   85.952   82.381
LGA    A    51_A      A    51_A     1.023     0    0.140   0.149     1.588   79.286   81.524
LGA    N    52_A      N    52_A     1.203     0    0.137   0.169     2.393   85.952   77.381
LGA    L    53_A      L    53_A     1.049     0    0.072   0.881     3.000   81.429   78.750
LGA    K    54_A      K    54_A     1.430     0    0.110   1.218     4.314   81.429   71.111
LGA    N    55_A      N    55_A     1.958     0    0.050   0.094     2.913   67.143   70.060
LGA    S    56_A      S    56_A     4.168     0    0.152   0.675     6.647   37.619   32.540
LGA    K    57_A      K    57_A     3.217     0    0.164   0.544     5.413   50.000   45.979
LGA    G    58_A      G    58_A     3.016     0    0.140   0.140     3.016   55.357   55.357
LGA    G    59_A      G    59_A     1.788     0    0.039   0.039     2.084   75.119   75.119
LGA    H    60_A      H    60_A     1.517     0    0.173   1.010     5.886   75.000   55.905
LGA    K    61_A      K    61_A     1.343     0    0.036   0.737     1.782   77.143   82.646
LGA    C    62_A      C    62_A     1.970     0    0.037   0.049     2.263   72.857   70.159
LGA    P    63_A      P    63_A     1.635     0    0.331   0.483     2.126   70.833   72.925

# 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):     1.929          1.954                  2.495           74.658   69.538

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63   63    4.0     63    1.93    80.159    90.233     3.105

LGA_LOCAL      RMSD:   1.929  Number of atoms:   63  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.929  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:   1.929  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.295894 * X  +   0.415980 * Y  +   0.859888 * Z  +  -9.617526
  Y_new =   0.165996 * X  +   0.908894 * Y  +  -0.382567 * Z  +   1.602511
  Z_new =  -0.940687 * X  +   0.029538 * Y  +  -0.337988 * Z  + -14.949541 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.630346  1.224649  3.054419   [DEG:  150.7077   70.1672  175.0053 ]
ZXZ:  1.152189  1.915574 -1.539406   [DEG:   66.0156  109.7543  -88.2015 ]
 
# END of job
