
#######################################################
#                                                     #
#                        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   64 (  508),  selected   51 , name one
# Molecule2: number of CA atoms   51 (  404),  selected   51 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:C  -ch2:C  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    51       6_C - 56_C        2.81     2.81
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    48       6_C - 53_C        1.92     3.03
  LCS_AVERAGE:     91.35

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    23      29_C - 51_C        0.91     3.22
  LCS_AVERAGE:     37.87

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   51
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     P     6_C     P     6_C     12   48   51      3    6   20   31   39   43   44   45   47   47   48   50   51   51   51   51   51   51   51   51 
LCS_GDT     T     7_C     T     7_C     14   48   51      3    6   16   29   33   38   43   45   46   47   48   50   51   51   51   51   51   51   51   51 
LCS_GDT     K     8_C     K     8_C     19   48   51      3   13   27   37   39   43   44   45   47   47   48   50   51   51   51   51   51   51   51   51 
LCS_GDT     I     9_C     I     9_C     19   48   51     10   28   38   40   42   43   44   45   47   47   48   50   51   51   51   51   51   51   51   51 
LCS_GDT     L    10_C     L    10_C     19   48   51     10   31   38   40   42   43   44   45   47   47   48   50   51   51   51   51   51   51   51   51 
LCS_GDT     P    11_C     P    11_C     19   48   51     12   33   38   40   42   43   44   45   47   47   48   50   51   51   51   51   51   51   51   51 
LCS_GDT     C    12_C     C    12_C     19   48   51     20   33   38   40   42   43   44   45   47   47   48   50   51   51   51   51   51   51   51   51 
LCS_GDT     P    13_C     P    13_C     19   48   51     15   33   38   40   42   43   44   45   47   47   48   50   51   51   51   51   51   51   51   51 
LCS_GDT     R    14_C     R    14_C     19   48   51     15   33   38   40   42   43   44   45   47   47   48   50   51   51   51   51   51   51   51   51 
LCS_GDT     C    15_C     C    15_C     19   48   51     20   33   38   40   42   43   44   45   47   47   48   50   51   51   51   51   51   51   51   51 
LCS_GDT     N    16_C     N    16_C     19   48   51     20   33   38   40   42   43   44   45   47   47   48   50   51   51   51   51   51   51   51   51 
LCS_GDT     S    17_C     S    17_C     19   48   51     20   33   38   40   42   43   44   45   47   47   48   50   51   51   51   51   51   51   51   51 
LCS_GDT     M    18_C     M    18_C     19   48   51     18   33   38   40   42   43   44   45   47   47   48   50   51   51   51   51   51   51   51   51 
LCS_GDT     E    19_C     E    19_C     19   48   51     16   33   38   40   42   43   44   45   47   47   48   50   51   51   51   51   51   51   51   51 
LCS_GDT     T    20_C     T    20_C     19   48   51     11   33   38   40   42   43   44   45   47   47   48   50   51   51   51   51   51   51   51   51 
LCS_GDT     K    21_C     K    21_C     19   48   51     20   33   38   40   42   43   44   45   47   47   48   50   51   51   51   51   51   51   51   51 
LCS_GDT     F    22_C     F    22_C     19   48   51     20   33   38   40   42   43   44   45   47   47   48   50   51   51   51   51   51   51   51   51 
LCS_GDT     C    23_C     C    23_C     19   48   51     20   33   38   40   42   43   44   45   47   47   48   50   51   51   51   51   51   51   51   51 
LCS_GDT     Y    24_C     Y    24_C     19   48   51     19   33   38   40   42   43   44   45   47   47   48   50   51   51   51   51   51   51   51   51 
LCS_GDT     Y    25_C     Y    25_C     19   48   51     19   33   38   40   42   43   44   45   47   47   48   50   51   51   51   51   51   51   51   51 
LCS_GDT     N    26_C     N    26_C     19   48   51      4   33   38   40   42   43   44   45   47   47   48   50   51   51   51   51   51   51   51   51 
LCS_GDT     N    27_C     N    27_C     19   48   51      3   22   36   40   42   43   44   45   47   47   48   50   51   51   51   51   51   51   51   51 
LCS_GDT     Y    28_C     Y    28_C     13   48   51      5   11   14   20   38   42   44   45   47   47   48   50   51   51   51   51   51   51   51   51 
LCS_GDT     N    29_C     N    29_C     23   48   51      5   25   33   40   42   43   44   45   47   47   48   50   51   51   51   51   51   51   51   51 
LCS_GDT     V    30_C     V    30_C     23   48   51      5   11   33   40   42   43   44   45   47   47   48   50   51   51   51   51   51   51   51   51 
LCS_GDT     N    31_C     N    31_C     23   48   51     11   28   38   40   42   43   44   45   47   47   48   50   51   51   51   51   51   51   51   51 
LCS_GDT     Q    32_C     Q    32_C     23   48   51     20   33   38   40   42   43   44   45   47   47   48   50   51   51   51   51   51   51   51   51 
LCS_GDT     P    33_C     P    33_C     23   48   51     20   33   38   40   42   43   44   45   47   47   48   50   51   51   51   51   51   51   51   51 
LCS_GDT     R    34_C     R    34_C     23   48   51     20   33   38   40   42   43   44   45   47   47   48   50   51   51   51   51   51   51   51   51 
LCS_GDT     H    35_C     H    35_C     23   48   51     20   33   38   40   42   43   44   45   47   47   48   50   51   51   51   51   51   51   51   51 
LCS_GDT     F    36_C     F    36_C     23   48   51     20   33   38   40   42   43   44   45   47   47   48   50   51   51   51   51   51   51   51   51 
LCS_GDT     C    37_C     C    37_C     23   48   51     20   33   38   40   42   43   44   45   47   47   48   50   51   51   51   51   51   51   51   51 
LCS_GDT     K    38_C     K    38_C     23   48   51     20   33   38   40   42   43   44   45   47   47   48   50   51   51   51   51   51   51   51   51 
LCS_GDT     A    39_C     A    39_C     23   48   51     20   33   38   40   42   43   44   45   47   47   48   50   51   51   51   51   51   51   51   51 
LCS_GDT     C    40_C     C    40_C     23   48   51     20   33   38   40   42   43   44   45   47   47   48   49   51   51   51   51   51   51   51   51 
LCS_GDT     Q    41_C     Q    41_C     23   48   51     20   33   38   40   42   43   44   45   47   47   48   50   51   51   51   51   51   51   51   51 
LCS_GDT     R    42_C     R    42_C     23   48   51     20   33   38   40   42   43   44   45   47   47   48   50   51   51   51   51   51   51   51   51 
LCS_GDT     Y    43_C     Y    43_C     23   48   51     20   33   38   40   42   43   44   45   47   47   48   50   51   51   51   51   51   51   51   51 
LCS_GDT     W    44_C     W    44_C     23   48   51     20   33   38   40   42   43   44   45   47   47   48   50   51   51   51   51   51   51   51   51 
LCS_GDT     T    45_C     T    45_C     23   48   51      8   33   38   40   42   43   44   45   47   47   48   50   51   51   51   51   51   51   51   51 
LCS_GDT     S    46_C     S    46_C     23   48   51     14   33   38   40   42   43   44   45   47   47   48   50   51   51   51   51   51   51   51   51 
LCS_GDT     G    47_C     G    47_C     23   48   51     14   33   38   40   42   43   44   45   47   47   48   50   51   51   51   51   51   51   51   51 
LCS_GDT     G    48_C     G    48_C     23   48   51     14   33   38   40   42   43   44   45   47   47   48   50   51   51   51   51   51   51   51   51 
LCS_GDT     T    49_C     T    49_C     23   48   51      5   29   38   40   42   43   44   45   47   47   48   50   51   51   51   51   51   51   51   51 
LCS_GDT     M    50_C     M    50_C     23   48   51      7   29   38   40   42   43   44   45   47   47   48   50   51   51   51   51   51   51   51   51 
LCS_GDT     R    51_C     R    51_C     23   48   51      3   29   38   40   42   43   44   45   47   47   48   50   51   51   51   51   51   51   51   51 
LCS_GDT     S    52_C     S    52_C      9   48   51      3    5   12   27   41   43   44   45   47   47   48   50   51   51   51   51   51   51   51   51 
LCS_GDT     V    53_C     V    53_C      7   48   51      3    5   12   26   38   43   44   45   47   47   48   50   51   51   51   51   51   51   51   51 
LCS_GDT     P    54_C     P    54_C      7   46   51      3    5    7   12   14   16   23   41   44   47   48   50   51   51   51   51   51   51   51   51 
LCS_GDT     I    55_C     I    55_C      7   13   51      3    5    8   12   14   20   23   39   42   47   48   50   51   51   51   51   51   51   51   51 
LCS_GDT     G    56_C     G    56_C      7   13   51      3    5    8   12   14   16   21   27   36   40   48   50   51   51   51   51   51   51   51   51 
LCS_AVERAGE  LCS_A:  76.41  (  37.87   91.35  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     20     33     38     40     42     43     44     45     47     47     48     50     51     51     51     51     51     51     51     51 
GDT PERCENT_AT  39.22  64.71  74.51  78.43  82.35  84.31  86.27  88.24  92.16  92.16  94.12  98.04 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.35   0.58   0.79   0.92   1.05   1.18   1.32   1.54   1.77   1.77   1.92   2.81   2.81   2.81   2.81   2.81   2.81   2.81   2.81   2.81
GDT RMS_ALL_AT   3.31   3.27   3.16   3.15   3.16   3.20   3.24   2.98   3.00   3.00   3.03   2.81   2.81   2.81   2.81   2.81   2.81   2.81   2.81   2.81

# Checking swapping
#   possible swapping detected:  F    22_C      F    22_C
#   possible swapping detected:  Y    28_C      Y    28_C
#   possible swapping detected:  F    36_C      F    36_C

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    P     6_C      P     6_C     5.057     2    0.202   0.213     6.440   21.548   17.619
LGA    T     7_C      T     7_C     6.438     0    0.073   0.108     7.864   19.286   14.898
LGA    K     8_C      K     8_C     4.616     4    0.276   0.300     5.085   36.071   20.159
LGA    I     9_C      I     9_C     2.506     0    0.148   0.743     4.316   57.262   58.690
LGA    L    10_C      L    10_C     1.878     0    0.059   0.249     3.575   75.119   67.321
LGA    P    11_C      P    11_C     1.009     0    0.007   0.038     1.777   83.690   80.272
LGA    C    12_C      C    12_C     0.580     0    0.031   0.121     1.139   88.214   88.968
LGA    P    13_C      P    13_C     1.300     0    0.093   0.289     1.958   79.286   78.980
LGA    R    14_C      R    14_C     1.420     0    0.230   1.020     3.425   73.214   73.247
LGA    C    15_C      C    15_C     0.964     0    0.040   0.219     1.185   88.214   87.460
LGA    N    16_C      N    16_C     0.746     0    0.090   0.298     1.885   90.476   86.012
LGA    S    17_C      S    17_C     0.268     0    0.046   0.491     1.777  100.000   95.476
LGA    M    18_C      M    18_C     0.548     0    0.070   0.859     4.287   92.857   78.810
LGA    E    19_C      E    19_C     0.705     4    0.027   0.033     0.778   90.476   50.265
LGA    T    20_C      T    20_C     0.821     0    0.096   0.128     1.169   88.214   89.184
LGA    K    21_C      K    21_C     0.530     0    0.020   0.420     3.716   95.238   79.894
LGA    F    22_C      F    22_C     0.496     0    0.031   0.075     0.769   95.238   92.208
LGA    C    23_C      C    23_C     0.708     0    0.057   0.679     2.429   90.476   86.190
LGA    Y    24_C      Y    24_C     0.900     0    0.019   0.119     1.579   90.476   83.016
LGA    Y    25_C      Y    25_C     1.058     0    0.104   0.136     1.316   81.429   85.952
LGA    N    26_C      N    26_C     1.371     0    0.088   0.221     3.025   75.119   70.119
LGA    N    27_C      N    27_C     2.896     0    0.353   0.355     8.268   67.024   39.524
LGA    Y    28_C      Y    28_C     4.066     0    0.296   1.357     7.652   44.167   25.278
LGA    N    29_C      N    29_C     1.930     0    0.079   0.836     3.770   72.976   64.405
LGA    V    30_C      V    30_C     2.233     0    0.039   1.108     5.559   68.810   58.707
LGA    N    31_C      N    31_C     1.405     0    0.030   0.352     3.518   79.286   69.524
LGA    Q    32_C      Q    32_C     0.532     0    0.138   0.387     2.501   95.238   86.878
LGA    P    33_C      P    33_C     0.472     0    0.057   0.096     0.667   92.857   91.837
LGA    R    34_C      R    34_C     0.653     0    0.032   0.894     5.067   90.476   71.732
LGA    H    35_C      H    35_C     0.379     0    0.111   0.237     0.689   92.857   95.238
LGA    F    36_C      F    36_C     0.968     0    0.023   0.166     1.833   90.476   82.381
LGA    C    37_C      C    37_C     0.830     0    0.095   0.127     1.442   88.214   88.968
LGA    K    38_C      K    38_C     0.779     0    0.101   0.483     1.902   90.476   85.556
LGA    A    39_C      A    39_C     0.690     0    0.110   0.111     0.805   90.476   90.476
LGA    C    40_C      C    40_C     1.237     0    0.023   0.057     1.463   81.429   81.429
LGA    Q    41_C      Q    41_C     1.434     0    0.016   0.760     2.853   77.143   73.016
LGA    R    42_C      R    42_C     1.452     0    0.015   1.274     6.905   81.429   60.779
LGA    Y    43_C      Y    43_C     0.944     0    0.064   0.180     1.250   88.214   89.722
LGA    W    44_C      W    44_C     0.699     0    0.090   0.184     1.004   90.476   91.190
LGA    T    45_C      T    45_C     1.045     0    0.043   0.967     2.386   83.690   77.959
LGA    S    46_C      S    46_C     0.683     0    0.074   0.671     1.701   90.476   87.540
LGA    G    47_C      G    47_C     0.612     0    0.041   0.041     0.612   92.857   92.857
LGA    G    48_C      G    48_C     0.551     0    0.095   0.095     0.551   95.238   95.238
LGA    T    49_C      T    49_C     0.748     0    0.151   0.212     1.290   88.214   87.891
LGA    M    50_C      M    50_C     0.746     0    0.074   1.296     4.661   90.476   77.560
LGA    R    51_C      R    51_C     1.151     0    0.151   0.786     7.972   79.405   56.234
LGA    S    52_C      S    52_C     3.569     0    0.071   0.146     5.527   46.786   40.952
LGA    V    53_C      V    53_C     4.455     0    0.149   1.173     5.731   32.024   33.401
LGA    P    54_C      P    54_C     8.661     0    0.070   0.112    10.076    4.643    3.741
LGA    I    55_C      I    55_C     8.725     0    0.068   1.305    10.498    1.548    1.726
LGA    G    56_C      G    56_C    10.338     0    0.690   0.690    10.595    0.357    0.357

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       51     204    204  100.00     404    404  100.00                51
SUMMARY(RMSD_GDC):     2.807          2.830                  3.132           74.503   68.369

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   64   51    4.0     45    1.54    82.843    87.087     2.747

LGA_LOCAL      RMSD:   1.538  Number of atoms:   45  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.980  Number of assigned atoms:   51 
Std_ASGN_ATOMS RMSD:   2.807  Standard rmsd on all 51 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.516241 * X  +  -0.384022 * Y  +  -0.765521 * Z  + -27.545319
  Y_new =   0.224350 * X  +  -0.801987 * Y  +   0.553610 * Z  +  -7.945256
  Z_new =  -0.826536 * X  +  -0.457541 * Y  +  -0.327863 * Z  +   4.214149 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.409961  0.972926 -2.192561   [DEG:   23.4890   55.7445 -125.6245 ]
ZXZ: -2.196911  1.904837 -2.076372   [DEG: -125.8737  109.1391 -118.9674 ]
 
# END of job
