
#######################################################
#                                                     #
#                        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   65 (  516),  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        2.30     2.30
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    50       7_C - 56_C        1.71     2.33
  LCS_AVERAGE:     97.96

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    45       8_C - 52_C        0.95     2.43
  LONGEST_CONTINUOUS_SEGMENT:    45       9_C - 53_C        0.94     2.41
  LCS_AVERAGE:     82.51

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      3   48   51      3    3    3    4    5    5    7    8    9   14   17   18   47   51   51   51   51   51   51   51 
LCS_GDT     T     7_C     T     7_C     42   50   51      3    5   14   20   33   45   45   46   48   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     K     8_C     K     8_C     45   50   51      3   15   40   44   44   46   47   49   49   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     I     9_C     I     9_C     45   50   51     19   39   43   44   45   46   48   49   49   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     L    10_C     L    10_C     45   50   51     18   39   43   44   45   46   48   49   49   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     P    11_C     P    11_C     45   50   51     32   39   43   44   45   46   48   49   49   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     C    12_C     C    12_C     45   50   51     32   39   43   44   45   46   48   49   49   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     P    13_C     P    13_C     45   50   51     32   39   43   44   45   46   48   49   49   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     R    14_C     R    14_C     45   50   51     32   39   43   44   45   46   48   49   49   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     C    15_C     C    15_C     45   50   51     32   39   43   44   45   46   48   49   49   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     N    16_C     N    16_C     45   50   51     32   39   43   44   45   46   48   49   49   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     S    17_C     S    17_C     45   50   51     32   39   43   44   45   46   48   49   49   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     M    18_C     M    18_C     45   50   51     32   39   43   44   45   46   48   49   49   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     E    19_C     E    19_C     45   50   51     32   39   43   44   45   46   48   49   49   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     T    20_C     T    20_C     45   50   51     32   39   43   44   45   46   48   49   49   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     K    21_C     K    21_C     45   50   51     32   39   43   44   45   46   48   49   49   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     F    22_C     F    22_C     45   50   51     32   39   43   44   45   46   48   49   49   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     C    23_C     C    23_C     45   50   51     32   39   43   44   45   46   48   49   49   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     Y    24_C     Y    24_C     45   50   51     32   39   43   44   45   46   48   49   49   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     Y    25_C     Y    25_C     45   50   51     32   39   43   44   45   46   48   49   49   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     N    26_C     N    26_C     45   50   51     30   39   43   44   45   46   48   49   49   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     N    27_C     N    27_C     45   50   51      7   39   43   44   45   46   48   49   49   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     Y    28_C     Y    28_C     45   50   51     20   39   43   44   45   46   48   49   49   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     N    29_C     N    29_C     45   50   51     32   39   43   44   45   46   48   49   49   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     V    30_C     V    30_C     45   50   51     32   39   43   44   45   46   48   49   49   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     N    31_C     N    31_C     45   50   51     32   39   43   44   45   46   48   49   49   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     Q    32_C     Q    32_C     45   50   51     32   39   43   44   45   46   48   49   49   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     P    33_C     P    33_C     45   50   51     32   39   43   44   45   46   48   49   49   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     R    34_C     R    34_C     45   50   51     32   39   43   44   45   46   48   49   49   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     H    35_C     H    35_C     45   50   51     32   39   43   44   45   46   48   49   49   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     F    36_C     F    36_C     45   50   51     32   39   43   44   45   46   48   49   49   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     C    37_C     C    37_C     45   50   51     32   39   43   44   45   46   48   49   49   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     K    38_C     K    38_C     45   50   51     32   39   43   44   45   46   48   49   49   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     A    39_C     A    39_C     45   50   51     32   39   43   44   45   46   48   49   49   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     C    40_C     C    40_C     45   50   51     32   39   43   44   45   46   48   49   49   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     Q    41_C     Q    41_C     45   50   51     32   39   43   44   45   46   48   49   49   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     R    42_C     R    42_C     45   50   51     32   39   43   44   45   46   48   49   49   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     Y    43_C     Y    43_C     45   50   51     32   39   43   44   45   46   48   49   49   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     W    44_C     W    44_C     45   50   51     32   39   43   44   45   46   48   49   49   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     T    45_C     T    45_C     45   50   51     32   39   43   44   45   46   48   49   49   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     S    46_C     S    46_C     45   50   51     32   39   43   44   45   46   48   49   49   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     G    47_C     G    47_C     45   50   51     11   38   43   44   45   46   48   49   49   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     G    48_C     G    48_C     45   50   51     25   39   43   44   45   46   48   49   49   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     T    49_C     T    49_C     45   50   51     11   38   43   44   45   46   48   49   49   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     M    50_C     M    50_C     45   50   51     11   38   43   44   45   46   48   49   49   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     R    51_C     R    51_C     45   50   51      3   28   43   44   45   46   48   49   49   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     S    52_C     S    52_C     45   50   51      3    6   31   44   45   46   48   49   49   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     V    53_C     V    53_C     45   50   51      4   15   36   44   45   46   48   49   49   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     P    54_C     P    54_C     12   50   51      3    4   14   25   38   46   48   49   49   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     I    55_C     I    55_C     12   50   51      3    9   19   32   44   46   48   49   49   50   50   50   50   51   51   51   51   51   51   51 
LCS_GDT     G    56_C     G    56_C      7   50   51      3    6   12   20   34   44   48   49   49   50   50   50   50   51   51   51   51   51   51   51 
LCS_AVERAGE  LCS_A:  93.49  (  82.51   97.96  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     32     39     43     44     45     46     48     49     49     50     50     50     50     51     51     51     51     51     51     51 
GDT PERCENT_AT  62.75  76.47  84.31  86.27  88.24  90.20  94.12  96.08  96.08  98.04  98.04  98.04  98.04 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.29   0.47   0.69   0.80   0.94   1.04   1.44   1.53   1.53   1.71   1.71   1.71   1.71   2.30   2.30   2.30   2.30   2.30   2.30   2.30
GDT RMS_ALL_AT   2.62   2.61   2.48   2.49   2.41   2.39   2.42   2.37   2.37   2.33   2.33   2.33   2.33   2.30   2.30   2.30   2.30   2.30   2.30   2.30

# Checking swapping
#   possible swapping detected:  F    22_C      F    22_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    11.750     2    0.338   0.345    13.744    0.119    0.068
LGA    T     7_C      T     7_C     5.921     0    0.621   0.477     7.749   21.548   23.537
LGA    K     8_C      K     8_C     3.601     4    0.256   0.273     4.135   48.690   27.196
LGA    I     9_C      I     9_C     1.863     0    0.076   0.699     4.130   70.833   67.440
LGA    L    10_C      L    10_C     1.145     0    0.100   0.247     2.573   85.952   81.786
LGA    P    11_C      P    11_C     0.502     0    0.007   0.069     1.008   90.476   89.184
LGA    C    12_C      C    12_C     0.839     0    0.061   0.109     1.353   85.952   85.952
LGA    P    13_C      P    13_C     1.389     0    0.078   0.245     1.881   77.143   77.755
LGA    R    14_C      R    14_C     1.787     0    0.159   1.022     5.651   68.929   53.896
LGA    C    15_C      C    15_C     1.327     0    0.051   0.153     1.386   81.429   81.429
LGA    N    16_C      N    16_C     0.779     0    0.060   0.242     1.577   90.476   86.012
LGA    S    17_C      S    17_C     0.693     0    0.094   0.141     0.785   92.857   92.063
LGA    M    18_C      M    18_C     0.361     0    0.039   0.587     1.733   97.619   93.036
LGA    E    19_C      E    19_C     0.644     4    0.017   0.017     0.793   90.476   50.265
LGA    T    20_C      T    20_C     0.790     0    0.099   0.175     1.095   88.214   89.184
LGA    K    21_C      K    21_C     0.650     0    0.022   0.493     4.040   90.476   77.090
LGA    F    22_C      F    22_C     0.432     0    0.017   0.063     0.687   95.238   96.537
LGA    C    23_C      C    23_C     0.488     0    0.057   0.164     0.981   95.238   93.651
LGA    Y    24_C      Y    24_C     0.590     0    0.024   0.086     2.040   95.238   83.968
LGA    Y    25_C      Y    25_C     0.236     0    0.068   0.097     1.346  100.000   92.976
LGA    N    26_C      N    26_C     0.664     0    0.109   0.328     1.885   90.476   86.012
LGA    N    27_C      N    27_C     1.449     0    0.040   0.800     4.990   83.690   64.940
LGA    Y    28_C      Y    28_C     1.141     0    0.096   0.138     4.126   83.690   65.119
LGA    N    29_C      N    29_C     0.578     0    0.090   0.192     1.473   90.476   87.083
LGA    V    30_C      V    30_C     0.716     0    0.036   1.148     3.333   90.476   81.020
LGA    N    31_C      N    31_C     0.822     0    0.019   0.412     1.126   90.476   89.345
LGA    Q    32_C      Q    32_C     0.534     0    0.018   0.217     1.612   90.476   88.519
LGA    P    33_C      P    33_C     0.523     0    0.022   0.123     0.757   90.476   93.197
LGA    R    34_C      R    34_C     0.664     0    0.024   1.034     5.267   95.238   76.970
LGA    H    35_C      H    35_C     0.401     0    0.071   1.054     2.621   92.857   86.476
LGA    F    36_C      F    36_C     1.061     0    0.016   0.113     2.116   85.952   76.926
LGA    C    37_C      C    37_C     1.218     0    0.087   0.124     1.694   79.286   80.000
LGA    K    38_C      K    38_C     1.370     0    0.098   0.490     1.854   81.429   78.571
LGA    A    39_C      A    39_C     1.317     0    0.084   0.082     1.390   81.429   81.429
LGA    C    40_C      C    40_C     1.681     0    0.038   0.044     1.738   72.857   74.286
LGA    Q    41_C      Q    41_C     1.798     0    0.023   0.759     3.150   72.857   67.619
LGA    R    42_C      R    42_C     1.475     0    0.014   1.251     7.031   77.143   53.290
LGA    Y    43_C      Y    43_C     1.135     0    0.088   0.154     1.443   81.429   81.429
LGA    W    44_C      W    44_C     0.908     0    0.035   1.751     5.771   90.476   71.463
LGA    T    45_C      T    45_C     0.761     0    0.047   0.164     1.059   90.476   89.184
LGA    S    46_C      S    46_C     0.650     0    0.060   0.091     1.099   88.214   88.968
LGA    G    47_C      G    47_C     0.866     0    0.023   0.023     0.866   90.476   90.476
LGA    G    48_C      G    48_C     0.617     0    0.073   0.073     0.724   92.857   92.857
LGA    T    49_C      T    49_C     0.220     0    0.134   0.337     1.165   97.619   95.986
LGA    M    50_C      M    50_C     0.460     0    0.153   1.128     5.207   95.238   79.643
LGA    R    51_C      R    51_C     1.617     0    0.152   0.466     3.761   79.286   64.199
LGA    S    52_C      S    52_C     2.012     0    0.163   0.281     3.844   70.833   63.968
LGA    V    53_C      V    53_C     1.710     0    0.070   1.144     3.306   66.905   65.170
LGA    P    54_C      P    54_C     4.095     0    0.122   0.220     5.177   43.452   38.503
LGA    I    55_C      I    55_C     3.306     0    0.096   1.368     4.543   42.024   44.643
LGA    G    56_C      G    56_C     4.749     0    0.613   0.613     5.117   31.548   31.548

# 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):     2.296          2.288                  2.361           79.942   73.958

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   65   51    4.0     49    1.53    89.706    93.101     3.010

LGA_LOCAL      RMSD:   1.528  Number of atoms:   49  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.374  Number of assigned atoms:   51 
Std_ASGN_ATOMS RMSD:   2.296  Standard rmsd on all 51 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.737534 * X  +   0.487953 * Y  +  -0.466846 * Z  + -31.762468
  Y_new =  -0.289356 * X  +   0.852974 * Y  +   0.434407 * Z  + -10.050414
  Z_new =   0.610178 * X  +  -0.185305 * Y  +   0.770289 * Z  +   4.870037 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.373876 -0.656285 -0.236080   [DEG:  -21.4215  -37.6024  -13.5264 ]
ZXZ: -2.320216  0.691502  1.865635   [DEG: -132.9386   39.6202  106.8930 ]
 
# END of job
