 
####################################################### 
#                                                     # 
#                        ACE                          # 
#                                                     # 
#        Ab-initio protein structure prediction       # 
#                         &                           # 
#               Comparative modeling                  # 
#                                                     # 
#                     Evaluator                       # 
#                                                     # 
#                ----------------- 11/1998            # 
#                                                     # 
#                         by                          # 
#           Adam Zemla & Ceslovas Venclovas           # 
#                                                     # 
#         Protein Structure Prediction Center         # 
#      Lawrence Livermore National Laboratory, CA     # 
#                                                     # 
####################################################### 
########################## 
#                        # 
#    ACE parameters:     # 
#                        # 
########################## 
# 
CONANA-INTER           ../CONANA/T0058.inter 
# 
NUMBER-OF-PARENTS      2 
ALIGNMENT-DALI(1)      ../PARENTS/casp3.T0058.1akz.rot 
ALIGNMENT-DALI(2)      ../PARENTS/casp3.T0058.1udh.rot 
# 
ITER-CUTOFF            2.5       #    DISTANCE cutoff (for CA (iter))  
# 
# 
# MEASURES: 
# 
# For AB: 0 3 9 13 14 
# For CM: 0 1 2 3 6 7 8 9 10 11 12 13 14 18 
# 
ARMSMC  0 1 2     7 8 9    11 12 13 14 18 
ARMSSC  0 1 2 3 6 7 8 9    11 12 13 14 18 
# 
CRMSCA  0 1 2     7 8 9 10 11 12 13 14 18 
CRMSMC  0 1 2     7 8 9 10 11 12 13 14 18 
CRMSSC  0 1 2 3 6     9    11 12 13 14 18 
CRMSALL 0 1 2     7 8 9    11 12 13 14 18 
# 
D-E_CA  0 1 2     7 8 9    11 12 13 14 18 
D-E_MC  0 1 2     7 8 9    11 12 13 14 18 
D-E_SC  0 1 2 3 6 7 8 9    11 12 13 14 18 
D-E_ALL 0 1 2     7 8 9    11 12 13 14 18 
# 
# Output parameters 
# 
DIHED-OUTPUT        0         #    1 - ON, 0 - OFF 
SS-OUTPUT           0         #    1 - ON, 0 - OFF  
PHI-PSI             0         #    1 - SEPARATELY, 0 - NO  
ALIGNMENT-OUTPUT    0         #    1 - ON, 0 - OFF 
# 
# Calculation parameters 
# 
TEMP-FACTOR         30.0      #    Target structure temperature factor cutoff  
ACCESS-CUTOFF       0.20      #    Solvent accessibility cutoff  
ANGLES-CORRECT      30.0      #    target-model  (diff < 30.0)  
ROTAMERS-LIMIT      30.0      #    target-parent (diff > 30.0) 
SC-SWAPPING         1         #    1 - ON, 0 - OFF  
DSSP-HELIX          6         #    Secondary Structure subset: helix cutoff  
DSSP-STRAND         3         #    Secondary Structure subset: strand cutoff 
LIGAND-DIST1        4.0       #    Ligand contact: contact with ligand cutoff 
LIGAND-DIST2        6.0       #    Ligand contact: protein neighborhood cutoff 
PARENT-DIST3        2.5       #    target-parent (dist > 2.5) 
# 
CRMS-METHOD         3         #    0 - ALL, 1 - CA, 2 - MC+CB, 3 - CA (iter)  
# 
########################## 
#                        # 
#      ACE results:      # 
#                        # 
########################## 
 
# Reading the coordinates set (1) 
 
 
# Evaluating the coordinates set (1) 
 
# WARNING! TARGET 1784 atoms, MODEL 1820 atoms, 1784 common with TARGET 
           Number of atoms possible to evaluate: 1740 
 
 
 CA-RMS TARGET<->PARENT(1akz)	 1.191923 
 
 CA-RMS TARGET<->PARENT(1udh)	 1.648171 
 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    37.63           83.9   436    97.3   448     ARMSMC  
     WELL ORDERED  . . . . .    37.07           84.3   433    97.3   445     ARMSMC  
     NO INTER CONTACTS . . .    37.37           86.0   314    99.7   315     ARMSMC  
     SHIFTED CHAIN . . . . .    46.36           76.2   122    91.0   134     ARMSMC  
     ALTERNATIVE PARENT  . .    40.47           75.0     4   100.0     4     ARMSMC  
     SECONDARY STRUCTURE . .    19.51           96.2   158   100.0   158     ARMSMC  
     LARGE SHIFTS/INSERTIONS    90.71           40.0    10    45.5    22     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    45.23           79.6   216    94.7   228     ARMSMC  
     BURIED  . . . . . . . .    28.25           88.2   220   100.0   220     ARMSMC  
     CORE  . . . . . . . . .    35.44           85.0   426   100.0   426     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    62.60           64.3   185    97.4   190     ARMSSC1 
     WELL ORDERED  . . . . .    61.30           66.5   173    98.3   176     ARMSSC1 
     NO INTER CONTACTS . . .    61.38           65.9   135   100.0   135     ARMSSC1 
     RELIABLE SIDE CHAINS  .    62.71           63.7   168    97.1   173     ARMSSC1 
     CHANGED ANGLES  . . . .    67.16           54.7    53    91.4    58     ARMSSC1 
     SHIFTED CHAIN . . . . .    76.43           49.1    53    91.4    58     ARMSSC1 
     ALTERNATIVE PARENT  . .     4.86          100.0     2   100.0     2     ARMSSC1 
     SECONDARY STRUCTURE . .    57.27           75.7    74   100.0    74     ARMSSC1 
     LARGE SHIFTS/INSERTIONS    86.37           20.0     5    50.0    10     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .    70.30           53.3    92    94.8    97     ARMSSC1 
     BURIED  . . . . . . . .    53.92           75.3    93   100.0    93     ARMSSC1 
     CORE  . . . . . . . . .    61.81           65.6   180   100.0   180     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    72.24           56.9   144    97.3   148     ARMSSC2 
     WELL ORDERED  . . . . .    70.77           62.0   129    97.7   132     ARMSSC2 
     NO INTER CONTACTS . . .    72.94           60.8   102   100.0   102     ARMSSC2 
     RELIABLE SIDE CHAINS  .    64.41           60.6    99    97.1   102     ARMSSC2 
     CHANGED ANGLES  . . . .    88.27           41.4    70    94.6    74     ARMSSC2 
     SHIFTED CHAIN . . . . .    89.07           32.5    40    90.9    44     ARMSSC2 
     ALTERNATIVE PARENT  . .     4.56          100.0     1   100.0     1     ARMSSC2 
     SECONDARY STRUCTURE . .    68.96           70.2    57   100.0    57     ARMSSC2 
     LARGE SHIFTS/INSERTIONS    73.94           50.0     2    33.3     6     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .    77.14           47.4    76    95.0    80     ARMSSC2 
     BURIED  . . . . . . . .    66.34           67.6    68   100.0    68     ARMSSC2 
     CORE  . . . . . . . . .    72.22           57.0   142   100.0   142     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    92.60           15.6    45    95.7    47     ARMSSC3 
     WELL ORDERED  . . . . .    86.56           15.6    32    97.0    33     ARMSSC3 
     NO INTER CONTACTS . . .    85.37           18.2    22   100.0    22     ARMSSC3 
     RELIABLE SIDE CHAINS  .    83.44           16.1    31    93.9    33     ARMSSC3 
     CHANGED ANGLES  . . . .   101.12            3.3    30    93.8    32     ARMSSC3 
     SHIFTED CHAIN . . . . .    95.41           11.8    17    89.5    19     ARMSSC3 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SECONDARY STRUCTURE . .    85.35           23.5    17   100.0    17     ARMSSC3 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0     2     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .    98.23           16.2    37    94.9    39     ARMSSC3 
     BURIED  . . . . . . . .    60.12           12.5     8   100.0     8     ARMSSC3 
     CORE  . . . . . . . . .    92.60           15.6    45   100.0    45     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    97.16           22.2    18   100.0    18     ARMSSC4 
     WELL ORDERED  . . . . .    92.66           27.3    11   100.0    11     ARMSSC4 
     NO INTER CONTACTS . . .    90.36           28.6     7   100.0     7     ARMSSC4 
     RELIABLE SIDE CHAINS  .    97.16           22.2    18   100.0    18     ARMSSC4 
     CHANGED ANGLES  . . . .   108.03           30.8    13   100.0    13     ARMSSC4 
     SHIFTED CHAIN . . . . .   124.14            0.0     5   100.0     5     ARMSSC4 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SECONDARY STRUCTURE . .    57.81           33.3     6   100.0     6     ARMSSC4 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0     0     ARMSSC4 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SURFACE . . . . . . . .    95.43           20.0    15   100.0    15     ARMSSC4 
     BURIED  . . . . . . . .   105.36           33.3     3   100.0     3     ARMSSC4 
     CORE  . . . . . . . . .    97.16           22.2    18   100.0    18     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =   0.88968     r(1,2) =  -0.28683     r(1,3) =  -0.35524 
 r(2,1) =  -0.39019     r(2,2) =  -0.07362     r(2,3) =  -0.91778 
 r(3,1) =   0.23710     r(3,2) =   0.95515     r(3,3) =  -0.17742 
THE OFFSET VECTOR: 
 v(1) =  36.52699     v(2) =  74.85875     v(3) =  22.15448 
 
 Number of iteration 31                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   0.99           (Number of atoms:  180) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    2.27        219    97.3   225     CRMSCA  
     CRN = ALL/NP  . . . . .    0.0104                            CRMSCA  
     WELL ORDERED  . . . . .    2.25        218    97.3   224     CRMSCA  
     NO INTER CONTACTS . . .    2.29        158   100.0   158     CRMSCA  
     SHIFTED CHAIN . . . . .    3.56         62    91.2    68     CRMSCA  
     ALTERNATIVE PARENT  . .    1.71          2   100.0     2     CRMSCA  
     SECONDARY STRUCTURE . .    2.23         79   100.0    79     CRMSCA  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSCA  
     LARGE SHIFTS/INSERTIONS    6.22          6    50.0    12     CRMSCA  
     SURFACE . . . . . . . .    2.74        109    94.8   115     CRMSCA  
     BURIED  . . . . . . . .    1.69        110   100.0   110     CRMSCA  
     CORE  . . . . . . . . .    2.05        213   100.0   213     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    2.32       1077    97.3  1107     CRMSMC  
     WELL ORDERED  . . . . .    2.30       1066    97.4  1095     CRMSMC  
     NO INTER CONTACTS . . .    2.29        778   100.0   778     CRMSMC  
     SHIFTED CHAIN . . . . .    3.62        304    91.0   334     CRMSMC  
     ALTERNATIVE PARENT  . .    1.80         10   100.0    10     CRMSMC  
     SECONDARY STRUCTURE . .    2.24        394   100.0   394     CRMSMC  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSMC  
     LARGE SHIFTS/INSERTIONS    6.12         29    49.2    59     CRMSMC  
     SURFACE . . . . . . . .    2.78        536    94.7   566     CRMSMC  
     BURIED  . . . . . . . .    1.75        541   100.0   541     CRMSMC  
     CORE  . . . . . . . . .    2.12       1048   100.0  1048     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    4.04        864    97.7   884     CRMSSC  
     WELL ORDERED  . . . . .    3.90        802    98.3   816     CRMSSC  
     NO INTER CONTACTS . . .    3.84        630   100.0   630     CRMSSC  
     RELIABLE SIDE CHAINS  .    4.05        686    97.4   704     CRMSSC  
     CHANGED ANGLES  . . . .    4.87        314    95.7   328     CRMSSC  
     SECONDARY STRUCTURE . .    4.06        341   100.0   341     CRMSSC  
     LARGE SHIFTS/INSERTIONS    8.03         16    44.4    36     CRMSSC  
     SURFACE . . . . . . . .    4.69        428    95.5   448     CRMSSC  
     BURIED  . . . . . . . .    3.27        436   100.0   436     CRMSSC  
     CORE  . . . . . . . . .    3.92        848   100.0   848     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    3.25       1740    97.5  1784     CRMSALL 
     WELL ORDERED  . . . . .    3.13       1670    97.8  1708     CRMSALL 
     NO INTER CONTACTS . . .    3.13       1262   100.0  1262     CRMSALL 
     SHIFTED CHAIN . . . . .    4.89        486    91.7   530     CRMSALL 
     ALTERNATIVE PARENT  . .    1.91         13   100.0    13     CRMSALL 
     SECONDARY STRUCTURE . .    3.27        657   100.0   657     CRMSALL 
     LARGE SHIFTS/INSERTIONS    6.87         40    47.6    84     CRMSALL 
     SURFACE . . . . . . . .    3.80        864    95.2   908     CRMSALL 
     BURIED  . . . . . . . .    2.58        876   100.0   876     CRMSALL 
     CORE  . . . . . . . . .    3.11       1700   100.0  1700     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     2.40      2    25.0     8     222-PVLPAESE-229  
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     3.02     10    25.0    40     222-PVLPAESE-229  
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     3.27     14    24.1    58     222-PVLPAESE-229  
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 WARNING! LOOP  1 cannot be considered (not enough atoms). 
 
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 WARNING! LOOP  1 cannot be considered (not enough atoms). 
 
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 WARNING! LOOP  1 cannot be considered (not enough atoms). 
 
 
 
Accuracy of estimates of atomic coordinate errors: model <-> target 
 
 (CA)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    8.508      0.768       0.795    219    97.3   225     ERRCA  
     WELL ORDERED  . . . . .    8.524      0.770       0.796    218    97.3   224     ERRCA  
     NO INTER CONTACTS . . .    8.569      0.778       0.800    158   100.0   158     ERRCA  
     SHIFTED CHAIN . . . . .    7.211      0.596       0.655     62    91.2    68     ERRCA  
     ALTERNATIVE PARENT  . .    8.659      0.779       0.811      2   100.0     2     ERRCA  
     SECONDARY STRUCTURE . .    8.585      0.785       0.809     79   100.0    79     ERRCA  
     LARGE SHIFTS/INSERTIONS    5.543      0.411       0.456      6    50.0    12     ERRCA  
     SURFACE . . . . . . . .    8.116      0.715       0.751    109    94.8   115     ERRCA  
     BURIED  . . . . . . . .    8.896      0.820       0.838    110   100.0   110     ERRCA  
     CORE  . . . . . . . . .    8.591      0.778       0.804    213   100.0   213     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    8.455      0.761       0.790   1077    97.3  1107     ERRMC  
     WELL ORDERED  . . . . .    8.476      0.764       0.792   1066    97.4  1095     ERRMC  
     NO INTER CONTACTS . . .    8.538      0.773       0.798    778   100.0   778     ERRMC  
     SHIFTED CHAIN . . . . .    7.144      0.589       0.648    304    91.0   334     ERRMC  
     ALTERNATIVE PARENT  . .    8.569      0.766       0.800     10   100.0    10     ERRMC  
     SECONDARY STRUCTURE . .    8.550      0.779       0.805    394   100.0   394     ERRMC  
     LARGE SHIFTS/INSERTIONS    5.478      0.403       0.459     29    49.2    59     ERRMC  
     SURFACE . . . . . . . .    8.063      0.709       0.746    536    94.7   566     ERRMC  
     BURIED  . . . . . . . .    8.843      0.812       0.833    541   100.0   541     ERRMC  
     CORE  . . . . . . . . .    8.538      0.771       0.799   1048   100.0  1048     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    7.524      0.650       0.678    864    97.7   884     ERRSC  
     WELL ORDERED  . . . . .    7.632      0.664       0.691    802    98.3   816     ERRSC  
     NO INTER CONTACTS . . .    7.727      0.674       0.700    630   100.0   630     ERRSC  
     RELIABLE SIDE CHAINS  .    7.563      0.654       0.682    686    97.4   704     ERRSC  
     CHANGED ANGLES  . . . .    6.687      0.543       0.582    314    95.7   328     ERRSC  
     SHIFTED CHAIN . . . . .    5.756      0.445       0.477    238    92.2   258     ERRSC  
     ALTERNATIVE PARENT  . .    8.192      0.715       0.764      5   100.0     5     ERRSC  
     SECONDARY STRUCTURE . .    7.593      0.665       0.687    341   100.0   341     ERRSC  
     LARGE SHIFTS/INSERTIONS    5.327      0.358       0.385     16    44.4    36     ERRSC  
     SURFACE . . . . . . . .    6.902      0.574       0.608    428    95.5   448     ERRSC  
     BURIED  . . . . . . . .    8.135      0.725       0.748    436   100.0   436     ERRSC  
     CORE  . . . . . . . . .    7.566      0.656       0.684    848   100.0   848     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    8.022      0.709       0.738   1740    97.5  1784     ERRALL 
     WELL ORDERED  . . . . .    8.103      0.719       0.747   1670    97.8  1708     ERRALL 
     NO INTER CONTACTS . . .    8.157      0.727       0.752   1262   100.0  1262     ERRALL 
     SHIFTED CHAIN . . . . .    6.536      0.526       0.573    486    91.7   530     ERRALL 
     ALTERNATIVE PARENT  . .    8.461      0.750       0.788     13   100.0    13     ERRALL 
     SECONDARY STRUCTURE . .    8.086      0.723       0.749    657   100.0   657     ERRALL 
     LARGE SHIFTS/INSERTIONS    5.421      0.387       0.433     40    47.6    84     ERRALL 
     SURFACE . . . . . . . .    7.525      0.646       0.682    864    95.2   908     ERRALL 
     BURIED  . . . . . . . .    8.512      0.771       0.793    876   100.0   876     ERRALL 
     CORE  . . . . . . . . .    8.083      0.717       0.745   1700   100.0  1700     ERRALL 
 
 
 
DISTANCES: Percent of total atoms where distance (target <-> model) in global 
           superposition is less than: 1 , 2 , 3 , 5 , 10 Angstroms 
            D < 1     D < 2     D < 3     D < 5    D < 10      NP      TN 
CA  (N)       131       171       184       206       218     219     225   DISTCA 
CA  (P)     58.22     76.00     81.78     91.56     96.89             225   DISTCA 
CA  (RMS)    0.61      0.86      1.06      1.67      2.12                   DISTCA 
 
ALL (N)       858      1185      1352      1545      1706    1740    1784   DISTALL 
ALL (P)     48.09     66.42     75.78     86.60     95.63            1784   DISTALL 
ALL (RMS)    0.63      0.92      1.22      1.84      2.70                   DISTALL 
 
CA RMS: P<->T (parent <-> target), and T<->M (target <-> model) calculated using 
        CA positions for which there exists an alignment with principal parent, 
        and for which does not (LARGE SHIFTS/INSERTIONS): 
              P<->T         T<->M         T<->M (LSI) 
CA  (N)         213           213             6          RMSLSI 
CA  (P)       94.67         94.67          2.67          RMSLSI 
CA  (RMS)      0.91          2.05          6.22          RMSLSI 
 
 
 
END of the results output 
