 
####################################################### 
#                                                     # 
#                        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 1821 atoms, 1784 common with TARGET 
           Number of atoms possible to evaluate: 1784 
 
 
 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 . . . . . . . . . .    34.16           89.7   448   100.0   448     ARMSMC  
     WELL ORDERED  . . . . .    32.52           90.1   445   100.0   445     ARMSMC  
     NO INTER CONTACTS . . .    32.00           91.4   315   100.0   315     ARMSMC  
     SHIFTED CHAIN . . . . .    46.78           79.1   134   100.0   134     ARMSMC  
     ALTERNATIVE PARENT  . .    87.88           50.0     4   100.0     4     ARMSMC  
     SECONDARY STRUCTURE . .     9.49           98.7   158   100.0   158     ARMSMC  
     LARGE SHIFTS/INSERTIONS    75.76           40.9    22   100.0    22     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    42.28           85.1   228   100.0   228     ARMSMC  
     BURIED  . . . . . . . .    22.87           94.5   220   100.0   220     ARMSMC  
     CORE  . . . . . . . . .    30.51           92.3   426   100.0   426     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    67.26           64.2   190   100.0   190     ARMSSC1 
     WELL ORDERED  . . . . .    66.32           67.0   176   100.0   176     ARMSSC1 
     NO INTER CONTACTS . . .    62.96           68.1   135   100.0   135     ARMSSC1 
     RELIABLE SIDE CHAINS  .    68.19           63.0   173   100.0   173     ARMSSC1 
     CHANGED ANGLES  . . . .    93.12           29.3    58   100.0    58     ARMSSC1 
     SHIFTED CHAIN . . . . .    81.02           46.6    58   100.0    58     ARMSSC1 
     ALTERNATIVE PARENT  . .   101.54            0.0     2   100.0     2     ARMSSC1 
     SECONDARY STRUCTURE . .    61.30           68.9    74   100.0    74     ARMSSC1 
     LARGE SHIFTS/INSERTIONS    83.17           30.0    10   100.0    10     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .    80.07           50.5    97   100.0    97     ARMSSC1 
     BURIED  . . . . . . . .    50.55           78.5    93   100.0    93     ARMSSC1 
     CORE  . . . . . . . . .    66.26           66.1   180   100.0   180     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    71.65           59.5   148   100.0   148     ARMSSC2 
     WELL ORDERED  . . . . .    71.54           62.1   132   100.0   132     ARMSSC2 
     NO INTER CONTACTS . . .    71.45           61.8   102   100.0   102     ARMSSC2 
     RELIABLE SIDE CHAINS  .    58.68           63.7   102   100.0   102     ARMSSC2 
     CHANGED ANGLES  . . . .    89.89           40.5    74   100.0    74     ARMSSC2 
     SHIFTED CHAIN . . . . .    80.13           43.2    44   100.0    44     ARMSSC2 
     ALTERNATIVE PARENT  . .    67.43            0.0     1   100.0     1     ARMSSC2 
     SECONDARY STRUCTURE . .    70.73           66.7    57   100.0    57     ARMSSC2 
     LARGE SHIFTS/INSERTIONS    81.67           33.3     6   100.0     6     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .    78.58           53.8    80   100.0    80     ARMSSC2 
     BURIED  . . . . . . . .    62.52           66.2    68   100.0    68     ARMSSC2 
     CORE  . . . . . . . . .    71.20           60.6   142   100.0   142     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    84.07           27.7    47   100.0    47     ARMSSC3 
     WELL ORDERED  . . . . .    83.91           33.3    33   100.0    33     ARMSSC3 
     NO INTER CONTACTS . . .    85.41           31.8    22   100.0    22     ARMSSC3 
     RELIABLE SIDE CHAINS  .    76.61           36.4    33   100.0    33     ARMSSC3 
     CHANGED ANGLES  . . . .    82.44           31.2    32   100.0    32     ARMSSC3 
     SHIFTED CHAIN . . . . .    82.02           36.8    19   100.0    19     ARMSSC3 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SECONDARY STRUCTURE . .    75.81           41.2    17   100.0    17     ARMSSC3 
     LARGE SHIFTS/INSERTIONS    34.46           50.0     2   100.0     2     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .    90.44           20.5    39   100.0    39     ARMSSC3 
     BURIED  . . . . . . . .    40.63           62.5     8   100.0     8     ARMSSC3 
     CORE  . . . . . . . . .    85.61           26.7    45   100.0    45     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    68.57           50.0    18   100.0    18     ARMSSC4 
     WELL ORDERED  . . . . .    54.50           63.6    11   100.0    11     ARMSSC4 
     NO INTER CONTACTS . . .    72.48           42.9     7   100.0     7     ARMSSC4 
     RELIABLE SIDE CHAINS  .    68.57           50.0    18   100.0    18     ARMSSC4 
     CHANGED ANGLES  . . . .    74.74           53.8    13   100.0    13     ARMSSC4 
     SHIFTED CHAIN . . . . .    63.44           40.0     5   100.0     5     ARMSSC4 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SECONDARY STRUCTURE . .    67.43           66.7     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 . . . . . . . .    70.20           46.7    15   100.0    15     ARMSSC4 
     BURIED  . . . . . . . .    59.80           66.7     3   100.0     3     ARMSSC4 
     CORE  . . . . . . . . .    68.57           50.0    18   100.0    18     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =  -0.16315     r(1,2) =   0.64343     r(1,3) =  -0.74791 
 r(2,1) =   0.97712     r(2,2) =   0.21020     r(2,3) =  -0.03232 
 r(3,1) =   0.13642     r(3,2) =  -0.73608     r(3,3) =  -0.66301 
THE OFFSET VECTOR: 
 v(1) =  10.99319     v(2) =  21.43703     v(3) =  -4.61666 
 
 Number of iteration 24                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   0.95           (Number of atoms:  215) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    2.83        225   100.0   225     CRMSCA  
     CRN = ALL/NP  . . . . .    0.0126                            CRMSCA  
     WELL ORDERED  . . . . .    2.83        224   100.0   224     CRMSCA  
     NO INTER CONTACTS . . .    1.30        158   100.0   158     CRMSCA  
     SHIFTED CHAIN . . . . .    5.06         68   100.0    68     CRMSCA  
     ALTERNATIVE PARENT  . .    3.24          2   100.0     2     CRMSCA  
     SECONDARY STRUCTURE . .    0.73         79   100.0    79     CRMSCA  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSCA  
     LARGE SHIFTS/INSERTIONS   11.59         12   100.0    12     CRMSCA  
     SURFACE . . . . . . . .    3.87        115   100.0   115     CRMSCA  
     BURIED  . . . . . . . .    0.84        110   100.0   110     CRMSCA  
     CORE  . . . . . . . . .    0.93        213   100.0   213     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    2.94       1107   100.0  1107     CRMSMC  
     WELL ORDERED  . . . . .    2.88       1095   100.0  1095     CRMSMC  
     NO INTER CONTACTS . . .    1.33        778   100.0   778     CRMSMC  
     SHIFTED CHAIN . . . . .    5.25        334   100.0   334     CRMSMC  
     ALTERNATIVE PARENT  . .    3.59         10   100.0    10     CRMSMC  
     SECONDARY STRUCTURE . .    0.75        394   100.0   394     CRMSMC  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSMC  
     LARGE SHIFTS/INSERTIONS   12.06         59   100.0    59     CRMSMC  
     SURFACE . . . . . . . .    4.01        566   100.0   566     CRMSMC  
     BURIED  . . . . . . . .    0.91        541   100.0   541     CRMSMC  
     CORE  . . . . . . . . .    0.97       1048   100.0  1048     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    3.61        884   100.0   884     CRMSSC  
     WELL ORDERED  . . . . .    3.13        816   100.0   816     CRMSSC  
     NO INTER CONTACTS . . .    2.40        630   100.0   630     CRMSSC  
     RELIABLE SIDE CHAINS  .    3.74        704   100.0   704     CRMSSC  
     CHANGED ANGLES  . . . .    5.05        328   100.0   328     CRMSSC  
     SECONDARY STRUCTURE . .    2.02        341   100.0   341     CRMSSC  
     LARGE SHIFTS/INSERTIONS   14.10         36   100.0    36     CRMSSC  
     SURFACE . . . . . . . .    4.85        448   100.0   448     CRMSSC  
     BURIED  . . . . . . . .    1.48        436   100.0   436     CRMSSC  
     CORE  . . . . . . . . .    2.26        848   100.0   848     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    3.26       1784   100.0  1784     CRMSALL 
     WELL ORDERED  . . . . .    3.01       1708   100.0  1708     CRMSALL 
     NO INTER CONTACTS . . .    1.92       1262   100.0  1262     CRMSALL 
     SHIFTED CHAIN . . . . .    5.57        530   100.0   530     CRMSALL 
     ALTERNATIVE PARENT  . .    4.52         13   100.0    13     CRMSALL 
     SECONDARY STRUCTURE . .    1.54        657   100.0   657     CRMSALL 
     LARGE SHIFTS/INSERTIONS   12.86         84   100.0    84     CRMSALL 
     SURFACE . . . . . . . .    4.42        908   100.0   908     CRMSALL 
     BURIED  . . . . . . . .    1.21        876   100.0   876     CRMSALL 
     CORE  . . . . . . . . .    1.73       1700   100.0  1700     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1    13.65      8   100.0     8     222-PVLPAESE-229  
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1    14.12     40   100.0    40     222-PVLPAESE-229  
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1    14.72     58   100.0    58     222-PVLPAESE-229  
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     3.45      8   100.0     8     222-PVLPAESE-229  
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     3.62     40   100.0    40     222-PVLPAESE-229  
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     4.02     58   100.0    58     222-PVLPAESE-229  
 
 
Accuracy of estimates of atomic coordinate errors: model <-> target 
 
 (CA)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    0.906      0.420       0.220    225   100.0   225     ERRCA  
     WELL ORDERED  . . . . .    0.908      0.420       0.220    224   100.0   224     ERRCA  
     NO INTER CONTACTS . . .    0.563      0.391       0.206    158   100.0   158     ERRCA  
     SHIFTED CHAIN . . . . .    2.295      0.606       0.303     68   100.0    68     ERRCA  
     ALTERNATIVE PARENT  . .    2.370      0.635       0.318      2   100.0     2     ERRCA  
     SECONDARY STRUCTURE . .    0.390      0.391       0.210     79   100.0    79     ERRCA  
     LARGE SHIFTS/INSERTIONS    8.055      0.742       0.371     12   100.0    12     ERRCA  
     SURFACE . . . . . . . .    1.402      0.480       0.248    115   100.0   115     ERRCA  
     BURIED  . . . . . . . .    0.388      0.357       0.191    110   100.0   110     ERRCA  
     CORE  . . . . . . . . .    0.503      0.402       0.212    213   100.0   213     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    0.949      0.427       0.224   1107   100.0  1107     ERRMC  
     WELL ORDERED  . . . . .    0.928      0.426       0.223   1095   100.0  1095     ERRMC  
     NO INTER CONTACTS . . .    0.588      0.402       0.211    778   100.0   778     ERRMC  
     SHIFTED CHAIN . . . . .    2.354      0.599       0.300    334   100.0   334     ERRMC  
     ALTERNATIVE PARENT  . .    2.486      0.602       0.301     10   100.0    10     ERRMC  
     SECONDARY STRUCTURE . .    0.408      0.402       0.215    394   100.0   394     ERRMC  
     LARGE SHIFTS/INSERTIONS    8.497      0.758       0.379     59   100.0    59     ERRMC  
     SURFACE . . . . . . . .    1.453      0.481       0.248    566   100.0   566     ERRMC  
     BURIED  . . . . . . . .    0.421      0.371       0.198    541   100.0   541     ERRMC  
     CORE  . . . . . . . . .    0.524      0.408       0.215   1048   100.0  1048     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    1.725      0.568       0.287    884   100.0   884     ERRSC  
     WELL ORDERED  . . . . .    1.484      0.554       0.280    816   100.0   816     ERRSC  
     NO INTER CONTACTS . . .    1.271      0.538       0.272    630   100.0   630     ERRSC  
     RELIABLE SIDE CHAINS  .    1.690      0.548       0.277    704   100.0   704     ERRSC  
     CHANGED ANGLES  . . . .    2.961      0.684       0.343    328   100.0   328     ERRSC  
     SHIFTED CHAIN . . . . .    3.360      0.689       0.344    258   100.0   258     ERRSC  
     ALTERNATIVE PARENT  . .    5.073      0.783       0.391      5   100.0     5     ERRSC  
     SECONDARY STRUCTURE . .    1.154      0.547       0.276    341   100.0   341     ERRSC  
     LARGE SHIFTS/INSERTIONS   10.866      0.824       0.412     36   100.0    36     ERRSC  
     SURFACE . . . . . . . .    2.615      0.642       0.323    448   100.0   448     ERRSC  
     BURIED  . . . . . . . .    0.811      0.491       0.249    436   100.0   436     ERRSC  
     CORE  . . . . . . . . .    1.337      0.557       0.281    848   100.0   848     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    1.319      0.494       0.254   1784   100.0  1784     ERRALL 
     WELL ORDERED  . . . . .    1.189      0.484       0.249   1708   100.0  1708     ERRALL 
     NO INTER CONTACTS . . .    0.920      0.467       0.240   1262   100.0  1262     ERRALL 
     SHIFTED CHAIN . . . . .    2.805      0.639       0.320    530   100.0   530     ERRALL 
     ALTERNATIVE PARENT  . .    3.275      0.655       0.328     13   100.0    13     ERRALL 
     SECONDARY STRUCTURE . .    0.791      0.475       0.246    657   100.0   657     ERRALL 
     LARGE SHIFTS/INSERTIONS    9.356      0.780       0.390     84   100.0    84     ERRALL 
     SURFACE . . . . . . . .    2.004      0.557       0.283    908   100.0   908     ERRALL 
     BURIED  . . . . . . . .    0.609      0.429       0.223    876   100.0   876     ERRALL 
     CORE  . . . . . . . . .    0.922      0.480       0.247   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)       155       208       216       219       220     225     225   DISTCA 
CA  (P)     68.89     92.44     96.00     97.33     97.78             225   DISTCA 
CA  (RMS)    0.60      0.87      0.96      1.05      1.15                   DISTCA 
 
ALL (N)       995      1446      1585      1687      1750    1784    1784   DISTALL 
ALL (P)     55.77     81.05     88.85     94.56     98.09            1784   DISTALL 
ALL (RMS)    0.61      0.94      1.15      1.46      1.90                   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            12          RMSLSI 
CA  (P)       94.67         94.67          5.33          RMSLSI 
CA  (RMS)      0.91          0.93         11.59          RMSLSI 
 
 
 
END of the results output 
