 
####################################################### 
#                                                     # 
#                        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 1867 atoms, 1783 common with TARGET 
           Number of atoms possible to evaluate: 1732 
 
 
 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 . . . . . . . . . .    38.02           83.2   434    96.9   448     ARMSMC  
     WELL ORDERED  . . . . .    36.58           83.8   431    96.9   445     ARMSMC  
     NO INTER CONTACTS . . .    37.60           83.3   312    99.0   315     ARMSMC  
     SHIFTED CHAIN . . . . .    51.94           75.0   120    89.6   134     ARMSMC  
     ALTERNATIVE PARENT  . .    99.52           66.7     3    75.0     4     ARMSMC  
     SECONDARY STRUCTURE . .    14.44           97.5   158   100.0   158     ARMSMC  
     LARGE SHIFTS/INSERTIONS   105.10           25.0     8    36.4    22     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    46.42           80.0   215    94.3   228     ARMSMC  
     BURIED  . . . . . . . .    27.37           86.3   219    99.5   220     ARMSMC  
     CORE  . . . . . . . . .    35.57           84.3   426   100.0   426     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    51.06           69.0   184    96.8   190     ARMSSC1 
     WELL ORDERED  . . . . .    47.97           71.5   172    97.7   176     ARMSSC1 
     NO INTER CONTACTS . . .    47.79           71.6   134    99.3   135     ARMSSC1 
     RELIABLE SIDE CHAINS  .    52.68           67.3   168    97.1   173     ARMSSC1 
     CHANGED ANGLES  . . . .    72.47           43.4    53    91.4    58     ARMSSC1 
     SHIFTED CHAIN . . . . .    57.65           59.6    52    89.7    58     ARMSSC1 
     ALTERNATIVE PARENT  . .    79.09           50.0     2   100.0     2     ARMSSC1 
     SECONDARY STRUCTURE . .    42.33           82.4    74   100.0    74     ARMSSC1 
     LARGE SHIFTS/INSERTIONS    93.30           25.0     4    40.0    10     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .    63.35           54.9    91    93.8    97     ARMSSC1 
     BURIED  . . . . . . . .    35.07           82.8    93   100.0    93     ARMSSC1 
     CORE  . . . . . . . . .    49.71           70.0   180   100.0   180     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    66.50           59.7   144    97.3   148     ARMSSC2 
     WELL ORDERED  . . . . .    65.87           62.0   129    97.7   132     ARMSSC2 
     NO INTER CONTACTS . . .    65.60           62.7   102   100.0   102     ARMSSC2 
     RELIABLE SIDE CHAINS  .    58.24           61.6    99    97.1   102     ARMSSC2 
     CHANGED ANGLES  . . . .    85.86           40.0    70    94.6    74     ARMSSC2 
     SHIFTED CHAIN . . . . .    80.53           42.5    40    90.9    44     ARMSSC2 
     ALTERNATIVE PARENT  . .     7.08          100.0     1   100.0     1     ARMSSC2 
     SECONDARY STRUCTURE . .    60.55           75.4    57   100.0    57     ARMSSC2 
     LARGE SHIFTS/INSERTIONS    61.83           50.0     2    33.3     6     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .    71.78           51.3    76    95.0    80     ARMSSC2 
     BURIED  . . . . . . . .    60.05           69.1    68   100.0    68     ARMSSC2 
     CORE  . . . . . . . . .    66.56           59.9   142   100.0   142     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    76.83           26.7    45    95.7    47     ARMSSC3 
     WELL ORDERED  . . . . .    76.07           28.1    32    97.0    33     ARMSSC3 
     NO INTER CONTACTS . . .    73.94           27.3    22   100.0    22     ARMSSC3 
     RELIABLE SIDE CHAINS  .    75.44           22.6    31    93.9    33     ARMSSC3 
     CHANGED ANGLES  . . . .    84.65           16.7    30    93.8    32     ARMSSC3 
     SHIFTED CHAIN . . . . .    85.59           23.5    17    89.5    19     ARMSSC3 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SECONDARY STRUCTURE . .    61.74           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 . . . . . . . .    77.61           27.0    37    94.9    39     ARMSSC3 
     BURIED  . . . . . . . .    73.15           25.0     8   100.0     8     ARMSSC3 
     CORE  . . . . . . . . .    76.83           26.7    45   100.0    45     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    98.62           11.1    18   100.0    18     ARMSSC4 
     WELL ORDERED  . . . . .    84.57           18.2    11   100.0    11     ARMSSC4 
     NO INTER CONTACTS . . .   111.01            0.0     7   100.0     7     ARMSSC4 
     RELIABLE SIDE CHAINS  .    98.62           11.1    18   100.0    18     ARMSSC4 
     CHANGED ANGLES  . . . .   114.37            0.0    13   100.0    13     ARMSSC4 
     SHIFTED CHAIN . . . . .    61.25            0.0     5   100.0     5     ARMSSC4 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SECONDARY STRUCTURE . .    86.69           16.7     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 . . . . . . . .    98.52           13.3    15   100.0    15     ARMSSC4 
     BURIED  . . . . . . . .    99.11            0.0     3   100.0     3     ARMSSC4 
     CORE  . . . . . . . . .    98.62           11.1    18   100.0    18     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =  -0.63562     r(1,2) =  -0.64984     r(1,3) =  -0.41676 
 r(2,1) =   0.67018     r(2,2) =  -0.73244     r(2,3) =   0.11996 
 r(3,1) =  -0.38321     r(3,2) =  -0.20306     r(3,3) =   0.90107 
THE OFFSET VECTOR: 
 v(1) =  14.59837     v(2) =   7.69084     v(3) =  22.62194 
 
 Number of iteration 25                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.07           (Number of atoms:  207) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    1.42        218    96.9   225     CRMSCA  
     CRN = ALL/NP  . . . . .    0.0065                            CRMSCA  
     WELL ORDERED  . . . . .    1.41        217    96.9   224     CRMSCA  
     NO INTER CONTACTS . . .    1.47        157    99.4   158     CRMSCA  
     SHIFTED CHAIN . . . . .    2.28         61    89.7    68     CRMSCA  
     ALTERNATIVE PARENT  . .    2.49          2   100.0     2     CRMSCA  
     SECONDARY STRUCTURE . .    0.90         79   100.0    79     CRMSCA  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSCA  
     LARGE SHIFTS/INSERTIONS    5.04          5    41.7    12     CRMSCA  
     SURFACE . . . . . . . .    1.75        108    93.9   115     CRMSCA  
     BURIED  . . . . . . . .    0.98        110   100.0   110     CRMSCA  
     CORE  . . . . . . . . .    1.21        213   100.0   213     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    1.48       1071    96.7  1107     CRMSMC  
     WELL ORDERED  . . . . .    1.46       1060    96.8  1095     CRMSMC  
     NO INTER CONTACTS . . .    1.52        772    99.2   778     CRMSMC  
     SHIFTED CHAIN . . . . .    2.33        298    89.2   334     CRMSMC  
     ALTERNATIVE PARENT  . .    2.73          9    90.0    10     CRMSMC  
     SECONDARY STRUCTURE . .    0.95        394   100.0   394     CRMSMC  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSMC  
     LARGE SHIFTS/INSERTIONS    5.23         23    39.0    59     CRMSMC  
     SURFACE . . . . . . . .    1.80        531    93.8   566     CRMSMC  
     BURIED  . . . . . . . .    1.06        540    99.8   541     CRMSMC  
     CORE  . . . . . . . . .    1.28       1048   100.0  1048     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    2.55        861    97.4   884     CRMSSC  
     WELL ORDERED  . . . . .    2.29        799    97.9   816     CRMSSC  
     NO INTER CONTACTS . . .    2.43        627    99.5   630     CRMSSC  
     RELIABLE SIDE CHAINS  .    2.42        685    97.3   704     CRMSSC  
     CHANGED ANGLES  . . . .    3.54        314    95.7   328     CRMSSC  
     SECONDARY STRUCTURE . .    1.93        341   100.0   341     CRMSSC  
     LARGE SHIFTS/INSERTIONS    7.50         13    36.1    36     CRMSSC  
     SURFACE . . . . . . . .    3.20        425    94.9   448     CRMSSC  
     BURIED  . . . . . . . .    1.70        436   100.0   436     CRMSSC  
     CORE  . . . . . . . . .    2.40        848   100.0   848     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    2.06       1732    97.1  1784     CRMSALL 
     WELL ORDERED  . . . . .    1.88       1662    97.3  1708     CRMSALL 
     NO INTER CONTACTS . . .    2.01       1254    99.4  1262     CRMSALL 
     SHIFTED CHAIN . . . . .    2.93        478    90.2   530     CRMSALL 
     ALTERNATIVE PARENT  . .    3.59         12    92.3    13     CRMSALL 
     SECONDARY STRUCTURE . .    1.53        657   100.0   657     CRMSALL 
     LARGE SHIFTS/INSERTIONS    6.12         32    38.1    84     CRMSALL 
     SURFACE . . . . . . . .    2.57        857    94.4   908     CRMSALL 
     BURIED  . . . . . . . .    1.41        875    99.9   876     CRMSALL 
     CORE  . . . . . . . . .    1.91       1700   100.0  1700     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     2.97      1    12.5     8     222-PVLPAESE-229  
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     3.53      4    10.0    40     222-PVLPAESE-229  
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     4.53      6    10.3    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 . . . . . . . . . .    0.538      0.250       0.225    218    96.9   225     ERRCA  
     WELL ORDERED  . . . . .    0.533      0.249       0.225    217    96.9   224     ERRCA  
     NO INTER CONTACTS . . .    0.575      0.265       0.246    157    99.4   158     ERRCA  
     SHIFTED CHAIN . . . . .    0.943      0.263       0.139     61    89.7    68     ERRCA  
     ALTERNATIVE PARENT  . .    1.425      0.401       0.200      2   100.0     2     ERRCA  
     SECONDARY STRUCTURE . .    0.481      0.306       0.326     79   100.0    79     ERRCA  
     LARGE SHIFTS/INSERTIONS    3.211      0.543       0.272      5    41.7    12     ERRCA  
     SURFACE . . . . . . . .    0.630      0.230       0.171    108    93.9   115     ERRCA  
     BURIED  . . . . . . . .    0.448      0.270       0.278    110   100.0   110     ERRCA  
     CORE  . . . . . . . . .    0.475      0.243       0.224    213   100.0   213     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    0.565      0.252       0.220   1071    96.7  1107     ERRMC  
     WELL ORDERED  . . . . .    0.557      0.251       0.220   1060    96.8  1095     ERRMC  
     NO INTER CONTACTS . . .    0.597      0.266       0.240    772    99.2   778     ERRMC  
     SHIFTED CHAIN . . . . .    0.965      0.265       0.141    298    89.2   334     ERRMC  
     ALTERNATIVE PARENT  . .    1.436      0.362       0.181      9    90.0    10     ERRMC  
     SECONDARY STRUCTURE . .    0.476      0.294       0.308    394   100.0   394     ERRMC  
     LARGE SHIFTS/INSERTIONS    3.360      0.541       0.270     23    39.0    59     ERRMC  
     SURFACE . . . . . . . .    0.670      0.240       0.176    531    93.8   566     ERRMC  
     BURIED  . . . . . . . .    0.461      0.264       0.263    540    99.8   541     ERRMC  
     CORE  . . . . . . . . .    0.504      0.246       0.219   1048   100.0  1048     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    1.164      0.314       0.213    861    97.4   884     ERRSC  
     WELL ORDERED  . . . . .    1.021      0.299       0.210    799    97.9   816     ERRSC  
     NO INTER CONTACTS . . .    1.090      0.313       0.223    627    99.5   630     ERRSC  
     RELIABLE SIDE CHAINS  .    1.090      0.306       0.212    685    97.3   704     ERRSC  
     CHANGED ANGLES  . . . .    2.010      0.416       0.226    314    95.7   328     ERRSC  
     SHIFTED CHAIN . . . . .    1.895      0.387       0.197    235    91.1   258     ERRSC  
     ALTERNATIVE PARENT  . .    3.704      0.614       0.307      5   100.0     5     ERRSC  
     SECONDARY STRUCTURE . .    0.871      0.314       0.257    341   100.0   341     ERRSC  
     LARGE SHIFTS/INSERTIONS    5.522      0.664       0.332     13    36.1    36     ERRSC  
     SURFACE . . . . . . . .    1.643      0.360       0.206    425    94.9   448     ERRSC  
     BURIED  . . . . . . . .    0.697      0.269       0.221    436   100.0   436     ERRSC  
     CORE  . . . . . . . . .    1.097      0.309       0.212    848   100.0   848     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    0.852      0.282       0.216   1732    97.1  1784     ERRALL 
     WELL ORDERED  . . . . .    0.768      0.273       0.215   1662    97.3  1708     ERRALL 
     NO INTER CONTACTS . . .    0.832      0.288       0.231   1254    99.4  1262     ERRALL 
     SHIFTED CHAIN . . . . .    1.386      0.320       0.167    478    90.2   530     ERRALL 
     ALTERNATIVE PARENT  . .    2.140      0.439       0.219     12    92.3    13     ERRALL 
     SECONDARY STRUCTURE . .    0.677      0.304       0.283    657   100.0   657     ERRALL 
     LARGE SHIFTS/INSERTIONS    4.103      0.583       0.291     32    38.1    84     ERRALL 
     SURFACE . . . . . . . .    1.134      0.297       0.190    857    94.4   908     ERRALL 
     BURIED  . . . . . . . .    0.575      0.266       0.242    875    99.9   876     ERRALL 
     CORE  . . . . . . . . .    0.791      0.276       0.215   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)       126       199       213       217       218     218     225   DISTCA 
CA  (P)     56.00     88.44     94.67     96.44     96.89             225   DISTCA 
CA  (RMS)    0.66      1.00      1.16      1.25      1.42                   DISTCA 
 
ALL (N)       800      1379      1547      1668      1727    1732    1784   DISTALL 
ALL (P)     44.84     77.30     86.72     93.50     96.80            1784   DISTALL 
ALL (RMS)    0.66      1.04      1.28      1.60      1.97                   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             5          RMSLSI 
CA  (P)       94.67         94.67          2.22          RMSLSI 
CA  (RMS)      0.91          1.21          5.04          RMSLSI 
 
 
 
END of the results output 
