 
####################################################### 
#                                                     # 
#                        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 3544 atoms, 1784 common with TARGET 
           Number of atoms possible to evaluate: 1726 
 
 
 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 . . . . . . . . . .    34.90           90.5   432    96.4   448     ARMSMC  
     WELL ORDERED  . . . . .    34.26           91.1   429    96.4   445     ARMSMC  
     NO INTER CONTACTS . . .    33.05           91.3   310    98.4   315     ARMSMC  
     SHIFTED CHAIN . . . . .    49.04           78.8   118    88.1   134     ARMSMC  
     ALTERNATIVE PARENT  . .   119.78           50.0     2    50.0     4     ARMSMC  
     SECONDARY STRUCTURE . .    11.30           98.7   158   100.0   158     ARMSMC  
     LARGE SHIFTS/INSERTIONS   104.87           14.3     7    31.8    22     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    43.37           84.6   214    93.9   228     ARMSMC  
     BURIED  . . . . . . . .    23.80           96.3   218    99.1   220     ARMSMC  
     CORE  . . . . . . . . .    32.51           91.8   425    99.8   426     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    55.30           71.0   183    96.3   190     ARMSSC1 
     WELL ORDERED  . . . . .    53.98           72.5   171    97.2   176     ARMSSC1 
     NO INTER CONTACTS . . .    48.65           75.9   133    98.5   135     ARMSSC1 
     RELIABLE SIDE CHAINS  .    56.54           69.5   167    96.5   173     ARMSSC1 
     CHANGED ANGLES  . . . .    70.49           48.1    52    89.7    58     ARMSSC1 
     SHIFTED CHAIN . . . . .    64.74           60.8    51    87.9    58     ARMSSC1 
     ALTERNATIVE PARENT  . .   128.02            0.0     1    50.0     2     ARMSSC1 
     SECONDARY STRUCTURE . .    49.02           75.7    74   100.0    74     ARMSSC1 
     LARGE SHIFTS/INSERTIONS    74.07           33.3     3    30.0    10     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .    69.64           57.1    91    93.8    97     ARMSSC1 
     BURIED  . . . . . . . .    35.87           84.8    92    98.9    93     ARMSSC1 
     CORE  . . . . . . . . .    54.93           71.7   180   100.0   180     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    64.70           61.5   143    96.6   148     ARMSSC2 
     WELL ORDERED  . . . . .    63.26           64.1   128    97.0   132     ARMSSC2 
     NO INTER CONTACTS . . .    66.73           64.4   101    99.0   102     ARMSSC2 
     RELIABLE SIDE CHAINS  .    59.46           60.2    98    96.1   102     ARMSSC2 
     CHANGED ANGLES  . . . .    79.00           43.5    69    93.2    74     ARMSSC2 
     SHIFTED CHAIN . . . . .    68.67           46.2    39    88.6    44     ARMSSC2 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     1     ARMSSC2 
     SECONDARY STRUCTURE . .    65.12           64.9    57   100.0    57     ARMSSC2 
     LARGE SHIFTS/INSERTIONS     4.51          100.0     1    16.7     6     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .    74.57           47.4    76    95.0    80     ARMSSC2 
     BURIED  . . . . . . . .    51.25           77.6    67    98.5    68     ARMSSC2 
     CORE  . . . . . . . . .    64.92           61.3   142   100.0   142     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    82.52           37.8    45    95.7    47     ARMSSC3 
     WELL ORDERED  . . . . .    74.67           46.9    32    97.0    33     ARMSSC3 
     NO INTER CONTACTS . . .    86.32           36.4    22   100.0    22     ARMSSC3 
     RELIABLE SIDE CHAINS  .    77.24           38.7    31    93.9    33     ARMSSC3 
     CHANGED ANGLES  . . . .    87.53           26.7    30    93.8    32     ARMSSC3 
     SHIFTED CHAIN . . . . .    82.36           35.3    17    89.5    19     ARMSSC3 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SECONDARY STRUCTURE . .    69.82           41.2    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 . . . . . . . .    82.38           35.1    37    94.9    39     ARMSSC3 
     BURIED  . . . . . . . .    83.16           50.0     8   100.0     8     ARMSSC3 
     CORE  . . . . . . . . .    82.52           37.8    45   100.0    45     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    91.88           33.3    18   100.0    18     ARMSSC4 
     WELL ORDERED  . . . . .    89.87           36.4    11   100.0    11     ARMSSC4 
     NO INTER CONTACTS . . .   115.81           14.3     7   100.0     7     ARMSSC4 
     RELIABLE SIDE CHAINS  .    91.88           33.3    18   100.0    18     ARMSSC4 
     CHANGED ANGLES  . . . .    92.37           30.8    13   100.0    13     ARMSSC4 
     SHIFTED CHAIN . . . . .    77.15           60.0     5   100.0     5     ARMSSC4 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SECONDARY STRUCTURE . .   101.94           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 . . . . . . . .    88.14           40.0    15   100.0    15     ARMSSC4 
     BURIED  . . . . . . . .   108.68            0.0     3   100.0     3     ARMSSC4 
     CORE  . . . . . . . . .    91.88           33.3    18   100.0    18     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =  -0.40348     r(1,2) =   0.66036     r(1,3) =  -0.63335 
 r(2,1) =   0.91225     r(2,2) =   0.23679     r(2,3) =  -0.33427 
 r(3,1) =  -0.07077     r(3,2) =  -0.71264     r(3,3) =  -0.69795 
THE OFFSET VECTOR: 
 v(1) =  10.46872     v(2) =  14.30384     v(3) =  -9.07152 
 
 Number of iteration 27                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   0.96           (Number of atoms:  211) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    1.22        217    96.4   225     CRMSCA  
     CRN = ALL/NP  . . . . .    0.0056                            CRMSCA  
     WELL ORDERED  . . . . .    1.21        216    96.4   224     CRMSCA  
     NO INTER CONTACTS . . .    1.26        156    98.7   158     CRMSCA  
     SHIFTED CHAIN . . . . .    2.00         60    88.2    68     CRMSCA  
     ALTERNATIVE PARENT  . .    1.31          1    50.0     2     CRMSCA  
     SECONDARY STRUCTURE . .    0.71         79   100.0    79     CRMSCA  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSCA  
     LARGE SHIFTS/INSERTIONS    5.35          4    33.3    12     CRMSCA  
     SURFACE . . . . . . . .    1.55        108    93.9   115     CRMSCA  
     BURIED  . . . . . . . .    0.76        109    99.1   110     CRMSCA  
     CORE  . . . . . . . . .    0.99        213   100.0   213     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    1.26       1067    96.4  1107     CRMSMC  
     WELL ORDERED  . . . . .    1.25       1056    96.4  1095     CRMSMC  
     NO INTER CONTACTS . . .    1.28        768    98.7   778     CRMSMC  
     SHIFTED CHAIN . . . . .    2.02        294    88.0   334     CRMSMC  
     ALTERNATIVE PARENT  . .    1.16          5    50.0    10     CRMSMC  
     SECONDARY STRUCTURE . .    0.73        394   100.0   394     CRMSMC  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSMC  
     LARGE SHIFTS/INSERTIONS    5.38         19    32.2    59     CRMSMC  
     SURFACE . . . . . . . .    1.59        531    93.8   566     CRMSMC  
     BURIED  . . . . . . . .    0.82        536    99.1   541     CRMSMC  
     CORE  . . . . . . . . .    1.05       1048   100.0  1048     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    2.33        858    97.1   884     CRMSSC  
     WELL ORDERED  . . . . .    2.04        796    97.5   816     CRMSSC  
     NO INTER CONTACTS . . .    2.21        624    99.0   630     CRMSSC  
     RELIABLE SIDE CHAINS  .    2.14        682    96.9   704     CRMSSC  
     CHANGED ANGLES  . . . .    3.16        312    95.1   328     CRMSSC  
     SECONDARY STRUCTURE . .    1.84        341   100.0   341     CRMSSC  
     LARGE SHIFTS/INSERTIONS    8.84         10    27.8    36     CRMSSC  
     SURFACE . . . . . . . .    3.05        425    94.9   448     CRMSSC  
     BURIED  . . . . . . . .    1.27        433    99.3   436     CRMSSC  
     CORE  . . . . . . . . .    2.13        848   100.0   848     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    1.86       1726    96.7  1784     CRMSALL 
     WELL ORDERED  . . . . .    1.66       1656    97.0  1708     CRMSALL 
     NO INTER CONTACTS . . .    1.79       1248    98.9  1262     CRMSALL 
     SHIFTED CHAIN . . . . .    2.66        472    89.1   530     CRMSALL 
     ALTERNATIVE PARENT  . .    1.87          6    46.2    13     CRMSALL 
     SECONDARY STRUCTURE . .    1.41        657   100.0   657     CRMSALL 
     LARGE SHIFTS/INSERTIONS    6.78         26    31.0    84     CRMSALL 
     SURFACE . . . . . . . .    2.41        857    94.4   908     CRMSALL 
     BURIED  . . . . . . . .    1.06        869    99.2   876     CRMSALL 
     CORE  . . . . . . . . .    1.67       1700   100.0  1700     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     0.00      0     0.0     8     222-PVLPAESE-229  
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     0.00      0     0.0    40     222-PVLPAESE-229  
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     0.00      0     0.0    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 . . . . . . . . . .    1.011      0.376       0.426    217    96.4   225     ERRCA  
     WELL ORDERED  . . . . .    1.014      0.378       0.428    216    96.4   224     ERRCA  
     NO INTER CONTACTS . . .    0.929      0.371       0.419    156    98.7   158     ERRCA  
     SHIFTED CHAIN . . . . .    1.111      0.269       0.294     60    88.2    68     ERRCA  
     ALTERNATIVE PARENT  . .    1.012      0.279       0.316      1    50.0     2     ERRCA  
     SECONDARY STRUCTURE . .    0.988      0.410       0.472     79   100.0    79     ERRCA  
     LARGE SHIFTS/INSERTIONS    1.765      0.151       0.076      4    33.3    12     ERRCA  
     SURFACE . . . . . . . .    1.238      0.378       0.429    108    93.9   115     ERRCA  
     BURIED  . . . . . . . .    0.786      0.374       0.423    109    99.1   110     ERRCA  
     CORE  . . . . . . . . .    0.997      0.380       0.432    213   100.0   213     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    1.005      0.372       0.420   1067    96.4  1107     ERRMC  
     WELL ORDERED  . . . . .    1.005      0.374       0.422   1056    96.4  1095     ERRMC  
     NO INTER CONTACTS . . .    0.933      0.369       0.416    768    98.7   778     ERRMC  
     SHIFTED CHAIN . . . . .    1.152      0.283       0.314    294    88.0   334     ERRMC  
     ALTERNATIVE PARENT  . .    1.261      0.405       0.428      5    50.0    10     ERRMC  
     SECONDARY STRUCTURE . .    0.978      0.404       0.459    394   100.0   394     ERRMC  
     LARGE SHIFTS/INSERTIONS    2.087      0.210       0.116     19    32.2    59     ERRMC  
     SURFACE . . . . . . . .    1.232      0.377       0.427    531    93.8   566     ERRMC  
     BURIED  . . . . . . . .    0.779      0.368       0.413    536    99.1   541     ERRMC  
     CORE  . . . . . . . . .    0.985      0.375       0.426   1048   100.0  1048     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    1.064      0.315       0.314    858    97.1   884     ERRSC  
     WELL ORDERED  . . . . .    0.996      0.317       0.323    796    97.5   816     ERRSC  
     NO INTER CONTACTS . . .    1.013      0.324       0.331    624    99.0   630     ERRSC  
     RELIABLE SIDE CHAINS  .    1.038      0.321       0.328    682    96.9   704     ERRSC  
     CHANGED ANGLES  . . . .    1.269      0.270       0.221    312    95.1   328     ERRSC  
     SHIFTED CHAIN . . . . .    1.214      0.235       0.212    232    89.9   258     ERRSC  
     ALTERNATIVE PARENT  . .    1.093      0.213       0.135      2    40.0     5     ERRSC  
     SECONDARY STRUCTURE . .    1.027      0.346       0.348    341   100.0   341     ERRSC  
     LARGE SHIFTS/INSERTIONS    4.580      0.322       0.166     10    27.8    36     ERRSC  
     SURFACE . . . . . . . .    1.325      0.296       0.265    425    94.9   448     ERRSC  
     BURIED  . . . . . . . .    0.809      0.334       0.363    433    99.3   436     ERRSC  
     CORE  . . . . . . . . .    1.023      0.315       0.316    848   100.0   848     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    1.041      0.346       0.371   1726    96.7  1784     ERRALL 
     WELL ORDERED  . . . . .    1.007      0.349       0.378   1656    97.0  1708     ERRALL 
     NO INTER CONTACTS . . .    0.976      0.349       0.376   1248    98.9  1262     ERRALL 
     SHIFTED CHAIN . . . . .    1.189      0.262       0.268    472    89.1   530     ERRALL 
     ALTERNATIVE PARENT  . .    1.293      0.377       0.377      6    46.2    13     ERRALL 
     SECONDARY STRUCTURE . .    1.006      0.376       0.404    657   100.0   657     ERRALL 
     LARGE SHIFTS/INSERTIONS    2.942      0.249       0.134     26    31.0    84     ERRALL 
     SURFACE . . . . . . . .    1.288      0.340       0.351    857    94.4   908     ERRALL 
     BURIED  . . . . . . . .    0.796      0.353       0.390    869    99.2   876     ERRALL 
     CORE  . . . . . . . . .    1.011      0.348       0.375   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)       149       202       216       216       217     217     225   DISTCA 
CA  (P)     66.22     89.78     96.00     96.00     96.44             225   DISTCA 
CA  (RMS)    0.61      0.86      1.04      1.04      1.22                   DISTCA 
 
ALL (N)      1031      1441      1593      1678      1721    1726    1784   DISTALL 
ALL (P)     57.79     80.77     89.29     94.06     96.47            1784   DISTALL 
ALL (RMS)    0.62      0.92      1.16      1.41      1.72                   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             4          RMSLSI 
CA  (P)       94.67         94.67          1.78          RMSLSI 
CA  (RMS)      0.91          0.99          5.35          RMSLSI 
 
 
 
END of the results output 
