 
####################################################### 
#                                                     # 
#                        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/T0073.inter 
CONANA-PAIR            ../CONANA/T0073.pair 
# 
NUMBER-OF-PARENTS      1 
ALIGNMENT-DALI(1)      ../PARENTS/casp3.T0073.1cos.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 358 atoms, MODEL 426 atoms, 358 common with TARGET 
           Number of atoms possible to evaluate: 312 
 
 
 CA-RMS TARGET<->PARENT(1cos)	 1.128383 
 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    28.67           93.8    80    85.1    94     ARMSMC  
     WELL ORDERED  . . . . .    28.67           93.8    80    85.1    94     ARMSMC  
     NO INTER CONTACTS . . .    32.41           91.7    12    63.2    19     ARMSMC  
     SHIFTED CHAIN . . . . .    40.01           89.5    38    82.6    46     ARMSMC  
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSMC  
     SECONDARY STRUCTURE . .    11.06           97.3    75    91.5    82     ARMSMC  
     LARGE SHIFTS/INSERTIONS    51.34           80.0    15    88.2    17     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    27.06           94.6    74    85.1    87     ARMSMC  
     BURIED  . . . . . . . .    43.90           83.3     6    85.7     7     ARMSMC  
     CORE  . . . . . . . . .    20.08           96.9    65    84.4    77     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    81.48           40.6    32    86.5    37     ARMSSC1 
     WELL ORDERED  . . . . .    81.48           40.6    32    86.5    37     ARMSSC1 
     NO INTER CONTACTS . . .   113.18            0.0     4    66.7     6     ARMSSC1 
     RELIABLE SIDE CHAINS  .    81.48           40.6    32    86.5    37     ARMSSC1 
     CHANGED ANGLES  . . . .    89.32           30.4    23    85.2    27     ARMSSC1 
     SHIFTED CHAIN . . . . .    99.33           20.0    15    88.2    17     ARMSSC1 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SECONDARY STRUCTURE . .    77.72           44.8    29    90.6    32     ARMSSC1 
     LARGE SHIFTS/INSERTIONS    73.88           33.3     6    85.7     7     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .    82.44           41.4    29    85.3    34     ARMSSC1 
     BURIED  . . . . . . . .    71.49           33.3     3   100.0     3     ARMSSC1 
     CORE  . . . . . . . . .    83.13           42.3    26    86.7    30     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    78.10           42.9    28    87.5    32     ARMSSC2 
     WELL ORDERED  . . . . .    78.66           44.0    25    86.2    29     ARMSSC2 
     NO INTER CONTACTS . . .    53.69           50.0     4    80.0     5     ARMSSC2 
     RELIABLE SIDE CHAINS  .    73.61           43.8    16    80.0    20     ARMSSC2 
     CHANGED ANGLES  . . . .    84.01           35.3    17    89.5    19     ARMSSC2 
     SHIFTED CHAIN . . . . .    76.66           33.3    12    92.3    13     ARMSSC2 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SECONDARY STRUCTURE . .    78.35           42.3    26    89.7    29     ARMSSC2 
     LARGE SHIFTS/INSERTIONS    74.77           40.0     5    83.3     6     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .    76.77           44.0    25    86.2    29     ARMSSC2 
     BURIED  . . . . . . . .    88.38           33.3     3   100.0     3     ARMSSC2 
     CORE  . . . . . . . . .    78.80           43.5    23    88.5    26     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    82.09           25.0    16    88.9    18     ARMSSC3 
     WELL ORDERED  . . . . .    76.72           23.1    13    86.7    15     ARMSSC3 
     NO INTER CONTACTS . . .    81.30            0.0     3   100.0     3     ARMSSC3 
     RELIABLE SIDE CHAINS  .    89.29           15.4    13    86.7    15     ARMSSC3 
     CHANGED ANGLES  . . . .    83.36           26.7    15    88.2    17     ARMSSC3 
     SHIFTED CHAIN . . . . .   100.79           25.0     8   100.0     8     ARMSSC3 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SECONDARY STRUCTURE . .    73.26           28.6    14    87.5    16     ARMSSC3 
     LARGE SHIFTS/INSERTIONS   127.95           33.3     3   100.0     3     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .    82.09           25.0    16    88.9    18     ARMSSC3 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     CORE  . . . . . . . . .    67.19           23.1    13    86.7    15     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    74.12           37.5     8   100.0     8     ARMSSC4 
     WELL ORDERED  . . . . .    54.69           40.0     5   100.0     5     ARMSSC4 
     NO INTER CONTACTS . . .   105.54            0.0     1   100.0     1     ARMSSC4 
     RELIABLE SIDE CHAINS  .    74.12           37.5     8   100.0     8     ARMSSC4 
     CHANGED ANGLES  . . . .    79.23           28.6     7   100.0     7     ARMSSC4 
     SHIFTED CHAIN . . . . .    69.84           40.0     5   100.0     5     ARMSSC4 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SECONDARY STRUCTURE . .    79.24           28.6     7   100.0     7     ARMSSC4 
     LARGE SHIFTS/INSERTIONS    73.31           50.0     2   100.0     2     ARMSSC4 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SURFACE . . . . . . . .    74.12           37.5     8   100.0     8     ARMSSC4 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     CORE  . . . . . . . . .    74.39           33.3     6   100.0     6     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =  -0.82308     r(1,2) =  -0.42621     r(1,3) =   0.37535 
 r(2,1) =  -0.11233     r(2,2) =   0.77002     r(2,3) =   0.62805 
 r(3,1) =  -0.55671     r(3,2) =   0.47477     r(3,3) =  -0.68166 
THE OFFSET VECTOR: 
 v(1) =  15.68834     v(2) =  29.78258     v(3) =   8.26466 
 
 Number of iteration 35                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   0.93           (Number of atoms:   26) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    7.80         42    87.5    48     CRMSCA  
     CRN = ALL/NP  . . . . .    0.1858                            CRMSCA  
     WELL ORDERED  . . . . .    7.80         42    87.5    48     CRMSCA  
     NO INTER CONTACTS . . .    8.19          7    70.0    10     CRMSCA  
     SHIFTED CHAIN . . . . .    8.10         21    87.5    24     CRMSCA  
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSCA  
     SECONDARY STRUCTURE . .    7.53         38    92.7    41     CRMSCA  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSCA  
     LARGE SHIFTS/INSERTIONS    1.72          8    88.9     9     CRMSCA  
     SURFACE . . . . . . . .    8.07         38    86.4    44     CRMSCA  
     BURIED  . . . . . . . .    4.58          4   100.0     4     CRMSCA  
     CORE  . . . . . . . . .    8.63         34    87.2    39     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    7.87        208    87.8   237     CRMSMC  
     WELL ORDERED  . . . . .    7.87        208    87.8   237     CRMSMC  
     NO INTER CONTACTS . . .    8.05         33    70.2    47     CRMSMC  
     SHIFTED CHAIN . . . . .    8.16        103    88.0   117     CRMSMC  
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSMC  
     SECONDARY STRUCTURE . .    7.61        190    92.7   205     CRMSMC  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSMC  
     LARGE SHIFTS/INSERTIONS    1.64         38    88.4    43     CRMSMC  
     SURFACE . . . . . . . .    8.08        190    86.8   219     CRMSMC  
     BURIED  . . . . . . . .    5.12         18   100.0    18     CRMSMC  
     CORE  . . . . . . . . .    8.67        170    87.6   194     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    8.88        145    86.8   167     CRMSSC  
     WELL ORDERED  . . . . .    9.16        135    86.5   156     CRMSSC  
     NO INTER CONTACTS . . .    5.23         21    80.8    26     CRMSSC  
     RELIABLE SIDE CHAINS  .    9.52        115    83.9   137     CRMSSC  
     CHANGED ANGLES  . . . .    9.52         85    85.0   100     CRMSSC  
     SECONDARY STRUCTURE . .    8.64        133    91.1   146     CRMSSC  
     LARGE SHIFTS/INSERTIONS    2.55         26    78.8    33     CRMSSC  
     SURFACE . . . . . . . .    9.22        133    85.8   155     CRMSSC  
     BURIED  . . . . . . . .    3.31         12   100.0    12     CRMSSC  
     CORE  . . . . . . . . .    9.73        119    88.8   134     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    8.32        312    87.2   358     CRMSALL 
     WELL ORDERED  . . . . .    8.43        302    87.0   347     CRMSALL 
     NO INTER CONTACTS . . .    6.81         48    73.8    65     CRMSALL 
     SHIFTED CHAIN . . . . .    8.98        150    87.7   171     CRMSALL 
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSALL 
     SECONDARY STRUCTURE . .    8.08        285    91.9   310     CRMSALL 
     LARGE SHIFTS/INSERTIONS    2.12         57    83.8    68     CRMSALL 
     SURFACE . . . . . . . .    8.59        285    86.1   331     CRMSALL 
     BURIED  . . . . . . . .    4.50         27   100.0    27     CRMSALL 
     CORE  . . . . . . . . .    9.15        255    87.9   290     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     1.72      8   100.0     8      41-SKLQALKG-48   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     1.64     38   100.0    38      41-SKLQALKG-48   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     2.12     57   100.0    57      41-SKLQALKG-48   
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     0.53      8   100.0     8      41-SKLQALKG-48   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     0.82     38   100.0    38      41-SKLQALKG-48   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     1.69     57   100.0    57      41-SKLQALKG-48   
 
 
Accuracy of estimates of atomic coordinate errors: model <-> target 
 
 (CA)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    4.420      0.478       0.364     42    87.5    48     ERRCA  
     WELL ORDERED  . . . . .    4.420      0.478       0.364     42    87.5    48     ERRCA  
     NO INTER CONTACTS . . .    4.540      0.464       0.344      7    70.0    10     ERRCA  
     SHIFTED CHAIN . . . . .    4.471      0.450       0.330     21    87.5    24     ERRCA  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRCA  
     SECONDARY STRUCTURE . .    4.175      0.474       0.376     38    92.7    41     ERRCA  
     LARGE SHIFTS/INSERTIONS    0.753      0.280       0.277      8    88.9     9     ERRCA  
     SURFACE . . . . . . . .    4.618      0.482       0.370     38    86.4    44     ERRCA  
     BURIED  . . . . . . . .    2.538      0.438       0.312      4   100.0     4     ERRCA  
     CORE  . . . . . . . . .    5.283      0.525       0.385     34    87.2    39     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    4.488      0.491       0.375    208    87.8   237     ERRMC  
     WELL ORDERED  . . . . .    4.488      0.491       0.375    208    87.8   237     ERRMC  
     NO INTER CONTACTS . . .    4.522      0.487       0.379     33    70.2    47     ERRMC  
     SHIFTED CHAIN . . . . .    4.553      0.464       0.342    103    88.0   117     ERRMC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRMC  
     SECONDARY STRUCTURE . .    4.240      0.485       0.384    190    92.7   205     ERRMC  
     LARGE SHIFTS/INSERTIONS    0.751      0.290       0.284     38    88.4    43     ERRMC  
     SURFACE . . . . . . . .    4.644      0.494       0.378    190    86.8   219     ERRMC  
     BURIED  . . . . . . . .    2.839      0.460       0.343     18   100.0    18     ERRMC  
     CORE  . . . . . . . . .    5.323      0.536       0.395    170    87.6   194     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    4.849      0.432       0.254    145    86.8   167     ERRSC  
     WELL ORDERED  . . . . .    5.091      0.444       0.263    135    86.5   156     ERRSC  
     NO INTER CONTACTS . . .    2.045      0.270       0.172     21    80.8    26     ERRSC  
     RELIABLE SIDE CHAINS  .    5.393      0.453       0.274    115    83.9   137     ERRSC  
     CHANGED ANGLES  . . . .    5.344      0.449       0.235     85    85.0   100     ERRSC  
     SHIFTED CHAIN . . . . .    5.583      0.442       0.252     67    88.2    76     ERRSC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRSC  
     SECONDARY STRUCTURE . .    4.574      0.421       0.250    133    91.1   146     ERRSC  
     LARGE SHIFTS/INSERTIONS    1.068      0.260       0.178     26    78.8    33     ERRSC  
     SURFACE . . . . . . . .    5.150      0.444       0.259    133    85.8   155     ERRSC  
     BURIED  . . . . . . . .    1.518      0.296       0.206     12   100.0    12     ERRSC  
     CORE  . . . . . . . . .    5.676      0.470       0.271    119    88.8   134     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    4.653      0.469       0.324    312    87.2   358     ERRALL 
     WELL ORDERED  . . . . .    4.755      0.475       0.331    302    87.0   347     ERRALL 
     NO INTER CONTACTS . . .    3.367      0.395       0.291     48    73.8    65     ERRALL 
     SHIFTED CHAIN . . . . .    4.980      0.458       0.308    150    87.7   171     ERRALL 
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRALL 
     SECONDARY STRUCTURE . .    4.401      0.461       0.328    285    91.9   310     ERRALL 
     LARGE SHIFTS/INSERTIONS    0.911      0.282       0.241     57    83.8    68     ERRALL 
     SURFACE . . . . . . . .    4.874      0.475       0.328    285    86.1   331     ERRALL 
     BURIED  . . . . . . . .    2.317      0.399       0.288     27   100.0    27     ERRALL 
     CORE  . . . . . . . . .    5.489      0.511       0.343    255    87.9   290     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)        19        26        26        27        30      42      48   DISTCA 
CA  (P)     39.58     54.17     54.17     56.25     62.50              48   DISTCA 
CA  (RMS)    0.70      0.93      0.93      1.17      2.75                   DISTCA 
 
ALL (N)       100       153       177       203       225     312     358   DISTALL 
ALL (P)     27.93     42.74     49.44     56.70     62.85             358   DISTALL 
ALL (RMS)    0.70      1.02      1.30      1.87      2.89                   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)          39            34             8          RMSLSI 
CA  (P)       81.25         70.83         16.67          RMSLSI 
CA  (RMS)      1.02          8.63          1.72          RMSLSI 
 
 
 
END of the results output 
