 
####################################################### 
#                                                     # 
#                        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 340 atoms, 339 common with TARGET 
           Number of atoms possible to evaluate: 139 
 
 
 CA-RMS TARGET<->PARENT(1cos)	 1.128383 
 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    10.95           97.5    40    42.6    94     ARMSMC  
     WELL ORDERED  . . . . .    10.95           97.5    40    42.6    94     ARMSMC  
     NO INTER CONTACTS . . .    17.81           80.0     5    26.3    19     ARMSMC  
     SHIFTED CHAIN . . . . .    13.03           95.7    23    50.0    46     ARMSMC  
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSMC  
     SECONDARY STRUCTURE . .     9.63          100.0    37    45.1    82     ARMSMC  
     LARGE SHIFTS/INSERTIONS    15.66           93.3    15    88.2    17     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .     9.65          100.0    37    42.5    87     ARMSMC  
     BURIED  . . . . . . . .    21.23           66.7     3    42.9     7     ARMSMC  
     CORE  . . . . . . . . .     6.70          100.0    25    32.5    77     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    55.75           50.0    12    32.4    37     ARMSSC1 
     WELL ORDERED  . . . . .    55.75           50.0    12    32.4    37     ARMSSC1 
     NO INTER CONTACTS . . .     0.50          100.0     1    16.7     6     ARMSSC1 
     RELIABLE SIDE CHAINS  .    55.75           50.0    12    32.4    37     ARMSSC1 
     CHANGED ANGLES  . . . .    61.73           44.4     9    33.3    27     ARMSSC1 
     SHIFTED CHAIN . . . . .    60.34           60.0     5    29.4    17     ARMSSC1 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SECONDARY STRUCTURE . .    55.75           50.0    12    37.5    32     ARMSSC1 
     LARGE SHIFTS/INSERTIONS    60.34           60.0     5    71.4     7     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .    55.75           50.0    12    35.3    34     ARMSSC1 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     3     ARMSSC1 
     CORE  . . . . . . . . .    52.22           42.9     7    23.3    30     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    52.35           63.6    11    34.4    32     ARMSSC2 
     WELL ORDERED  . . . . .    45.45           75.0     8    27.6    29     ARMSSC2 
     NO INTER CONTACTS . . .    10.99          100.0     1    20.0     5     ARMSSC2 
     RELIABLE SIDE CHAINS  .    50.49           66.7     6    30.0    20     ARMSSC2 
     CHANGED ANGLES  . . . .    57.17           55.6     9    47.4    19     ARMSSC2 
     SHIFTED CHAIN . . . . .    77.94           50.0     4    30.8    13     ARMSSC2 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SECONDARY STRUCTURE . .    52.35           63.6    11    37.9    29     ARMSSC2 
     LARGE SHIFTS/INSERTIONS    77.94           50.0     4    66.7     6     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .    52.35           63.6    11    37.9    29     ARMSSC2 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     3     ARMSSC2 
     CORE  . . . . . . . . .    28.90           71.4     7    26.9    26     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    32.22           66.7     6    33.3    18     ARMSSC3 
     WELL ORDERED  . . . . .    30.59           66.7     3    20.0    15     ARMSSC3 
     NO INTER CONTACTS . . .    44.17            0.0     1    33.3     3     ARMSSC3 
     RELIABLE SIDE CHAINS  .    33.04           60.0     5    33.3    15     ARMSSC3 
     CHANGED ANGLES  . . . .    32.22           66.7     6    35.3    17     ARMSSC3 
     SHIFTED CHAIN . . . . .    26.74          100.0     2    25.0     8     ARMSSC3 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SECONDARY STRUCTURE . .    32.22           66.7     6    37.5    16     ARMSSC3 
     LARGE SHIFTS/INSERTIONS    26.74          100.0     2    66.7     3     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .    32.22           66.7     6    33.3    18     ARMSSC3 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     CORE  . . . . . . . . .    34.64           50.0     4    26.7    15     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    97.47            0.0     3    37.5     8     ARMSSC4 
     WELL ORDERED  . . . . .    37.72            0.0     1    20.0     5     ARMSSC4 
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0     1     ARMSSC4 
     RELIABLE SIDE CHAINS  .    97.47            0.0     3    37.5     8     ARMSSC4 
     CHANGED ANGLES  . . . .   116.36            0.0     2    28.6     7     ARMSSC4 
     SHIFTED CHAIN . . . . .   133.30            0.0     1    20.0     5     ARMSSC4 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SECONDARY STRUCTURE . .    97.47            0.0     3    42.9     7     ARMSSC4 
     LARGE SHIFTS/INSERTIONS   133.30            0.0     1    50.0     2     ARMSSC4 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SURFACE . . . . . . . .    97.47            0.0     3    37.5     8     ARMSSC4 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     CORE  . . . . . . . . .    73.27            0.0     2    33.3     6     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =   0.61525     r(1,2) =  -0.14940     r(1,3) =  -0.77405 
 r(2,1) =   0.25486     r(2,2) =  -0.89146     r(2,3) =   0.37464 
 r(3,1) =  -0.74600     r(3,2) =  -0.42777     r(3,3) =  -0.51039 
THE OFFSET VECTOR: 
 v(1) =   7.20760     v(2) =  22.32667     v(3) =  20.05101 
 
 Number of iteration 26                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   0.65           (Number of atoms:   21) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    0.65         21    43.8    48     CRMSCA  
     CRN = ALL/NP  . . . . .    0.0311                            CRMSCA  
     WELL ORDERED  . . . . .    0.65         21    43.8    48     CRMSCA  
     NO INTER CONTACTS . . .    0.95          3    30.0    10     CRMSCA  
     SHIFTED CHAIN . . . . .    0.62         12    50.0    24     CRMSCA  
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSCA  
     SECONDARY STRUCTURE . .    0.57         19    46.3    41     CRMSCA  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSCA  
     LARGE SHIFTS/INSERTIONS    0.68          8    88.9     9     CRMSCA  
     SURFACE . . . . . . . .    0.55         19    43.2    44     CRMSCA  
     BURIED  . . . . . . . .    1.24          2    50.0     4     CRMSCA  
     CORE  . . . . . . . . .    0.64         13    33.3    39     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    0.70         99    41.8   237     CRMSMC  
     WELL ORDERED  . . . . .    0.70         99    41.8   237     CRMSMC  
     NO INTER CONTACTS . . .    1.05         12    25.5    47     CRMSMC  
     SHIFTED CHAIN . . . . .    0.70         55    47.0   117     CRMSMC  
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSMC  
     SECONDARY STRUCTURE . .    0.60         92    44.9   205     CRMSMC  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSMC  
     LARGE SHIFTS/INSERTIONS    0.78         37    86.0    43     CRMSMC  
     SURFACE . . . . . . . .    0.61         92    42.0   219     CRMSMC  
     BURIED  . . . . . . . .    1.40          7    38.9    18     CRMSMC  
     CORE  . . . . . . . . .    0.64         62    32.0   194     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    2.15         56    33.5   167     CRMSSC  
     WELL ORDERED  . . . . .    1.97         47    30.1   156     CRMSSC  
     NO INTER CONTACTS . . .    0.46          5    19.2    26     CRMSSC  
     RELIABLE SIDE CHAINS  .    2.11         44    32.1   137     CRMSSC  
     CHANGED ANGLES  . . . .    2.61         35    35.0   100     CRMSSC  
     SECONDARY STRUCTURE . .    2.15         56    38.4   146     CRMSSC  
     LARGE SHIFTS/INSERTIONS    2.26         21    63.6    33     CRMSSC  
     SURFACE . . . . . . . .    2.15         56    36.1   155     CRMSSC  
     BURIED  . . . . . . . .    0.00          0     0.0    12     CRMSSC  
     CORE  . . . . . . . . .    2.08         35    26.1   134     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    1.46        139    38.8   358     CRMSALL 
     WELL ORDERED  . . . . .    1.30        130    37.5   347     CRMSALL 
     NO INTER CONTACTS . . .    0.94         16    24.6    65     CRMSALL 
     SHIFTED CHAIN . . . . .    1.37         70    40.9   171     CRMSALL 
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSALL 
     SECONDARY STRUCTURE . .    1.46        132    42.6   310     CRMSALL 
     LARGE SHIFTS/INSERTIONS    1.57         52    76.5    68     CRMSALL 
     SURFACE . . . . . . . .    1.47        132    39.9   331     CRMSALL 
     BURIED  . . . . . . . .    1.40          7    25.9    27     CRMSALL 
     CORE  . . . . . . . . .    1.39         87    30.0   290     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     0.68      8   100.0     8      41-SKLQALKG-48   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     0.78     37    97.4    38      41-SKLQALKG-48   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     1.57     52    91.2    57      41-SKLQALKG-48   
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     0.35      8   100.0     8      41-SKLQALKG-48   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     0.51     37    97.4    38      41-SKLQALKG-48   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     1.43     52    91.2    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 . . . . . . . . . .    1.521      0.600       0.660     21    43.8    48     ERRCA  
     WELL ORDERED  . . . . .    1.521      0.600       0.660     21    43.8    48     ERRCA  
     NO INTER CONTACTS . . .    1.921      0.598       0.670      3    30.0    10     ERRCA  
     SHIFTED CHAIN . . . . .    1.648      0.637       0.697     12    50.0    24     ERRCA  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRCA  
     SECONDARY STRUCTURE . .    1.466      0.612       0.667     19    46.3    41     ERRCA  
     LARGE SHIFTS/INSERTIONS    1.653      0.634       0.695      8    88.9     9     ERRCA  
     SURFACE . . . . . . . .    1.455      0.613       0.668     19    43.2    44     ERRCA  
     BURIED  . . . . . . . .    2.155      0.475       0.584      2    50.0     4     ERRCA  
     CORE  . . . . . . . . .    1.440      0.580       0.638     13    33.3    39     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    1.456      0.584       0.648     99    41.8   237     ERRMC  
     WELL ORDERED  . . . . .    1.456      0.584       0.648     99    41.8   237     ERRMC  
     NO INTER CONTACTS . . .    1.766      0.607       0.657     12    25.5    47     ERRMC  
     SHIFTED CHAIN . . . . .    1.534      0.605       0.668     55    47.0   117     ERRMC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRMC  
     SECONDARY STRUCTURE . .    1.432      0.595       0.659     92    44.9   205     ERRMC  
     LARGE SHIFTS/INSERTIONS    1.487      0.583       0.650     37    86.0    43     ERRMC  
     SURFACE . . . . . . . .    1.409      0.591       0.655     92    42.0   219     ERRMC  
     BURIED  . . . . . . . .    2.071      0.500       0.567      7    38.9    18     ERRMC  
     CORE  . . . . . . . . .    1.438      0.585       0.648     62    32.0   194     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    1.120      0.343       0.336     56    33.5   167     ERRSC  
     WELL ORDERED  . . . . .    1.091      0.356       0.359     47    30.1   156     ERRSC  
     NO INTER CONTACTS . . .    1.345      0.599       0.667      5    19.2    26     ERRSC  
     RELIABLE SIDE CHAINS  .    1.233      0.391       0.395     44    32.1   137     ERRSC  
     CHANGED ANGLES  . . . .    1.096      0.269       0.221     35    35.0   100     ERRSC  
     SHIFTED CHAIN . . . . .    1.124      0.343       0.330     23    30.3    76     ERRSC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRSC  
     SECONDARY STRUCTURE . .    1.120      0.343       0.336     56    38.4   146     ERRSC  
     LARGE SHIFTS/INSERTIONS    1.084      0.311       0.292     21    63.6    33     ERRSC  
     SURFACE . . . . . . . .    1.120      0.343       0.336     56    36.1   155     ERRSC  
     BURIED  . . . . . . . .    0.000      0.000       0.000      0     0.0    12     ERRSC  
     CORE  . . . . . . . . .    1.142      0.362       0.362     35    26.1   134     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    1.344      0.495       0.530    139    38.8   358     ERRALL 
     WELL ORDERED  . . . . .    1.350      0.510       0.551    130    37.5   347     ERRALL 
     NO INTER CONTACTS . . .    1.654      0.600       0.656     16    24.6    65     ERRALL 
     SHIFTED CHAIN . . . . .    1.420      0.524       0.560     70    40.9   171     ERRALL 
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRALL 
     SECONDARY STRUCTURE . .    1.322      0.498       0.530    132    42.6   310     ERRALL 
     LARGE SHIFTS/INSERTIONS    1.348      0.480       0.509     52    76.5    68     ERRALL 
     SURFACE . . . . . . . .    1.306      0.495       0.528    132    39.9   331     ERRALL 
     BURIED  . . . . . . . .    2.071      0.500       0.567      7    25.9    27     ERRALL 
     CORE  . . . . . . . . .    1.343      0.504       0.542     87    30.0   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        21        21        21        21      21      48   DISTCA 
CA  (P)     39.58     43.75     43.75     43.75     43.75              48   DISTCA 
CA  (RMS)    0.52      0.65      0.65      0.65      0.65                   DISTCA 
 
ALL (N)        99       119       130       138       139     139     358   DISTALL 
ALL (P)     27.65     33.24     36.31     38.55     38.83             358   DISTALL 
ALL (RMS)    0.54      0.77      1.04      1.38      1.46                   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            13             8          RMSLSI 
CA  (P)       81.25         27.08         16.67          RMSLSI 
CA  (RMS)      1.02          0.64          0.68          RMSLSI 
 
 
 
END of the results output 
