 
####################################################### 
#                                                     # 
#                        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/T0003.inter 
# 
NUMBER-OF-PARENTS      2 
ALIGNMENT-DALI(1)      ../PARENTS/casp2.T0003.1gpr.rot 
ALIGNMENT-DALI(2)      ../PARENTS/casp2.T0003.1f3g.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 1162 atoms, MODEL 1175 atoms, 1162 common with TARGET 
           Number of atoms possible to evaluate: 1085 
 
 
 CA-RMS TARGET<->PARENT(1gpr)	 1.649883 
 
 CA-RMS TARGET<->PARENT(1f3g)	 1.280893 
 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    33.03           84.0   288    94.1   306     ARMSMC  
     WELL ORDERED  . . . . .    31.94           88.7   159    97.0   164     ARMSMC  
     NO INTER CONTACTS . . .    27.10           86.2   203    97.6   208     ARMSMC  
     SHIFTED CHAIN . . . . .    41.78           77.5   138    88.5   156     ARMSMC  
     ALTERNATIVE PARENT  . .    64.32           54.5    22    81.5    27     ARMSMC  
     SECONDARY STRUCTURE . .    28.75           88.4   121    96.0   126     ARMSMC  
     LARGE SHIFTS/INSERTIONS    77.88           42.9    21    55.3    38     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    36.62           81.0   163    91.6   178     ARMSMC  
     BURIED  . . . . . . . .    27.66           88.0   125    97.7   128     ARMSMC  
     CORE  . . . . . . . . .    26.46           87.3   267    99.6   268     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    79.87           50.8   122    93.8   130     ARMSSC1 
     WELL ORDERED  . . . . .    77.93           58.9    56    98.2    57     ARMSSC1 
     NO INTER CONTACTS . . .    79.79           47.6    82    98.8    83     ARMSSC1 
     RELIABLE SIDE CHAINS  .    80.89           49.5   105    92.9   113     ARMSSC1 
     CHANGED ANGLES  . . . .    91.84           33.3    66    90.4    73     ARMSSC1 
     SHIFTED CHAIN . . . . .    87.60           39.0    59    88.1    67     ARMSSC1 
     ALTERNATIVE PARENT  . .    90.91           30.0    10    83.3    12     ARMSSC1 
     SECONDARY STRUCTURE . .    78.98           48.1    52    96.3    54     ARMSSC1 
     LARGE SHIFTS/INSERTIONS   103.92           33.3     9    52.9    17     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .    88.50           43.7    71    91.0    78     ARMSSC1 
     BURIED  . . . . . . . .    66.01           60.8    51    98.1    52     ARMSSC1 
     CORE  . . . . . . . . .    77.63           52.2   113   100.0   113     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    83.45           40.7    86    91.5    94     ARMSSC2 
     WELL ORDERED  . . . . .    84.68           47.1    34    97.1    35     ARMSSC2 
     NO INTER CONTACTS . . .    85.70           39.3    56    98.2    57     ARMSSC2 
     RELIABLE SIDE CHAINS  .    70.42           46.2    65    92.9    70     ARMSSC2 
     CHANGED ANGLES  . . . .    89.66           30.2    63    88.7    71     ARMSSC2 
     SHIFTED CHAIN . . . . .    87.93           35.9    39    83.0    47     ARMSSC2 
     ALTERNATIVE PARENT  . .   108.72           33.3     6    75.0     8     ARMSSC2 
     SECONDARY STRUCTURE . .    94.26           32.4    37    94.9    39     ARMSSC2 
     LARGE SHIFTS/INSERTIONS   111.52           42.9     7    46.7    15     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .    78.63           39.6    53    88.3    60     ARMSSC2 
     BURIED  . . . . . . . .    90.67           42.4    33    97.1    34     ARMSSC2 
     CORE  . . . . . . . . .    80.50           40.5    79   100.0    79     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    93.80           13.8    29    90.6    32     ARMSSC3 
     WELL ORDERED  . . . . .    97.98            0.0     5   100.0     5     ARMSSC3 
     NO INTER CONTACTS . . .   110.51            6.7    15   100.0    15     ARMSSC3 
     RELIABLE SIDE CHAINS  .    86.50           16.0    25    89.3    28     ARMSSC3 
     CHANGED ANGLES  . . . .    92.13           15.4    26    89.7    29     ARMSSC3 
     SHIFTED CHAIN . . . . .   103.72           26.7    15    83.3    18     ARMSSC3 
     ALTERNATIVE PARENT  . .   108.08            0.0     2    66.7     3     ARMSSC3 
     SECONDARY STRUCTURE . .    82.60           22.2     9    90.0    10     ARMSSC3 
     LARGE SHIFTS/INSERTIONS    97.81            0.0     3    50.0     6     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .    93.80           13.8    29    90.6    32     ARMSSC3 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     CORE  . . . . . . . . .    93.33           15.4    26   100.0    26     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    84.14           53.3    15    88.2    17     ARMSSC4 
     WELL ORDERED  . . . . .   102.93            0.0     2   100.0     2     ARMSSC4 
     NO INTER CONTACTS . . .    95.60           50.0    10   100.0    10     ARMSSC4 
     RELIABLE SIDE CHAINS  .    84.14           53.3    15    88.2    17     ARMSSC4 
     CHANGED ANGLES  . . . .    84.14           53.3    15    88.2    17     ARMSSC4 
     SHIFTED CHAIN . . . . .    85.81           50.0     8    80.0    10     ARMSSC4 
     ALTERNATIVE PARENT  . .   101.39            0.0     1    50.0     2     ARMSSC4 
     SECONDARY STRUCTURE . .    66.31           80.0     5    83.3     6     ARMSSC4 
     LARGE SHIFTS/INSERTIONS   107.94            0.0     2    50.0     4     ARMSSC4 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SURFACE . . . . . . . .    84.14           53.3    15    88.2    17     ARMSSC4 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     CORE  . . . . . . . . .    79.84           61.5    13   100.0    13     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =   0.51003     r(1,2) =  -0.84802     r(1,3) =  -0.14399 
 r(2,1) =   0.37003     r(2,2) =   0.36744     r(2,3) =  -0.85327 
 r(3,1) =   0.77650     r(3,2) =   0.38191     r(3,3) =   0.50120 
THE OFFSET VECTOR: 
 v(1) =  63.56362     v(2) =  44.46712     v(3) = -11.76448 
 
 Number of iteration 24                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.09           (Number of atoms:  134) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    1.47        145    94.2   154     CRMSCA  
     CRN = ALL/NP  . . . . .    0.0102                            CRMSCA  
     WELL ORDERED  . . . . .    1.44         86    97.7    88     CRMSCA  
     NO INTER CONTACTS . . .    1.31        102    98.1   104     CRMSCA  
     SHIFTED CHAIN . . . . .    1.93         70    88.6    79     CRMSCA  
     ALTERNATIVE PARENT  . .    2.32         12    85.7    14     CRMSCA  
     SECONDARY STRUCTURE . .    1.34         61    96.8    63     CRMSCA  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSCA  
     LARGE SHIFTS/INSERTIONS    3.10         11    55.0    20     CRMSCA  
     SURFACE . . . . . . . .    1.62         82    91.1    90     CRMSCA  
     BURIED  . . . . . . . .    1.26         63    98.4    64     CRMSCA  
     CORE  . . . . . . . . .    1.25        134   100.0   134     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    1.57        711    94.0   756     CRMSMC  
     WELL ORDERED  . . . . .    1.49        431    97.5   442     CRMSMC  
     NO INTER CONTACTS . . .    1.39        497    98.0   507     CRMSMC  
     SHIFTED CHAIN . . . . .    2.04        344    88.4   389     CRMSMC  
     ALTERNATIVE PARENT  . .    2.58         58    85.3    68     CRMSMC  
     SECONDARY STRUCTURE . .    1.49        300    96.8   310     CRMSMC  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSMC  
     LARGE SHIFTS/INSERTIONS    3.32         53    54.1    98     CRMSMC  
     SURFACE . . . . . . . .    1.70        402    91.0   442     CRMSMC  
     BURIED  . . . . . . . .    1.38        309    98.4   314     CRMSMC  
     CORE  . . . . . . . . .    1.33        658   100.0   658     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    2.90        505    92.5   546     CRMSSC  
     WELL ORDERED  . . . . .    2.79        261    98.1   266     CRMSSC  
     NO INTER CONTACTS . . .    2.48        336    98.5   341     CRMSSC  
     RELIABLE SIDE CHAINS  .    2.81        415    92.2   450     CRMSSC  
     CHANGED ANGLES  . . . .    3.63        256    89.2   287     CRMSSC  
     SECONDARY STRUCTURE . .    2.82        220    96.1   229     CRMSSC  
     LARGE SHIFTS/INSERTIONS    6.59         37    47.4    78     CRMSSC  
     SURFACE . . . . . . . .    3.17        296    88.9   333     CRMSSC  
     BURIED  . . . . . . . .    2.47        209    98.1   213     CRMSSC  
     CORE  . . . . . . . . .    2.38        468   100.0   468     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    2.25       1085    93.4  1162     CRMSALL 
     WELL ORDERED  . . . . .    2.09        613    97.8   627     CRMSALL 
     NO INTER CONTACTS . . .    1.93        744    98.3   757     CRMSALL 
     SHIFTED CHAIN . . . . .    2.85        508    86.8   585     CRMSALL 
     ALTERNATIVE PARENT  . .    4.05         85    83.3   102     CRMSALL 
     SECONDARY STRUCTURE . .    2.18        464    96.5   481     CRMSALL 
     LARGE SHIFTS/INSERTIONS    4.96         81    51.3   158     CRMSALL 
     SURFACE . . . . . . . .    2.46        624    90.0   693     CRMSALL 
     BURIED  . . . . . . . .    1.92        461    98.3   469     CRMSALL 
     CORE  . . . . . . . . .    1.87       1004   100.0  1004     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     0.00      0     0.0     9       1-MWFFNKNLK-9    
 CA  LOOP  2     2.78      8   100.0     8     132-GGKTLEIV-139  
 CA  LOOP  3     3.83      3   100.0     3     152-ILK-154  
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     0.00      0     0.0    45       1-MWFFNKNLK-9    
 MC  LOOP  2     2.94     38   100.0    38     132-GGKTLEIV-139  
 MC  LOOP  3     4.14     15   100.0    15     152-ILK-154  
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     0.00      0     0.0    77       1-MWFFNKNLK-9    
 ALL LOOP  2     3.91     56   100.0    56     132-GGKTLEIV-139  
 ALL LOOP  3     6.74     25   100.0    25     152-ILK-154  
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 WARNING! LOOP  1 cannot be considered (not enough atoms). 
 
 CA  LOOP  2     2.11      8   100.0     8     132-GGKTLEIV-139  
 CA  LOOP  3     0.49      3   100.0     3     152-ILK-154  
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 WARNING! LOOP  1 cannot be considered (not enough atoms). 
 
 MC  LOOP  2     2.37     38   100.0    38     132-GGKTLEIV-139  
 MC  LOOP  3     0.84     15   100.0    15     152-ILK-154  
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 WARNING! LOOP  1 cannot be considered (not enough atoms). 
 
 ALL LOOP  2     3.55     56   100.0    56     132-GGKTLEIV-139  
 ALL LOOP  3     2.33     25   100.0    25     152-ILK-154  
 
 
Accuracy of estimates of atomic coordinate errors: model <-> target 
 
 (CA)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    2.284      0.467       0.492    145    94.2   154     ERRCA  
     WELL ORDERED  . . . . .    2.302      0.474       0.498     86    97.7    88     ERRCA  
     NO INTER CONTACTS . . .    2.316      0.475       0.505    102    98.1   104     ERRCA  
     SHIFTED CHAIN . . . . .    2.133      0.395       0.409     70    88.6    79     ERRCA  
     ALTERNATIVE PARENT  . .    1.740      0.340       0.304     12    85.7    14     ERRCA  
     SECONDARY STRUCTURE . .    2.445      0.540       0.566     61    96.8    63     ERRCA  
     LARGE SHIFTS/INSERTIONS    1.460      0.212       0.161     11    55.0    20     ERRCA  
     SURFACE . . . . . . . .    2.579      0.478       0.503     82    91.1    90     ERRCA  
     BURIED  . . . . . . . .    1.901      0.452       0.476     63    98.4    64     ERRCA  
     CORE  . . . . . . . . .    2.352      0.488       0.519    134   100.0   134     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    2.301      0.463       0.486    711    94.0   756     ERRMC  
     WELL ORDERED  . . . . .    2.221      0.469       0.492    431    97.5   442     ERRMC  
     NO INTER CONTACTS . . .    2.337      0.470       0.498    497    98.0   507     ERRMC  
     SHIFTED CHAIN . . . . .    2.167      0.398       0.412    344    88.4   389     ERRMC  
     ALTERNATIVE PARENT  . .    1.868      0.358       0.325     58    85.3    68     ERRMC  
     SECONDARY STRUCTURE . .    2.443      0.527       0.550    300    96.8   310     ERRMC  
     LARGE SHIFTS/INSERTIONS    1.643      0.239       0.199     53    54.1    98     ERRMC  
     SURFACE . . . . . . . .    2.596      0.477       0.505    402    91.0   442     ERRMC  
     BURIED  . . . . . . . .    1.917      0.444       0.461    309    98.4   314     ERRMC  
     CORE  . . . . . . . . .    2.354      0.480       0.509    658   100.0   658     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    2.186      0.368       0.376    505    92.5   546     ERRSC  
     WELL ORDERED  . . . . .    2.129      0.388       0.391    261    98.1   266     ERRSC  
     NO INTER CONTACTS . . .    2.242      0.391       0.409    336    98.5   341     ERRSC  
     RELIABLE SIDE CHAINS  .    2.291      0.385       0.399    415    92.2   450     ERRSC  
     CHANGED ANGLES  . . . .    2.355      0.336       0.324    256    89.2   287     ERRSC  
     SHIFTED CHAIN . . . . .    2.241      0.334       0.332    228    84.8   269     ERRSC  
     ALTERNATIVE PARENT  . .    3.171      0.375       0.286     37    80.4    46     ERRSC  
     SECONDARY STRUCTURE . .    2.289      0.412       0.404    220    96.1   229     ERRSC  
     LARGE SHIFTS/INSERTIONS    2.860      0.284       0.180     37    47.4    78     ERRSC  
     SURFACE . . . . . . . .    2.320      0.351       0.371    296    88.9   333     ERRSC  
     BURIED  . . . . . . . .    1.996      0.392       0.383    209    98.1   213     ERRSC  
     CORE  . . . . . . . . .    2.133      0.375       0.392    468   100.0   468     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    2.240      0.420       0.436   1085    93.4  1162     ERRALL 
     WELL ORDERED  . . . . .    2.181      0.438       0.453    613    97.8   627     ERRALL 
     NO INTER CONTACTS . . .    2.289      0.436       0.459    744    98.3   757     ERRALL 
     SHIFTED CHAIN . . . . .    2.192      0.370       0.377    508    86.8   585     ERRALL 
     ALTERNATIVE PARENT  . .    2.366      0.359       0.302     85    83.3   102     ERRALL 
     SECONDARY STRUCTURE . .    2.351      0.474       0.483    464    96.5   481     ERRALL 
     LARGE SHIFTS/INSERTIONS    2.171      0.257       0.191     81    51.3   158     ERRALL 
     SURFACE . . . . . . . .    2.464      0.420       0.443    624    90.0   693     ERRALL 
     BURIED  . . . . . . . .    1.936      0.420       0.427    461    98.3   469     ERRALL 
     CORE  . . . . . . . . .    2.245      0.433       0.456   1004   100.0  1004     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)        82       127       136       144       145     145     154   DISTCA 
CA  (P)     53.25     82.47     88.31     93.51     94.16             154   DISTCA 
CA  (RMS)    0.68      0.98      1.11      1.41      1.47                   DISTCA 
 
ALL (N)       440       813       937      1038      1081    1085    1162   DISTALL 
ALL (P)     37.87     69.97     80.64     89.33     93.03            1162   DISTALL 
ALL (RMS)    0.68      1.10      1.35      1.73      2.15                   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)         134           134            11          RMSLSI 
CA  (P)       87.01         87.01          7.14          RMSLSI 
CA  (RMS)      1.12          1.25          3.10          RMSLSI 
 
 
 
END of the results output 
