 
####################################################### 
#                                                     # 
#                        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/T0064.inter 
CONANA-PAIR            ../CONANA/T0064.pair 
# 
NUMBER-OF-PARENTS      2 
ALIGNMENT-DALI(1)      ../PARENTS/casp3.T0064.1r69.rot 
ALIGNMENT-DALI(2)      ../PARENTS/casp3.T0064.2cro.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 845 atoms, MODEL 914 atoms, 845 common with TARGET 
           Number of atoms possible to evaluate: 845 
 
 
 CA-RMS TARGET<->PARENT(1r69)	 1.473148 
 
 CA-RMS TARGET<->PARENT(2cro)	 1.394009 
 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    67.33           51.0   194    96.5   201     ARMSMC  
     WELL ORDERED  . . . . .    67.03           49.7   161   100.0   161     ARMSMC  
     NO INTER CONTACTS . . .    59.76           54.0   100    95.2   105     ARMSMC  
     SHIFTED CHAIN . . . . .    71.35           47.8   134    95.0   141     ARMSMC  
     ALTERNATIVE PARENT  . .    79.27           25.0     4   100.0     4     ARMSMC  
     SECONDARY STRUCTURE . .    55.78           57.9   121    95.3   127     ARMSMC  
     LARGE SHIFTS/INSERTIONS    71.39           48.8    82    92.1    89     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    72.13           49.3   144    95.4   151     ARMSMC  
     BURIED  . . . . . . . .    51.06           56.0    50   100.0    50     ARMSMC  
     CORE  . . . . . . . . .    64.20           52.7   112   100.0   112     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    78.01           55.2    87    95.6    91     ARMSSC1 
     WELL ORDERED  . . . . .    72.69           59.3    54   100.0    54     ARMSSC1 
     NO INTER CONTACTS . . .    85.58           42.9    42    93.3    45     ARMSSC1 
     RELIABLE SIDE CHAINS  .    78.25           58.8    80    95.2    84     ARMSSC1 
     CHANGED ANGLES  . . . .    81.99           51.6    62    93.9    66     ARMSSC1 
     SHIFTED CHAIN . . . . .    77.34           55.0    60    93.8    64     ARMSSC1 
     ALTERNATIVE PARENT  . .    20.85          100.0     2   100.0     2     ARMSSC1 
     SECONDARY STRUCTURE . .    77.17           55.6    54    94.7    57     ARMSSC1 
     LARGE SHIFTS/INSERTIONS    61.59           68.4    38    90.5    42     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .    73.50           61.5    65    94.2    69     ARMSSC1 
     BURIED  . . . . . . . .    90.03           36.4    22   100.0    22     ARMSSC1 
     CORE  . . . . . . . . .    88.67           44.9    49   100.0    49     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    75.77           44.3    61    95.3    64     ARMSSC2 
     WELL ORDERED  . . . . .    71.81           46.4    28   100.0    28     ARMSSC2 
     NO INTER CONTACTS . . .    76.38           41.9    31    93.9    33     ARMSSC2 
     RELIABLE SIDE CHAINS  .    70.59           45.7    46    93.9    49     ARMSSC2 
     CHANGED ANGLES  . . . .    84.79           34.1    44    93.6    47     ARMSSC2 
     SHIFTED CHAIN . . . . .    75.22           46.3    41    93.2    44     ARMSSC2 
     ALTERNATIVE PARENT  . .    29.84          100.0     1   100.0     1     ARMSSC2 
     SECONDARY STRUCTURE . .    70.84           45.0    40    95.2    42     ARMSSC2 
     LARGE SHIFTS/INSERTIONS    79.87           40.0    25    89.3    28     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .    78.44           41.3    46    93.9    49     ARMSSC2 
     BURIED  . . . . . . . .    66.93           53.3    15   100.0    15     ARMSSC2 
     CORE  . . . . . . . . .    72.78           47.2    36   100.0    36     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    73.60           32.1    28    90.3    31     ARMSSC3 
     WELL ORDERED  . . . . .    45.00           60.0    10   100.0    10     ARMSSC3 
     NO INTER CONTACTS . . .    78.70           38.5    13    86.7    15     ARMSSC3 
     RELIABLE SIDE CHAINS  .    70.39           33.3    24    92.3    26     ARMSSC3 
     CHANGED ANGLES  . . . .    81.47           23.8    21    87.5    24     ARMSSC3 
     SHIFTED CHAIN . . . . .    77.86           29.4    17    85.0    20     ARMSSC3 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SECONDARY STRUCTURE . .    70.82           38.1    21    91.3    23     ARMSSC3 
     LARGE SHIFTS/INSERTIONS    72.03           27.3    11    78.6    14     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .    73.99           32.0    25    89.3    28     ARMSSC3 
     BURIED  . . . . . . . .    70.21           33.3     3   100.0     3     ARMSSC3 
     CORE  . . . . . . . . .    74.59           35.3    17   100.0    17     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    83.71           10.0    10    83.3    12     ARMSSC4 
     WELL ORDERED  . . . . .   122.32            0.0     3   100.0     3     ARMSSC4 
     NO INTER CONTACTS . . .    72.34            0.0     5    83.3     6     ARMSSC4 
     RELIABLE SIDE CHAINS  .    83.71           10.0    10    83.3    12     ARMSSC4 
     CHANGED ANGLES  . . . .    77.05           11.1     9    81.8    11     ARMSSC4 
     SHIFTED CHAIN . . . . .    91.59           25.0     4    66.7     6     ARMSSC4 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SECONDARY STRUCTURE . .    78.42            0.0     7    77.8     9     ARMSSC4 
     LARGE SHIFTS/INSERTIONS   116.59            0.0     1    33.3     3     ARMSSC4 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SURFACE . . . . . . . .    80.52           12.5     8    80.0    10     ARMSSC4 
     BURIED  . . . . . . . .    95.40            0.0     2   100.0     2     ARMSSC4 
     CORE  . . . . . . . . .    79.22           11.1     9   100.0     9     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =  -0.70130     r(1,2) =   0.16787     r(1,3) =   0.69282 
 r(2,1) =  -0.15915     r(2,2) =  -0.98422     r(2,3) =   0.07737 
 r(3,1) =   0.69488     r(3,2) =  -0.05600     r(3,3) =   0.71694 
THE OFFSET VECTOR: 
 v(1) =   9.09202     v(2) =  50.79578     v(3) =  49.22067 
 
 Number of iteration 55                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.67           (Number of atoms:   20) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .   19.38        103   100.0   103     CRMSCA  
     CRN = ALL/NP  . . . . .    0.1882                            CRMSCA  
     WELL ORDERED  . . . . .   18.88         85   100.0    85     CRMSCA  
     NO INTER CONTACTS . . .   15.90         54   100.0    54     CRMSCA  
     SHIFTED CHAIN . . . . .   22.64         73   100.0    73     CRMSCA  
     ALTERNATIVE PARENT  . .    5.05          2   100.0     2     CRMSCA  
     SECONDARY STRUCTURE . .   21.07         65   100.0    65     CRMSCA  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSCA  
     LARGE SHIFTS/INSERTIONS   27.85         47   100.0    47     CRMSCA  
     SURFACE . . . . . . . .   22.06         78   100.0    78     CRMSCA  
     BURIED  . . . . . . . .    5.45         25   100.0    25     CRMSCA  
     CORE  . . . . . . . . .    6.32         56   100.0    56     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .   19.44        511   100.0   511     CRMSMC  
     WELL ORDERED  . . . . .   18.90        420   100.0   420     CRMSMC  
     NO INTER CONTACTS . . .   15.93        267   100.0   267     CRMSMC  
     SHIFTED CHAIN . . . . .   22.67        363   100.0   363     CRMSMC  
     ALTERNATIVE PARENT  . .    5.19         10   100.0    10     CRMSMC  
     SECONDARY STRUCTURE . .   21.22        324   100.0   324     CRMSMC  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSMC  
     LARGE SHIFTS/INSERTIONS   27.87        234   100.0   234     CRMSMC  
     SURFACE . . . . . . . .   22.12        387   100.0   387     CRMSMC  
     BURIED  . . . . . . . .    5.57        124   100.0   124     CRMSMC  
     CORE  . . . . . . . . .    6.40        277   100.0   277     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .   21.62        433   100.0   433     CRMSSC  
     WELL ORDERED  . . . . .   21.34        248   100.0   248     CRMSSC  
     NO INTER CONTACTS . . .   20.30        210   100.0   210     CRMSSC  
     RELIABLE SIDE CHAINS  .   22.15        371   100.0   371     CRMSSC  
     CHANGED ANGLES  . . . .   23.75        281   100.0   281     CRMSSC  
     SECONDARY STRUCTURE . .   23.80        297   100.0   297     CRMSSC  
     LARGE SHIFTS/INSERTIONS   29.52        213   100.0   213     CRMSSC  
     SURFACE . . . . . . . .   23.94        344   100.0   344     CRMSSC  
     BURIED  . . . . . . . .    7.57         89   100.0    89     CRMSSC  
     CORE  . . . . . . . . .    8.73        220   100.0   220     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .   20.54        845   100.0   845     CRMSALL 
     WELL ORDERED  . . . . .   19.89        593   100.0   593     CRMSALL 
     NO INTER CONTACTS . . .   18.16        426   100.0   426     CRMSALL 
     SHIFTED CHAIN . . . . .   23.78        601   100.0   601     CRMSALL 
     ALTERNATIVE PARENT  . .    5.50         14   100.0    14     CRMSALL 
     SECONDARY STRUCTURE . .   22.59        557   100.0   557     CRMSALL 
     LARGE SHIFTS/INSERTIONS   28.73        401   100.0   401     CRMSALL 
     SURFACE . . . . . . . .   23.04        656   100.0   656     CRMSALL 
     BURIED  . . . . . . . .    6.52        189   100.0   189     CRMSALL 
     CORE  . . . . . . . . .    7.56        444   100.0   444     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     4.44      6   100.0     6      40-TNPSIQ-45   
 CA  LOOP  2    30.12     40   100.0    40      64-EKHETLDSEWEKLVRDAMTSGVSKKQFREFLDYQKWRKSQ-108  
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     4.57     30   100.0    30      40-TNPSIQ-45   
 MC  LOOP  2    30.15    199   100.0   199      64-EKHETLDSEWEKLVRDAMTSGVSKKQFREFLDYQKWRKSQ-108  
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     5.03     45   100.0    45      40-TNPSIQ-45   
 ALL LOOP  2    30.77    348   100.0   348      64-EKHETLDSEWEKLVRDAMTSGVSKKQFREFLDYQKWRKSQ-108  
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     2.69      6   100.0     6      40-TNPSIQ-45   
 CA  LOOP  2     6.68     40   100.0    40      64-EKHETLDSEWEKLVRDAMTSGVSKKQFREFLDYQKWRKSQ-108  
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     3.22     30   100.0    30      40-TNPSIQ-45   
 MC  LOOP  2     6.85    199   100.0   199      64-EKHETLDSEWEKLVRDAMTSGVSKKQFREFLDYQKWRKSQ-108  
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     4.20     45   100.0    45      40-TNPSIQ-45   
 ALL LOOP  2     7.67    348   100.0   348      64-EKHETLDSEWEKLVRDAMTSGVSKKQFREFLDYQKWRKSQ-108  
 
 
Accuracy of estimates of atomic coordinate errors: model <-> target 
 
 (CA)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   10.794      0.438       0.365    103   100.0   103     ERRCA  
     WELL ORDERED  . . . . .   10.320      0.421       0.349     85   100.0    85     ERRCA  
     NO INTER CONTACTS . . .    8.890      0.441       0.426     54   100.0    54     ERRCA  
     SHIFTED CHAIN . . . . .   13.489      0.476       0.365     73   100.0    73     ERRCA  
     ALTERNATIVE PARENT  . .    3.953      0.282       0.324      2   100.0     2     ERRCA  
     SECONDARY STRUCTURE . .   12.557      0.485       0.400     65   100.0    65     ERRCA  
     LARGE SHIFTS/INSERTIONS   18.398      0.529       0.337     47   100.0    47     ERRCA  
     SURFACE . . . . . . . .   12.830      0.458       0.349     78   100.0    78     ERRCA  
     BURIED  . . . . . . . .    4.442      0.375       0.416     25   100.0    25     ERRCA  
     CORE  . . . . . . . . .    4.412      0.362       0.389     56   100.0    56     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   10.747      0.428       0.359    511   100.0   511     ERRMC  
     WELL ORDERED  . . . . .   10.269      0.414       0.347    420   100.0   420     ERRMC  
     NO INTER CONTACTS . . .    8.792      0.430       0.416    267   100.0   267     ERRMC  
     SHIFTED CHAIN . . . . .   13.433      0.466       0.359    363   100.0   363     ERRMC  
     ALTERNATIVE PARENT  . .    3.930      0.287       0.338     10   100.0    10     ERRMC  
     SECONDARY STRUCTURE . .   12.566      0.477       0.390    324   100.0   324     ERRMC  
     LARGE SHIFTS/INSERTIONS   18.330      0.521       0.331    234   100.0   234     ERRMC  
     SURFACE . . . . . . . .   12.787      0.449       0.344    387   100.0   387     ERRMC  
     BURIED  . . . . . . . .    4.380      0.364       0.407    124   100.0   124     ERRMC  
     CORE  . . . . . . . . .    4.341      0.350       0.382    277   100.0   277     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   11.274      0.365       0.262    433   100.0   433     ERRSC  
     WELL ORDERED  . . . . .   11.239      0.375       0.273    248   100.0   248     ERRSC  
     NO INTER CONTACTS . . .    9.855      0.334       0.268    210   100.0   210     ERRSC  
     RELIABLE SIDE CHAINS  .   11.707      0.371       0.264    371   100.0   371     ERRSC  
     CHANGED ANGLES  . . . .   12.891      0.377       0.246    281   100.0   281     ERRSC  
     SHIFTED CHAIN . . . . .   14.351      0.424       0.286    309   100.0   309     ERRSC  
     ALTERNATIVE PARENT  . .    2.813      0.189       0.167      6   100.0     6     ERRSC  
     SECONDARY STRUCTURE . .   13.367      0.409       0.285    297   100.0   297     ERRSC  
     LARGE SHIFTS/INSERTIONS   19.140      0.491       0.286    213   100.0   213     ERRSC  
     SURFACE . . . . . . . .   13.412      0.402       0.271    344   100.0   344     ERRSC  
     BURIED  . . . . . . . .    3.009      0.220       0.229     89   100.0    89     ERRSC  
     CORE  . . . . . . . . .    3.658      0.242       0.239    220   100.0   220     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   11.025      0.399       0.313    845   100.0   845     ERRALL 
     WELL ORDERED  . . . . .   10.677      0.401       0.320    593   100.0   593     ERRALL 
     NO INTER CONTACTS . . .    9.355      0.388       0.350    426   100.0   426     ERRALL 
     SHIFTED CHAIN . . . . .   13.924      0.448       0.326    601   100.0   601     ERRALL 
     ALTERNATIVE PARENT  . .    3.621      0.260       0.289     14   100.0    14     ERRALL 
     SECONDARY STRUCTURE . .   12.986      0.442       0.336    557   100.0   557     ERRALL 
     LARGE SHIFTS/INSERTIONS   18.778      0.508       0.311    401   100.0   401     ERRALL 
     SURFACE . . . . . . . .   13.107      0.427       0.308    656   100.0   656     ERRALL 
     BURIED  . . . . . . . .    3.797      0.302       0.331    189   100.0   189     ERRALL 
     CORE  . . . . . . . . .    4.023      0.300       0.315    444   100.0   444     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)         3        13        23        39        61     103     103   DISTCA 
CA  (P)      2.91     12.62     22.33     37.86     59.22             103   DISTCA 
CA  (RMS)    0.67      1.32      1.86      2.96      4.91                   DISTCA 
 
ALL (N)         9        60       117       253       460     845     845   DISTALL 
ALL (P)      1.07      7.10     13.85     29.94     54.44             845   DISTALL 
ALL (RMS)    0.72      1.42      2.06      3.30      5.50                   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)          56            56            47          RMSLSI 
CA  (P)       54.37         54.37         45.63          RMSLSI 
CA  (RMS)      1.04          6.32         27.85          RMSLSI 
 
 
 
END of the results output 
