 
####################################################### 
#                                                     # 
#                        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:     # 
#                        # 
########################## 
NUMBER-OF-PARENTS      2 
ALIGNMENT-DALI(1)      ../PARENTS/casp2.T0004.1csp.rot 
ALIGNMENT-DALI(2)      ../PARENTS/casp2.T0004.1mjc.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 588 atoms, MODEL 556 atoms, 499 common with TARGET 
           Number of atoms possible to evaluate: 155 
 
 
 CA-RMS TARGET<->PARENT(1csp)	 2.141282 
 
 CA-RMS TARGET<->PARENT(1mjc)	 2.434782 
 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    83.50           28.1    64    42.7   150     ARMSMC  
     WELL ORDERED  . . . . .    83.50           28.1    64    42.7   150     ARMSMC  
     NO INTER CONTACTS . . .    83.50           28.1    64    42.7   150     ARMSMC  
     SHIFTED CHAIN . . . . .    83.63           26.8    56    40.6   138     ARMSMC  
     ALTERNATIVE PARENT  . .    14.18          100.0     1    10.0    10     ARMSMC  
     SECONDARY STRUCTURE . .    70.03           40.0    30    55.6    54     ARMSMC  
     LARGE SHIFTS/INSERTIONS    86.00           13.3    15    24.2    62     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    89.17           25.6    39    36.8   106     ARMSMC  
     BURIED  . . . . . . . .    73.80           32.0    25    56.8    44     ARMSMC  
     CORE  . . . . . . . . .    82.73           32.7    49    55.7    88     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    62     ARMSSC1 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0    62     ARMSSC1 
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0    62     ARMSSC1 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    50     ARMSSC1 
     CHANGED ANGLES  . . . .     0.00            0.0     0     0.0    49     ARMSSC1 
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0    56     ARMSSC1 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     5     ARMSSC1 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    23     ARMSSC1 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0    23     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    46     ARMSSC1 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0    16     ARMSSC1 
     CORE  . . . . . . . . .     0.00            0.0     0     0.0    39     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    45     ARMSSC2 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0    45     ARMSSC2 
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0    45     ARMSSC2 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    40     ARMSSC2 
     CHANGED ANGLES  . . . .     0.00            0.0     0     0.0    41     ARMSSC2 
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0    42     ARMSSC2 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     4     ARMSSC2 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    13     ARMSSC2 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0    17     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    38     ARMSSC2 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     7     ARMSSC2 
     CORE  . . . . . . . . .     0.00            0.0     0     0.0    28     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    24     ARMSSC3 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0    24     ARMSSC3 
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0    24     ARMSSC3 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    20     ARMSSC3 
     CHANGED ANGLES  . . . .     0.00            0.0     0     0.0    24     ARMSSC3 
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0    23     ARMSSC3 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     2     ARMSSC3 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0     6     ARMSSC3 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0    11     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    24     ARMSSC3 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     CORE  . . . . . . . . .     0.00            0.0     0     0.0    13     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    12     ARMSSC4 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0    12     ARMSSC4 
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0    12     ARMSSC4 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    12     ARMSSC4 
     CHANGED ANGLES  . . . .     0.00            0.0     0     0.0    12     ARMSSC4 
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0    11     ARMSSC4 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     2     ARMSSC4 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0     4     ARMSSC4 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0     6     ARMSSC4 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    12     ARMSSC4 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     CORE  . . . . . . . . .     0.00            0.0     0     0.0     6     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =  -0.96309     r(1,2) =   0.20112     r(1,3) =  -0.17891 
 r(2,1) =  -0.25554     r(2,2) =  -0.89201     r(2,3) =   0.37285 
 r(3,1) =  -0.08460     r(3,2) =   0.40481     r(3,3) =   0.91048 
THE OFFSET VECTOR: 
 v(1) =   6.21242     v(2) =  19.50888     v(3) =  -8.09072 
 
 Number of iteration  2                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.49           (Number of atoms:    9) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    9.61         33    43.4    76     CRMSCA  
     CRN = ALL/NP  . . . . .    0.2914                            CRMSCA  
     WELL ORDERED  . . . . .    9.61         33    43.4    76     CRMSCA  
     NO INTER CONTACTS . . .    9.61         33    43.4    76     CRMSCA  
     SHIFTED CHAIN . . . . .   10.21         29    41.4    70     CRMSCA  
     ALTERNATIVE PARENT  . .    2.18          1    20.0     5     CRMSCA  
     SECONDARY STRUCTURE . .    4.93         15    55.6    27     CRMSCA  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     6     CRMSCA  
     LARGE SHIFTS/INSERTIONS   12.33          8    25.0    32     CRMSCA  
     SURFACE . . . . . . . .   10.31         20    37.0    54     CRMSCA  
     BURIED  . . . . . . . .    8.44         13    59.1    22     CRMSCA  
     CORE  . . . . . . . . .    8.57         25    56.8    44     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    9.54        155    41.8   371     CRMSMC  
     WELL ORDERED  . . . . .    9.54        155    41.8   371     CRMSMC  
     NO INTER CONTACTS . . .    9.54        155    41.8   371     CRMSMC  
     SHIFTED CHAIN . . . . .   10.09        137    40.2   341     CRMSMC  
     ALTERNATIVE PARENT  . .    2.26          5    20.0    25     CRMSMC  
     SECONDARY STRUCTURE . .    5.21         71    53.4   133     CRMSMC  
     SHIFTED SS UNITS  . . .    0.00          0     0.0    30     CRMSMC  
     LARGE SHIFTS/INSERTIONS   12.18         36    23.4   154     CRMSMC  
     SURFACE . . . . . . . .   10.13         93    35.2   264     CRMSMC  
     BURIED  . . . . . . . .    8.58         62    57.9   107     CRMSMC  
     CORE  . . . . . . . . .    8.59        119    54.8   217     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    9.40         23     8.1   284     CRMSSC  
     WELL ORDERED  . . . . .    9.40         23     8.1   284     CRMSSC  
     NO INTER CONTACTS . . .    9.40         23     8.1   284     CRMSSC  
     RELIABLE SIDE CHAINS  .    9.40         23     9.6   240     CRMSSC  
     CHANGED ANGLES  . . . .    0.00          0     0.0   192     CRMSSC  
     SECONDARY STRUCTURE . .    6.39         11    11.1    99     CRMSSC  
     LARGE SHIFTS/INSERTIONS   12.11          4     3.6   112     CRMSSC  
     SURFACE . . . . . . . .    9.79         13     5.9   222     CRMSSC  
     BURIED  . . . . . . . .    8.88         10    16.1    62     CRMSSC  
     CORE  . . . . . . . . .    8.73         19    11.0   172     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    9.54        155    26.4   588     CRMSALL 
     WELL ORDERED  . . . . .    9.54        155    26.4   588     CRMSALL 
     NO INTER CONTACTS . . .    9.54        155    26.4   588     CRMSALL 
     SHIFTED CHAIN . . . . .   10.09        137    25.3   542     CRMSALL 
     ALTERNATIVE PARENT  . .    2.26          5    11.1    45     CRMSALL 
     SECONDARY STRUCTURE . .    5.21         71    34.3   207     CRMSALL 
     LARGE SHIFTS/INSERTIONS   12.18         36    15.0   240     CRMSALL 
     SURFACE . . . . . . . .   10.13         93    21.2   438     CRMSALL 
     BURIED  . . . . . . . .    8.58         62    41.3   150     CRMSALL 
     CORE  . . . . . . . . .    8.59        119    34.2   348     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     2.18      1    14.3     7       1-AEIEVGR-7    
 CA  LOOP  2    15.04      3   100.0     3      26-GGG-28   
 CA  LOOP  3     0.00      0     0.0    10      40-DKRVEKVTDY-49   
 CA  LOOP  4     0.00      0     0.0     4      65-RQGR-68   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     2.26      5    14.7    34       1-AEIEVGR-7    
 MC  LOOP  2    14.75     12   100.0    12      26-GGG-28   
 MC  LOOP  3     0.00      0     0.0    50      40-DKRVEKVTDY-49   
 MC  LOOP  4     0.00      0     0.0    19      65-RQGR-68   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     2.26      5     9.4    53       1-AEIEVGR-7    
 ALL LOOP  2    14.75     12   100.0    12      26-GGG-28   
 ALL LOOP  3     0.00      0     0.0    87      40-DKRVEKVTDY-49   
 ALL LOOP  4     0.00      0     0.0    35      65-RQGR-68   
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 WARNING! LOOP  1 cannot be considered (not enough atoms). 
 
 CA  LOOP  2     0.10      3   100.0     3      26-GGG-28   
 WARNING! LOOP  3 cannot be considered (not enough atoms). 
 
 WARNING! LOOP  4 cannot be considered (not enough atoms). 
 
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 WARNING! LOOP  1 cannot be considered (not enough atoms). 
 
 MC  LOOP  2     1.94     12   100.0    12      26-GGG-28   
 WARNING! LOOP  3 cannot be considered (not enough atoms). 
 
 WARNING! LOOP  4 cannot be considered (not enough atoms). 
 
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 WARNING! LOOP  1 cannot be considered (not enough atoms). 
 
 ALL LOOP  2     1.94     12   100.0    12      26-GGG-28   
 WARNING! LOOP  3 cannot be considered (not enough atoms). 
 
 WARNING! LOOP  4 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 . . . . . . . . . .    8.008      1.000       0.500     33    43.4    76     ERRCA  
     WELL ORDERED  . . . . .    8.008      1.000       0.500     33    43.4    76     ERRCA  
     NO INTER CONTACTS . . .    8.008      1.000       0.500     33    43.4    76     ERRCA  
     SHIFTED CHAIN . . . . .    8.850      1.000       0.500     29    41.4    70     ERRCA  
     ALTERNATIVE PARENT  . .    2.176      1.000       0.500      1    20.0     5     ERRCA  
     SECONDARY STRUCTURE . .    3.875      1.000       0.500     15    55.6    27     ERRCA  
     LARGE SHIFTS/INSERTIONS   11.097      1.000       0.500      8    25.0    32     ERRCA  
     SURFACE . . . . . . . .    8.384      1.000       0.500     20    37.0    54     ERRCA  
     BURIED  . . . . . . . .    7.430      1.000       0.500     13    59.1    22     ERRCA  
     CORE  . . . . . . . . .    7.020      1.000       0.500     25    56.8    44     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    8.036      1.000       0.500    155    41.8   371     ERRMC  
     WELL ORDERED  . . . . .    8.036      1.000       0.500    155    41.8   371     ERRMC  
     NO INTER CONTACTS . . .    8.036      1.000       0.500    155    41.8   371     ERRMC  
     SHIFTED CHAIN . . . . .    8.756      1.000       0.500    137    40.2   341     ERRMC  
     ALTERNATIVE PARENT  . .    1.926      1.000       0.500      5    20.0    25     ERRMC  
     SECONDARY STRUCTURE . .    4.229      1.000       0.500     71    53.4   133     ERRMC  
     LARGE SHIFTS/INSERTIONS   10.829      1.000       0.500     36    23.4   154     ERRMC  
     SURFACE . . . . . . . .    8.334      1.000       0.500     93    35.2   264     ERRMC  
     BURIED  . . . . . . . .    7.588      1.000       0.500     62    57.9   107     ERRMC  
     CORE  . . . . . . . . .    7.191      1.000       0.500    119    54.8   217     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    8.314      1.000       0.500     23     8.1   284     ERRSC  
     WELL ORDERED  . . . . .    8.314      1.000       0.500     23     8.1   284     ERRSC  
     NO INTER CONTACTS . . .    8.314      1.000       0.500     23     8.1   284     ERRSC  
     RELIABLE SIDE CHAINS  .    8.314      1.000       0.500     23     9.6   240     ERRSC  
     CHANGED ANGLES  . . . .    0.000      0.000       0.000      0     0.0   192     ERRSC  
     SHIFTED CHAIN . . . . .    8.606      1.000       0.500     21     8.0   262     ERRSC  
     ALTERNATIVE PARENT  . .    4.113      1.000       0.500      1     4.0    25     ERRSC  
     SECONDARY STRUCTURE . .    5.709      1.000       0.500     11    11.1    99     ERRSC  
     LARGE SHIFTS/INSERTIONS   11.053      1.000       0.500      4     3.6   112     ERRSC  
     SURFACE . . . . . . . .    8.370      1.000       0.500     13     5.9   222     ERRSC  
     BURIED  . . . . . . . .    8.240      1.000       0.500     10    16.1    62     ERRSC  
     CORE  . . . . . . . . .    7.737      1.000       0.500     19    11.0   172     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    8.036      1.000       0.500    155    26.4   588     ERRALL 
     WELL ORDERED  . . . . .    8.036      1.000       0.500    155    26.4   588     ERRALL 
     NO INTER CONTACTS . . .    8.036      1.000       0.500    155    26.4   588     ERRALL 
     SHIFTED CHAIN . . . . .    8.756      1.000       0.500    137    25.3   542     ERRALL 
     ALTERNATIVE PARENT  . .    1.926      1.000       0.500      5    11.1    45     ERRALL 
     SECONDARY STRUCTURE . .    4.229      1.000       0.500     71    34.3   207     ERRALL 
     LARGE SHIFTS/INSERTIONS   10.829      1.000       0.500     36    15.0   240     ERRALL 
     SURFACE . . . . . . . .    8.334      1.000       0.500     93    21.2   438     ERRALL 
     BURIED  . . . . . . . .    7.588      1.000       0.500     62    41.3   150     ERRALL 
     CORE  . . . . . . . . .    7.191      1.000       0.500    119    34.2   348     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         8         9        11        22      33      76   DISTCA 
CA  (P)      3.95     10.53     11.84     14.47     28.95              76   DISTCA 
CA  (RMS)    0.61      1.38      1.49      2.25      5.64                   DISTCA 
 
ALL (N)        10        27        36        53       107     155     588   DISTALL 
ALL (P)      1.70      4.59      6.12      9.01     18.20             588   DISTALL 
ALL (RMS)    0.63      1.24      1.59      2.49      6.00                   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)          44            25             8          RMSLSI 
CA  (P)       57.89         32.89         10.53          RMSLSI 
CA  (RMS)      1.67          8.57         12.33          RMSLSI 
 
 
 
END of the results output 
