 
####################################################### 
#                                                     # 
#                        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 585 atoms, 528 common with TARGET 
           Number of atoms possible to evaluate: 94 
 
 
 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 . . . . . . . . . .    83.10           33.3    36    24.0   150     ARMSMC  
     WELL ORDERED  . . . . .    83.10           33.3    36    24.0   150     ARMSMC  
     NO INTER CONTACTS . . .    83.10           33.3    36    24.0   150     ARMSMC  
     SHIFTED CHAIN . . . . .    86.87           31.2    32    23.2   138     ARMSMC  
     ALTERNATIVE PARENT  . .    84.75           12.5     8    80.0    10     ARMSMC  
     SECONDARY STRUCTURE . .    76.46           38.1    21    38.9    54     ARMSMC  
     LARGE SHIFTS/INSERTIONS    95.70           25.0    12    19.4    62     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    80.53           40.0    25    23.6   106     ARMSMC  
     BURIED  . . . . . . . .    88.65           18.2    11    25.0    44     ARMSMC  
     CORE  . . . . . . . . .    76.01           37.5    24    27.3    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) =  -0.37160     r(1,2) =   0.55666     r(1,3) =  -0.74299 
 r(2,1) =  -0.77375     r(2,2) =   0.25657     r(2,3) =   0.57921 
 r(3,1) =   0.51305     r(3,2) =   0.79013     r(3,3) =   0.33538 
THE OFFSET VECTOR: 
 v(1) =  24.04103     v(2) = -15.10922     v(3) = -33.29638 
 
 Number of iteration  2                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   2.08           (Number of atoms:    4) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    8.42         19    25.0    76     CRMSCA  
     CRN = ALL/NP  . . . . .    0.4432                            CRMSCA  
     WELL ORDERED  . . . . .    8.42         19    25.0    76     CRMSCA  
     NO INTER CONTACTS . . .    8.42         19    25.0    76     CRMSCA  
     SHIFTED CHAIN . . . . .    8.80         17    24.3    70     CRMSCA  
     ALTERNATIVE PARENT  . .    6.07          4    80.0     5     CRMSCA  
     SECONDARY STRUCTURE . .   10.38         11    40.7    27     CRMSCA  
     SHIFTED SS UNITS  . . .   14.53          5    83.3     6     CRMSCA  
     LARGE SHIFTS/INSERTIONS    5.65          6    18.8    32     CRMSCA  
     SURFACE . . . . . . . .    6.82         13    24.1    54     CRMSCA  
     BURIED  . . . . . . . .   11.13          6    27.3    22     CRMSCA  
     CORE  . . . . . . . . .    9.43         13    29.5    44     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    8.50         94    25.3   371     CRMSMC  
     WELL ORDERED  . . . . .    8.50         94    25.3   371     CRMSMC  
     NO INTER CONTACTS . . .    8.50         94    25.3   371     CRMSMC  
     SHIFTED CHAIN . . . . .    8.86         84    24.6   341     CRMSMC  
     ALTERNATIVE PARENT  . .    5.93         20    80.0    25     CRMSMC  
     SECONDARY STRUCTURE . .   10.36         55    41.4   133     CRMSMC  
     SHIFTED SS UNITS  . . .   14.32         25    83.3    30     CRMSMC  
     LARGE SHIFTS/INSERTIONS    5.69         29    18.8   154     CRMSMC  
     SURFACE . . . . . . . .    7.07         64    24.2   264     CRMSMC  
     BURIED  . . . . . . . .   10.95         30    28.0   107     CRMSMC  
     CORE  . . . . . . . . .    9.49         65    30.0   217     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    9.66         18     6.3   284     CRMSSC  
     WELL ORDERED  . . . . .    9.66         18     6.3   284     CRMSSC  
     NO INTER CONTACTS . . .    9.66         18     6.3   284     CRMSSC  
     RELIABLE SIDE CHAINS  .    9.66         18     7.5   240     CRMSSC  
     CHANGED ANGLES  . . . .    0.00          0     0.0   192     CRMSSC  
     SECONDARY STRUCTURE . .   11.39         11    11.1    99     CRMSSC  
     LARGE SHIFTS/INSERTIONS    7.39          5     4.5   112     CRMSSC  
     SURFACE . . . . . . . .    8.20         12     5.4   222     CRMSSC  
     BURIED  . . . . . . . .   12.06          6     9.7    62     CRMSSC  
     CORE  . . . . . . . . .   10.40         13     7.6   172     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    8.50         94    16.0   588     CRMSALL 
     WELL ORDERED  . . . . .    8.50         94    16.0   588     CRMSALL 
     NO INTER CONTACTS . . .    8.50         94    16.0   588     CRMSALL 
     SHIFTED CHAIN . . . . .    8.86         84    15.5   542     CRMSALL 
     ALTERNATIVE PARENT  . .    5.93         20    44.4    45     CRMSALL 
     SECONDARY STRUCTURE . .   10.36         55    26.6   207     CRMSALL 
     LARGE SHIFTS/INSERTIONS    5.69         29    12.1   240     CRMSALL 
     SURFACE . . . . . . . .    7.07         64    14.6   438     CRMSALL 
     BURIED  . . . . . . . .   10.95         30    20.0   150     CRMSALL 
     CORE  . . . . . . . . .    9.49         65    18.7   348     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     0.00      0     0.0     7       1-AEIEVGR-7    
 CA  LOOP  2     0.00      0     0.0     3      26-GGG-28   
 CA  LOOP  3     0.00      0     0.0    10      40-DKRVEKVTDY-49   
 CA  LOOP  4     4.94      4   100.0     4      65-RQGR-68   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     0.00      0     0.0    34       1-AEIEVGR-7    
 MC  LOOP  2     0.00      0     0.0    12      26-GGG-28   
 MC  LOOP  3     0.00      0     0.0    50      40-DKRVEKVTDY-49   
 MC  LOOP  4     5.25     19   100.0    19      65-RQGR-68   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     0.00      0     0.0    53       1-AEIEVGR-7    
 ALL LOOP  2     0.00      0     0.0    12      26-GGG-28   
 ALL LOOP  3     0.00      0     0.0    87      40-DKRVEKVTDY-49   
 ALL LOOP  4     5.25     19    54.3    35      65-RQGR-68   
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 WARNING! LOOP  1 cannot be considered (not enough atoms). 
 
 WARNING! LOOP  2 cannot be considered (not enough atoms). 
 
 WARNING! LOOP  3 cannot be considered (not enough atoms). 
 
 CA  LOOP  4     0.74      4   100.0     4      65-RQGR-68   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 WARNING! LOOP  1 cannot be considered (not enough atoms). 
 
 WARNING! LOOP  2 cannot be considered (not enough atoms). 
 
 WARNING! LOOP  3 cannot be considered (not enough atoms). 
 
 MC  LOOP  4     1.69     19   100.0    19      65-RQGR-68   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 WARNING! LOOP  1 cannot be considered (not enough atoms). 
 
 WARNING! LOOP  2 cannot be considered (not enough atoms). 
 
 WARNING! LOOP  3 cannot be considered (not enough atoms). 
 
 ALL LOOP  4     1.69     19    54.3    35      65-RQGR-68   
 
 
Accuracy of estimates of atomic coordinate errors: model <-> target 
 
 (CA)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    6.689      1.000       0.500     19    25.0    76     ERRCA  
     WELL ORDERED  . . . . .    6.689      1.000       0.500     19    25.0    76     ERRCA  
     NO INTER CONTACTS . . .    6.689      1.000       0.500     19    25.0    76     ERRCA  
     SHIFTED CHAIN . . . . .    7.043      1.000       0.500     17    24.3    70     ERRCA  
     ALTERNATIVE PARENT  . .    5.966      1.000       0.500      4    80.0     5     ERRCA  
     SECONDARY STRUCTURE . .    8.578      1.000       0.500     11    40.7    27     ERRCA  
     LARGE SHIFTS/INSERTIONS    5.307      1.000       0.500      6    18.8    32     ERRCA  
     SURFACE . . . . . . . .    5.636      1.000       0.500     13    24.1    54     ERRCA  
     BURIED  . . . . . . . .    8.971      1.000       0.500      6    27.3    22     ERRCA  
     CORE  . . . . . . . . .    7.328      1.000       0.500     13    29.5    44     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    6.873      1.000       0.500     94    25.3   371     ERRMC  
     WELL ORDERED  . . . . .    6.873      1.000       0.500     94    25.3   371     ERRMC  
     NO INTER CONTACTS . . .    6.873      1.000       0.500     94    25.3   371     ERRMC  
     SHIFTED CHAIN . . . . .    7.198      1.000       0.500     84    24.6   341     ERRMC  
     ALTERNATIVE PARENT  . .    5.743      1.000       0.500     20    80.0    25     ERRMC  
     SECONDARY STRUCTURE . .    8.597      1.000       0.500     55    41.4   133     ERRMC  
     LARGE SHIFTS/INSERTIONS    5.349      1.000       0.500     29    18.8   154     ERRMC  
     SURFACE . . . . . . . .    6.007      1.000       0.500     64    24.2   264     ERRMC  
     BURIED  . . . . . . . .    8.718      1.000       0.500     30    28.0   107     ERRMC  
     CORE  . . . . . . . . .    7.552      1.000       0.500     65    30.0   217     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    8.145      1.000       0.500     18     6.3   284     ERRSC  
     WELL ORDERED  . . . . .    8.145      1.000       0.500     18     6.3   284     ERRSC  
     NO INTER CONTACTS . . .    8.145      1.000       0.500     18     6.3   284     ERRSC  
     RELIABLE SIDE CHAINS  .    8.145      1.000       0.500     18     7.5   240     ERRSC  
     CHANGED ANGLES  . . . .    0.000      0.000       0.000      0     0.0   192     ERRSC  
     SHIFTED CHAIN . . . . .    8.386      1.000       0.500     16     6.1   262     ERRSC  
     ALTERNATIVE PARENT  . .    7.099      1.000       0.500      4    16.0    25     ERRSC  
     SECONDARY STRUCTURE . .    9.782      1.000       0.500     11    11.1    99     ERRSC  
     LARGE SHIFTS/INSERTIONS    7.092      1.000       0.500      5     4.5   112     ERRSC  
     SURFACE . . . . . . . .    7.280      1.000       0.500     12     5.4   222     ERRSC  
     BURIED  . . . . . . . .    9.877      1.000       0.500      6     9.7    62     ERRSC  
     CORE  . . . . . . . . .    8.551      1.000       0.500     13     7.6   172     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    6.873      1.000       0.500     94    16.0   588     ERRALL 
     WELL ORDERED  . . . . .    6.873      1.000       0.500     94    16.0   588     ERRALL 
     NO INTER CONTACTS . . .    6.873      1.000       0.500     94    16.0   588     ERRALL 
     SHIFTED CHAIN . . . . .    7.198      1.000       0.500     84    15.5   542     ERRALL 
     ALTERNATIVE PARENT  . .    5.743      1.000       0.500     20    44.4    45     ERRALL 
     SECONDARY STRUCTURE . .    8.597      1.000       0.500     55    26.6   207     ERRALL 
     LARGE SHIFTS/INSERTIONS    5.349      1.000       0.500     29    12.1   240     ERRALL 
     SURFACE . . . . . . . .    6.007      1.000       0.500     64    14.6   438     ERRALL 
     BURIED  . . . . . . . .    8.718      1.000       0.500     30    20.0   150     ERRALL 
     CORE  . . . . . . . . .    7.552      1.000       0.500     65    18.7   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)         0         1         4         9        16      19      76   DISTCA 
CA  (P)      0.00      1.32      5.26     11.84     21.05              76   DISTCA 
CA  (RMS)    0.00      1.49      2.08      3.44      5.17                   DISTCA 
 
ALL (N)         0         3        14        45        78      94     588   DISTALL 
ALL (P)      0.00      0.51      2.38      7.65     13.27             588   DISTALL 
ALL (RMS)    0.00      1.72      2.29      3.60      5.32                   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            13             6          RMSLSI 
CA  (P)       57.89         17.11          7.89          RMSLSI 
CA  (RMS)      1.67          9.43          5.65          RMSLSI 
 
 
 
END of the results output 
