 
####################################################### 
#                                                     # 
#                        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 800 atoms, 588 common with TARGET 
           Number of atoms possible to evaluate: 588 
 
 
 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 . . . . . . . . . .    96.02           28.0   150   100.0   150     ARMSMC  
     WELL ORDERED  . . . . .    96.02           28.0   150   100.0   150     ARMSMC  
     NO INTER CONTACTS . . .    96.02           28.0   150   100.0   150     ARMSMC  
     SHIFTED CHAIN . . . . .    93.50           29.0   138   100.0   138     ARMSMC  
     ALTERNATIVE PARENT  . .   102.18           40.0    10   100.0    10     ARMSMC  
     SECONDARY STRUCTURE . .   109.88           16.7    54   100.0    54     ARMSMC  
     LARGE SHIFTS/INSERTIONS    91.49           35.5    62   100.0    62     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    91.24           33.0   106   100.0   106     ARMSMC  
     BURIED  . . . . . . . .   106.66           15.9    44   100.0    44     ARMSMC  
     CORE  . . . . . . . . .    99.09           22.7    88   100.0    88     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    96.23           29.0    62   100.0    62     ARMSSC1 
     WELL ORDERED  . . . . .    96.23           29.0    62   100.0    62     ARMSSC1 
     NO INTER CONTACTS . . .    96.23           29.0    62   100.0    62     ARMSSC1 
     RELIABLE SIDE CHAINS  .    95.81           28.0    50   100.0    50     ARMSSC1 
     CHANGED ANGLES  . . . .   101.90           22.4    49   100.0    49     ARMSSC1 
     SHIFTED CHAIN . . . . .    98.54           28.6    56   100.0    56     ARMSSC1 
     ALTERNATIVE PARENT  . .   116.85           20.0     5   100.0     5     ARMSSC1 
     SECONDARY STRUCTURE . .   104.09           21.7    23   100.0    23     ARMSSC1 
     LARGE SHIFTS/INSERTIONS    86.30           39.1    23   100.0    23     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .    94.62           30.4    46   100.0    46     ARMSSC1 
     BURIED  . . . . . . . .   100.70           25.0    16   100.0    16     ARMSSC1 
     CORE  . . . . . . . . .   101.63           23.1    39   100.0    39     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    86.99           22.2    45   100.0    45     ARMSSC2 
     WELL ORDERED  . . . . .    86.99           22.2    45   100.0    45     ARMSSC2 
     NO INTER CONTACTS . . .    86.99           22.2    45   100.0    45     ARMSSC2 
     RELIABLE SIDE CHAINS  .    86.87           25.0    40   100.0    40     ARMSSC2 
     CHANGED ANGLES  . . . .    90.13           19.5    41   100.0    41     ARMSSC2 
     SHIFTED CHAIN . . . . .    87.81           21.4    42   100.0    42     ARMSSC2 
     ALTERNATIVE PARENT  . .    76.80            0.0     4   100.0     4     ARMSSC2 
     SECONDARY STRUCTURE . .    87.01           15.4    13   100.0    13     ARMSSC2 
     LARGE SHIFTS/INSERTIONS    86.27           23.5    17   100.0    17     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .    86.08           23.7    38   100.0    38     ARMSSC2 
     BURIED  . . . . . . . .    91.76           14.3     7   100.0     7     ARMSSC2 
     CORE  . . . . . . . . .    87.42           21.4    28   100.0    28     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    60.09           50.0    24   100.0    24     ARMSSC3 
     WELL ORDERED  . . . . .    60.09           50.0    24   100.0    24     ARMSSC3 
     NO INTER CONTACTS . . .    60.09           50.0    24   100.0    24     ARMSSC3 
     RELIABLE SIDE CHAINS  .    61.57           50.0    20   100.0    20     ARMSSC3 
     CHANGED ANGLES  . . . .    60.09           50.0    24   100.0    24     ARMSSC3 
     SHIFTED CHAIN . . . . .    60.22           52.2    23   100.0    23     ARMSSC3 
     ALTERNATIVE PARENT  . .    42.10           50.0     2   100.0     2     ARMSSC3 
     SECONDARY STRUCTURE . .    85.92           16.7     6   100.0     6     ARMSSC3 
     LARGE SHIFTS/INSERTIONS    43.89           63.6    11   100.0    11     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .    60.09           50.0    24   100.0    24     ARMSSC3 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     CORE  . . . . . . . . .    70.96           38.5    13   100.0    13     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    86.48           25.0    12   100.0    12     ARMSSC4 
     WELL ORDERED  . . . . .    86.48           25.0    12   100.0    12     ARMSSC4 
     NO INTER CONTACTS . . .    86.48           25.0    12   100.0    12     ARMSSC4 
     RELIABLE SIDE CHAINS  .    86.48           25.0    12   100.0    12     ARMSSC4 
     CHANGED ANGLES  . . . .    86.48           25.0    12   100.0    12     ARMSSC4 
     SHIFTED CHAIN . . . . .    87.62           27.3    11   100.0    11     ARMSSC4 
     ALTERNATIVE PARENT  . .    72.55           50.0     2   100.0     2     ARMSSC4 
     SECONDARY STRUCTURE . .    64.69           25.0     4   100.0     4     ARMSSC4 
     LARGE SHIFTS/INSERTIONS    97.79           16.7     6   100.0     6     ARMSSC4 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SURFACE . . . . . . . .    86.48           25.0    12   100.0    12     ARMSSC4 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     CORE  . . . . . . . . .    73.45           33.3     6   100.0     6     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =   0.03233     r(1,2) =   0.98077     r(1,3) =   0.19248 
 r(2,1) =  -0.99793     r(2,2) =   0.04238     r(2,3) =  -0.04836 
 r(3,1) =  -0.05558     r(3,2) =  -0.19052     r(3,3) =   0.98011 
THE OFFSET VECTOR: 
 v(1) =   3.33475     v(2) =  -9.65608     v(3) = -10.97254 
 
 Number of iteration  2                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.41           (Number of atoms:    7) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .   12.59         76   100.0    76     CRMSCA  
     CRN = ALL/NP  . . . . .    0.1656                            CRMSCA  
     WELL ORDERED  . . . . .   12.59         76   100.0    76     CRMSCA  
     NO INTER CONTACTS . . .   12.59         76   100.0    76     CRMSCA  
     SHIFTED CHAIN . . . . .   12.26         70   100.0    70     CRMSCA  
     ALTERNATIVE PARENT  . .   14.06          5   100.0     5     CRMSCA  
     SECONDARY STRUCTURE . .   15.48         27   100.0    27     CRMSCA  
     SHIFTED SS UNITS  . . .   19.21          6   100.0     6     CRMSCA  
     LARGE SHIFTS/INSERTIONS   11.31         32   100.0    32     CRMSCA  
     SURFACE . . . . . . . .   12.24         54   100.0    54     CRMSCA  
     BURIED  . . . . . . . .   13.40         22   100.0    22     CRMSCA  
     CORE  . . . . . . . . .   13.44         44   100.0    44     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .   12.70        371   100.0   371     CRMSMC  
     WELL ORDERED  . . . . .   12.70        371   100.0   371     CRMSMC  
     NO INTER CONTACTS . . .   12.70        371   100.0   371     CRMSMC  
     SHIFTED CHAIN . . . . .   12.35        341   100.0   341     CRMSMC  
     ALTERNATIVE PARENT  . .   14.07         25   100.0    25     CRMSMC  
     SECONDARY STRUCTURE . .   15.55        133   100.0   133     CRMSMC  
     SHIFTED SS UNITS  . . .   19.45         30   100.0    30     CRMSMC  
     LARGE SHIFTS/INSERTIONS   11.38        154   100.0   154     CRMSMC  
     SURFACE . . . . . . . .   12.41        264   100.0   264     CRMSMC  
     BURIED  . . . . . . . .   13.39        107   100.0   107     CRMSMC  
     CORE  . . . . . . . . .   13.56        217   100.0   217     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .   14.20        284   100.0   284     CRMSSC  
     WELL ORDERED  . . . . .   14.20        284   100.0   284     CRMSSC  
     NO INTER CONTACTS . . .   14.20        284   100.0   284     CRMSSC  
     RELIABLE SIDE CHAINS  .   14.31        240   100.0   240     CRMSSC  
     CHANGED ANGLES  . . . .   14.52        192   100.0   192     CRMSSC  
     SECONDARY STRUCTURE . .   16.16         99   100.0    99     CRMSSC  
     LARGE SHIFTS/INSERTIONS   13.74        112   100.0   112     CRMSSC  
     SURFACE . . . . . . . .   14.38        222   100.0   222     CRMSSC  
     BURIED  . . . . . . . .   13.50         62   100.0    62     CRMSSC  
     CORE  . . . . . . . . .   14.49        172   100.0   172     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .   13.34        588   100.0   588     CRMSALL 
     WELL ORDERED  . . . . .   13.34        588   100.0   588     CRMSALL 
     NO INTER CONTACTS . . .   13.34        588   100.0   588     CRMSALL 
     SHIFTED CHAIN . . . . .   13.04        542   100.0   542     CRMSALL 
     ALTERNATIVE PARENT  . .   14.65         45   100.0    45     CRMSALL 
     SECONDARY STRUCTURE . .   15.81        207   100.0   207     CRMSALL 
     LARGE SHIFTS/INSERTIONS   12.40        240   100.0   240     CRMSALL 
     SURFACE . . . . . . . .   13.31        438   100.0   438     CRMSALL 
     BURIED  . . . . . . . .   13.44        150   100.0   150     CRMSALL 
     CORE  . . . . . . . . .   13.96        348   100.0   348     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     5.33      7   100.0     7       1-AEIEVGR-7    
 CA  LOOP  2     1.51      3   100.0     3      26-GGG-28   
 CA  LOOP  3    11.42     10   100.0    10      40-DKRVEKVTDY-49   
 CA  LOOP  4     5.12      4   100.0     4      65-RQGR-68   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     5.39     34   100.0    34       1-AEIEVGR-7    
 MC  LOOP  2     2.10     12   100.0    12      26-GGG-28   
 MC  LOOP  3    11.20     50   100.0    50      40-DKRVEKVTDY-49   
 MC  LOOP  4     5.35     19   100.0    19      65-RQGR-68   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     6.66     53   100.0    53       1-AEIEVGR-7    
 ALL LOOP  2     2.10     12   100.0    12      26-GGG-28   
 ALL LOOP  3    12.58     87   100.0    87      40-DKRVEKVTDY-49   
 ALL LOOP  4     9.30     35   100.0    35      65-RQGR-68   
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     2.84      7   100.0     7       1-AEIEVGR-7    
 CA  LOOP  2     0.25      3   100.0     3      26-GGG-28   
 CA  LOOP  3     2.68     10   100.0    10      40-DKRVEKVTDY-49   
 CA  LOOP  4     1.89      4   100.0     4      65-RQGR-68   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     2.95     34   100.0    34       1-AEIEVGR-7    
 MC  LOOP  2     1.60     12   100.0    12      26-GGG-28   
 MC  LOOP  3     2.92     50   100.0    50      40-DKRVEKVTDY-49   
 MC  LOOP  4     1.89     19   100.0    19      65-RQGR-68   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     3.84     53   100.0    53       1-AEIEVGR-7    
 ALL LOOP  2     1.60     12   100.0    12      26-GGG-28   
 ALL LOOP  3     4.11     87   100.0    87      40-DKRVEKVTDY-49   
 ALL LOOP  4     3.79     35   100.0    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 . . . . . . . . . .   11.177      1.000       0.500     76   100.0    76     ERRCA  
     WELL ORDERED  . . . . .   11.177      1.000       0.500     76   100.0    76     ERRCA  
     NO INTER CONTACTS . . .   11.177      1.000       0.500     76   100.0    76     ERRCA  
     SHIFTED CHAIN . . . . .   10.786      1.000       0.500     70   100.0    70     ERRCA  
     ALTERNATIVE PARENT  . .   12.529      1.000       0.500      5   100.0     5     ERRCA  
     SECONDARY STRUCTURE . .   14.788      1.000       0.500     27   100.0    27     ERRCA  
     LARGE SHIFTS/INSERTIONS    9.222      1.000       0.500     32   100.0    32     ERRCA  
     SURFACE . . . . . . . .   10.691      1.000       0.500     54   100.0    54     ERRCA  
     BURIED  . . . . . . . .   12.370      1.000       0.500     22   100.0    22     ERRCA  
     CORE  . . . . . . . . .   12.599      1.000       0.500     44   100.0    44     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   11.355      1.000       0.500    371   100.0   371     ERRMC  
     WELL ORDERED  . . . . .   11.355      1.000       0.500    371   100.0   371     ERRMC  
     NO INTER CONTACTS . . .   11.355      1.000       0.500    371   100.0   371     ERRMC  
     SHIFTED CHAIN . . . . .   10.951      1.000       0.500    341   100.0   341     ERRMC  
     ALTERNATIVE PARENT  . .   12.380      1.000       0.500     25   100.0    25     ERRMC  
     SECONDARY STRUCTURE . .   14.851      1.000       0.500    133   100.0   133     ERRMC  
     LARGE SHIFTS/INSERTIONS    9.434      1.000       0.500    154   100.0   154     ERRMC  
     SURFACE . . . . . . . .   10.950      1.000       0.500    264   100.0   264     ERRMC  
     BURIED  . . . . . . . .   12.353      1.000       0.500    107   100.0   107     ERRMC  
     CORE  . . . . . . . . .   12.718      1.000       0.500    217   100.0   217     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   13.033      1.000       0.500    284   100.0   284     ERRSC  
     WELL ORDERED  . . . . .   13.033      1.000       0.500    284   100.0   284     ERRSC  
     NO INTER CONTACTS . . .   13.033      1.000       0.500    284   100.0   284     ERRSC  
     RELIABLE SIDE CHAINS  .   13.178      1.000       0.500    240   100.0   240     ERRSC  
     CHANGED ANGLES  . . . .   13.310      1.000       0.500    192   100.0   192     ERRSC  
     SHIFTED CHAIN . . . . .   12.708      1.000       0.500    262   100.0   262     ERRSC  
     ALTERNATIVE PARENT  . .   14.434      1.000       0.500     25   100.0    25     ERRSC  
     SECONDARY STRUCTURE . .   15.332      1.000       0.500     99   100.0    99     ERRSC  
     LARGE SHIFTS/INSERTIONS   12.236      1.000       0.500    112   100.0   112     ERRSC  
     SURFACE . . . . . . . .   13.168      1.000       0.500    222   100.0   222     ERRSC  
     BURIED  . . . . . . . .   12.551      1.000       0.500     62   100.0    62     ERRSC  
     CORE  . . . . . . . . .   13.553      1.000       0.500    172   100.0   172     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   12.049      1.000       0.500    588   100.0   588     ERRALL 
     WELL ORDERED  . . . . .   12.049      1.000       0.500    588   100.0   588     ERRALL 
     NO INTER CONTACTS . . .   12.049      1.000       0.500    588   100.0   588     ERRALL 
     SHIFTED CHAIN . . . . .   11.688      1.000       0.500    542   100.0   542     ERRALL 
     ALTERNATIVE PARENT  . .   13.366      1.000       0.500     45   100.0    45     ERRALL 
     SECONDARY STRUCTURE . .   15.052      1.000       0.500    207   100.0   207     ERRALL 
     LARGE SHIFTS/INSERTIONS   10.566      1.000       0.500    240   100.0   240     ERRALL 
     SURFACE . . . . . . . .   11.912      1.000       0.500    438   100.0   438     ERRALL 
     BURIED  . . . . . . . .   12.447      1.000       0.500    150   100.0   150     ERRALL 
     CORE  . . . . . . . . .   13.071      1.000       0.500    348   100.0   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)         1         7         7        13        34      76      76   DISTCA 
CA  (P)      1.32      9.21      9.21     17.11     44.74              76   DISTCA 
CA  (RMS)    0.67      1.41      1.41      3.22      6.27                   DISTCA 
 
ALL (N)         3        19        31        73       234     588     588   DISTALL 
ALL (P)      0.51      3.23      5.27     12.41     39.80             588   DISTALL 
ALL (RMS)    0.62      1.37      1.92      3.36      6.73                   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            44            32          RMSLSI 
CA  (P)       57.89         57.89         42.11          RMSLSI 
CA  (RMS)      1.67         13.44         11.31          RMSLSI 
 
 
 
END of the results output 
