 
####################################################### 
#                                                     # 
#                        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 459 atoms, 419 common with TARGET 
           Number of atoms possible to evaluate: 283 
 
 
 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 . . . . . . . . . .    85.04           30.4   112    74.7   150     ARMSMC  
     WELL ORDERED  . . . . .    85.04           30.4   112    74.7   150     ARMSMC  
     NO INTER CONTACTS . . .    85.04           30.4   112    74.7   150     ARMSMC  
     SHIFTED CHAIN . . . . .    85.29           29.9   107    77.5   138     ARMSMC  
     ALTERNATIVE PARENT  . .    71.66           25.0     4    40.0    10     ARMSMC  
     SECONDARY STRUCTURE . .    71.90           33.3    30    55.6    54     ARMSMC  
     LARGE SHIFTS/INSERTIONS    89.94           29.5    44    71.0    62     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    84.94           28.6    77    72.6   106     ARMSMC  
     BURIED  . . . . . . . .    85.28           34.3    35    79.5    44     ARMSMC  
     CORE  . . . . . . . . .    81.72           30.9    68    77.3    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) =  -0.52108     r(1,2) =  -0.56701     r(1,3) =   0.63795 
 r(2,1) =   0.29689     r(2,2) =   0.58035     r(2,3) =   0.75832 
 r(3,1) =  -0.80020     r(3,2) =   0.58455     r(3,3) =  -0.13407 
THE OFFSET VECTOR: 
 v(1) =  -3.38622     v(2) = -137.23233     v(3) =  11.43490 
 
 Number of iteration  3                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.73           (Number of atoms:    7) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .   17.83         59    77.6    76     CRMSCA  
     CRN = ALL/NP  . . . . .    0.3021                            CRMSCA  
     WELL ORDERED  . . . . .   17.83         59    77.6    76     CRMSCA  
     NO INTER CONTACTS . . .   17.83         59    77.6    76     CRMSCA  
     SHIFTED CHAIN . . . . .   17.64         56    80.0    70     CRMSCA  
     ALTERNATIVE PARENT  . .   29.42          3    60.0     5     CRMSCA  
     SECONDARY STRUCTURE . .   19.60         17    63.0    27     CRMSCA  
     SHIFTED SS UNITS  . . .   24.58          6   100.0     6     CRMSCA  
     LARGE SHIFTS/INSERTIONS   17.43         23    71.9    32     CRMSCA  
     SURFACE . . . . . . . .   18.59         40    74.1    54     CRMSCA  
     BURIED  . . . . . . . .   16.09         19    86.4    22     CRMSCA  
     CORE  . . . . . . . . .   18.07         36    81.8    44     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .   17.78        283    76.3   371     CRMSMC  
     WELL ORDERED  . . . . .   17.78        283    76.3   371     CRMSMC  
     NO INTER CONTACTS . . .   17.78        283    76.3   371     CRMSMC  
     SHIFTED CHAIN . . . . .   17.57        268    78.6   341     CRMSMC  
     ALTERNATIVE PARENT  . .   29.30         15    60.0    25     CRMSMC  
     SECONDARY STRUCTURE . .   19.60         83    62.4   133     CRMSMC  
     SHIFTED SS UNITS  . . .   24.80         29    96.7    30     CRMSMC  
     LARGE SHIFTS/INSERTIONS   17.29        109    70.8   154     CRMSMC  
     SURFACE . . . . . . . .   18.44        192    72.7   264     CRMSMC  
     BURIED  . . . . . . . .   16.30         91    85.0   107     CRMSMC  
     CORE  . . . . . . . . .   18.08        174    80.2   217     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .   17.85         47    16.5   284     CRMSSC  
     WELL ORDERED  . . . . .   17.85         47    16.5   284     CRMSSC  
     NO INTER CONTACTS . . .   17.85         47    16.5   284     CRMSSC  
     RELIABLE SIDE CHAINS  .   17.85         47    19.6   240     CRMSSC  
     CHANGED ANGLES  . . . .    0.00          0     0.0   192     CRMSSC  
     SECONDARY STRUCTURE . .   19.55         15    15.2    99     CRMSSC  
     LARGE SHIFTS/INSERTIONS   16.88         17    15.2   112     CRMSSC  
     SURFACE . . . . . . . .   18.33         32    14.4   222     CRMSSC  
     BURIED  . . . . . . . .   16.79         15    24.2    62     CRMSSC  
     CORE  . . . . . . . . .   18.38         30    17.4   172     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .   17.78        283    48.1   588     CRMSALL 
     WELL ORDERED  . . . . .   17.78        283    48.1   588     CRMSALL 
     NO INTER CONTACTS . . .   17.78        283    48.1   588     CRMSALL 
     SHIFTED CHAIN . . . . .   17.57        268    49.4   542     CRMSALL 
     ALTERNATIVE PARENT  . .   29.30         15    33.3    45     CRMSALL 
     SECONDARY STRUCTURE . .   19.60         83    40.1   207     CRMSALL 
     LARGE SHIFTS/INSERTIONS   17.29        109    45.4   240     CRMSALL 
     SURFACE . . . . . . . .   18.44        192    43.8   438     CRMSALL 
     BURIED  . . . . . . . .   16.30         91    60.7   150     CRMSALL 
     CORE  . . . . . . . . .   18.08        174    50.0   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    18.56      3   100.0     3      26-GGG-28   
 CA  LOOP  3     5.60     10   100.0    10      40-DKRVEKVTDY-49   
 CA  LOOP  4    34.36      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    17.89     12   100.0    12      26-GGG-28   
 MC  LOOP  3     5.86     50   100.0    50      40-DKRVEKVTDY-49   
 MC  LOOP  4    34.20     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    17.89     12   100.0    12      26-GGG-28   
 ALL LOOP  3     5.86     50    57.5    87      40-DKRVEKVTDY-49   
 ALL LOOP  4    34.20     19    54.3    35      65-RQGR-68   
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 WARNING! LOOP  1 cannot be considered (not enough atoms). 
 
 CA  LOOP  2     0.25      3   100.0     3      26-GGG-28   
 CA  LOOP  3     4.73     10   100.0    10      40-DKRVEKVTDY-49   
 CA  LOOP  4     1.15      4   100.0     4      65-RQGR-68   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 WARNING! LOOP  1 cannot be considered (not enough atoms). 
 
 MC  LOOP  2     1.49     12   100.0    12      26-GGG-28   
 MC  LOOP  3     4.98     50   100.0    50      40-DKRVEKVTDY-49   
 MC  LOOP  4     1.67     19   100.0    19      65-RQGR-68   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 WARNING! LOOP  1 cannot be considered (not enough atoms). 
 
 ALL LOOP  2     1.49     12   100.0    12      26-GGG-28   
 ALL LOOP  3     4.98     50    57.5    87      40-DKRVEKVTDY-49   
 ALL LOOP  4     1.67     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 . . . . . . . . . .   14.948      1.000       0.500     59    77.6    76     ERRCA  
     WELL ORDERED  . . . . .   14.948      1.000       0.500     59    77.6    76     ERRCA  
     NO INTER CONTACTS . . .   14.948      1.000       0.500     59    77.6    76     ERRCA  
     SHIFTED CHAIN . . . . .   14.676      1.000       0.500     56    80.0    70     ERRCA  
     ALTERNATIVE PARENT  . .   29.242      1.000       0.500      3    60.0     5     ERRCA  
     SECONDARY STRUCTURE . .   18.406      1.000       0.500     17    63.0    27     ERRCA  
     LARGE SHIFTS/INSERTIONS   12.798      1.000       0.500     23    71.9    32     ERRCA  
     SURFACE . . . . . . . .   15.492      1.000       0.500     40    74.1    54     ERRCA  
     BURIED  . . . . . . . .   13.802      1.000       0.500     19    86.4    22     ERRCA  
     CORE  . . . . . . . . .   16.321      1.000       0.500     36    81.8    44     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   14.862      1.000       0.500    283    76.3   371     ERRMC  
     WELL ORDERED  . . . . .   14.862      1.000       0.500    283    76.3   371     ERRMC  
     NO INTER CONTACTS . . .   14.862      1.000       0.500    283    76.3   371     ERRMC  
     SHIFTED CHAIN . . . . .   14.565      1.000       0.500    268    78.6   341     ERRMC  
     ALTERNATIVE PARENT  . .   29.170      1.000       0.500     15    60.0    25     ERRMC  
     SECONDARY STRUCTURE . .   18.359      1.000       0.500     83    62.4   133     ERRMC  
     LARGE SHIFTS/INSERTIONS   12.615      1.000       0.500    109    70.8   154     ERRMC  
     SURFACE . . . . . . . .   15.286      1.000       0.500    192    72.7   264     ERRMC  
     BURIED  . . . . . . . .   13.967      1.000       0.500     91    85.0   107     ERRMC  
     CORE  . . . . . . . . .   16.270      1.000       0.500    174    80.2   217     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   15.073      1.000       0.500     47    16.5   284     ERRSC  
     WELL ORDERED  . . . . .   15.073      1.000       0.500     47    16.5   284     ERRSC  
     NO INTER CONTACTS . . .   15.073      1.000       0.500     47    16.5   284     ERRSC  
     RELIABLE SIDE CHAINS  .   15.073      1.000       0.500     47    19.6   240     ERRSC  
     CHANGED ANGLES  . . . .    0.000      0.000       0.000      0     0.0   192     ERRSC  
     SHIFTED CHAIN . . . . .   14.723      1.000       0.500     44    16.8   262     ERRSC  
     ALTERNATIVE PARENT  . .   29.939      1.000       0.500      3    12.0    25     ERRSC  
     SECONDARY STRUCTURE . .   18.185      1.000       0.500     15    15.2    99     ERRSC  
     LARGE SHIFTS/INSERTIONS   12.172      1.000       0.500     17    15.2   112     ERRSC  
     SURFACE . . . . . . . .   15.209      1.000       0.500     32    14.4   222     ERRSC  
     BURIED  . . . . . . . .   14.784      1.000       0.500     15    24.2    62     ERRSC  
     CORE  . . . . . . . . .   16.717      1.000       0.500     30    17.4   172     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   14.862      1.000       0.500    283    48.1   588     ERRALL 
     WELL ORDERED  . . . . .   14.862      1.000       0.500    283    48.1   588     ERRALL 
     NO INTER CONTACTS . . .   14.862      1.000       0.500    283    48.1   588     ERRALL 
     SHIFTED CHAIN . . . . .   14.565      1.000       0.500    268    49.4   542     ERRALL 
     ALTERNATIVE PARENT  . .   29.170      1.000       0.500     15    33.3    45     ERRALL 
     SECONDARY STRUCTURE . .   18.359      1.000       0.500     83    40.1   207     ERRALL 
     LARGE SHIFTS/INSERTIONS   12.615      1.000       0.500    109    45.4   240     ERRALL 
     SURFACE . . . . . . . .   15.286      1.000       0.500    192    43.8   438     ERRALL 
     BURIED  . . . . . . . .   13.967      1.000       0.500     91    60.7   150     ERRALL 
     CORE  . . . . . . . . .   16.270      1.000       0.500    174    50.0   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)         0         6         7        10        21      59      76   DISTCA 
CA  (P)      0.00      7.89      9.21     13.16     27.63              76   DISTCA 
CA  (RMS)    0.00      1.68      1.73      2.44      5.43                   DISTCA 
 
ALL (N)         2        25        35        55       104     283     588   DISTALL 
ALL (P)      0.34      4.25      5.95      9.35     17.69             588   DISTALL 
ALL (RMS)    0.90      1.45      1.85      2.85      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)          44            36            23          RMSLSI 
CA  (P)       57.89         47.37         30.26          RMSLSI 
CA  (RMS)      1.67         18.07         17.43          RMSLSI 
 
 
 
END of the results output 
