 
####################################################### 
#                                                     # 
#                        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 521 atoms, 464 common with TARGET 
           Number of atoms possible to evaluate: 190 
 
 
 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 . . . . . . . . . .    80.61           29.5    78    52.0   150     ARMSMC  
     WELL ORDERED  . . . . .    80.61           29.5    78    52.0   150     ARMSMC  
     NO INTER CONTACTS . . .    80.61           29.5    78    52.0   150     ARMSMC  
     SHIFTED CHAIN . . . . .    80.97           28.9    76    55.1   138     ARMSMC  
     ALTERNATIVE PARENT  . .    62.52           50.0     4    40.0    10     ARMSMC  
     SECONDARY STRUCTURE . .    65.48           37.5    16    29.6    54     ARMSMC  
     LARGE SHIFTS/INSERTIONS    87.79           29.4    34    54.8    62     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    77.35           29.3    58    54.7   106     ARMSMC  
     BURIED  . . . . . . . .    89.40           30.0    20    45.5    44     ARMSMC  
     CORE  . . . . . . . . .    74.60           29.5    44    50.0    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) =  -0.84994     r(1,2) =  -0.42136     r(1,3) =  -0.31631 
 r(2,1) =  -0.25227     r(2,2) =  -0.20160     r(2,3) =   0.94642 
 r(3,1) =  -0.46255     r(3,2) =   0.88420     r(3,3) =   0.06505 
THE OFFSET VECTOR: 
 v(1) =  32.34084     v(2) = -13.58673     v(3) =  32.66964 
 
 Number of iteration  2                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.78           (Number of atoms:    8) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .   12.18         40    52.6    76     CRMSCA  
     CRN = ALL/NP  . . . . .    0.3046                            CRMSCA  
     WELL ORDERED  . . . . .   12.18         40    52.6    76     CRMSCA  
     NO INTER CONTACTS . . .   12.18         40    52.6    76     CRMSCA  
     SHIFTED CHAIN . . . . .   11.95         39    55.7    70     CRMSCA  
     ALTERNATIVE PARENT  . .    7.20          2    40.0     5     CRMSCA  
     SECONDARY STRUCTURE . .    6.26          8    29.6    27     CRMSCA  
     SHIFTED SS UNITS  . . .    2.32          6   100.0     6     CRMSCA  
     LARGE SHIFTS/INSERTIONS   13.51         18    56.2    32     CRMSCA  
     SURFACE . . . . . . . .   13.26         30    55.6    54     CRMSCA  
     BURIED  . . . . . . . .    8.12         10    45.5    22     CRMSCA  
     CORE  . . . . . . . . .   10.98         22    50.0    44     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .   12.20        190    51.2   371     CRMSMC  
     WELL ORDERED  . . . . .   12.20        190    51.2   371     CRMSMC  
     NO INTER CONTACTS . . .   12.20        190    51.2   371     CRMSMC  
     SHIFTED CHAIN . . . . .   11.92        185    54.3   341     CRMSMC  
     ALTERNATIVE PARENT  . .    8.07         10    40.0    25     CRMSMC  
     SECONDARY STRUCTURE . .    6.26         39    29.3   133     CRMSMC  
     SHIFTED SS UNITS  . . .    2.76         30   100.0    30     CRMSMC  
     LARGE SHIFTS/INSERTIONS   13.59         83    53.9   154     CRMSMC  
     SURFACE . . . . . . . .   13.33        144    54.5   264     CRMSMC  
     BURIED  . . . . . . . .    7.65         46    43.0   107     CRMSMC  
     CORE  . . . . . . . . .   11.00        107    49.3   217     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .   12.93         30    10.6   284     CRMSSC  
     WELL ORDERED  . . . . .   12.93         30    10.6   284     CRMSSC  
     NO INTER CONTACTS . . .   12.93         30    10.6   284     CRMSSC  
     RELIABLE SIDE CHAINS  .   12.93         30    12.5   240     CRMSSC  
     CHANGED ANGLES  . . . .    0.00          0     0.0   192     CRMSSC  
     SECONDARY STRUCTURE . .    4.84          7     7.1    99     CRMSSC  
     LARGE SHIFTS/INSERTIONS   15.30         11     9.8   112     CRMSSC  
     SURFACE . . . . . . . .   14.02         24    10.8   222     CRMSSC  
     BURIED  . . . . . . . .    7.06          6     9.7    62     CRMSSC  
     CORE  . . . . . . . . .   11.34         19    11.0   172     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .   12.20        190    32.3   588     CRMSALL 
     WELL ORDERED  . . . . .   12.20        190    32.3   588     CRMSALL 
     NO INTER CONTACTS . . .   12.20        190    32.3   588     CRMSALL 
     SHIFTED CHAIN . . . . .   11.92        185    34.1   542     CRMSALL 
     ALTERNATIVE PARENT  . .    8.07         10    22.2    45     CRMSALL 
     SECONDARY STRUCTURE . .    6.26         39    18.8   207     CRMSALL 
     LARGE SHIFTS/INSERTIONS   13.59         83    34.6   240     CRMSALL 
     SURFACE . . . . . . . .   13.33        144    32.9   438     CRMSALL 
     BURIED  . . . . . . . .    7.65         46    30.7   150     CRMSALL 
     CORE  . . . . . . . . .   11.00        107    30.7   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    22.40      1    33.3     3      26-GGG-28   
 CA  LOOP  3     8.00     10   100.0    10      40-DKRVEKVTDY-49   
 CA  LOOP  4    25.34      3    75.0     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    22.03      4    33.3    12      26-GGG-28   
 MC  LOOP  3     8.28     46    92.0    50      40-DKRVEKVTDY-49   
 MC  LOOP  4    25.45     14    73.7    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    22.03      4    33.3    12      26-GGG-28   
 ALL LOOP  3     8.28     46    52.9    87      40-DKRVEKVTDY-49   
 ALL LOOP  4    25.45     14    40.0    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). 
 
 CA  LOOP  3     3.62     10   100.0    10      40-DKRVEKVTDY-49   
 CA  LOOP  4     0.04      3    75.0     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). 
 
 MC  LOOP  3     3.75     46    92.0    50      40-DKRVEKVTDY-49   
 MC  LOOP  4     1.48     14    73.7    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). 
 
 ALL LOOP  3     3.75     46    52.9    87      40-DKRVEKVTDY-49   
 ALL LOOP  4     1.48     14    40.0    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 . . . . . . . . . .    9.711      1.000       0.500     40    52.6    76     ERRCA  
     WELL ORDERED  . . . . .    9.711      1.000       0.500     40    52.6    76     ERRCA  
     NO INTER CONTACTS . . .    9.711      1.000       0.500     40    52.6    76     ERRCA  
     SHIFTED CHAIN . . . . .    9.468      1.000       0.500     39    55.7    70     ERRCA  
     ALTERNATIVE PARENT  . .    6.731      1.000       0.500      2    40.0     5     ERRCA  
     SECONDARY STRUCTURE . .    4.463      1.000       0.500      8    29.6    27     ERRCA  
     LARGE SHIFTS/INSERTIONS   11.293      1.000       0.500     18    56.2    32     ERRCA  
     SURFACE . . . . . . . .   10.648      1.000       0.500     30    55.6    54     ERRCA  
     BURIED  . . . . . . . .    6.902      1.000       0.500     10    45.5    22     ERRCA  
     CORE  . . . . . . . . .    8.417      1.000       0.500     22    50.0    44     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    9.769      1.000       0.500    190    51.2   371     ERRMC  
     WELL ORDERED  . . . . .    9.769      1.000       0.500    190    51.2   371     ERRMC  
     NO INTER CONTACTS . . .    9.769      1.000       0.500    190    51.2   371     ERRMC  
     SHIFTED CHAIN . . . . .    9.492      1.000       0.500    185    54.3   341     ERRMC  
     ALTERNATIVE PARENT  . .    7.315      1.000       0.500     10    40.0    25     ERRMC  
     SECONDARY STRUCTURE . .    4.513      1.000       0.500     39    29.3   133     ERRMC  
     LARGE SHIFTS/INSERTIONS   11.435      1.000       0.500     83    53.9   154     ERRMC  
     SURFACE . . . . . . . .   10.813      1.000       0.500    144    54.5   264     ERRMC  
     BURIED  . . . . . . . .    6.499      1.000       0.500     46    43.0   107     ERRMC  
     CORE  . . . . . . . . .    8.476      1.000       0.500    107    49.3   217     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   10.411      1.000       0.500     30    10.6   284     ERRSC  
     WELL ORDERED  . . . . .   10.411      1.000       0.500     30    10.6   284     ERRSC  
     NO INTER CONTACTS . . .   10.411      1.000       0.500     30    10.6   284     ERRSC  
     RELIABLE SIDE CHAINS  .   10.411      1.000       0.500     30    12.5   240     ERRSC  
     CHANGED ANGLES  . . . .    0.000      0.000       0.000      0     0.0   192     ERRSC  
     SHIFTED CHAIN . . . . .   10.068      1.000       0.500     29    11.1   262     ERRSC  
     ALTERNATIVE PARENT  . .    6.905      1.000       0.500      2     8.0    25     ERRSC  
     SECONDARY STRUCTURE . .    3.991      1.000       0.500      7     7.1    99     ERRSC  
     LARGE SHIFTS/INSERTIONS   12.877      1.000       0.500     11     9.8   112     ERRSC  
     SURFACE . . . . . . . .   11.518      1.000       0.500     24    10.8   222     ERRSC  
     BURIED  . . . . . . . .    5.983      1.000       0.500      6     9.7    62     ERRSC  
     CORE  . . . . . . . . .    8.984      1.000       0.500     19    11.0   172     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    9.769      1.000       0.500    190    32.3   588     ERRALL 
     WELL ORDERED  . . . . .    9.769      1.000       0.500    190    32.3   588     ERRALL 
     NO INTER CONTACTS . . .    9.769      1.000       0.500    190    32.3   588     ERRALL 
     SHIFTED CHAIN . . . . .    9.492      1.000       0.500    185    34.1   542     ERRALL 
     ALTERNATIVE PARENT  . .    7.315      1.000       0.500     10    22.2    45     ERRALL 
     SECONDARY STRUCTURE . .    4.513      1.000       0.500     39    18.8   207     ERRALL 
     LARGE SHIFTS/INSERTIONS   11.435      1.000       0.500     83    34.6   240     ERRALL 
     SURFACE . . . . . . . .   10.813      1.000       0.500    144    32.9   438     ERRALL 
     BURIED  . . . . . . . .    6.499      1.000       0.500     46    30.7   150     ERRALL 
     CORE  . . . . . . . . .    8.476      1.000       0.500    107    30.7   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)         1         6         8        12        27      40      76   DISTCA 
CA  (P)      1.32      7.89     10.53     15.79     35.53              76   DISTCA 
CA  (RMS)    0.92      1.63      1.78      2.80      6.06                   DISTCA 
 
ALL (N)         5        25        36        53       122     190     588   DISTALL 
ALL (P)      0.85      4.25      6.12      9.01     20.75             588   DISTALL 
ALL (RMS)    0.73      1.54      1.93      2.77      5.92                   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            22            18          RMSLSI 
CA  (P)       57.89         28.95         23.68          RMSLSI 
CA  (RMS)      1.67         10.98         13.51          RMSLSI 
 
 
 
END of the results output 
