 
####################################################### 
#                                                     # 
#                        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 . . . . . . . . . .    79.13           36.7   150   100.0   150     ARMSMC  
     WELL ORDERED  . . . . .    79.13           36.7   150   100.0   150     ARMSMC  
     NO INTER CONTACTS . . .    79.13           36.7   150   100.0   150     ARMSMC  
     SHIFTED CHAIN . . . . .    77.44           37.0   138   100.0   138     ARMSMC  
     ALTERNATIVE PARENT  . .    50.68           20.0    10   100.0    10     ARMSMC  
     SECONDARY STRUCTURE . .    78.92           33.3    54   100.0    54     ARMSMC  
     LARGE SHIFTS/INSERTIONS    74.74           40.3    62   100.0    62     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    73.77           39.6   106   100.0   106     ARMSMC  
     BURIED  . . . . . . . .    90.75           29.5    44   100.0    44     ARMSMC  
     CORE  . . . . . . . . .    82.08           34.1    88   100.0    88     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    98.74           21.0    62   100.0    62     ARMSSC1 
     WELL ORDERED  . . . . .    98.74           21.0    62   100.0    62     ARMSSC1 
     NO INTER CONTACTS . . .    98.74           21.0    62   100.0    62     ARMSSC1 
     RELIABLE SIDE CHAINS  .   103.39           20.0    50   100.0    50     ARMSSC1 
     CHANGED ANGLES  . . . .   103.61           16.3    49   100.0    49     ARMSSC1 
     SHIFTED CHAIN . . . . .   101.10           21.4    56   100.0    56     ARMSSC1 
     ALTERNATIVE PARENT  . .   107.54            0.0     5   100.0     5     ARMSSC1 
     SECONDARY STRUCTURE . .    94.54            8.7    23   100.0    23     ARMSSC1 
     LARGE SHIFTS/INSERTIONS    97.01           26.1    23   100.0    23     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .   106.19           17.4    46   100.0    46     ARMSSC1 
     BURIED  . . . . . . . .    73.23           31.2    16   100.0    16     ARMSSC1 
     CORE  . . . . . . . . .    99.75           17.9    39   100.0    39     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    85.77           17.8    45   100.0    45     ARMSSC2 
     WELL ORDERED  . . . . .    85.77           17.8    45   100.0    45     ARMSSC2 
     NO INTER CONTACTS . . .    85.77           17.8    45   100.0    45     ARMSSC2 
     RELIABLE SIDE CHAINS  .    85.71           17.5    40   100.0    40     ARMSSC2 
     CHANGED ANGLES  . . . .    85.17           17.1    41   100.0    41     ARMSSC2 
     SHIFTED CHAIN . . . . .    84.51           16.7    42   100.0    42     ARMSSC2 
     ALTERNATIVE PARENT  . .   119.70           25.0     4   100.0     4     ARMSSC2 
     SECONDARY STRUCTURE . .    79.70            7.7    13   100.0    13     ARMSSC2 
     LARGE SHIFTS/INSERTIONS    94.71           17.6    17   100.0    17     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .    85.81           15.8    38   100.0    38     ARMSSC2 
     BURIED  . . . . . . . .    85.52           28.6     7   100.0     7     ARMSSC2 
     CORE  . . . . . . . . .    79.85           17.9    28   100.0    28     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    87.01           25.0    24   100.0    24     ARMSSC3 
     WELL ORDERED  . . . . .    87.01           25.0    24   100.0    24     ARMSSC3 
     NO INTER CONTACTS . . .    87.01           25.0    24   100.0    24     ARMSSC3 
     RELIABLE SIDE CHAINS  .    88.29           30.0    20   100.0    20     ARMSSC3 
     CHANGED ANGLES  . . . .    87.01           25.0    24   100.0    24     ARMSSC3 
     SHIFTED CHAIN . . . . .    82.87           26.1    23   100.0    23     ARMSSC3 
     ALTERNATIVE PARENT  . .   123.45           50.0     2   100.0     2     ARMSSC3 
     SECONDARY STRUCTURE . .   109.81           33.3     6   100.0     6     ARMSSC3 
     LARGE SHIFTS/INSERTIONS    74.55           36.4    11   100.0    11     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .    87.01           25.0    24   100.0    24     ARMSSC3 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     CORE  . . . . . . . . .    96.30           15.4    13   100.0    13     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .   105.23           41.7    12   100.0    12     ARMSSC4 
     WELL ORDERED  . . . . .   105.23           41.7    12   100.0    12     ARMSSC4 
     NO INTER CONTACTS . . .   105.23           41.7    12   100.0    12     ARMSSC4 
     RELIABLE SIDE CHAINS  .   105.23           41.7    12   100.0    12     ARMSSC4 
     CHANGED ANGLES  . . . .   105.23           41.7    12   100.0    12     ARMSSC4 
     SHIFTED CHAIN . . . . .    97.36           45.5    11   100.0    11     ARMSSC4 
     ALTERNATIVE PARENT  . .   125.48           50.0     2   100.0     2     ARMSSC4 
     SECONDARY STRUCTURE . .   106.10           50.0     4   100.0     4     ARMSSC4 
     LARGE SHIFTS/INSERTIONS   105.88           33.3     6   100.0     6     ARMSSC4 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SURFACE . . . . . . . .   105.23           41.7    12   100.0    12     ARMSSC4 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     CORE  . . . . . . . . .   104.57           50.0     6   100.0     6     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =   0.57922     r(1,2) =  -0.77273     r(1,3) =  -0.25961 
 r(2,1) =  -0.80141     r(2,2) =  -0.48150     r(2,3) =  -0.35484 
 r(3,1) =   0.14920     r(3,2) =   0.41358     r(3,3) =  -0.89816 
THE OFFSET VECTOR: 
 v(1) =   3.37325     v(2) = -18.12167     v(3) =  -0.67198 
 
 Number of iteration  2                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.67           (Number of atoms:   15) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    8.13         76   100.0    76     CRMSCA  
     CRN = ALL/NP  . . . . .    0.1069                            CRMSCA  
     WELL ORDERED  . . . . .    8.13         76   100.0    76     CRMSCA  
     NO INTER CONTACTS . . .    8.13         76   100.0    76     CRMSCA  
     SHIFTED CHAIN . . . . .    8.30         70   100.0    70     CRMSCA  
     ALTERNATIVE PARENT  . .    2.37          5   100.0     5     CRMSCA  
     SECONDARY STRUCTURE . .    4.95         27   100.0    27     CRMSCA  
     SHIFTED SS UNITS  . . .    3.00          6   100.0     6     CRMSCA  
     LARGE SHIFTS/INSERTIONS    8.40         32   100.0    32     CRMSCA  
     SURFACE . . . . . . . .    8.25         54   100.0    54     CRMSCA  
     BURIED  . . . . . . . .    7.81         22   100.0    22     CRMSCA  
     CORE  . . . . . . . . .    7.92         44   100.0    44     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    8.21        371   100.0   371     CRMSMC  
     WELL ORDERED  . . . . .    8.21        371   100.0   371     CRMSMC  
     NO INTER CONTACTS . . .    8.21        371   100.0   371     CRMSMC  
     SHIFTED CHAIN . . . . .    8.38        341   100.0   341     CRMSMC  
     ALTERNATIVE PARENT  . .    2.78         25   100.0    25     CRMSMC  
     SECONDARY STRUCTURE . .    4.98        133   100.0   133     CRMSMC  
     SHIFTED SS UNITS  . . .    3.09         30   100.0    30     CRMSMC  
     LARGE SHIFTS/INSERTIONS    8.52        154   100.0   154     CRMSMC  
     SURFACE . . . . . . . .    8.39        264   100.0   264     CRMSMC  
     BURIED  . . . . . . . .    7.76        107   100.0   107     CRMSMC  
     CORE  . . . . . . . . .    7.99        217   100.0   217     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    9.30        284   100.0   284     CRMSSC  
     WELL ORDERED  . . . . .    9.30        284   100.0   284     CRMSSC  
     NO INTER CONTACTS . . .    9.30        284   100.0   284     CRMSSC  
     RELIABLE SIDE CHAINS  .    9.56        240   100.0   240     CRMSSC  
     CHANGED ANGLES  . . . .    9.41        192   100.0   192     CRMSSC  
     SECONDARY STRUCTURE . .    6.23         99   100.0    99     CRMSSC  
     LARGE SHIFTS/INSERTIONS   10.21        112   100.0   112     CRMSSC  
     SURFACE . . . . . . . .    9.59        222   100.0   222     CRMSSC  
     BURIED  . . . . . . . .    8.15         62   100.0    62     CRMSSC  
     CORE  . . . . . . . . .    8.65        172   100.0   172     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    8.67        588   100.0   588     CRMSALL 
     WELL ORDERED  . . . . .    8.67        588   100.0   588     CRMSALL 
     NO INTER CONTACTS . . .    8.67        588   100.0   588     CRMSALL 
     SHIFTED CHAIN . . . . .    8.86        542   100.0   542     CRMSALL 
     ALTERNATIVE PARENT  . .    3.73         45   100.0    45     CRMSALL 
     SECONDARY STRUCTURE . .    5.57        207   100.0   207     CRMSALL 
     LARGE SHIFTS/INSERTIONS    9.24        240   100.0   240     CRMSALL 
     SURFACE . . . . . . . .    8.93        438   100.0   438     CRMSALL 
     BURIED  . . . . . . . .    7.84        150   100.0   150     CRMSALL 
     CORE  . . . . . . . . .    8.25        348   100.0   348     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1    10.29      7   100.0     7       1-AEIEVGR-7    
 CA  LOOP  2     6.29      3   100.0     3      26-GGG-28   
 CA  LOOP  3    10.52     10   100.0    10      40-DKRVEKVTDY-49   
 CA  LOOP  4     2.69      4   100.0     4      65-RQGR-68   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1    10.26     34   100.0    34       1-AEIEVGR-7    
 MC  LOOP  2     5.96     12   100.0    12      26-GGG-28   
 MC  LOOP  3    10.43     50   100.0    50      40-DKRVEKVTDY-49   
 MC  LOOP  4     3.06     19   100.0    19      65-RQGR-68   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1    10.00     53   100.0    53       1-AEIEVGR-7    
 ALL LOOP  2     5.96     12   100.0    12      26-GGG-28   
 ALL LOOP  3    11.81     87   100.0    87      40-DKRVEKVTDY-49   
 ALL LOOP  4     3.82     35   100.0    35      65-RQGR-68   
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     3.19      7   100.0     7       1-AEIEVGR-7    
 CA  LOOP  2     0.39      3   100.0     3      26-GGG-28   
 CA  LOOP  3     3.73     10   100.0    10      40-DKRVEKVTDY-49   
 CA  LOOP  4     0.41      4   100.0     4      65-RQGR-68   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     3.57     34   100.0    34       1-AEIEVGR-7    
 MC  LOOP  2     1.43     12   100.0    12      26-GGG-28   
 MC  LOOP  3     3.90     50   100.0    50      40-DKRVEKVTDY-49   
 MC  LOOP  4     1.18     19   100.0    19      65-RQGR-68   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     4.05     53   100.0    53       1-AEIEVGR-7    
 ALL LOOP  2     1.43     12   100.0    12      26-GGG-28   
 ALL LOOP  3     5.82     87   100.0    87      40-DKRVEKVTDY-49   
 ALL LOOP  4     1.99     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 . . . . . . . . . .    6.696      1.000       0.500     76   100.0    76     ERRCA  
     WELL ORDERED  . . . . .    6.696      1.000       0.500     76   100.0    76     ERRCA  
     NO INTER CONTACTS . . .    6.696      1.000       0.500     76   100.0    76     ERRCA  
     SHIFTED CHAIN . . . . .    6.790      1.000       0.500     70   100.0    70     ERRCA  
     ALTERNATIVE PARENT  . .    2.277      1.000       0.500      5   100.0     5     ERRCA  
     SECONDARY STRUCTURE . .    4.419      1.000       0.500     27   100.0    27     ERRCA  
     LARGE SHIFTS/INSERTIONS    7.016      1.000       0.500     32   100.0    32     ERRCA  
     SURFACE . . . . . . . .    6.969      1.000       0.500     54   100.0    54     ERRCA  
     BURIED  . . . . . . . .    6.026      1.000       0.500     22   100.0    22     ERRCA  
     CORE  . . . . . . . . .    6.464      1.000       0.500     44   100.0    44     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    6.818      1.000       0.500    371   100.0   371     ERRMC  
     WELL ORDERED  . . . . .    6.818      1.000       0.500    371   100.0   371     ERRMC  
     NO INTER CONTACTS . . .    6.818      1.000       0.500    371   100.0   371     ERRMC  
     SHIFTED CHAIN . . . . .    6.901      1.000       0.500    341   100.0   341     ERRMC  
     ALTERNATIVE PARENT  . .    2.539      1.000       0.500     25   100.0    25     ERRMC  
     SECONDARY STRUCTURE . .    4.458      1.000       0.500    133   100.0   133     ERRMC  
     LARGE SHIFTS/INSERTIONS    7.167      1.000       0.500    154   100.0   154     ERRMC  
     SURFACE . . . . . . . .    7.156      1.000       0.500    264   100.0   264     ERRMC  
     BURIED  . . . . . . . .    5.983      1.000       0.500    107   100.0   107     ERRMC  
     CORE  . . . . . . . . .    6.571      1.000       0.500    217   100.0   217     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    8.053      1.000       0.500    284   100.0   284     ERRSC  
     WELL ORDERED  . . . . .    8.053      1.000       0.500    284   100.0   284     ERRSC  
     NO INTER CONTACTS . . .    8.053      1.000       0.500    284   100.0   284     ERRSC  
     RELIABLE SIDE CHAINS  .    8.264      1.000       0.500    240   100.0   240     ERRSC  
     CHANGED ANGLES  . . . .    8.245      1.000       0.500    192   100.0   192     ERRSC  
     SHIFTED CHAIN . . . . .    8.263      1.000       0.500    262   100.0   262     ERRSC  
     ALTERNATIVE PARENT  . .    4.111      1.000       0.500     25   100.0    25     ERRSC  
     SECONDARY STRUCTURE . .    5.666      1.000       0.500     99   100.0    99     ERRSC  
     LARGE SHIFTS/INSERTIONS    8.923      1.000       0.500    112   100.0   112     ERRSC  
     SURFACE . . . . . . . .    8.417      1.000       0.500    222   100.0   222     ERRSC  
     BURIED  . . . . . . . .    6.752      1.000       0.500     62   100.0    62     ERRSC  
     CORE  . . . . . . . . .    7.487      1.000       0.500    172   100.0   172     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    7.335      1.000       0.500    588   100.0   588     ERRALL 
     WELL ORDERED  . . . . .    7.335      1.000       0.500    588   100.0   588     ERRALL 
     NO INTER CONTACTS . . .    7.335      1.000       0.500    588   100.0   588     ERRALL 
     SHIFTED CHAIN . . . . .    7.466      1.000       0.500    542   100.0   542     ERRALL 
     ALTERNATIVE PARENT  . .    3.365      1.000       0.500     45   100.0    45     ERRALL 
     SECONDARY STRUCTURE . .    4.986      1.000       0.500    207   100.0   207     ERRALL 
     LARGE SHIFTS/INSERTIONS    7.873      1.000       0.500    240   100.0   240     ERRALL 
     SURFACE . . . . . . . .    7.710      1.000       0.500    438   100.0   438     ERRALL 
     BURIED  . . . . . . . .    6.240      1.000       0.500    150   100.0   150     ERRALL 
     CORE  . . . . . . . . .    6.964      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        11        16        29        63      76      76   DISTCA 
CA  (P)      1.32     14.47     21.05     38.16     82.89              76   DISTCA 
CA  (RMS)    0.65      1.43      1.75      2.90      5.57                   DISTCA 
 
ALL (N)         6        47        97       204       450     588     588   DISTALL 
ALL (P)      1.02      7.99     16.50     34.69     76.53             588   DISTALL 
ALL (RMS)    0.75      1.48      2.05      3.27      5.69                   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          7.92          8.40          RMSLSI 
 
 
 
END of the results output 
