 
####################################################### 
#                                                     # 
#                        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 646 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 . . . . . . . . . .    74.88           44.0   150   100.0   150     ARMSMC  
     WELL ORDERED  . . . . .    74.88           44.0   150   100.0   150     ARMSMC  
     NO INTER CONTACTS . . .    74.88           44.0   150   100.0   150     ARMSMC  
     SHIFTED CHAIN . . . . .    77.36           42.0   138   100.0   138     ARMSMC  
     ALTERNATIVE PARENT  . .    87.68            0.0    10   100.0    10     ARMSMC  
     SECONDARY STRUCTURE . .    59.10           61.1    54   100.0    54     ARMSMC  
     LARGE SHIFTS/INSERTIONS    97.02           16.1    62   100.0    62     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    79.12           39.6   106   100.0   106     ARMSMC  
     BURIED  . . . . . . . .    63.51           54.5    44   100.0    44     ARMSMC  
     CORE  . . . . . . . . .    54.09           63.6    88   100.0    88     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    98.40           29.0    62   100.0    62     ARMSSC1 
     WELL ORDERED  . . . . .    98.40           29.0    62   100.0    62     ARMSSC1 
     NO INTER CONTACTS . . .    98.40           29.0    62   100.0    62     ARMSSC1 
     RELIABLE SIDE CHAINS  .    98.01           30.0    50   100.0    50     ARMSSC1 
     CHANGED ANGLES  . . . .   106.16           20.4    49   100.0    49     ARMSSC1 
     SHIFTED CHAIN . . . . .    98.57           30.4    56   100.0    56     ARMSSC1 
     ALTERNATIVE PARENT  . .   102.97           20.0     5   100.0     5     ARMSSC1 
     SECONDARY STRUCTURE . .    99.12           21.7    23   100.0    23     ARMSSC1 
     LARGE SHIFTS/INSERTIONS   104.89           21.7    23   100.0    23     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .   100.03           28.3    46   100.0    46     ARMSSC1 
     BURIED  . . . . . . . .    93.55           31.2    16   100.0    16     ARMSSC1 
     CORE  . . . . . . . . .    94.37           33.3    39   100.0    39     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    78.14           33.3    45   100.0    45     ARMSSC2 
     WELL ORDERED  . . . . .    78.14           33.3    45   100.0    45     ARMSSC2 
     NO INTER CONTACTS . . .    78.14           33.3    45   100.0    45     ARMSSC2 
     RELIABLE SIDE CHAINS  .    72.53           35.0    40   100.0    40     ARMSSC2 
     CHANGED ANGLES  . . . .    76.92           34.1    41   100.0    41     ARMSSC2 
     SHIFTED CHAIN . . . . .    76.56           33.3    42   100.0    42     ARMSSC2 
     ALTERNATIVE PARENT  . .    69.65           25.0     4   100.0     4     ARMSSC2 
     SECONDARY STRUCTURE . .    86.87           23.1    13   100.0    13     ARMSSC2 
     LARGE SHIFTS/INSERTIONS    83.75           35.3    17   100.0    17     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .    77.63           31.6    38   100.0    38     ARMSSC2 
     BURIED  . . . . . . . .    80.88           42.9     7   100.0     7     ARMSSC2 
     CORE  . . . . . . . . .    74.53           32.1    28   100.0    28     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    91.62           16.7    24   100.0    24     ARMSSC3 
     WELL ORDERED  . . . . .    91.62           16.7    24   100.0    24     ARMSSC3 
     NO INTER CONTACTS . . .    91.62           16.7    24   100.0    24     ARMSSC3 
     RELIABLE SIDE CHAINS  .    88.85           20.0    20   100.0    20     ARMSSC3 
     CHANGED ANGLES  . . . .    91.62           16.7    24   100.0    24     ARMSSC3 
     SHIFTED CHAIN . . . . .    87.93           17.4    23   100.0    23     ARMSSC3 
     ALTERNATIVE PARENT  . .   119.73           50.0     2   100.0     2     ARMSSC3 
     SECONDARY STRUCTURE . .   111.31            0.0     6   100.0     6     ARMSSC3 
     LARGE SHIFTS/INSERTIONS    77.14           27.3    11   100.0    11     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .    91.62           16.7    24   100.0    24     ARMSSC3 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     CORE  . . . . . . . . .   102.28            7.7    13   100.0    13     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    70.65           25.0    12   100.0    12     ARMSSC4 
     WELL ORDERED  . . . . .    70.65           25.0    12   100.0    12     ARMSSC4 
     NO INTER CONTACTS . . .    70.65           25.0    12   100.0    12     ARMSSC4 
     RELIABLE SIDE CHAINS  .    70.65           25.0    12   100.0    12     ARMSSC4 
     CHANGED ANGLES  . . . .    70.65           25.0    12   100.0    12     ARMSSC4 
     SHIFTED CHAIN . . . . .    73.05           27.3    11   100.0    11     ARMSSC4 
     ALTERNATIVE PARENT  . .    57.76           50.0     2   100.0     2     ARMSSC4 
     SECONDARY STRUCTURE . .    39.50           25.0     4   100.0     4     ARMSSC4 
     LARGE SHIFTS/INSERTIONS    72.04           33.3     6   100.0     6     ARMSSC4 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SURFACE . . . . . . . .    70.65           25.0    12   100.0    12     ARMSSC4 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     CORE  . . . . . . . . .    69.23           16.7     6   100.0     6     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =  -0.94726     r(1,2) =  -0.30434     r(1,3) =  -0.10038 
 r(2,1) =   0.32017     r(2,2) =  -0.88533     r(2,3) =  -0.33718 
 r(3,1) =   0.01375     r(3,2) =  -0.35153     r(3,3) =   0.93608 
THE OFFSET VECTOR: 
 v(1) =  35.61049     v(2) =  23.57507     v(3) = -18.83231 
 
 Number of iteration 46                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.31           (Number of atoms:   34) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    7.81         76   100.0    76     CRMSCA  
     CRN = ALL/NP  . . . . .    0.1027                            CRMSCA  
     WELL ORDERED  . . . . .    7.81         76   100.0    76     CRMSCA  
     NO INTER CONTACTS . . .    7.81         76   100.0    76     CRMSCA  
     SHIFTED CHAIN . . . . .    8.11         70   100.0    70     CRMSCA  
     ALTERNATIVE PARENT  . .    3.53          5   100.0     5     CRMSCA  
     SECONDARY STRUCTURE . .    2.90         27   100.0    27     CRMSCA  
     SHIFTED SS UNITS  . . .    0.96          6   100.0     6     CRMSCA  
     LARGE SHIFTS/INSERTIONS   11.57         32   100.0    32     CRMSCA  
     SURFACE . . . . . . . .    8.89         54   100.0    54     CRMSCA  
     BURIED  . . . . . . . .    4.08         22   100.0    22     CRMSCA  
     CORE  . . . . . . . . .    2.81         44   100.0    44     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    7.77        371   100.0   371     CRMSMC  
     WELL ORDERED  . . . . .    7.77        371   100.0   371     CRMSMC  
     NO INTER CONTACTS . . .    7.77        371   100.0   371     CRMSMC  
     SHIFTED CHAIN . . . . .    8.08        341   100.0   341     CRMSMC  
     ALTERNATIVE PARENT  . .    3.81         25   100.0    25     CRMSMC  
     SECONDARY STRUCTURE . .    3.01        133   100.0   133     CRMSMC  
     SHIFTED SS UNITS  . . .    1.05         30   100.0    30     CRMSMC  
     LARGE SHIFTS/INSERTIONS   11.53        154   100.0   154     CRMSMC  
     SURFACE . . . . . . . .    8.81        264   100.0   264     CRMSMC  
     BURIED  . . . . . . . .    4.21        107   100.0   107     CRMSMC  
     CORE  . . . . . . . . .    2.98        217   100.0   217     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    9.01        284   100.0   284     CRMSSC  
     WELL ORDERED  . . . . .    9.01        284   100.0   284     CRMSSC  
     NO INTER CONTACTS . . .    9.01        284   100.0   284     CRMSSC  
     RELIABLE SIDE CHAINS  .    9.48        240   100.0   240     CRMSSC  
     CHANGED ANGLES  . . . .    9.64        192   100.0   192     CRMSSC  
     SECONDARY STRUCTURE . .    4.58         99   100.0    99     CRMSSC  
     LARGE SHIFTS/INSERTIONS   13.12        112   100.0   112     CRMSSC  
     SURFACE . . . . . . . .    9.77        222   100.0   222     CRMSSC  
     BURIED  . . . . . . . .    5.50         62   100.0    62     CRMSSC  
     CORE  . . . . . . . . .    4.69        172   100.0   172     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    8.32        588   100.0   588     CRMSALL 
     WELL ORDERED  . . . . .    8.32        588   100.0   588     CRMSALL 
     NO INTER CONTACTS . . .    8.32        588   100.0   588     CRMSALL 
     SHIFTED CHAIN . . . . .    8.63        542   100.0   542     CRMSALL 
     ALTERNATIVE PARENT  . .    7.15         45   100.0    45     CRMSALL 
     SECONDARY STRUCTURE . .    3.81        207   100.0   207     CRMSALL 
     LARGE SHIFTS/INSERTIONS   12.15        240   100.0   240     CRMSALL 
     SURFACE . . . . . . . .    9.24        438   100.0   438     CRMSALL 
     BURIED  . . . . . . . .    4.68        150   100.0   150     CRMSALL 
     CORE  . . . . . . . . .    3.88        348   100.0   348     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1    22.01      7   100.0     7       1-AEIEVGR-7    
 CA  LOOP  2     6.32      3   100.0     3      26-GGG-28   
 CA  LOOP  3     7.77     10   100.0    10      40-DKRVEKVTDY-49   
 CA  LOOP  4     3.91      4   100.0     4      65-RQGR-68   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1    21.75     34   100.0    34       1-AEIEVGR-7    
 MC  LOOP  2     6.15     12   100.0    12      26-GGG-28   
 MC  LOOP  3     7.78     50   100.0    50      40-DKRVEKVTDY-49   
 MC  LOOP  4     3.99     19   100.0    19      65-RQGR-68   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1    21.33     53   100.0    53       1-AEIEVGR-7    
 ALL LOOP  2     6.15     12   100.0    12      26-GGG-28   
 ALL LOOP  3     9.69     87   100.0    87      40-DKRVEKVTDY-49   
 ALL LOOP  4     6.65     35   100.0    35      65-RQGR-68   
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     2.13      7   100.0     7       1-AEIEVGR-7    
 CA  LOOP  2     0.21      3   100.0     3      26-GGG-28   
 CA  LOOP  3     3.64     10   100.0    10      40-DKRVEKVTDY-49   
 CA  LOOP  4     1.24      4   100.0     4      65-RQGR-68   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     2.40     34   100.0    34       1-AEIEVGR-7    
 MC  LOOP  2     1.55     12   100.0    12      26-GGG-28   
 MC  LOOP  3     3.96     50   100.0    50      40-DKRVEKVTDY-49   
 MC  LOOP  4     1.90     19   100.0    19      65-RQGR-68   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     3.36     53   100.0    53       1-AEIEVGR-7    
 ALL LOOP  2     1.55     12   100.0    12      26-GGG-28   
 ALL LOOP  3     6.17     87   100.0    87      40-DKRVEKVTDY-49   
 ALL LOOP  4     4.76     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 . . . . . . . . . .    3.484      0.382       0.330     76   100.0    76     ERRCA  
     WELL ORDERED  . . . . .    3.484      0.382       0.330     76   100.0    76     ERRCA  
     NO INTER CONTACTS . . .    3.484      0.382       0.330     76   100.0    76     ERRCA  
     SHIFTED CHAIN . . . . .    3.550      0.373       0.311     70   100.0    70     ERRCA  
     ALTERNATIVE PARENT  . .    1.112      0.158       0.161      5   100.0     5     ERRCA  
     SECONDARY STRUCTURE . .    2.172      0.393       0.384     27   100.0    27     ERRCA  
     LARGE SHIFTS/INSERTIONS    5.300      0.347       0.232     32   100.0    32     ERRCA  
     SURFACE . . . . . . . .    3.996      0.388       0.323     54   100.0    54     ERRCA  
     BURIED  . . . . . . . .    2.226      0.367       0.347     22   100.0    22     ERRCA  
     CORE  . . . . . . . . .    2.163      0.407       0.401     44   100.0    44     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    3.440      0.372       0.319    371   100.0   371     ERRMC  
     WELL ORDERED  . . . . .    3.440      0.372       0.319    371   100.0   371     ERRMC  
     NO INTER CONTACTS . . .    3.440      0.372       0.319    371   100.0   371     ERRMC  
     SHIFTED CHAIN . . . . .    3.522      0.367       0.306    341   100.0   341     ERRMC  
     ALTERNATIVE PARENT  . .    1.494      0.221       0.211     25   100.0    25     ERRMC  
     SECONDARY STRUCTURE . .    2.160      0.388       0.365    133   100.0   133     ERRMC  
     LARGE SHIFTS/INSERTIONS    5.302      0.352       0.242    154   100.0   154     ERRMC  
     SURFACE . . . . . . . .    3.954      0.381       0.315    264   100.0   264     ERRMC  
     BURIED  . . . . . . . .    2.170      0.350       0.327    107   100.0   107     ERRMC  
     CORE  . . . . . . . . .    2.118      0.386       0.373    217   100.0   217     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    3.951      0.337       0.251    284   100.0   284     ERRSC  
     WELL ORDERED  . . . . .    3.951      0.337       0.251    284   100.0   284     ERRSC  
     NO INTER CONTACTS . . .    3.951      0.337       0.251    284   100.0   284     ERRSC  
     RELIABLE SIDE CHAINS  .    4.253      0.347       0.259    240   100.0   240     ERRSC  
     CHANGED ANGLES  . . . .    4.294      0.330       0.236    192   100.0   192     ERRSC  
     SHIFTED CHAIN . . . . .    4.037      0.331       0.238    262   100.0   262     ERRSC  
     ALTERNATIVE PARENT  . .    4.276      0.309       0.166     25   100.0    25     ERRSC  
     SECONDARY STRUCTURE . .    2.304      0.323       0.268     99   100.0    99     ERRSC  
     LARGE SHIFTS/INSERTIONS    6.437      0.349       0.211    112   100.0   112     ERRSC  
     SURFACE . . . . . . . .    4.296      0.334       0.243    222   100.0   222     ERRSC  
     BURIED  . . . . . . . .    2.714      0.347       0.278     62   100.0    62     ERRSC  
     CORE  . . . . . . . . .    2.332      0.328       0.277    172   100.0   172     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    3.662      0.357       0.289    588   100.0   588     ERRALL 
     WELL ORDERED  . . . . .    3.662      0.357       0.289    588   100.0   588     ERRALL 
     NO INTER CONTACTS . . .    3.662      0.357       0.289    588   100.0   588     ERRALL 
     SHIFTED CHAIN . . . . .    3.747      0.352       0.276    542   100.0   542     ERRALL 
     ALTERNATIVE PARENT  . .    3.045      0.276       0.198     45   100.0    45     ERRALL 
     SECONDARY STRUCTURE . .    2.234      0.362       0.325    207   100.0   207     ERRALL 
     LARGE SHIFTS/INSERTIONS    5.772      0.355       0.232    240   100.0   240     ERRALL 
     SURFACE . . . . . . . .    4.110      0.359       0.281    438   100.0   438     ERRALL 
     BURIED  . . . . . . . .    2.355      0.351       0.312    150   100.0   150     ERRALL 
     CORE  . . . . . . . . .    2.207      0.359       0.328    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)        13        31        35        56        68      76      76   DISTCA 
CA  (P)     17.11     40.79     46.05     73.68     89.47              76   DISTCA 
CA  (RMS)    0.69      1.21      1.37      2.84      3.87                   DISTCA 
 
ALL (N)        73       177       240       371       502     588     588   DISTALL 
ALL (P)     12.41     30.10     40.82     63.10     85.37             588   DISTALL 
ALL (RMS)    0.73      1.22      1.66      2.76      4.33                   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          2.81         11.57          RMSLSI 
 
 
 
END of the results output 
