 
####################################################### 
#                                                     # 
#                        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 645 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 . . . . . . . . . .    76.43           36.7   150   100.0   150     ARMSMC  
     WELL ORDERED  . . . . .    76.43           36.7   150   100.0   150     ARMSMC  
     NO INTER CONTACTS . . .    76.43           36.7   150   100.0   150     ARMSMC  
     SHIFTED CHAIN . . . . .    77.30           36.2   138   100.0   138     ARMSMC  
     ALTERNATIVE PARENT  . .    79.00           10.0    10   100.0    10     ARMSMC  
     SECONDARY STRUCTURE . .    69.10           40.7    54   100.0    54     ARMSMC  
     LARGE SHIFTS/INSERTIONS    87.54           32.3    62   100.0    62     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    78.98           37.7   106   100.0   106     ARMSMC  
     BURIED  . . . . . . . .    69.92           34.1    44   100.0    44     ARMSMC  
     CORE  . . . . . . . . .    67.52           39.8    88   100.0    88     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    79.15           45.2    62   100.0    62     ARMSSC1 
     WELL ORDERED  . . . . .    79.15           45.2    62   100.0    62     ARMSSC1 
     NO INTER CONTACTS . . .    79.15           45.2    62   100.0    62     ARMSSC1 
     RELIABLE SIDE CHAINS  .    81.56           42.0    50   100.0    50     ARMSSC1 
     CHANGED ANGLES  . . . .    82.37           42.9    49   100.0    49     ARMSSC1 
     SHIFTED CHAIN . . . . .    78.73           46.4    56   100.0    56     ARMSSC1 
     ALTERNATIVE PARENT  . .    47.56           80.0     5   100.0     5     ARMSSC1 
     SECONDARY STRUCTURE . .    73.64           52.2    23   100.0    23     ARMSSC1 
     LARGE SHIFTS/INSERTIONS    77.39           34.8    23   100.0    23     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .    80.88           45.7    46   100.0    46     ARMSSC1 
     BURIED  . . . . . . . .    73.98           43.8    16   100.0    16     ARMSSC1 
     CORE  . . . . . . . . .    80.18           51.3    39   100.0    39     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    63.68           37.8    45   100.0    45     ARMSSC2 
     WELL ORDERED  . . . . .    63.68           37.8    45   100.0    45     ARMSSC2 
     NO INTER CONTACTS . . .    63.68           37.8    45   100.0    45     ARMSSC2 
     RELIABLE SIDE CHAINS  .    61.37           40.0    40   100.0    40     ARMSSC2 
     CHANGED ANGLES  . . . .    65.76           36.6    41   100.0    41     ARMSSC2 
     SHIFTED CHAIN . . . . .    65.61           33.3    42   100.0    42     ARMSSC2 
     ALTERNATIVE PARENT  . .    50.56           25.0     4   100.0     4     ARMSSC2 
     SECONDARY STRUCTURE . .    54.26           61.5    13   100.0    13     ARMSSC2 
     LARGE SHIFTS/INSERTIONS    51.26           47.1    17   100.0    17     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .    60.11           39.5    38   100.0    38     ARMSSC2 
     BURIED  . . . . . . . .    80.32           28.6     7   100.0     7     ARMSSC2 
     CORE  . . . . . . . . .    70.15           32.1    28   100.0    28     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    82.10           25.0    24   100.0    24     ARMSSC3 
     WELL ORDERED  . . . . .    82.10           25.0    24   100.0    24     ARMSSC3 
     NO INTER CONTACTS . . .    82.10           25.0    24   100.0    24     ARMSSC3 
     RELIABLE SIDE CHAINS  .    77.32           25.0    20   100.0    20     ARMSSC3 
     CHANGED ANGLES  . . . .    82.10           25.0    24   100.0    24     ARMSSC3 
     SHIFTED CHAIN . . . . .    82.88           26.1    23   100.0    23     ARMSSC3 
     ALTERNATIVE PARENT  . .    95.85            0.0     2   100.0     2     ARMSSC3 
     SECONDARY STRUCTURE . .    64.02           16.7     6   100.0     6     ARMSSC3 
     LARGE SHIFTS/INSERTIONS    96.09           27.3    11   100.0    11     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .    82.10           25.0    24   100.0    24     ARMSSC3 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     CORE  . . . . . . . . .    68.05           23.1    13   100.0    13     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    52.19           25.0    12   100.0    12     ARMSSC4 
     WELL ORDERED  . . . . .    52.19           25.0    12   100.0    12     ARMSSC4 
     NO INTER CONTACTS . . .    52.19           25.0    12   100.0    12     ARMSSC4 
     RELIABLE SIDE CHAINS  .    52.19           25.0    12   100.0    12     ARMSSC4 
     CHANGED ANGLES  . . . .    52.19           25.0    12   100.0    12     ARMSSC4 
     SHIFTED CHAIN . . . . .    51.45           27.3    11   100.0    11     ARMSSC4 
     ALTERNATIVE PARENT  . .    43.49           50.0     2   100.0     2     ARMSSC4 
     SECONDARY STRUCTURE . .    46.14            0.0     4   100.0     4     ARMSSC4 
     LARGE SHIFTS/INSERTIONS    49.41           33.3     6   100.0     6     ARMSSC4 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SURFACE . . . . . . . .    52.19           25.0    12   100.0    12     ARMSSC4 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     CORE  . . . . . . . . .    54.82           16.7     6   100.0     6     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =  -0.76598     r(1,2) =  -0.08432     r(1,3) =  -0.63731 
 r(2,1) =  -0.20535     r(2,2) =  -0.90733     r(2,3) =   0.36686 
 r(3,1) =  -0.60919     r(3,2) =   0.41188     r(3,3) =   0.67768 
THE OFFSET VECTOR: 
 v(1) =  21.53833     v(2) =  17.79066     v(3) =  -2.95507 
 
 Number of iteration 36                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.39           (Number of atoms:   25) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    8.17         76   100.0    76     CRMSCA  
     CRN = ALL/NP  . . . . .    0.1074                            CRMSCA  
     WELL ORDERED  . . . . .    8.17         76   100.0    76     CRMSCA  
     NO INTER CONTACTS . . .    8.17         76   100.0    76     CRMSCA  
     SHIFTED CHAIN . . . . .    7.88         70   100.0    70     CRMSCA  
     ALTERNATIVE PARENT  . .    8.41          5   100.0     5     CRMSCA  
     SECONDARY STRUCTURE . .    8.65         27   100.0    27     CRMSCA  
     SHIFTED SS UNITS  . . .    1.14          6   100.0     6     CRMSCA  
     LARGE SHIFTS/INSERTIONS    9.66         32   100.0    32     CRMSCA  
     SURFACE . . . . . . . .    8.71         54   100.0    54     CRMSCA  
     BURIED  . . . . . . . .    6.65         22   100.0    22     CRMSCA  
     CORE  . . . . . . . . .    6.88         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 . . . . .    7.92        341   100.0   341     CRMSMC  
     ALTERNATIVE PARENT  . .    8.25         25   100.0    25     CRMSMC  
     SECONDARY STRUCTURE . .    8.72        133   100.0   133     CRMSMC  
     SHIFTED SS UNITS  . . .    1.24         30   100.0    30     CRMSMC  
     LARGE SHIFTS/INSERTIONS    9.68        154   100.0   154     CRMSMC  
     SURFACE . . . . . . . .    8.70        264   100.0   264     CRMSMC  
     BURIED  . . . . . . . .    6.88        107   100.0   107     CRMSMC  
     CORE  . . . . . . . . .    6.99        217   100.0   217     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    9.97        284   100.0   284     CRMSSC  
     WELL ORDERED  . . . . .    9.97        284   100.0   284     CRMSSC  
     NO INTER CONTACTS . . .    9.97        284   100.0   284     CRMSSC  
     RELIABLE SIDE CHAINS  .   10.33        240   100.0   240     CRMSSC  
     CHANGED ANGLES  . . . .   10.53        192   100.0   192     CRMSSC  
     SECONDARY STRUCTURE . .   11.33         99   100.0    99     CRMSSC  
     LARGE SHIFTS/INSERTIONS   10.82        112   100.0   112     CRMSSC  
     SURFACE . . . . . . . .   10.31        222   100.0   222     CRMSSC  
     BURIED  . . . . . . . .    8.65         62   100.0    62     CRMSSC  
     CORE  . . . . . . . . .    9.38        172   100.0   172     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    9.04        588   100.0   588     CRMSALL 
     WELL ORDERED  . . . . .    9.04        588   100.0   588     CRMSALL 
     NO INTER CONTACTS . . .    9.04        588   100.0   588     CRMSALL 
     SHIFTED CHAIN . . . . .    8.75        542   100.0   542     CRMSALL 
     ALTERNATIVE PARENT  . .    9.84         45   100.0    45     CRMSALL 
     SECONDARY STRUCTURE . .   10.00        207   100.0   207     CRMSALL 
     LARGE SHIFTS/INSERTIONS   10.15        240   100.0   240     CRMSALL 
     SURFACE . . . . . . . .    9.47        438   100.0   438     CRMSALL 
     BURIED  . . . . . . . .    7.66        150   100.0   150     CRMSALL 
     CORE  . . . . . . . . .    8.19        348   100.0   348     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1    16.52      7   100.0     7       1-AEIEVGR-7    
 CA  LOOP  2     5.49      3   100.0     3      26-GGG-28   
 CA  LOOP  3     7.84     10   100.0    10      40-DKRVEKVTDY-49   
 CA  LOOP  4     5.03      4   100.0     4      65-RQGR-68   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1    16.36     34   100.0    34       1-AEIEVGR-7    
 MC  LOOP  2     5.32     12   100.0    12      26-GGG-28   
 MC  LOOP  3     7.94     50   100.0    50      40-DKRVEKVTDY-49   
 MC  LOOP  4     5.18     19   100.0    19      65-RQGR-68   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1    16.38     53   100.0    53       1-AEIEVGR-7    
 ALL LOOP  2     5.32     12   100.0    12      26-GGG-28   
 ALL LOOP  3     9.20     87   100.0    87      40-DKRVEKVTDY-49   
 ALL LOOP  4     4.99     35   100.0    35      65-RQGR-68   
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     2.15      7   100.0     7       1-AEIEVGR-7    
 CA  LOOP  2     0.52      3   100.0     3      26-GGG-28   
 CA  LOOP  3     3.77     10   100.0    10      40-DKRVEKVTDY-49   
 CA  LOOP  4     0.81      4   100.0     4      65-RQGR-68   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     2.72     34   100.0    34       1-AEIEVGR-7    
 MC  LOOP  2     1.70     12   100.0    12      26-GGG-28   
 MC  LOOP  3     4.03     50   100.0    50      40-DKRVEKVTDY-49   
 MC  LOOP  4     1.40     19   100.0    19      65-RQGR-68   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     4.99     53   100.0    53       1-AEIEVGR-7    
 ALL LOOP  2     1.70     12   100.0    12      26-GGG-28   
 ALL LOOP  3     6.78     87   100.0    87      40-DKRVEKVTDY-49   
 ALL LOOP  4     2.16     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 . . . . . . . . . .    4.356      0.400       0.263     76   100.0    76     ERRCA  
     WELL ORDERED  . . . . .    4.356      0.400       0.263     76   100.0    76     ERRCA  
     NO INTER CONTACTS . . .    4.356      0.400       0.263     76   100.0    76     ERRCA  
     SHIFTED CHAIN . . . . .    4.129      0.393       0.265     70   100.0    70     ERRCA  
     ALTERNATIVE PARENT  . .    4.389      0.357       0.197      5   100.0     5     ERRCA  
     SECONDARY STRUCTURE . .    5.121      0.465       0.290     27   100.0    27     ERRCA  
     LARGE SHIFTS/INSERTIONS    5.437      0.394       0.200     32   100.0    32     ERRCA  
     SURFACE . . . . . . . .    4.569      0.381       0.244     54   100.0    54     ERRCA  
     BURIED  . . . . . . . .    3.831      0.447       0.310     22   100.0    22     ERRCA  
     CORE  . . . . . . . . .    3.569      0.405       0.309     44   100.0    44     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    4.374      0.391       0.251    371   100.0   371     ERRMC  
     WELL ORDERED  . . . . .    4.374      0.391       0.251    371   100.0   371     ERRMC  
     NO INTER CONTACTS . . .    4.374      0.391       0.251    371   100.0   371     ERRMC  
     SHIFTED CHAIN . . . . .    4.140      0.383       0.252    341   100.0   341     ERRMC  
     ALTERNATIVE PARENT  . .    4.394      0.386       0.239     25   100.0    25     ERRMC  
     SECONDARY STRUCTURE . .    5.202      0.468       0.296    133   100.0   133     ERRMC  
     LARGE SHIFTS/INSERTIONS    5.487      0.401       0.208    154   100.0   154     ERRMC  
     SURFACE . . . . . . . .    4.574      0.380       0.236    264   100.0   264     ERRMC  
     BURIED  . . . . . . . .    3.882      0.420       0.288    107   100.0   107     ERRMC  
     CORE  . . . . . . . . .    3.585      0.384       0.281    217   100.0   217     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    5.752      0.426       0.239    284   100.0   284     ERRSC  
     WELL ORDERED  . . . . .    5.752      0.426       0.239    284   100.0   284     ERRSC  
     NO INTER CONTACTS . . .    5.752      0.426       0.239    284   100.0   284     ERRSC  
     RELIABLE SIDE CHAINS  .    6.072      0.439       0.245    240   100.0   240     ERRSC  
     CHANGED ANGLES  . . . .    6.241      0.443       0.238    192   100.0   192     ERRSC  
     SHIFTED CHAIN . . . . .    5.470      0.415       0.235    262   100.0   262     ERRSC  
     ALTERNATIVE PARENT  . .    6.388      0.440       0.258     25   100.0    25     ERRSC  
     SECONDARY STRUCTURE . .    7.084      0.494       0.280     99   100.0    99     ERRSC  
     LARGE SHIFTS/INSERTIONS    6.710      0.466       0.245    112   100.0   112     ERRSC  
     SURFACE . . . . . . . .    5.917      0.423       0.234    222   100.0   222     ERRSC  
     BURIED  . . . . . . . .    5.159      0.436       0.255     62   100.0    62     ERRSC  
     CORE  . . . . . . . . .    5.128      0.400       0.234    172   100.0   172     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    4.986      0.406       0.245    588   100.0   588     ERRALL 
     WELL ORDERED  . . . . .    4.986      0.406       0.245    588   100.0   588     ERRALL 
     NO INTER CONTACTS . . .    4.986      0.406       0.245    588   100.0   588     ERRALL 
     SHIFTED CHAIN . . . . .    4.738      0.397       0.243    542   100.0   542     ERRALL 
     ALTERNATIVE PARENT  . .    5.460      0.412       0.245     45   100.0    45     ERRALL 
     SECONDARY STRUCTURE . .    6.063      0.480       0.288    207   100.0   207     ERRALL 
     LARGE SHIFTS/INSERTIONS    5.993      0.428       0.223    240   100.0   240     ERRALL 
     SURFACE . . . . . . . .    5.184      0.399       0.234    438   100.0   438     ERRALL 
     BURIED  . . . . . . . .    4.407      0.428       0.277    150   100.0   150     ERRALL 
     CORE  . . . . . . . . .    4.291      0.391       0.259    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)         9        20        25        32        57      76      76   DISTCA 
CA  (P)     11.84     26.32     32.89     42.11     75.00              76   DISTCA 
CA  (RMS)    0.75      1.12      1.39      2.21      4.52                   DISTCA 
 
ALL (N)        39       119       169       244       421     588     588   DISTALL 
ALL (P)      6.63     20.24     28.74     41.50     71.60             588   DISTALL 
ALL (RMS)    0.76      1.28      1.72      2.67      4.99                   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          6.88          9.66          RMSLSI 
 
 
 
END of the results output 
