 
####################################################### 
#                                                     # 
#                        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 418 atoms, 378 common with TARGET 
           Number of atoms possible to evaluate: 344 
 
 
 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 . . . . . . . . . .    84.74           35.8   134    89.3   150     ARMSMC  
     WELL ORDERED  . . . . .    84.74           35.8   134    89.3   150     ARMSMC  
     NO INTER CONTACTS . . .    84.74           35.8   134    89.3   150     ARMSMC  
     SHIFTED CHAIN . . . . .    85.09           35.2   122    88.4   138     ARMSMC  
     ALTERNATIVE PARENT  . .    83.79           42.9     7    70.0    10     ARMSMC  
     SECONDARY STRUCTURE . .    84.49           28.6    49    90.7    54     ARMSMC  
     LARGE SHIFTS/INSERTIONS    82.67           38.9    54    87.1    62     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    86.55           37.2    94    88.7   106     ARMSMC  
     BURIED  . . . . . . . .    80.32           32.5    40    90.9    44     ARMSMC  
     CORE  . . . . . . . . .    86.10           33.8    80    90.9    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) =  -0.22508     r(1,2) =  -0.20951     r(1,3) =  -0.95155 
 r(2,1) =   0.29908     r(2,2) =   0.91460     r(2,3) =  -0.27212 
 r(3,1) =   0.92730     r(3,2) =  -0.34584     r(3,3) =  -0.14320 
THE OFFSET VECTOR: 
 v(1) =  19.49637     v(2) = -25.97589     v(3) = -21.44427 
 
 Number of iteration  3                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.61           (Number of atoms:    4) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .   12.98         71    93.4    76     CRMSCA  
     CRN = ALL/NP  . . . . .    0.1829                            CRMSCA  
     WELL ORDERED  . . . . .   12.98         71    93.4    76     CRMSCA  
     NO INTER CONTACTS . . .   12.98         71    93.4    76     CRMSCA  
     SHIFTED CHAIN . . . . .   12.90         65    92.9    70     CRMSCA  
     ALTERNATIVE PARENT  . .   16.54          4    80.0     5     CRMSCA  
     SECONDARY STRUCTURE . .   12.68         26    96.3    27     CRMSCA  
     SHIFTED SS UNITS  . . .   15.82          6   100.0     6     CRMSCA  
     LARGE SHIFTS/INSERTIONS   12.72         29    90.6    32     CRMSCA  
     SURFACE . . . . . . . .   13.72         50    92.6    54     CRMSCA  
     BURIED  . . . . . . . .   11.05         21    95.5    22     CRMSCA  
     CORE  . . . . . . . . .   13.16         42    95.5    44     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .   13.12        344    92.7   371     CRMSMC  
     WELL ORDERED  . . . . .   13.12        344    92.7   371     CRMSMC  
     NO INTER CONTACTS . . .   13.12        344    92.7   371     CRMSMC  
     SHIFTED CHAIN . . . . .   13.02        314    92.1   341     CRMSMC  
     ALTERNATIVE PARENT  . .   16.17         20    80.0    25     CRMSMC  
     SECONDARY STRUCTURE . .   12.66        126    94.7   133     CRMSMC  
     SHIFTED SS UNITS  . . .   15.53         29    96.7    30     CRMSMC  
     LARGE SHIFTS/INSERTIONS   12.92        138    89.6   154     CRMSMC  
     SURFACE . . . . . . . .   13.89        242    91.7   264     CRMSMC  
     BURIED  . . . . . . . .   11.10        102    95.3   107     CRMSMC  
     CORE  . . . . . . . . .   13.26        206    94.9   217     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .   13.66         60    21.1   284     CRMSSC  
     WELL ORDERED  . . . . .   13.66         60    21.1   284     CRMSSC  
     NO INTER CONTACTS . . .   13.66         60    21.1   284     CRMSSC  
     RELIABLE SIDE CHAINS  .   13.66         60    25.0   240     CRMSSC  
     CHANGED ANGLES  . . . .    0.00          0     0.0   192     CRMSSC  
     SECONDARY STRUCTURE . .   13.15         22    22.2    99     CRMSSC  
     LARGE SHIFTS/INSERTIONS   13.55         22    19.6   112     CRMSSC  
     SURFACE . . . . . . . .   14.51         42    18.9   222     CRMSSC  
     BURIED  . . . . . . . .   11.43         18    29.0    62     CRMSSC  
     CORE  . . . . . . . . .   13.73         38    22.1   172     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .   13.12        344    58.5   588     CRMSALL 
     WELL ORDERED  . . . . .   13.12        344    58.5   588     CRMSALL 
     NO INTER CONTACTS . . .   13.12        344    58.5   588     CRMSALL 
     SHIFTED CHAIN . . . . .   13.02        314    57.9   542     CRMSALL 
     ALTERNATIVE PARENT  . .   16.17         20    44.4    45     CRMSALL 
     SECONDARY STRUCTURE . .   12.66        126    60.9   207     CRMSALL 
     LARGE SHIFTS/INSERTIONS   12.92        138    57.5   240     CRMSALL 
     SURFACE . . . . . . . .   13.89        242    55.3   438     CRMSALL 
     BURIED  . . . . . . . .   11.10        102    68.0   150     CRMSALL 
     CORE  . . . . . . . . .   13.26        206    59.2   348     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     5.89      5    71.4     7       1-AEIEVGR-7    
 CA  LOOP  2     5.93      3   100.0     3      26-GGG-28   
 CA  LOOP  3    10.85     10   100.0    10      40-DKRVEKVTDY-49   
 CA  LOOP  4    24.59      4   100.0     4      65-RQGR-68   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     5.97     23    67.6    34       1-AEIEVGR-7    
 MC  LOOP  2     5.30     12   100.0    12      26-GGG-28   
 MC  LOOP  3    11.10     50   100.0    50      40-DKRVEKVTDY-49   
 MC  LOOP  4    24.58     19   100.0    19      65-RQGR-68   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     5.97     23    43.4    53       1-AEIEVGR-7    
 ALL LOOP  2     5.30     12   100.0    12      26-GGG-28   
 ALL LOOP  3    11.10     50    57.5    87      40-DKRVEKVTDY-49   
 ALL LOOP  4    24.58     19    54.3    35      65-RQGR-68   
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     1.70      5    71.4     7       1-AEIEVGR-7    
 CA  LOOP  2     0.08      3   100.0     3      26-GGG-28   
 CA  LOOP  3     3.74     10   100.0    10      40-DKRVEKVTDY-49   
 CA  LOOP  4     1.75      4   100.0     4      65-RQGR-68   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     2.30     23    67.6    34       1-AEIEVGR-7    
 MC  LOOP  2     1.14     12   100.0    12      26-GGG-28   
 MC  LOOP  3     3.86     50   100.0    50      40-DKRVEKVTDY-49   
 MC  LOOP  4     2.39     19   100.0    19      65-RQGR-68   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     2.30     23    43.4    53       1-AEIEVGR-7    
 ALL LOOP  2     1.14     12   100.0    12      26-GGG-28   
 ALL LOOP  3     3.86     50    57.5    87      40-DKRVEKVTDY-49   
 ALL LOOP  4     2.39     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 . . . . . . . . . .   11.226      1.000       0.500     71    93.4    76     ERRCA  
     WELL ORDERED  . . . . .   11.226      1.000       0.500     71    93.4    76     ERRCA  
     NO INTER CONTACTS . . .   11.226      1.000       0.500     71    93.4    76     ERRCA  
     SHIFTED CHAIN . . . . .   11.007      1.000       0.500     65    92.9    70     ERRCA  
     ALTERNATIVE PARENT  . .   13.585      1.000       0.500      4    80.0     5     ERRCA  
     SECONDARY STRUCTURE . .   11.555      1.000       0.500     26    96.3    27     ERRCA  
     LARGE SHIFTS/INSERTIONS   10.422      1.000       0.500     29    90.6    32     ERRCA  
     SURFACE . . . . . . . .   11.848      1.000       0.500     50    92.6    54     ERRCA  
     BURIED  . . . . . . . .    9.746      1.000       0.500     21    95.5    22     ERRCA  
     CORE  . . . . . . . . .   11.781      1.000       0.500     42    95.5    44     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   11.358      1.000       0.500    344    92.7   371     ERRMC  
     WELL ORDERED  . . . . .   11.358      1.000       0.500    344    92.7   371     ERRMC  
     NO INTER CONTACTS . . .   11.358      1.000       0.500    344    92.7   371     ERRMC  
     SHIFTED CHAIN . . . . .   11.113      1.000       0.500    314    92.1   341     ERRMC  
     ALTERNATIVE PARENT  . .   13.288      1.000       0.500     20    80.0    25     ERRMC  
     SECONDARY STRUCTURE . .   11.483      1.000       0.500    126    94.7   133     ERRMC  
     LARGE SHIFTS/INSERTIONS   10.575      1.000       0.500    138    89.6   154     ERRMC  
     SURFACE . . . . . . . .   12.054      1.000       0.500    242    91.7   264     ERRMC  
     BURIED  . . . . . . . .    9.707      1.000       0.500    102    95.3   107     ERRMC  
     CORE  . . . . . . . . .   11.882      1.000       0.500    206    94.9   217     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   12.005      1.000       0.500     60    21.1   284     ERRSC  
     WELL ORDERED  . . . . .   12.005      1.000       0.500     60    21.1   284     ERRSC  
     NO INTER CONTACTS . . .   12.005      1.000       0.500     60    21.1   284     ERRSC  
     RELIABLE SIDE CHAINS  .   12.005      1.000       0.500     60    25.0   240     ERRSC  
     CHANGED ANGLES  . . . .    0.000      0.000       0.000      0     0.0   192     ERRSC  
     SHIFTED CHAIN . . . . .   11.828      1.000       0.500     54    20.6   262     ERRSC  
     ALTERNATIVE PARENT  . .   13.199      1.000       0.500      4    16.0    25     ERRSC  
     SECONDARY STRUCTURE . .   12.074      1.000       0.500     22    22.2    99     ERRSC  
     LARGE SHIFTS/INSERTIONS   11.173      1.000       0.500     22    19.6   112     ERRSC  
     SURFACE . . . . . . . .   12.878      1.000       0.500     42    18.9   222     ERRSC  
     BURIED  . . . . . . . .    9.967      1.000       0.500     18    29.0    62     ERRSC  
     CORE  . . . . . . . . .   12.487      1.000       0.500     38    22.1   172     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   11.358      1.000       0.500    344    58.5   588     ERRALL 
     WELL ORDERED  . . . . .   11.358      1.000       0.500    344    58.5   588     ERRALL 
     NO INTER CONTACTS . . .   11.358      1.000       0.500    344    58.5   588     ERRALL 
     SHIFTED CHAIN . . . . .   11.113      1.000       0.500    314    57.9   542     ERRALL 
     ALTERNATIVE PARENT  . .   13.288      1.000       0.500     20    44.4    45     ERRALL 
     SECONDARY STRUCTURE . .   11.483      1.000       0.500    126    60.9   207     ERRALL 
     LARGE SHIFTS/INSERTIONS   10.575      1.000       0.500    138    57.5   240     ERRALL 
     SURFACE . . . . . . . .   12.054      1.000       0.500    242    55.3   438     ERRALL 
     BURIED  . . . . . . . .    9.707      1.000       0.500    102    68.0   150     ERRALL 
     CORE  . . . . . . . . .   11.882      1.000       0.500    206    59.2   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)         2         3         4        16        35      71      76   DISTCA 
CA  (P)      2.63      3.95      5.26     21.05     46.05              76   DISTCA 
CA  (RMS)    0.60      1.22      1.61      3.63      6.17                   DISTCA 
 
ALL (N)         4        10        25        77       161     344     588   DISTALL 
ALL (P)      0.68      1.70      4.25     13.10     27.38             588   DISTALL 
ALL (RMS)    0.60      1.40      2.09      3.53      5.94                   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            42            29          RMSLSI 
CA  (P)       57.89         55.26         38.16          RMSLSI 
CA  (RMS)      1.67         13.16         12.72          RMSLSI 
 
 
 
END of the results output 
