 
####################################################### 
#                                                     # 
#                        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:     # 
#                        # 
########################## 
# 
CONANA-INTER           ../CONANA/T0003.inter 
# 
NUMBER-OF-PARENTS      2 
ALIGNMENT-DALI(1)      ../PARENTS/casp2.T0003.1gpr.rot 
ALIGNMENT-DALI(2)      ../PARENTS/casp2.T0003.1f3g.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 1162 atoms, MODEL 1176 atoms, 1162 common with TARGET 
           Number of atoms possible to evaluate: 1162 
 
 
 CA-RMS TARGET<->PARENT(1gpr)	 1.649883 
 
 CA-RMS TARGET<->PARENT(1f3g)	 1.280893 
 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    44.72           72.9   306   100.0   306     ARMSMC  
     WELL ORDERED  . . . . .    41.35           79.9   164   100.0   164     ARMSMC  
     NO INTER CONTACTS . . .    38.86           75.5   208   100.0   208     ARMSMC  
     SHIFTED CHAIN . . . . .    55.30           62.2   156   100.0   156     ARMSMC  
     ALTERNATIVE PARENT  . .    62.36           51.9    27   100.0    27     ARMSMC  
     SECONDARY STRUCTURE . .    31.89           79.4   126   100.0   126     ARMSMC  
     LARGE SHIFTS/INSERTIONS    80.40           36.8    38   100.0    38     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    53.76           66.9   178   100.0   178     ARMSMC  
     BURIED  . . . . . . . .    27.58           81.2   128   100.0   128     ARMSMC  
     CORE  . . . . . . . . .    36.97           78.0   268   100.0   268     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    76.14           48.5   130   100.0   130     ARMSSC1 
     WELL ORDERED  . . . . .    77.04           54.4    57   100.0    57     ARMSSC1 
     NO INTER CONTACTS . . .    75.36           47.0    83   100.0    83     ARMSSC1 
     RELIABLE SIDE CHAINS  .    74.04           46.9   113   100.0   113     ARMSSC1 
     CHANGED ANGLES  . . . .    97.87           17.8    73   100.0    73     ARMSSC1 
     SHIFTED CHAIN . . . . .    85.98           38.8    67   100.0    67     ARMSSC1 
     ALTERNATIVE PARENT  . .    80.42           50.0    12   100.0    12     ARMSSC1 
     SECONDARY STRUCTURE . .    82.41           46.3    54   100.0    54     ARMSSC1 
     LARGE SHIFTS/INSERTIONS    91.71           29.4    17   100.0    17     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .    79.58           38.5    78   100.0    78     ARMSSC1 
     BURIED  . . . . . . . .    70.69           63.5    52   100.0    52     ARMSSC1 
     CORE  . . . . . . . . .    73.52           51.3   113   100.0   113     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    80.77           37.2    94   100.0    94     ARMSSC2 
     WELL ORDERED  . . . . .    85.19           40.0    35   100.0    35     ARMSSC2 
     NO INTER CONTACTS . . .    73.06           38.6    57   100.0    57     ARMSSC2 
     RELIABLE SIDE CHAINS  .    70.70           41.4    70   100.0    70     ARMSSC2 
     CHANGED ANGLES  . . . .    90.73           25.4    71   100.0    71     ARMSSC2 
     SHIFTED CHAIN . . . . .    88.63           31.9    47   100.0    47     ARMSSC2 
     ALTERNATIVE PARENT  . .   121.94           12.5     8   100.0     8     ARMSSC2 
     SECONDARY STRUCTURE . .    80.60           46.2    39   100.0    39     ARMSSC2 
     LARGE SHIFTS/INSERTIONS   101.69           20.0    15   100.0    15     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .    78.88           35.0    60   100.0    60     ARMSSC2 
     BURIED  . . . . . . . .    83.99           41.2    34   100.0    34     ARMSSC2 
     CORE  . . . . . . . . .    76.15           40.5    79   100.0    79     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .   101.70           21.9    32   100.0    32     ARMSSC3 
     WELL ORDERED  . . . . .   114.31           20.0     5   100.0     5     ARMSSC3 
     NO INTER CONTACTS . . .   111.15           20.0    15   100.0    15     ARMSSC3 
     RELIABLE SIDE CHAINS  .   103.03           21.4    28   100.0    28     ARMSSC3 
     CHANGED ANGLES  . . . .   105.78           24.1    29   100.0    29     ARMSSC3 
     SHIFTED CHAIN . . . . .   106.37           22.2    18   100.0    18     ARMSSC3 
     ALTERNATIVE PARENT  . .    93.80           33.3     3   100.0     3     ARMSSC3 
     SECONDARY STRUCTURE . .    86.16           10.0    10   100.0    10     ARMSSC3 
     LARGE SHIFTS/INSERTIONS    95.94           50.0     6   100.0     6     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .   101.70           21.9    32   100.0    32     ARMSSC3 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     CORE  . . . . . . . . .   102.98           15.4    26   100.0    26     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    99.51           11.8    17   100.0    17     ARMSSC4 
     WELL ORDERED  . . . . .   136.90            0.0     2   100.0     2     ARMSSC4 
     NO INTER CONTACTS . . .    96.21           10.0    10   100.0    10     ARMSSC4 
     RELIABLE SIDE CHAINS  .    99.51           11.8    17   100.0    17     ARMSSC4 
     CHANGED ANGLES  . . . .    99.51           11.8    17   100.0    17     ARMSSC4 
     SHIFTED CHAIN . . . . .    98.51           10.0    10   100.0    10     ARMSSC4 
     ALTERNATIVE PARENT  . .    78.73            0.0     2   100.0     2     ARMSSC4 
     SECONDARY STRUCTURE . .    55.72           16.7     6   100.0     6     ARMSSC4 
     LARGE SHIFTS/INSERTIONS   121.82            0.0     4   100.0     4     ARMSSC4 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SURFACE . . . . . . . .    99.51           11.8    17   100.0    17     ARMSSC4 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     CORE  . . . . . . . . .    91.55           15.4    13   100.0    13     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =   0.94591     r(1,2) =  -0.02196     r(1,3) =   0.32368 
 r(2,1) =  -0.05726     r(2,2) =  -0.99335     r(2,3) =   0.09993 
 r(3,1) =   0.31934     r(3,2) =  -0.11306     r(3,3) =  -0.94087 
THE OFFSET VECTOR: 
 v(1) = -19.38442     v(2) =  55.10491     v(3) =  43.17004 
 
 Number of iteration 28                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.10           (Number of atoms:  131) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    2.47        154   100.0   154     CRMSCA  
     CRN = ALL/NP  . . . . .    0.0160                            CRMSCA  
     WELL ORDERED  . . . . .    1.82         88   100.0    88     CRMSCA  
     NO INTER CONTACTS . . .    1.79        104   100.0   104     CRMSCA  
     SHIFTED CHAIN . . . . .    3.26         79   100.0    79     CRMSCA  
     ALTERNATIVE PARENT  . .    3.82         14   100.0    14     CRMSCA  
     SECONDARY STRUCTURE . .    1.49         63   100.0    63     CRMSCA  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSCA  
     LARGE SHIFTS/INSERTIONS    5.72         20   100.0    20     CRMSCA  
     SURFACE . . . . . . . .    3.01         90   100.0    90     CRMSCA  
     BURIED  . . . . . . . .    1.39         64   100.0    64     CRMSCA  
     CORE  . . . . . . . . .    1.45        134   100.0   134     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    2.52        756   100.0   756     CRMSMC  
     WELL ORDERED  . . . . .    1.88        442   100.0   442     CRMSMC  
     NO INTER CONTACTS . . .    1.83        507   100.0   507     CRMSMC  
     SHIFTED CHAIN . . . . .    3.33        389   100.0   389     CRMSMC  
     ALTERNATIVE PARENT  . .    3.79         68   100.0    68     CRMSMC  
     SECONDARY STRUCTURE . .    1.64        310   100.0   310     CRMSMC  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSMC  
     LARGE SHIFTS/INSERTIONS    5.73         98   100.0    98     CRMSMC  
     SURFACE . . . . . . . .    3.03        442   100.0   442     CRMSMC  
     BURIED  . . . . . . . .    1.52        314   100.0   314     CRMSMC  
     CORE  . . . . . . . . .    1.54        658   100.0   658     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    4.08        546   100.0   546     CRMSSC  
     WELL ORDERED  . . . . .    3.24        266   100.0   266     CRMSSC  
     NO INTER CONTACTS . . .    2.84        341   100.0   341     CRMSSC  
     RELIABLE SIDE CHAINS  .    4.17        450   100.0   450     CRMSSC  
     CHANGED ANGLES  . . . .    5.12        287   100.0   287     CRMSSC  
     SECONDARY STRUCTURE . .    2.70        229   100.0   229     CRMSSC  
     LARGE SHIFTS/INSERTIONS    8.42         78   100.0    78     CRMSSC  
     SURFACE . . . . . . . .    4.84        333   100.0   333     CRMSSC  
     BURIED  . . . . . . . .    2.46        213   100.0   213     CRMSSC  
     CORE  . . . . . . . . .    2.75        468   100.0   468     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    3.30       1162   100.0  1162     CRMSALL 
     WELL ORDERED  . . . . .    2.50        627   100.0   627     CRMSALL 
     NO INTER CONTACTS . . .    2.34        757   100.0   757     CRMSALL 
     SHIFTED CHAIN . . . . .    4.30        585   100.0   585     CRMSALL 
     ALTERNATIVE PARENT  . .    4.89        102   100.0   102     CRMSALL 
     SECONDARY STRUCTURE . .    2.17        481   100.0   481     CRMSALL 
     LARGE SHIFTS/INSERTIONS    7.08        158   100.0   158     CRMSALL 
     SURFACE . . . . . . . .    3.95        693   100.0   693     CRMSALL 
     BURIED  . . . . . . . .    1.96        469   100.0   469     CRMSALL 
     CORE  . . . . . . . . .    2.17       1004   100.0  1004     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     6.96      9   100.0     9       1-MWFFNKNLK-9    
 CA  LOOP  2     4.50      8   100.0     8     132-GGKTLEIV-139  
 CA  LOOP  3     4.33      3   100.0     3     152-ILK-154  
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     6.95     45   100.0    45       1-MWFFNKNLK-9    
 MC  LOOP  2     4.35     38   100.0    38     132-GGKTLEIV-139  
 MC  LOOP  3     4.64     15   100.0    15     152-ILK-154  
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     8.33     77   100.0    77       1-MWFFNKNLK-9    
 ALL LOOP  2     5.03     56   100.0    56     132-GGKTLEIV-139  
 ALL LOOP  3     6.80     25   100.0    25     152-ILK-154  
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     3.47      9   100.0     9       1-MWFFNKNLK-9    
 CA  LOOP  2     2.35      8   100.0     8     132-GGKTLEIV-139  
 CA  LOOP  3     0.05      3   100.0     3     152-ILK-154  
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     3.73     45   100.0    45       1-MWFFNKNLK-9    
 MC  LOOP  2     2.62     38   100.0    38     132-GGKTLEIV-139  
 MC  LOOP  3     0.68     15   100.0    15     152-ILK-154  
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     5.19     77   100.0    77       1-MWFFNKNLK-9    
 ALL LOOP  2     3.86     56   100.0    56     132-GGKTLEIV-139  
 ALL LOOP  3     1.25     25   100.0    25     152-ILK-154  
 
 
Accuracy of estimates of atomic coordinate errors: model <-> target 
 
 (CA)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    8.366      0.748       0.774    154   100.0   154     ERRCA  
     WELL ORDERED  . . . . .    8.623      0.774       0.802     88   100.0    88     ERRCA  
     NO INTER CONTACTS . . .    8.723      0.791       0.810    104   100.0   104     ERRCA  
     SHIFTED CHAIN . . . . .    7.589      0.646       0.686     79   100.0    79     ERRCA  
     ALTERNATIVE PARENT  . .    6.562      0.511       0.584     14   100.0    14     ERRCA  
     SECONDARY STRUCTURE . .    8.868      0.808       0.831     63   100.0    63     ERRCA  
     LARGE SHIFTS/INSERTIONS    5.134      0.384       0.441     20   100.0    20     ERRCA  
     SURFACE . . . . . . . .    7.968      0.701       0.730     90   100.0    90     ERRCA  
     BURIED  . . . . . . . .    8.924      0.815       0.836     64   100.0    64     ERRCA  
     CORE  . . . . . . . . .    8.848      0.803       0.824    134   100.0   134     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    8.334      0.743       0.770    756   100.0   756     ERRMC  
     WELL ORDERED  . . . . .    8.610      0.774       0.800    442   100.0   442     ERRMC  
     NO INTER CONTACTS . . .    8.683      0.785       0.806    507   100.0   507     ERRMC  
     SHIFTED CHAIN . . . . .    7.570      0.643       0.684    389   100.0   389     ERRMC  
     ALTERNATIVE PARENT  . .    6.630      0.520       0.589     68   100.0    68     ERRMC  
     SECONDARY STRUCTURE . .    8.790      0.798       0.820    310   100.0   310     ERRMC  
     LARGE SHIFTS/INSERTIONS    5.246      0.391       0.447     98   100.0    98     ERRMC  
     SURFACE . . . . . . . .    7.963      0.698       0.730    442   100.0   442     ERRMC  
     BURIED  . . . . . . . .    8.856      0.806       0.826    314   100.0   314     ERRMC  
     CORE  . . . . . . . . .    8.794      0.796       0.818    658   100.0   658     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    7.429      0.631       0.663    546   100.0   546     ERRSC  
     WELL ORDERED  . . . . .    7.721      0.671       0.701    266   100.0   266     ERRSC  
     NO INTER CONTACTS . . .    7.975      0.695       0.729    341   100.0   341     ERRSC  
     RELIABLE SIDE CHAINS  .    7.471      0.636       0.667    450   100.0   450     ERRSC  
     CHANGED ANGLES  . . . .    6.545      0.524       0.565    287   100.0   287     ERRSC  
     SHIFTED CHAIN . . . . .    6.514      0.524       0.557    269   100.0   269     ERRSC  
     ALTERNATIVE PARENT  . .    4.960      0.376       0.405     46   100.0    46     ERRSC  
     SECONDARY STRUCTURE . .    7.939      0.687       0.724    229   100.0   229     ERRSC  
     LARGE SHIFTS/INSERTIONS    4.273      0.281       0.290     78   100.0    78     ERRSC  
     SURFACE . . . . . . . .    6.944      0.574       0.608    333   100.0   333     ERRSC  
     BURIED  . . . . . . . .    8.187      0.719       0.751    213   100.0   213     ERRSC  
     CORE  . . . . . . . . .    7.955      0.689       0.726    468   100.0   468     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    7.932      0.693       0.723   1162   100.0  1162     ERRALL 
     WELL ORDERED  . . . . .    8.270      0.735       0.762    627   100.0   627     ERRALL 
     NO INTER CONTACTS . . .    8.374      0.746       0.773    757   100.0   757     ERRALL 
     SHIFTED CHAIN . . . . .    7.118      0.592       0.629    585   100.0   585     ERRALL 
     ALTERNATIVE PARENT  . .    5.956      0.463       0.515    102   100.0   102     ERRALL 
     SECONDARY STRUCTURE . .    8.411      0.748       0.778    481   100.0   481     ERRALL 
     LARGE SHIFTS/INSERTIONS    4.800      0.341       0.375    158   100.0   158     ERRALL 
     SURFACE . . . . . . . .    7.499      0.642       0.675    693   100.0   693     ERRALL 
     BURIED  . . . . . . . .    8.573      0.769       0.794    469   100.0   469     ERRALL 
     CORE  . . . . . . . . .    8.425      0.749       0.778   1004   100.0  1004     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)        73       128       132       144       152     154     154   DISTCA 
CA  (P)     47.40     83.12     85.71     93.51     98.70             154   DISTCA 
CA  (RMS)    0.68      1.06      1.12      1.58      2.16                   DISTCA 
 
ALL (N)       430       815       916      1035      1136    1162    1162   DISTALL 
ALL (P)     37.01     70.14     78.83     89.07     97.76            1162   DISTALL 
ALL (RMS)    0.70      1.10      1.31      1.80      2.70                   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)         134           134            20          RMSLSI 
CA  (P)       87.01         87.01         12.99          RMSLSI 
CA  (RMS)      1.12          1.45          5.72          RMSLSI 
 
 
 
END of the results output 
