
 OPTIM version 22983, Copyright (C) David J. Wales
 OPTIM comes with ABSOLUTELY NO WARRANTY; for details supply WARRANTY as an input keyword.
 This is free software, and you are welcome to redistribute it
 under certain conditions; provide keyword COPYRIGHT to see the details.

 getparams> Number of atoms (or variables)  determined as    145
 keyword> Local permutational alignment: alignment threshold=        1.00000
 keyword> Local permutational alignment: alignment cutoff=           5.00000
 keyword> Number of groups of permutable atoms=     6
CHARMMTYPE set to  2
1
                 Chemistry at HARvard Macromolecular Mechanics
                   (CHARMM) - Developmental Version 35b4   February 15, 2010   
       Copyright(c) 1984-2001  President and Fellows of Harvard College
                              All Rights Reserved
      Current operating system: Linux-2.6.16.54-0.2.5-smp(x86_64)@comp19.ch.
                 Created on  5/28/12 at 13:12:35 by user: wales       

            Maximum number of ATOMS:     25140, and RESidues:       14000
            Current HEAP size:         2048000, and STACK size:    500000

 RDTITL> * INPUT FILE FOR TRYPZIP 1LE1
 RDTITL> *
  
 CHARMM>    BOMLev -2
 Parameter: TOP <- "toph19_eef1_bs360.inp"
 Parameter: PAR <- "param19_eef1_bs360.inp"
  
 CHARMM>    WRNLEV -1
  
 CHARMM>    PRNLEV 1
 NBOND          152
 NTHETA          223
 NPHI           88

chsetdihe> number of internal coordinates for segment    1
 chsetdihe> NPHIPSI           24
 chsetdihe> NOMEGAC           11
 chsetdihe> NSIDECHAIN           27
 chsetdihe> NCHIRAL           13

chsetdihe> total number of internal coordinates
 chsetdihe> NPHIPSITOT=            24
 chsetdihe> NOMEGACTOT=            11
 chsetdihe> NSIDECHAINTOT=            27
 chsetdihe> NCHIRALTOT=            13

 chsetdihe>            51  twistable dihedrals identified
chsetdihe> SEG-NR, NSEGATOMS :    1     145

 fetchz> Hybrid EF/BFGS transition state search, maximum steps= 250
         maximum tangent space steps=   5 or  100 when overlap is better than     0.999900
 fetchz> Uphill mode is    0 for initial step and    0 after that
 fetchz> Steps for largest Hessian e/vector= 100, smallest e/vector=2000 convergence at       0.0020%

 fetchz>  435 Cartesian coordinates will be optimised for  145 CHARMM atoms

 fetchz> Lowest   1 eigenvalues and eigenvectors will be calculated non-iteratively
 fetchz> Point group checked when RMS force <     0.00100000, highest symmetry axis tested for=  6
 fetchz> Initial distance and eigenvalue tolerances in symmetry determination=     0.00010000     0.00010000
 fetchz> Minimum number of optimization steps=     0
 keywords> Cutoff for identifying atoms in the same orbit=    0.2000000000    
 keywords> lpermdist neighbours, threshold, max sep=    10     1.000000000         3
 fetchz> Convergence criterion for LBFGS optimization: RMS force< 0.10000000E-05 maximum steps= 10000
 fetchz> Maximum energy rise in LBFGS minimization=    0.1000000000E-01
 fetchz> Number of updates in LBFGS=    10000
 fetchz> Number of updates in XLBFGS=   4
 fetchz> Number of updates in mind=   4
 fetchz> Initial guess for diagonal elements in LBFGS=     0.0100
 fetchz> Initial guess for diagonal elements in XLBFGS=    0.1000
 fetchz> Maximum step size in LBFGS energy minimization=     0.1000
 fetchz> Maximum step size in XLBFGS=    0.2000
 fetchz> Maximum step size in LBFGS neb image minimization=                 0.2000
 fetchz> Warnings will be issued if atoms become closer than 0.5 units
 fetchz> Coordinates for intermediate steps will not be dumped to file points


 natintsetup, NATOMS          145
 cartres           12
 KeyInt>> Using natural internal coordinates. # of coords =        429
 KeyInt>> Parameter file for internal coordinates is naturals-noH.par                                                                                    
 KeyInt>> KD, NNZ are         50      4500
 KeyInt>> Back transform convergence (for interpolation)     0.1000000000E-07
 KeyInt>> Back transform convergence criterion (except for interpolation)     0.1000000000E-03
 KeyInt>> Using internal coordinates for interpolation.
 KeyInt>> using simple internal interpolation.    Image points will not be evenly distributed in Cartesians
 KeyInt>> Permuting endpoint atoms to minimise torsion distance
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -392.1976999     RMS force=    0.8619930222E-06
 OPTIM> Final energy  =    -394.4130237     RMS force=    0.9481290240E-06
 KeyConnect> Maximum cycles = 50, maximum images = 23
 KeyConnect> Maximum attempts per pair of minima = 3, with increment image density of 2.00
 KeyConnect> Image density = 0.30, iteration density = 35.00
 KeyNEB> Initial and final NEB force constants     10.00000000        10.00000000     factor=    1.010000000    
 KeyNEB> Number of images will vary depending on the separation of the endpoints
 KeyGrad> Overall rotation and translation will NOT be removed
 KeyGrad> Using doubly nudged elastic band gradient
 KeyOutput> Transition state candidates will be optimized
 KeyOutput> Concise printing during transition states optimization
 KeyOutput> Transition state candidates are maxima along NEB
 KeyMin> Maximal number of iterations will vary, depending on the number of images in the band
 KeyMin> RMS convergence criterion is set to 0.001
 KeyMin> L-BFGS minimization
 KeyLBFGS> Maximum step size per image =     0.2000000000    
 KeyLBFGS> 4 Hessian updates per iteration
 KeyLBFGS> Guess for inverse Hessian diagonal elements =     0.1000000000E-02
 KeyTau> Using Henkelman and Jonsson's improved tangent
 KeyDecide> Cost function in Dijkstra algorithm is D^3

 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     4105.4    
 decide> The unconnected minima in the chain and their distances are:
     2       16.01     1 
 

 tryconnect> 140-iteration DNEB run for minima 1_S and 2_F using 4 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 140 RMS= 0.5307 Dev= 0.93% S= 21.67 time= 0.79
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         58
 DNEB run yielded 1 true transition state(s) time=   6.10

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     908 steps. Energy=    -394.5497349       time=       2.36
 Minus side of path:                     909 steps. Energy=    -394.6523294       time=       2.57

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -394.5497349 0.13243E-01     -394.5364916 0.11584         -394.6523294   1.017   1.014  39.326   3.687
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 4 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     3912.6    
 decide> The unconnected minima in the chain and their distances are:
     2       13.78     3     4       10.90     1 
 

 tryconnect> 140-iteration DNEB run for minima 2_F and 3_U using 4 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.568374182    
 Double-ended search iterations= 140 RMS= 4.0529 Dev= 0.94% S= 19.89 time= 0.79
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):        193
 DNEB run yielded 1 true transition state(s) time=  17.14

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1199 steps. Energy=    -394.6523294       time=       4.95
 Minus side of path:                     930 steps. Energy=    -391.8862401       time=       3.17

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -394.6523294  5.9399         -388.7124009  3.1738         -391.8862401  50.461  33.090  10.327  14.041
        Known (#4)                                              *NEW* (Placed in 5)
 Connection established between members of the U set.

 tryconnect> 105-iteration DNEB run for minima 1_S and 4_U using 3 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.1259 Dev= 0.46% S= 11.35 time= 0.46
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         25
 DNEB run yielded 1 true transition state(s) time=   4.31

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     939 steps. Energy=    -394.6523294       time=       3.25
 Minus side of path:                     908 steps. Energy=    -392.1976999       time=       2.85

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -394.6523294  3.3315         -391.3208421 0.87686         -392.1976999  12.054  10.902  19.145   7.574
        Known (#4)                                              Known (#1)
 Unconnected minimum 4 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     2640.4    
 decide> The unconnected minima in the chain and their distances are:
     2       13.82     4 
 

 tryconnect> 140-iteration DNEB run for minima 2_F and 4_S using 4 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.568374182    
 Double-ended search iterations= 140 RMS= 0.7190 Dev= 1.73% S= 19.83 time= 0.82
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         37
 DNEB run yielded 1 true transition state(s) time=   6.19
 isnewts> transition state is the same as number        1 energy=     -394.5364915536
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 4 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     902 steps. Energy=    -394.5497349       time=       2.91
 Minus side of path:                     898 steps. Energy=    -394.6523294       time=       2.16

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -394.5497349 0.13243E-01     -394.5364916 0.11584         -394.6523294   1.017   1.014  39.318   3.688
        Known (#3)                                              Known (#4)
 Alternative path found between members of the S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 5 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     5235.6    
 decide> The unconnected minima in the chain and their distances are:
     2       13.78     3 
 

 tryconnect> 805-iteration DNEB run for minima 2_F and 3_S using 23 images  (DNEB attempt #2)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.3450947594    
 Double-ended search iterations= 805 RMS= 0.1904 Dev= 4.78% S= 33.63 time= 24.40
 Following    1 images are candidates for TS:   10  
 Converged to TS (number of iterations):         32
 DNEB run yielded 1 true transition state(s) time=   4.18

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1017 steps. Energy=    -394.4130237       time=       2.70
 Minus side of path:                    1008 steps. Energy=    -394.7110446       time=       2.64

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -394.4130237  9.1194         -385.2935977  9.4174         -394.7110446  26.640  10.328  24.645   5.884
        Known (#2)                                              *NEW* (Placed in 6)
 Unconnected minimum 6 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 6 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     1196.5    
 decide> The unconnected minima in the chain and their distances are:
     6       10.62     3 
 

 tryconnect> 105-iteration DNEB run for minima 3_S and 6_F using 3 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.1210 Dev= 0.06% S= 10.72 time= 0.45
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         25
 DNEB run yielded 1 true transition state(s) time=   3.47

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     931 steps. Energy=    -394.6523294       time=       2.13
 Minus side of path:                     974 steps. Energy=    -394.7110446       time=       2.29

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -394.6523294 0.78979         -393.8625379 0.84851         -394.7110446  11.345  10.714   2.667  54.371
        Known (#4)                                              Known (#6)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   3     -392.1976999 0.87686        -391.3208421  3.3315        -394.6523294  12.054  10.902  19.145   7.574
   6     -394.6523294 0.78979        -393.8625379 0.84851        -394.7110446  11.345  10.714   2.667  54.371
   5     -394.7110446  9.4174        -385.2935977  9.1194        -394.4130237  26.640  10.328  24.645   5.884

 Number of TS in the path       =      3
 Number of cycles               =      5

 Elapsed time=                               103.21
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             38567 time=          50.63 %= 49.1
 OPTIM> # of energy+gradient+Hessian calls=       370 time=           1.74 %=  1.7
