
 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)@comp33.ch.
                 Created on  5/28/12 at 13:10:54 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>> Choosing internal or Cartesian coordinates for interpolation, based on max energy.
 KeyInt>> Permuting endpoint atoms to minimise torsion distance
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -382.2945320     RMS force=    0.9711961287E-06
 OPTIM> Final energy  =    -378.3909776     RMS force=    0.7549428702E-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=     45608.    
 decide> The unconnected minima in the chain and their distances are:
     2       35.73     1 
 

 tryconnect> 350-iteration DNEB run for minima 1_S and 2_F using 10 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.3286616756    
 Double-ended search iterations= 350 RMS= 0.0879 Dev= 2.66% S= 41.27 time= 4.22
 Following    2 images are candidates for TS:    2    8  
 bfgsts> WARNING *** initial eigenvalue is positive - increase NEBK?
 Converged to TS (number of iterations):        144
 Converged to TS (number of iterations):         55
 DNEB run yielded 2 true transition state(s) time=  17.26

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1008 steps. Energy=    -385.0249047       time=       3.36
 Minus side of path:                     989 steps. Energy=    -382.2945320       time=       3.36

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.0249047  3.0944         -381.9305045 0.36403         -382.2945320  23.668  21.977   2.813  51.555
        *NEW* (Placed in 3)                                     Known (#1)
 Unconnected minimum 3 found its way to S set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1131 steps. Energy=    -383.7903472       time=       4.46
 Minus side of path:                    1014 steps. Energy=    -379.7128734       time=       2.33

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -383.7903472  4.5543         -379.2359975 0.47688         -379.7128734  22.705  18.504   3.032  47.829
        *NEW* (Placed in 4)                                     *NEW* (Placed in 5)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 5 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     3349.3    
 decide> The unconnected minima in the chain and their distances are:
     2       11.52     5     4       12.21     1 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 5_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.2576 Dev= 0.52% S= 12.03 time= 0.41
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         37
 DNEB run yielded 1 true transition state(s) time=   4.17

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1046 steps. Energy=    -378.3909776       time=       3.16
 Minus side of path:                    1093 steps. Energy=    -383.7903472       time=       3.88

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -378.3909776  1.2412         -377.1497735  6.6406         -383.7903472  28.736  26.648   2.549  56.878
        Known (#2)                                              Known (#4)
 Unconnected minimum 4 found its way to F set.

 tryconnect> 105-iteration DNEB run for minima 1_S and 4_F using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.2553 Dev= 0.69% S= 12.75 time= 0.45
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         35
 DNEB run yielded 1 true transition state(s) time=   6.08

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1029 steps. Energy=    -384.1799149       time=       2.62
 Minus side of path:                     993 steps. Energy=    -383.8167775       time=       2.30

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.1799149  4.0651         -380.1147793  3.7020         -383.8167775  16.819  15.298   1.986  73.017
        *NEW* (Placed in 6)                                     *NEW* (Placed in 7)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 7 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     1330.8    
 decide> The unconnected minima in the chain and their distances are:
     4        9.45     7     7        7.87     1 
 

 tryconnect> 70-iteration DNEB run for minima 4_F and 7_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2120 Dev= 0.27% S= 9.64 time= 0.22
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         25
 DNEB run yielded 1 true transition state(s) time=   3.68

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     990 steps. Energy=    -383.7903472       time=       2.49
 Minus side of path:                    1002 steps. Energy=    -384.1799149       time=       2.58

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -383.7903472 0.49931         -383.2910326 0.88888         -384.1799149  11.985  10.577   1.506  96.297
        Known (#4)                                              Known (#6)
 Unconnected minimum 6 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 7_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.4209 Dev= 0.32% S= 8.26 time= 0.23
 Following    1 images are candidates for TS:    1  
 bfgsts> WARNING *** initial eigenvalue is positive - increase NEBK?
 Converged to TS (number of iterations):        106
 DNEB run yielded 1 true transition state(s) time=  11.66
 isnewts> transition state is the same as number        1 energy=     -381.9305044734
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 6 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    1022 steps. Energy=    -385.0249047       time=       3.19
 Minus side of path:                     998 steps. Energy=    -382.2945320       time=       3.20

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.0249047  3.0944         -381.9305045 0.36403         -382.2945320  23.668  21.978   2.810  51.592
        Known (#3)                                              Known (#1)
 Alternative path found between members of the S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 7 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     976.05    
 decide> The unconnected minima in the chain and their distances are:
     7        7.87     1 
 

 tryconnect> 630-iteration DNEB run for minima 1_S and 7_F using 18 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.2452524026    
 Double-ended search iterations= 630 RMS= 0.0205 Dev= 4.37% S= 12.96 time= 13.28
 Following    1 images are candidates for TS:    8  
 Converged to TS (number of iterations):         15
 DNEB run yielded 1 true transition state(s) time=   2.92

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     992 steps. Energy=    -382.2945320       time=       2.38
 Minus side of path:                    1018 steps. Energy=    -384.1799149       time=       2.57

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.2945320  4.6994         -377.5951621  6.5848         -384.1799149  17.484  14.277   2.380  60.930
        Known (#1)                                              Known (#6)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   7     -382.2945320  4.6994        -377.5951621  6.5848        -384.1799149  17.484  14.277   2.380  60.930
   5     -384.1799149 0.88888        -383.2910326 0.49931        -383.7903472  11.985  10.577   1.506  96.297
   3     -383.7903472  6.6406        -377.1497735  1.2412        -378.3909776  28.736  26.648   2.549  56.878

 Number of TS in the path       =      3
 Number of cycles               =      4

 Elapsed time=                               106.63
 OPTIM> # of energy calls=                         76 time=           0.08 %=  0.1
 OPTIM> # of energy+gradient calls=             38035 time=          42.02 %= 39.4
 OPTIM> # of energy+gradient+Hessian calls=       417 time=           1.84 %=  1.7
