
 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)@comp24.ch.
                 Created on  5/28/12 at 13:11:34 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=    -382.6517516     RMS force=    0.9790532668E-06
 OPTIM> Final energy  =    -379.3011876     RMS force=    0.9720334003E-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=     55230.    
 decide> The unconnected minima in the chain and their distances are:
     2       38.08     1 
 

 tryconnect> 385-iteration DNEB run for minima 1_S and 2_F using 11 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.2335737168    
 Double-ended search iterations= 385 RMS= 0.0950 Dev= 4.23% S= 45.60 time= 5.01
 Following    2 images are candidates for TS:    3    9  
 Converged to TS (number of iterations):         57
 Converged to TS (number of iterations):         40
 DNEB run yielded 2 true transition state(s) time=   9.95

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1025 steps. Energy=    -382.6517516       time=       3.12
 Minus side of path:                     975 steps. Energy=    -381.8353908       time=       2.98

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.6517516 0.81700         -381.8347519 0.63893E-03     -381.8353908   4.763   4.723   3.587  40.418
        Known (#1)                                              *NEW* (Placed in 3)
 Unconnected minimum 3 found its way to S set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1009 steps. Energy=    -381.7644736       time=       3.22
 Minus side of path:                    1036 steps. Energy=    -380.2155834       time=       3.07

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.7644736  2.4603         -379.3041634 0.91142         -380.2155834  14.441  13.904   2.915  49.748
        *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      4 steps with      2 missing connections, weight=     30334.    
 decide> The unconnected minima in the chain and their distances are:
     2       13.09     4     5       30.40     3 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 4_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.0809 Dev= 0.06% S= 13.18 time= 0.43
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         52
 DNEB run yielded 1 true transition state(s) time=   6.80
 isnewts> transition state is the same as number        2 energy=     -379.3041634428
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 3 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    1042 steps. Energy=    -381.7644736       time=       3.10
 Minus side of path:                    1048 steps. Energy=    -380.2155834       time=       3.12

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.7644736  2.4603         -379.3041634 0.91142         -380.2155834  14.441  13.903   2.917  49.714
        Known (#4)                                              Known (#5)
 Connection established between members of the U set.

 tryconnect> 315-iteration DNEB run for minima 3_S and 5_U using 9 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.4624599827    
 Double-ended search iterations= 315 RMS= 0.0919 Dev= 0.43% S= 32.93 time= 3.34
 Following    2 images are candidates for TS:    2    8  
 Converged to TS (number of iterations):         88
 Converged to TS (number of iterations):         41
 DNEB run yielded 2 true transition state(s) time=  13.03

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1032 steps. Energy=    -383.4268737       time=       2.97
 Minus side of path:                    1036 steps. Energy=    -381.8353908       time=       2.93

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -383.4268737  2.2710         -381.1559056 0.67949         -381.8353908  15.642  13.201   2.358  61.503
        *NEW* (Placed in 6)                                     Known (#3)
 Unconnected minimum 6 found its way to S set.

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1001 steps. Energy=    -380.2155834       time=       3.13
 Minus side of path:                    1149 steps. Energy=    -383.4268737       time=       4.24

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.2155834 0.65889E-02     -380.2089945  3.2179         -383.4268737  29.557  28.787   2.248  64.490
        Known (#5)                                              Known (#6)
 Unconnected minimum 5 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     4489.8    
 decide> The unconnected minima in the chain and their distances are:
     2       13.09     4 
 

 tryconnect> 805-iteration DNEB run for minima 2_F and 4_S using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      14.07100423    
 Double-ended search iterations= 805 RMS= 0.1572 Dev= 2.64% S= 13.74 time= 21.62
 Following    1 images are candidates for TS:   11  
 Converged to TS (number of iterations):         37
 DNEB run yielded 1 true transition state(s) time=   4.25
 isnewts> transition state is the same as number        2 energy=     -379.3041634431
 tryconnect> Will not repeat search for TS      1 same as TS      2
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 6 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     6667.0    
 decide> The unconnected minima in the chain and their distances are:
     2       18.82     5 
 

 tryconnect> 175-iteration DNEB run for minima 2_F and 5_S using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.1476 Dev= 0.07% S= 19.02 time= 1.05
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         43
 DNEB run yielded 1 true transition state(s) time=   5.07

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1010 steps. Energy=    -379.3011876       time=       3.39
 Minus side of path:                    1088 steps. Energy=    -380.2155834       time=       3.94

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -379.3011876 0.16393E-01     -379.2847946 0.93079         -380.2155834  20.327  18.830   2.181  66.486
        Known (#2)                                              Known (#5)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -382.6517516 0.81700        -381.8347519 0.63893E-03    -381.8353908   4.763   4.723   3.587  40.418
   4     -381.8353908 0.67949        -381.1559056  2.2710        -383.4268737  15.642  13.201   2.358  61.503
   5     -383.4268737  3.2179        -380.2089945 0.65889E-02    -380.2155834  29.557  28.787   2.248  64.490
   6     -380.2155834 0.93079        -379.2847946 0.16393E-01    -379.3011876  20.327  18.830   2.181  66.486

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

 Elapsed time=                               109.88
 OPTIM> # of energy calls=                        102 time=           0.11 %=  0.1
 OPTIM> # of energy+gradient calls=             46532 time=          51.89 %= 47.2
 OPTIM> # of energy+gradient+Hessian calls=       358 time=           1.54 %=  1.4
