
 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 13:10:52 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=    -390.2596686     RMS force=    0.9377387882E-06
 OPTIM> Final energy  =    -389.0755876     RMS force=    0.9194710027E-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=     14826.    
 decide> The unconnected minima in the chain and their distances are:
     2       24.57     1 
 

 tryconnect> 245-iteration DNEB run for minima 1_S and 2_F using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 245 RMS= 0.3258 Dev= 1.10% S= 27.11 time= 2.42
 Following    2 images are candidates for TS:    2    5  
 Converged to TS (number of iterations):         38
 Converged to TS (number of iterations):         58
 DNEB run yielded 2 true transition state(s) time=  10.23

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     958 steps. Energy=    -390.2596686       time=       2.51
 Minus side of path:                     978 steps. Energy=    -389.9883114       time=       3.33

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.2596686  2.2769         -387.9827304  2.0056         -389.9883114  11.177  10.348   2.503  57.934
        Known (#1)                                              *NEW* (Placed in 3)
 Unconnected minimum 3 found its way to S set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     966 steps. Energy=    -390.2984981       time=       2.84
 Minus side of path:                     989 steps. Energy=    -390.4740503       time=       3.21

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.2984981  3.5793         -386.7191828  3.7549         -390.4740503  23.201  19.722   2.672  54.268
        *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=     951.85    
 decide> The unconnected minima in the chain and their distances are:
     2        7.12     4     5        8.39     3 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 4_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.768393620    
 Double-ended search iterations= 70 RMS= 0.1751 Dev= 0.54% S= 7.24 time= 0.26
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         20
 DNEB run yielded 1 true transition state(s) time=   4.14

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     940 steps. Energy=    -390.2984981       time=       3.23
 Minus side of path:                     945 steps. Energy=    -389.0755876       time=       3.07

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.2984981  1.6329         -388.6655860 0.41000         -389.0755876   7.723   7.118   6.978  20.779
        Known (#4)                                              Known (#2)
 Unconnected minimum 4 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 3_S and 5_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2827 Dev= 0.30% S= 8.63 time= 0.26
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         55
 DNEB run yielded 1 true transition state(s) time=   5.87

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     975 steps. Energy=    -390.5076396       time=       3.35
 Minus side of path:                     908 steps. Energy=    -390.4740503       time=       2.23

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.5076396 0.39708E-01     -390.4679315 0.61189E-02     -390.4740503   3.150   3.098  31.989   4.533
        *NEW* (Placed in 6)                                     Known (#5)
 Unconnected minimum 6 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     361.79    
 decide> The unconnected minima in the chain and their distances are:
     6        7.13     3 
 

 tryconnect> 70-iteration DNEB run for minima 3_S and 6_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.4682 Dev= 0.29% S= 7.35 time= 0.26
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         89
 DNEB run yielded 1 true transition state(s) time=   7.48

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     934 steps. Energy=    -391.9475241       time=       2.73
 Minus side of path:                     978 steps. Energy=    -390.5076396       time=       2.56

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.9475241  1.6606         -390.2869383 0.22070         -390.5076396  20.965  19.849   6.756  21.462
        *NEW* (Placed in 7)                                     Known (#6)
 Unconnected minimum 7 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 7 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     723.58    
 decide> The unconnected minima in the chain and their distances are:
     6        7.13     3 
 

 tryconnect> 560-iteration DNEB run for minima 3_S and 6_F using 16 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.2224511589    
 Double-ended search iterations= 560 RMS= 0.0112 Dev= 5.18% S= 12.01 time= 12.36
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         16
 DNEB run yielded 1 true transition state(s) time=   2.90

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     966 steps. Energy=    -389.9883114       time=       2.28
 Minus side of path:                     998 steps. Energy=    -390.5076396       time=       2.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -389.9883114 0.27958         -389.7087359 0.79890         -390.5076396  10.591   7.126   4.301  33.710
        Known (#3)                                              Known (#6)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -390.2596686  2.2769        -387.9827304  2.0056        -389.9883114  11.177  10.348   2.503  57.934
   6     -389.9883114 0.27958        -389.7087359 0.79890        -390.5076396  10.591   7.126   4.301  33.710
   4     -390.5076396 0.39708E-01    -390.4679315 0.61189E-02    -390.4740503   3.150   3.098  31.989   4.533
   2     -390.4740503  3.7549        -386.7191828  3.5793        -390.2984981  23.201  19.722   2.672  54.268
   3     -390.2984981  1.6329        -388.6655860 0.41000        -389.0755876   7.723   7.118   6.978  20.779

 Number of TS in the path       =      5
 Number of cycles               =      4

 Elapsed time=                                80.11
 OPTIM> # of energy calls=                         58 time=           0.08 %=  0.1
 OPTIM> # of energy+gradient calls=             28396 time=          38.09 %= 47.5
 OPTIM> # of energy+gradient+Hessian calls=       276 time=           1.29 %=  1.6
