
 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 13:10:49 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=    -378.3553468     RMS force=    0.9228756643E-06
 OPTIM> Final energy  =    -374.7352035     RMS force=    0.8428802569E-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=     8801.6    
 decide> The unconnected minima in the chain and their distances are:
     2       20.65     1 
 

 tryconnect> 210-iteration DNEB run for minima 1_S and 2_F using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.0949 Dev= 0.65% S= 22.87 time= 1.46
 Following    2 images are candidates for TS:    3    6  
 Converged to TS (number of iterations):         39
 Converged to TS (number of iterations):         16
 DNEB run yielded 2 true transition state(s) time=  10.11

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1054 steps. Energy=    -376.4429556       time=       3.77
 Minus side of path:                    1049 steps. Energy=    -378.1554128       time=       3.73

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -376.4429556  1.3815         -375.0614168  3.0940         -378.1554128  12.941  11.389  11.319  12.810
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 Connection established between members of the U set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     995 steps. Energy=    -374.7352035       time=       2.83
 Minus side of path:                    1007 steps. Energy=    -376.4429556       time=       3.36

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -374.7352035 0.22441         -374.5107946  1.9322         -376.4429556   2.949   2.852  37.491   3.868
        Known (#2)                                              Known (#3)
 Unconnected minimum 3 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 4 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     2199.9    
 decide> The unconnected minima in the chain and their distances are:
     4       13.01     1 
 

 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= 0.3610 Dev= 0.57% S= 13.92 time= 0.44
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         24
 DNEB run yielded 1 true transition state(s) time=   4.04

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1023 steps. Energy=    -375.5843107       time=       2.20
 Minus side of path:                    1026 steps. Energy=    -378.1554128       time=       2.21

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -375.5843107 0.91440         -374.6699151  3.4855         -378.1554128   9.106   8.229  26.466   5.479
        *NEW* (Placed in 5)                                     Known (#4)
 Unconnected minimum 5 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     169.33    
 decide> The unconnected minima in the chain and their distances are:
     5        5.53     1 
 

 tryconnect> 70-iteration DNEB run for minima 1_S and 5_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      7.462153966    
 Double-ended search iterations= 70 RMS= 0.4807 Dev= 3.02% S= 5.91 time= 0.21
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         79
 DNEB run yielded 1 true transition state(s) time=   6.27

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1053 steps. Energy=    -375.5843107       time=       2.41
 Minus side of path:                    1965 steps. Energy=    -382.3268629       time=       8.82

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -375.5843107 0.91961E-01     -375.4923500  6.8345         -382.3268629  59.108  56.956   1.703  85.139
        Known (#5)                                              *NEW* (Placed in 6)
 Unconnected minimum 6 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 6 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     338.66    
 decide> The unconnected minima in the chain and their distances are:
     5        5.53     1 
 

 tryconnect> 420-iteration DNEB run for minima 1_S and 5_F using 12 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      1.903547996    
 Double-ended search iterations= 420 RMS= 0.8785 Dev= 4.27% S= 10.13 time= 5.46
 Following    1 images are candidates for TS:    8  
 Converged to TS (number of iterations):         20
 DNEB run yielded 1 true transition state(s) time=   4.03

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1056 steps. Energy=    -378.3553468       time=       3.86
 Minus side of path:                    1022 steps. Energy=    -378.1554128       time=       3.63

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -378.3553468  5.2633         -373.0920065  5.0634         -378.1554128  14.629  13.009  21.195   6.841
        Known (#1)                                              Known (#4)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   5     -378.3553468  5.2633        -373.0920065  5.0634        -378.1554128  14.629  13.009  21.195   6.841
   1     -378.1554128  3.0940        -375.0614168  1.3815        -376.4429556  12.941  11.389  11.319  12.810
   2     -376.4429556  1.9322        -374.5107946 0.22441        -374.7352035   2.949   2.852  37.491   3.868

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

 Elapsed time=                                68.94
 OPTIM> # of energy calls=                         46 time=           0.05 %=  0.1
 OPTIM> # of energy+gradient calls=             23272 time=          25.03 %= 36.3
 OPTIM> # of energy+gradient+Hessian calls=       178 time=           0.70 %=  1.0
