
 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)@comp34.ch.
                 Created on  5/28/12 at 12:45:34 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


 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -386.9950363     RMS force=    0.9442932671E-06
 OPTIM> Final energy  =    -394.0946509     RMS force=    0.8441807438E-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=     77222.    
 decide> The unconnected minima in the chain and their distances are:
     2       42.58     1 
 

 tryconnect> 420-iteration DNEB run for minima 1_S and 2_F using 12 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.2224511589    
 Double-ended search iterations= 420 RMS= 0.0864 Dev= 4.51% S= 50.23 time= 7.20
 Following    2 images are candidates for TS:    4    6  
 Converged to TS (number of iterations):         90
 Converged to TS (number of iterations):         40
 DNEB run yielded 2 true transition state(s) time=  13.77

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1028 steps. Energy=    -390.8573318       time=       3.11
 Minus side of path:                    1050 steps. Energy=    -391.9279111       time=       3.19

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.8573318  1.8244         -389.0329029  2.8950         -391.9279111  36.400  32.092   3.744  38.726
        *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:                     971 steps. Energy=    -393.3015088       time=       2.70
 Minus side of path:                     949 steps. Energy=    -391.2704282       time=       2.62

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -393.3015088  4.0287         -389.2728484  1.9976         -391.2704282  37.389  35.026   3.729  38.879
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 6 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     2689.0    
 decide> The unconnected minima in the chain and their distances are:
     2       13.15     6     5        7.47     1 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 6_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.3823 Dev= 0.09% S= 13.76 time= 0.42
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):        100
 DNEB run yielded 1 true transition state(s) time=   8.56

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     953 steps. Energy=    -391.4223786       time=       2.70
 Minus side of path:                     930 steps. Energy=    -391.0933216       time=       2.38

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.4223786 0.35638         -391.0659938 0.27328E-01     -391.0933216   7.439   6.856   2.332  62.182
        *NEW* (Placed in 7)                                     *NEW* (Placed in 8)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 5_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.4111 Dev= 1.04% S= 7.97 time= 0.21
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         19
 DNEB run yielded 1 true transition state(s) time=   3.97

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     942 steps. Energy=    -386.9950363       time=       3.18
 Minus side of path:                     927 steps. Energy=    -391.9281723       time=       3.19

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.9950363  1.0861         -385.9089241  6.0192         -391.9281723   6.996   5.596  13.811  10.499
        Known (#1)                                              *NEW* (Placed in 9)
 Unconnected minimum 9 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 9 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      3 missing connections, weight=     494.84    
 decide> The unconnected minima in the chain and their distances are:
     2        6.75     7     8        4.97     6     5        4.01     9 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 7_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2597 Dev= 0.36% S= 7.14 time= 0.19
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):        208
 DNEB run yielded 1 true transition state(s) time=  25.89

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1079 steps. Energy=    -391.4223786       time=       3.33
 Minus side of path:                     910 steps. Energy=    -387.6035121       time=       2.70

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.4223786  4.4904         -386.9319304 0.67158         -387.6035121  37.029  35.291   3.270  44.343
        Known (#7)                                              *NEW* (Placed in 10)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 6_U and 8_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1126 Dev= 0.06% S= 5.03 time= 0.19
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         38
 DNEB run yielded 1 true transition state(s) time=   4.71
 isnewts> transition state is the same as number        3 energy=     -391.0659938005
 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:                     970 steps. Energy=    -391.4223786       time=       3.07
 Minus side of path:                     920 steps. Energy=    -391.0933216       time=       2.04

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.4223786 0.35638         -391.0659938 0.27328E-01     -391.0933216   7.439   6.856   2.334  62.137
        Known (#7)                                              Known (#8)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 5_U and 9_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 1.9208 Dev= 0.50% S= 4.17 time= 0.21
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         14
 DNEB run yielded 1 true transition state(s) time=   3.14

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     909 steps. Energy=    -393.3015088       time=       2.84
 Minus side of path:                     929 steps. Energy=    -391.9281723       time=       2.82

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -393.3015088  2.0180         -391.2834708 0.64470         -391.9281723   4.356   4.011  12.342  11.748
        Known (#5)                                              Known (#9)
 Unconnected minimum 5 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 10 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      2 missing connections, weight=     860.63    
 decide> The unconnected minima in the chain and their distances are:
     2        6.75     7     8        4.97     6 
 

 tryconnect> 525-iteration DNEB run for minima 2_F and 7_U using 15 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.3450947594    
 Double-ended search iterations= 525 RMS= 0.0260 Dev= 4.88% S= 9.32 time= 10.45
 Following    1 images are candidates for TS:    8  
 Converged to TS (number of iterations):         35
 DNEB run yielded 1 true transition state(s) time=   4.44

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     949 steps. Energy=    -391.4223786       time=       2.26
 Minus side of path:                     922 steps. Energy=    -394.0946509       time=       2.27

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.4223786  5.3114         -386.1109490  7.9837         -394.0946509  15.588   6.751   6.823  21.251
        Known (#7)                                              Known (#2)
 Unconnected minimum 7 found its way to F set.

 tryconnect> 385-iteration DNEB run for minima 6_S and 8_F using 11 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      1.644356330    
 Double-ended search iterations= 385 RMS= 0.0229 Dev= 5.15% S= 6.53 time= 5.61
 Following    2 images are candidates for TS:    5    9  
 Converged to TS (number of iterations):         18
 Converged to TS (number of iterations):         24
 DNEB run yielded 2 true transition state(s) time=   5.95
 isnewts> transition state is the same as number        3 energy=     -391.0659938006
 tryconnect> Will not repeat search for TS      2 same as TS      3

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     947 steps. Energy=    -391.4223786       time=       2.39
 Minus side of path:                     941 steps. Energy=    -391.2704282       time=       2.96

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.4223786 0.66119         -390.7611866 0.50924         -391.2704282   8.199   7.953   2.705  53.609
        Known (#7)                                              Known (#6)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   4     -386.9950363  1.0861        -385.9089241  6.0192        -391.9281723   6.996   5.596  13.811  10.499
   7     -391.9281723 0.64470        -391.2834708  2.0180        -393.3015088   4.356   4.011  12.342  11.748
   2     -393.3015088  4.0287        -389.2728484  1.9976        -391.2704282  37.389  35.026   3.729  38.879
   9     -391.2704282 0.50924        -390.7611866 0.66119        -391.4223786   8.199   7.953   2.705  53.609
   8     -391.4223786  5.3114        -386.1109490  7.9837        -394.0946509  15.588   6.751   6.823  21.251

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

 Elapsed time=                               144.92
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             46183 time=          61.99 %= 42.8
 OPTIM> # of energy+gradient+Hessian calls=       586 time=           2.92 %=  2.0
