
 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 12:40:21 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=    -386.8811822     RMS force=    0.9010287363E-06
 OPTIM> Final energy  =    -383.8347763     RMS force=    0.9097963389E-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=    0.21530E+06
 decide> The unconnected minima in the chain and their distances are:
     2       59.93     1 
 

 tryconnect> 595-iteration DNEB run for minima 1_S and 2_F using 17 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.3009354918E-01
 Double-ended search iterations= 595 RMS= 0.1581 Dev= 3.18% S= 69.86 time= 12.12
 Following    2 images are candidates for TS:    7   12  
 Converged to TS (number of iterations):         69
 Converged to TS (number of iterations):         45
 DNEB run yielded 2 true transition state(s) time=  16.16

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1292 steps. Energy=    -386.8811822       time=       3.86
 Minus side of path:                    1034 steps. Energy=    -385.2241429       time=       2.46

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.8811822  1.7857         -385.0955298 0.12861         -385.2241429  39.462  33.039   2.029  71.451
        Known (#1)                                              *NEW* (Placed in 3)
 Unconnected minimum 3 found its way to S set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1164 steps. Energy=    -383.7366609       time=       3.29
 Minus side of path:                    1023 steps. Energy=    -383.0612560       time=       2.64

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -383.7366609 0.87463         -382.8620343 0.19922         -383.0612560  40.766  39.127   2.705  53.603
        *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=     44381.    
 decide> The unconnected minima in the chain and their distances are:
     2        1.04     4     4       35.40     3 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 4_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0268 Dev= 0.11% S= 1.05 time= 0.16
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         11
 DNEB run yielded 1 true transition state(s) time=   2.41

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1014 steps. Energy=    -383.8347763       time=       2.24
 Minus side of path:                     999 steps. Energy=    -383.7366609       time=       2.21

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -383.8347763 0.11306         -383.7217202 0.14941E-01     -383.7366609   1.048   1.045  38.531   3.763
        Known (#2)                                              Known (#4)
 Unconnected minimum 4 found its way to F set.

 tryconnect> 350-iteration DNEB run for minima 3_S and 4_F using 10 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.3286616756    
 Double-ended search iterations= 350 RMS= 0.0209 Dev= 1.65% S= 37.33 time= 3.99
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         42
 DNEB run yielded 1 true transition state(s) time=   6.89
 isnewts> transition state is the same as number        2 energy=     -382.8620342745
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 4 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    1080 steps. Energy=    -383.0612560       time=       2.90
 Minus side of path:                    1149 steps. Energy=    -383.7366609       time=       3.46

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -383.0612560 0.19922         -382.8620343 0.87463         -383.7366609  40.772  39.133   2.699  53.716
        Known (#5)                                              Known (#4)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     45305.    
 decide> The unconnected minima in the chain and their distances are:
     2       35.65     3 
 

 tryconnect> 350-iteration DNEB run for minima 2_F and 3_S using 10 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.3286616756    
 Double-ended search iterations= 350 RMS= 0.0472 Dev= 1.92% S= 37.61 time= 4.03
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         38
 DNEB run yielded 1 true transition state(s) time=   9.10
 isnewts> transition state is the same as number        2 energy=     -382.8620342745
 tryconnect> Will not repeat search for TS      1 same as TS      2
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 5 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     48444.    
 decide> The unconnected minima in the chain and their distances are:
     5       36.45     3 
 

 tryconnect> 350-iteration DNEB run for minima 3_S and 5_F using 10 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.3286616756    
 Double-ended search iterations= 350 RMS= 0.0341 Dev= 0.47% S= 37.78 time= 4.36
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):         57
 DNEB run yielded 1 true transition state(s) time=   6.83

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1024 steps. Energy=    -383.0612560       time=       4.25
 Minus side of path:                    1061 steps. Energy=    -385.2241429       time=       4.68

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -383.0612560 0.26796         -382.7932931  2.4308         -385.2241429  38.748  36.503   2.271  63.838
        Known (#5)                                              Known (#3)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -386.8811822  1.7857        -385.0955298 0.12861        -385.2241429  39.462  33.039   2.029  71.451
   5     -385.2241429  2.4308        -382.7932931 0.26796        -383.0612560  38.748  36.503   2.271  63.838
   2     -383.0612560 0.19922        -382.8620343 0.87463        -383.7366609  40.766  39.127   2.705  53.603
   3     -383.7366609 0.14941E-01    -383.7217202 0.11306        -383.8347763   1.048   1.045  38.531   3.763

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

 Elapsed time=                                98.16
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             38647 time=          44.03 %= 44.9
 OPTIM> # of energy+gradient+Hessian calls=       262 time=           1.30 %=  1.3
