
 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)@comp23.ch.
                 Created on  5/28/12 at 12:53:58 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=    -383.5130933     RMS force=    0.8840672774E-06
 OPTIM> Final energy  =    -381.3326931     RMS force=    0.9898394155E-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=     53980.    
 decide> The unconnected minima in the chain and their distances are:
     2       37.79     1 
 

 tryconnect> 385-iteration DNEB run for minima 1_S and 2_F using 11 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      319.4774681    
 Double-ended search iterations= 385 RMS= 3.0677 Dev= 1.04% S= 38.13 time= 5.89
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         50
 DNEB run yielded 1 true transition state(s) time=   6.29

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     925 steps. Energy=    -381.5222420       time=       2.31
 Minus side of path:                     936 steps. Energy=    -381.6248082       time=       2.23

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.5222420 0.12836E-01     -381.5094059 0.11540         -381.6248082   1.087   1.084  40.626   3.569
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 4 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     56261.    
 decide> The unconnected minima in the chain and their distances are:
     2       11.21     4     3       38.00     1 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 4_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      10.50000000    
 Double-ended search iterations= 105 RMS= 0.4535 Dev= 0.54% S= 11.24 time= 0.42
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         29
 DNEB run yielded 1 true transition state(s) time=   5.46

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     973 steps. Energy=    -381.6248082       time=       3.82
 Minus side of path:                    1004 steps. Energy=    -383.0478394       time=       2.48

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.6248082 0.63202E-01     -381.5616064  1.4862         -383.0478394   3.239   3.064   4.242  34.183
        Known (#4)                                              *NEW* (Placed in 5)
 Connection established between members of the U set.

 tryconnect> 385-iteration DNEB run for minima 1_S and 3_U using 11 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      161.3578309    
 Double-ended search iterations= 385 RMS= 1.5616 Dev= 0.68% S= 38.31 time= 5.92
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         50
 DNEB run yielded 1 true transition state(s) time=   6.86
 isnewts> transition state is the same as number        1 energy=     -381.5094059250
 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:                     942 steps. Energy=    -381.6248082       time=       2.31
 Minus side of path:                     927 steps. Energy=    -381.5222420       time=       2.24

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.6248082 0.11540         -381.5094059 0.12836E-01     -381.5222420   1.087   1.084  40.630   3.569
        Known (#4)                                              Known (#3)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     56837.    
 decide> The unconnected minima in the chain and their distances are:
     2       11.59     3     4       38.09     1 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 3_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      9.523809524    
 Double-ended search iterations= 105 RMS= 0.8174 Dev= 0.55% S= 11.62 time= 0.42
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         37
 DNEB run yielded 1 true transition state(s) time=   4.32
 isnewts> transition state is the same as number        1 energy=     -381.5094059231
 tryconnect> Will not repeat search for TS      1 same as TS      1

 tryconnect> 385-iteration DNEB run for minima 1_S and 4_U using 11 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      89.85007793    
 Double-ended search iterations= 385 RMS= 0.4900 Dev= 0.27% S= 38.46 time= 6.00
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):        100
 DNEB run yielded 1 true transition state(s) time=   8.91

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     985 steps. Energy=    -381.7774156       time=       2.40
 Minus side of path:                     988 steps. Energy=    -381.5109421       time=       2.41

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.7774156 0.27462         -381.5027992 0.81430E-02     -381.5109421   3.286   3.088   6.129  23.657
        *NEW* (Placed in 6)                                     *NEW* (Placed in 7)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 7 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      2 missing connections, weight=     37588.    
 decide> The unconnected minima in the chain and their distances are:
     2        9.88     6     6       33.21     1 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 6_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      13.40095641    
 Double-ended search iterations= 70 RMS= 0.9281 Dev= 2.10% S= 9.90 time= 0.19
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         62
 DNEB run yielded 1 true transition state(s) time=   5.60
 isnewts> transition state is the same as number        4 energy=     -381.5027991906
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 5 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     986 steps. Energy=    -381.7774156       time=       2.36
 Minus side of path:                     985 steps. Energy=    -381.5109421       time=       2.43

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.7774156 0.27462         -381.5027992 0.81430E-02     -381.5109421   3.286   3.088   6.129  23.657
        Known (#6)                                              Known (#7)
 Connection established between members of the U set.

 tryconnect> 315-iteration DNEB run for minima 1_S and 6_U using 9 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      25.26950195    
 Double-ended search iterations= 315 RMS= 0.2684 Dev= 0.52% S= 33.55 time= 3.99
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         66
 DNEB run yielded 1 true transition state(s) time=   5.61

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1029 steps. Energy=    -381.5109421       time=       2.61
 Minus side of path:                    1038 steps. Energy=    -383.5130933       time=       2.80

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.5109421 0.60457         -380.9063747  2.6067         -383.5130933  35.219  34.224   2.123  68.310
        Known (#7)                                              Known (#1)
 Unconnected minimum 7 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 7 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     1001.4    
 decide> The unconnected minima in the chain and their distances are:
     2       10.00     7 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 7_S using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      8.638375985    
 Double-ended search iterations= 105 RMS= 0.0883 Dev= 0.67% S= 10.03 time= 0.42
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         52
 DNEB run yielded 1 true transition state(s) time=   4.75

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                    1028 steps. Energy=    -381.5109421       time=       2.47
 Minus side of path:                     957 steps. Energy=    -381.3326931       time=       2.18

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.5109421 0.57435         -380.9365940 0.39610         -381.3326931  11.313  10.006   1.761  82.354
        Known (#7)                                              Known (#2)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   6     -383.5130933  2.6067        -380.9063747 0.60457        -381.5109421  35.219  34.224   2.123  68.310
   7     -381.5109421 0.57435        -380.9365940 0.39610        -381.3326931  11.313  10.006   1.761  82.354

 Number of TS in the path       =      2
 Number of cycles               =      5

 Elapsed time=                               106.29
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             39153 time=          51.66 %= 48.6
 OPTIM> # of energy+gradient+Hessian calls=       446 time=           1.94 %=  1.8
