
 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)@comp29.ch.
                 Created on  5/28/12 at 13: 5:13 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=    -383.2316760     RMS force=    0.9326983595E-06
 OPTIM> Final energy  =    -391.3156109     RMS force=    0.9142348555E-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=     39462.    
 decide> The unconnected minima in the chain and their distances are:
     2       34.05     1 
 

 tryconnect> 350-iteration DNEB run for minima 1_S and 2_F using 10 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      304.2642554    
 Double-ended search iterations= 378 RMS= 58.3183 Dev= 23.98% S= 71.40 time= 5.59
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         25
 DNEB run yielded 1 true transition state(s) time=   4.41

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     949 steps. Energy=    -389.7215338       time=       2.79
 Minus side of path:                     929 steps. Energy=    -389.1057838       time=       2.89

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -389.7215338 0.64395         -389.0775860 0.28198E-01     -389.1057838   3.333   3.258   5.442  26.643
        *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=     19971.    
 decide> The unconnected minima in the chain and their distances are:
     2       10.54     3     4       26.59     1 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 3_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      14.07100423    
 Double-ended search iterations= 105 RMS= 0.1858 Dev= 0.64% S= 10.58 time= 0.47
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         40
 DNEB run yielded 1 true transition state(s) time=   4.24

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     959 steps. Energy=    -391.3156109       time=       2.50
 Minus side of path:                     922 steps. Energy=    -389.7215338       time=       2.28

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.3156109  2.0709         -389.2447121 0.47682         -389.7215338  11.493  10.545   2.010  72.153
        Known (#2)                                              Known (#3)
 Unconnected minimum 3 found its way to F set.

 tryconnect> 245-iteration DNEB run for minima 1_S and 4_F using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      109.2133313    
 Double-ended search iterations= 522 RMS= 3.2239 Dev= 0.13% S= 26.77 time= 5.24
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         29
 DNEB run yielded 1 true transition state(s) time=   4.90

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     957 steps. Energy=    -384.8532460       time=       3.21
 Minus side of path:                     957 steps. Energy=    -387.2420025       time=       2.41

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.8532460  1.5470         -383.3062792  3.9357         -387.2420025   5.236   4.743  15.391   9.421
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      2 missing connections, weight=     11659.    
 decide> The unconnected minima in the chain and their distances are:
     4       16.15     6     5       19.53     1 
 

 tryconnect> 140-iteration DNEB run for minima 4_F and 6_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      9.070294785    
 Double-ended search iterations= 140 RMS= 0.1478 Dev= 0.80% S= 16.25 time= 0.78
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         62
 DNEB run yielded 1 true transition state(s) time=   5.88

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     946 steps. Energy=    -388.7676323       time=       2.63
 Minus side of path:                     890 steps. Energy=    -387.2420025       time=       2.40

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -388.7676323  1.5507         -387.2168929 0.25110E-01     -387.2420025   6.698   6.060   6.820  21.260
        *NEW* (Placed in 7)                                     Known (#6)
 Connection established between members of the U set.

 tryconnect> 175-iteration DNEB run for minima 1_S and 5_U using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      55.16015368    
 Double-ended search iterations= 843 RMS= 3.8672 Dev= 0.11% S= 19.70 time= 5.97
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         71
 DNEB run yielded 1 true transition state(s) time=   6.42

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     969 steps. Energy=    -383.2316760       time=       2.80
 Minus side of path:                     960 steps. Energy=    -384.8532460       time=       3.06

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -383.2316760 0.17930         -383.0523749  1.8009         -384.8532460  20.294  19.552   7.519  19.284
        Known (#1)                                              Known (#5)
 Unconnected minimum 5 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 7 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     1993.5    
 decide> The unconnected minima in the chain and their distances are:
     4       12.59     7 
 

 tryconnect> 105-iteration DNEB run for minima 4_F and 7_S using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      12.76281563    
 Double-ended search iterations= 105 RMS= 0.1032 Dev= 0.42% S= 12.60 time= 0.45
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         28
 DNEB run yielded 1 true transition state(s) time=   3.78

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     956 steps. Energy=    -389.1788416       time=       2.57
 Minus side of path:                     887 steps. Energy=    -388.7676323       time=       2.34

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -389.1788416 0.49472         -388.6841213 0.83511E-01     -388.7676323  13.337  13.156   1.991  72.841
        *NEW* (Placed in 8)                                     Known (#7)
 Unconnected minimum 8 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 8 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      1 missing connections, weight=     2.4442    
 decide> The unconnected minima in the chain and their distances are:
     4        1.35     8 
 

 tryconnect> 70-iteration DNEB run for minima 4_F and 8_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.768393620    
 Double-ended search iterations= 70 RMS= 0.0212 Dev= 0.36% S= 1.35 time= 0.20
 No maximum in profile - using highest image
 Following    0 images are candidates for TS:    1  
 Converged to TS (number of iterations):         22
 DNEB run yielded 1 true transition state(s) time=   3.20

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     900 steps. Energy=    -389.1057838       time=       2.18
 Minus side of path:                     927 steps. Energy=    -389.1788416       time=       2.47

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -389.1057838 0.24419E-02     -389.1033419 0.75500E-01     -389.1788416   1.384   1.347   5.237  27.687
        Known (#4)                                              Known (#8)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   5     -383.2316760 0.17930        -383.0523749  1.8009        -384.8532460  20.294  19.552   7.519  19.284
   3     -384.8532460  1.5470        -383.3062792  3.9357        -387.2420025   5.236   4.743  15.391   9.421
   4     -387.2420025 0.25110E-01    -387.2168929  1.5507        -388.7676323   6.698   6.060   6.820  21.260
   6     -388.7676323 0.83511E-01    -388.6841213 0.49472        -389.1788416  13.337  13.156   1.991  72.841
   7     -389.1788416 0.75500E-01    -389.1033419 0.24419E-02    -389.1057838   1.384   1.347   5.237  27.687
   1     -389.1057838 0.28198E-01    -389.0775860 0.64395        -389.7215338   3.333   3.258   5.442  26.643
   2     -389.7215338 0.47682        -389.2447121  2.0709        -391.3156109  11.493  10.545   2.010  72.153

 Number of TS in the path       =      7
 Number of cycles               =      5

 Elapsed time=                                88.24
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             32719 time=          45.19 %= 51.2
 OPTIM> # of energy+gradient+Hessian calls=       277 time=           1.27 %=  1.4
