
 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)@comp25.ch.
                 Created on  5/28/12 at 13: 4:36 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=    -375.1744094     RMS force=    0.9932691612E-06
 OPTIM> Final energy  =    -371.2775909     RMS force=    0.9258943288E-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=     21296.    
 decide> The unconnected minima in the chain and their distances are:
     2       27.72     1 
 

 tryconnect> 280-iteration DNEB run for minima 1_S and 2_F using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      153.6741246    
 Double-ended search iterations= 405 RMS= 2.8451 Dev= 1.38% S= 28.03 time= 4.32
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         56
 DNEB run yielded 1 true transition state(s) time=   7.28

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     898 steps. Energy=    -375.2724866       time=       2.10
 Minus side of path:                     836 steps. Energy=    -375.1635639       time=       1.83

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -375.2724866 0.12046         -375.1520268 0.11537E-01     -375.1635639   0.994   0.991  40.144   3.612
        *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      2 steps with      2 missing connections, weight=     22043.    
 decide> The unconnected minima in the chain and their distances are:
     2       28.04     3     3        1.07     1 
 

 tryconnect> 280-iteration DNEB run for minima 2_F and 3_U using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      153.6741246    
 Double-ended search iterations= 312 RMS= 25.0006 Dev= 29.40% S= 49.31 time= 3.35
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):        129
 DNEB run yielded 1 true transition state(s) time=  10.06

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1381 steps. Energy=    -375.6732872       time=       4.87
 Minus side of path:                    1275 steps. Energy=    -371.2775909       time=       4.07

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -375.6732872  7.2610         -368.4122384  2.8654         -371.2775909  42.574  27.940   2.815  51.513
        *NEW* (Placed in 5)                                     Known (#2)
 Unconnected minimum 5 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 3_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      7.462153966    
 Double-ended search iterations= 70 RMS= 0.2565 Dev= 0.37% S= 1.08 time= 0.19
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         10
 DNEB run yielded 1 true transition state(s) time=   2.49

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     876 steps. Energy=    -375.1744094       time=       2.18
 Minus side of path:                     886 steps. Energy=    -375.2724866       time=       2.15

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -375.1744094 0.15164E-01     -375.1592456 0.11324         -375.2724866   1.077   1.074  41.449   3.498
        Known (#1)                                              Known (#3)
 Unconnected minimum 3 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     40.742    
 decide> The unconnected minima in the chain and their distances are:
     5        3.44     3 
 

 tryconnect> 70-iteration DNEB run for minima 3_S and 5_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      14.77455444    
 Double-ended search iterations= 70 RMS= 0.1917 Dev= 0.98% S= 3.47 time= 0.19
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         15
 DNEB run yielded 1 true transition state(s) time=   3.01

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     885 steps. Energy=    -375.2724866       time=       2.07
 Minus side of path:                     909 steps. Energy=    -375.7716026       time=       2.16

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -375.2724866 0.14196         -375.1305244 0.64108         -375.7716026   3.612   3.526   6.508  22.282
        Known (#3)                                              *NEW* (Placed in 6)
 Unconnected minimum 6 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 6 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     1.2501    
 decide> The unconnected minima in the chain and their distances are:
     5        1.08     6 
 

 tryconnect> 70-iteration DNEB run for minima 5_F and 6_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      8.227024748    
 Double-ended search iterations= 70 RMS= 0.0571 Dev= 0.18% S= 1.08 time= 0.19
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         10
 DNEB run yielded 1 true transition state(s) time=   2.48

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     854 steps. Energy=    -375.6732872       time=       2.12
 Minus side of path:                     888 steps. Energy=    -375.7716026       time=       3.01

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -375.6732872 0.14958E-01     -375.6583294 0.11327         -375.7716026   1.080   1.077  41.279   3.513
        Known (#5)                                              Known (#6)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   3     -375.1744094 0.15164E-01    -375.1592456 0.11324        -375.2724866   1.077   1.074  41.449   3.498
   4     -375.2724866 0.14196        -375.1305244 0.64108        -375.7716026   3.612   3.526   6.508  22.282
   5     -375.7716026 0.11327        -375.6583294 0.14958E-01    -375.6732872   1.080   1.077  41.279   3.513
   2     -375.6732872  7.2610        -368.4122384  2.8654        -371.2775909  42.574  27.940   2.815  51.513

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

 Elapsed time=                                60.24
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             20818 time=          26.69 %= 44.3
 OPTIM> # of energy+gradient+Hessian calls=       220 time=           0.99 %=  1.6
