
 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)@comp32.ch.
                 Created on  5/28/12 at 12:31:44 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=    -388.3743583     RMS force=    0.9589739517E-06
 OPTIM> Final energy  =    -385.9372500     RMS force=    0.9633571024E-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=     27170.    
 decide> The unconnected minima in the chain and their distances are:
     2       30.06     1 
 

 tryconnect> 315-iteration DNEB run for minima 1_S and 2_F using 9 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 315 RMS= 0.1043 Dev= 1.52% S= 35.59 time= 4.03
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         37
 DNEB run yielded 1 true transition state(s) time=   5.92

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1005 steps. Energy=    -389.1988082       time=       3.35
 Minus side of path:                     991 steps. Energy=    -384.6377338       time=       4.16

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -389.1988082  6.6562         -382.5425886  2.0951         -384.6377338  28.341  25.788  10.615  13.660
        *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=     962.12    
 decide> The unconnected minima in the chain and their distances are:
     2        5.34     4     3        9.32     1 
 

 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= 0.3680 Dev= 0.71% S= 5.81 time= 0.20
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         61
 DNEB run yielded 1 true transition state(s) time=   6.52

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     984 steps. Energy=    -384.7423728       time=       3.75
 Minus side of path:                     962 steps. Energy=    -384.6377338       time=       3.03

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.7423728 0.39353         -384.3488379 0.28890         -384.6377338  12.483  11.147   5.056  28.678
        *NEW* (Placed in 5)                                     Known (#4)
 Connection established between members of the U 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= 1.1090 Dev= 1.00% S= 10.29 time= 0.19
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         45
 DNEB run yielded 1 true transition state(s) time=   5.22

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     951 steps. Energy=    -390.7775518       time=       2.83
 Minus side of path:                     956 steps. Energy=    -388.3743583       time=       3.19

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.7775518  4.0148         -386.7627300  1.6116         -388.3743583  10.286   7.994  19.269   7.525
        *NEW* (Placed in 6)                                     Known (#1)
 Unconnected minimum 6 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     373.36    
 decide> The unconnected minima in the chain and their distances are:
     2        5.34     4     3        4.11     6 
 

 tryconnect> 420-iteration DNEB run for minima 2_F and 4_U using 12 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.3994903209    
 Double-ended search iterations= 420 RMS= 0.0148 Dev= 4.62% S= 7.22 time= 6.56
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):         13
 DNEB run yielded 1 true transition state(s) time=   3.02

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     951 steps. Energy=    -384.6377338       time=       2.86
 Minus side of path:                     970 steps. Energy=    -385.9372500       time=       3.25

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.6377338  2.1765         -382.4612796  3.4760         -385.9372500   6.171   5.356  39.846   3.639
        Known (#4)                                              Known (#2)
 Unconnected minimum 4 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 3_F and 6_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 1.8005 Dev= 1.32% S= 4.66 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=   4.11

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     933 steps. Energy=    -390.7775518       time=       2.91
 Minus side of path:                     955 steps. Energy=    -389.1988082       time=       3.09

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.7775518  4.5607         -386.2168067  2.9820         -389.1988082   4.832   4.113  34.249   4.234
        Known (#6)                                              Known (#3)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   3     -388.3743583  1.6116        -386.7627300  4.0148        -390.7775518  10.286   7.994  19.269   7.525
   5     -390.7775518  4.5607        -386.2168067  2.9820        -389.1988082   4.832   4.113  34.249   4.234
   1     -389.1988082  6.6562        -382.5425886  2.0951        -384.6377338  28.341  25.788  10.615  13.660
   4     -384.6377338  2.1765        -382.4612796  3.4760        -385.9372500   6.171   5.356  39.846   3.639

 Number of TS in the path       =      4
 Number of cycles               =      3

 Elapsed time=                                68.50
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             22779 time=          30.07 %= 43.9
 OPTIM> # of energy+gradient+Hessian calls=       171 time=           0.91 %=  1.3
