
 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)@comp24.ch.
                 Created on  5/28/12 at 12:44:37 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


 natintsetup, NATOMS          145
 cartres           12
 KeyInt>> Using natural internal coordinates. # of coords =        429
 KeyInt>> Parameter file for internal coordinates is naturals-noH.par                                                                                    
 KeyInt>> KD, NNZ are         50      4500
 KeyInt>> Back transform convergence (for interpolation)     0.1000000000E-07
 KeyInt>> Back transform convergence criterion (except for interpolation)     0.1000000000E-03
 KeyInt>> Using internal coordinates for interpolation.
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -384.9194479     RMS force=    0.8510596021E-06
 OPTIM> Final energy  =    -390.4183956     RMS force=    0.9028449365E-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=     56261.    
 decide> The unconnected minima in the chain and their distances are:
     2       38.32     1 
 

 tryconnect> 385-iteration DNEB run for minima 1_S and 2_F using 11 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.2335737168    
 Double-ended search iterations= 385 RMS= 0.0659 Dev= 2.45% S= 42.68 time= 5.73
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         54
 DNEB run yielded 1 true transition state(s) time=   7.54

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     969 steps. Energy=    -384.9194479       time=       2.58
 Minus side of path:                     992 steps. Energy=    -385.3447492       time=       2.58

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.9194479 0.24360         -384.6758460 0.66890         -385.3447492  25.701  24.909   2.527  57.389
        Known (#1)                                              *NEW* (Placed in 3)
 Unconnected minimum 3 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 3 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     6045.2    
 decide> The unconnected minima in the chain and their distances are:
     2       18.22     3 
 

 tryconnect> 175-iteration DNEB run for minima 2_F and 3_S using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.1732 Dev= 1.22% S= 18.97 time= 1.26
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         20
 DNEB run yielded 1 true transition state(s) time=   3.40

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     980 steps. Energy=    -386.3009340       time=       2.54
 Minus side of path:                     952 steps. Energy=    -385.3447492       time=       2.39

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.3009340  2.9772         -383.3237764  2.0210         -385.3447492   7.251   6.166  22.985   6.308
        *NEW* (Placed in 4)                                     Known (#3)
 Unconnected minimum 4 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 4 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     3375.8    
 decide> The unconnected minima in the chain and their distances are:
     2       15.00     4 
 

 tryconnect> 140-iteration DNEB run for minima 2_F and 4_S using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.100679103    
 Double-ended search iterations= 140 RMS= 0.0688 Dev= 0.39% S= 15.14 time= 0.84
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         29
 DNEB run yielded 1 true transition state(s) time=   4.10

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1021 steps. Energy=    -390.4557563       time=       4.04
 Minus side of path:                     987 steps. Energy=    -386.3009340       time=       2.91

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.4557563  4.3659         -386.0898136 0.21112         -386.3009340  16.039  15.236   3.008  48.204
        *NEW* (Placed in 5)                                     Known (#4)
 Unconnected minimum 5 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=    0.58796    
 decide> The unconnected minima in the chain and their distances are:
     2        0.84     5 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 5_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0128 Dev= 0.09% S= 0.84 time= 0.24
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):          9
 DNEB run yielded 1 true transition state(s) time=   2.66

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     859 steps. Energy=    -390.4183956       time=       2.72
 Minus side of path:                     867 steps. Energy=    -390.4557563       time=       2.56

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -390.4183956 0.11606E-01     -390.4067900 0.48966E-01     -390.4557563   0.871   0.838   6.659  21.775
        Known (#2)                                              Known (#5)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -384.9194479 0.24360        -384.6758460 0.66890        -385.3447492  25.701  24.909   2.527  57.389
   2     -385.3447492  2.0210        -383.3237764  2.9772        -386.3009340   7.251   6.166  22.985   6.308
   3     -386.3009340 0.21112        -386.0898136  4.3659        -390.4557563  16.039  15.236   3.008  48.204
   4     -390.4557563 0.48966E-01    -390.4067900 0.11606E-01    -390.4183956   0.871   0.838   6.659  21.775

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

 Elapsed time=                                48.18
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             17204 time=          22.87 %= 47.5
 OPTIM> # of energy+gradient+Hessian calls=       112 time=           0.58 %=  1.2
