
 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)@comp16.ch.
                 Created on  5/28/12 at 13:12:59 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.
 KeyInt>> using simple internal interpolation.    Image points will not be evenly distributed in Cartesians
 KeyInt>> Permuting endpoint atoms to minimise torsion distance
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -383.1678282     RMS force=    0.9687152806E-06
 OPTIM> Final energy  =    -388.7845356     RMS force=    0.9784241277E-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=     20781.    
 decide> The unconnected minima in the chain and their distances are:
     2       27.49     1 
 

 tryconnect> 280-iteration DNEB run for minima 1_S and 2_F using 8 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      1.726574146    
 Double-ended search iterations= 280 RMS= 0.4472 Dev= 0.43% S= 31.69 time= 2.71
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):        146
 DNEB run yielded 1 true transition state(s) time=  12.53

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     996 steps. Energy=    -383.5508335       time=       3.60
 Minus side of path:                     980 steps. Energy=    -387.6877387       time=       4.04

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -383.5508335 0.96367         -382.5871638  5.1006         -387.6877387  15.663  13.801   1.886  76.877
        *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=     10775.    
 decide> The unconnected minima in the chain and their distances are:
     2        9.95     4     3       21.39     1 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 4_U using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.7637 Dev= 0.56% S= 12.23 time= 0.19
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):        114
 DNEB run yielded 1 true transition state(s) time=   9.39

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     977 steps. Energy=    -389.5564792       time=       3.11
 Minus side of path:                     993 steps. Energy=    -387.6877387       time=       3.18

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -389.5564792  2.8692         -386.6872932  1.0004         -387.6877387  23.429  22.288   2.857  50.759
        *NEW* (Placed in 5)                                     Known (#4)
 Connection established between members of the U set.

 tryconnect> 210-iteration DNEB run for minima 1_S and 3_U using 6 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.0668 Dev= 0.22% S= 21.84 time= 1.52
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         96
 DNEB run yielded 1 true transition state(s) time=   7.15

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1167 steps. Energy=    -383.5508335       time=       2.95
 Minus side of path:                     967 steps. Energy=    -383.1761707       time=       2.08

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -383.5508335 0.43250         -383.1183294 0.57841E-01     -383.1761707  24.878  21.777   3.089  46.942
        Known (#3)                                              *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      4 steps with      2 missing connections, weight=     1968.5    
 decide> The unconnected minima in the chain and their distances are:
     2        9.95     4     6        0.90     1 
 

 tryconnect> 770-iteration DNEB run for minima 2_F and 4_U using 22 images  (DNEB attempt #2)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.2981058282    
 Double-ended search iterations= 770 RMS= 0.0485 Dev= 5.52% S= 23.05 time= 20.60
 Following    1 images are candidates for TS:   11  
 Converged to TS (number of iterations):         25
 DNEB run yielded 1 true transition state(s) time=   3.39

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     954 steps. Energy=    -385.2909508       time=       2.09
 Minus side of path:                    1014 steps. Energy=    -387.6877387       time=       2.31

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.2909508 0.16222         -385.1287336  2.5590         -387.6877387  18.502  12.943   4.978  29.128
        *NEW* (Placed in 7)                                     Known (#4)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 6_U using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0110 Dev= 0.18% S= 0.90 time= 0.17
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         12
 DNEB run yielded 1 true transition state(s) time=   2.64

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     983 steps. Energy=    -383.1761707       time=       2.12
 Minus side of path:                     924 steps. Energy=    -383.1678282       time=       1.90

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -383.1761707 0.32391E-01     -383.1437792 0.24049E-01     -383.1678282   0.913   0.899   8.087  17.929
        Known (#6)                                              Known (#1)
 Unconnected minimum 6 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 7 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     986.84    
 decide> The unconnected minima in the chain and their distances are:
     2        9.96     7 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 7_S using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1268 Dev= 0.34% S= 10.03 time= 0.18
 No maximum in profile - using highest image
 Following    0 images are candidates for TS:    2  
 Converged to TS (number of iterations):         45
 DNEB run yielded 1 true transition state(s) time=   4.12

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     878 steps. Energy=    -385.2909508       time=       1.82
 Minus side of path:                     937 steps. Energy=    -388.7845356       time=       2.01

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.2909508 0.15009E-01     -385.2759416  3.5086         -388.7845356  10.323   9.957   3.472  41.759
        Known (#7)                                              Known (#2)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   5     -383.1678282 0.24049E-01    -383.1437792 0.32391E-01    -383.1761707   0.913   0.899   8.087  17.929
   3     -383.1761707 0.57841E-01    -383.1183294 0.43250        -383.5508335  24.878  21.777   3.089  46.942
   1     -383.5508335 0.96367        -382.5871638  5.1006        -387.6877387  15.663  13.801   1.886  76.877
   4     -387.6877387  2.5590        -385.1287336 0.16222        -385.2909508  18.502  12.943   4.978  29.128
   6     -385.2909508 0.15009E-01    -385.2759416  3.5086        -388.7845356  10.323   9.957   3.472  41.759

 Number of TS in the path       =      5
 Number of cycles               =      4

 Elapsed time=                                95.92
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             39120 time=          45.73 %= 47.7
 OPTIM> # of energy+gradient+Hessian calls=       438 time=           1.86 %=  1.9
