
 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)@comp31.ch.
                 Created on  5/28/12 at 13:11:48 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=    -381.4115420     RMS force=    0.9091137211E-06
 OPTIM> Final energy  =    -384.3809262     RMS force=    0.9953443816E-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=    0.20578E+06
 decide> The unconnected minima in the chain and their distances are:
     2       59.04     1 
 

 tryconnect> 595-iteration DNEB run for minima 1_S and 2_F using 17 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.1300625854    
 Double-ended search iterations= 595 RMS= 0.0414 Dev= 2.26% S= 66.94 time= 11.75
 Following    1 images are candidates for TS:    9  
 Converged to TS (number of iterations):        116
 DNEB run yielded 1 true transition state(s) time=   9.36

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1044 steps. Energy=    -380.6818344       time=       2.66
 Minus side of path:                    1068 steps. Energy=    -380.6105130       time=       3.45

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -380.6818344 0.39374         -380.2880910 0.32242         -380.6105130  26.521  25.960   2.048  70.805
        *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=     55020.    
 decide> The unconnected minima in the chain and their distances are:
     2       36.87     3     4       16.97     1 
 

 tryconnect> 385-iteration DNEB run for minima 2_F and 3_U using 11 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.2335737168    
 Double-ended search iterations= 385 RMS= 0.0359 Dev= 0.32% S= 38.52 time= 4.96
 Following    1 images are candidates for TS:   10  
 Converged to TS (number of iterations):         42
 DNEB run yielded 1 true transition state(s) time=   5.40

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1130 steps. Energy=    -384.3395678       time=       3.72
 Minus side of path:                    1024 steps. Energy=    -380.6818344       time=       3.04

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.3395678  3.6781         -380.6614622 0.20372E-01     -380.6818344  36.352  35.679   1.640  88.423
        *NEW* (Placed in 5)                                     Known (#3)
 Connection established between members of the U set.

 tryconnect> 175-iteration DNEB run for minima 1_S and 4_U using 5 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.2730 Dev= 0.07% S= 17.18 time= 0.97
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         64
 DNEB run yielded 1 true transition state(s) time=   7.10

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1070 steps. Energy=    -381.2770161       time=       4.22
 Minus side of path:                    1003 steps. Energy=    -380.6105130       time=       2.72

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.2770161 0.70640         -380.5706150 0.39898E-01     -380.6105130  21.688  21.547   1.864  77.795
        *NEW* (Placed in 6)                                     Known (#4)
 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=     9827.0    
 decide> The unconnected minima in the chain and their distances are:
     2        3.67     5     4       16.97     1 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 5_U using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2474 Dev= 0.04% S= 3.67 time= 0.17
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         13
 DNEB run yielded 1 true transition state(s) time=   3.50

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     931 steps. Energy=    -384.3395678       time=       2.67
 Minus side of path:                     979 steps. Energy=    -384.3809262       time=       3.03

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.3395678 0.17609E-01     -384.3219585 0.58968E-01     -384.3809262   3.686   3.668   1.703  85.121
        Known (#5)                                              Known (#2)
 Unconnected minimum 5 found its way to F set.

 tryconnect> 805-iteration DNEB run for minima 1_S and 4_F using 23 images  (DNEB attempt #2)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.6569044378E-01
 Double-ended search iterations= 805 RMS= 0.0995 Dev= 21.90% S= 29.02 time= 20.22
 Following    2 images are candidates for TS:   14   19  
 Converged to TS (number of iterations):         34
 Converged to TS (number of iterations):         26
 DNEB run yielded 2 true transition state(s) time=   7.92
 isnewts> transition state is the same as number        3 energy=     -380.5706150299
 tryconnect> Try the path again for ts      2 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1030 steps. Energy=    -381.2770161       time=       2.38
 Minus side of path:                    1087 steps. Energy=    -381.4115420       time=       2.50

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.2770161 0.34998         -380.9270369 0.48451         -381.4115420  24.781  22.599   2.615  55.441
        Known (#6)                                              Known (#1)

 >>>>>  Path run for ts 6 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    1046 steps. Energy=    -381.2770161       time=       2.32
 Minus side of path:                    1027 steps. Energy=    -380.6105130       time=       2.23

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.2770161 0.70640         -380.5706150 0.39898E-01     -380.6105130  21.688  21.547   1.864  77.793
        Known (#6)                                              Known (#4)
 Alternative path found between members of the F set.
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   5     -381.4115420 0.48451        -380.9270369 0.34998        -381.2770161  24.781  22.599   2.615  55.441
   3     -381.2770161 0.70640        -380.5706150 0.39898E-01    -380.6105130  21.688  21.547   1.864  77.795
   1     -380.6105130 0.32242        -380.2880910 0.39374        -380.6818344  26.521  25.960   2.048  70.805
   2     -380.6818344 0.20372E-01    -380.6614622  3.6781        -384.3395678  36.352  35.679   1.640  88.423
   4     -384.3395678 0.17609E-01    -384.3219585 0.58968E-01    -384.3809262   3.686   3.668   1.703  85.121

 Number of TS in the path       =      5
 Number of cycles               =      3

 Elapsed time=                               106.42
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             52567 time=          56.08 %= 52.7
 OPTIM> # of energy+gradient+Hessian calls=       295 time=           1.29 %=  1.2
