
 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 13: 2:21 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>> Permuting endpoint atoms to minimise torsion distance
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -383.3551822     RMS force=    0.9284769086E-06
 OPTIM> Final energy  =    -386.9022817     RMS force=    0.9933692398E-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=     3046.4    
 decide> The unconnected minima in the chain and their distances are:
     2       14.50     1 
 

 tryconnect> 140-iteration DNEB run for minima 1_S and 2_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.1887 Dev= 0.43% S= 16.34 time= 0.76
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):        195
 DNEB run yielded 1 true transition state(s) time=  16.92

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     997 steps. Energy=    -386.8927998       time=       2.39
 Minus side of path:                     993 steps. Energy=    -386.9022817       time=       2.67

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.8927998 0.56580E-01     -386.8362201 0.66062E-01     -386.9022817   2.900   2.871   6.190  23.424
        *NEW* (Placed in 3)                                     Known (#2)
 Unconnected minimum 3 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 3 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     3669.8    
 decide> The unconnected minima in the chain and their distances are:
     3       15.42     1 
 

 tryconnect> 140-iteration DNEB run for minima 1_S and 3_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.2160 Dev= 0.32% S= 17.39 time= 0.73
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):        238
 DNEB run yielded 1 true transition state(s) time=  30.05

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1145 steps. Energy=    -386.9022817       time=       5.41
 Minus side of path:                    1009 steps. Energy=    -386.1138428       time=       4.14

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.9022817  1.4057         -385.4966052 0.61724         -386.1138428  35.297  30.931   4.309  33.648
        Known (#2)                                              *NEW* (Placed in 4)
 Unconnected minimum 4 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 4 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     6092.9    
 decide> The unconnected minima in the chain and their distances are:
     2       14.50     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 2_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.4624599827    
 Double-ended search iterations= 805 RMS= 0.0522 Dev= 5.00% S= 25.32 time= 22.51
 Following    3 images are candidates for TS:    2   10   20  
 Converged to TS (number of iterations):         20
 Failed to converge to TS (number of iterations):        251
 Converged to TS (number of iterations):         19
 DNEB run yielded 2 true transition state(s) time=  60.93

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1099 steps. Energy=    -387.1746544       time=       2.68
 Minus side of path:                     977 steps. Energy=    -383.3551822       time=       2.34

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -387.1746544  3.8532         -383.3214602 0.33722E-01     -383.3551822  14.701  13.700   5.339  27.159
        *NEW* (Placed in 5)                                     Known (#1)
 Unconnected minimum 5 found its way to S set.

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     992 steps. Energy=    -386.9022817       time=       2.86
 Minus side of path:                     987 steps. Energy=    -387.1746544       time=       3.56

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.9022817  2.7315         -384.1707759  3.0039         -387.1746544   7.156   5.892  27.228   5.325
        Known (#2)                                              Known (#5)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   3     -383.3551822 0.33722E-01    -383.3214602  3.8532        -387.1746544  14.701  13.700   5.339  27.159
   4     -387.1746544  3.0039        -384.1707759  2.7315        -386.9022817   7.156   5.892  27.228   5.325

 Number of TS in the path       =      2
 Number of cycles               =      3

 Elapsed time=                               158.01
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             37689 time=          44.86 %= 28.4
 OPTIM> # of energy+gradient+Hessian calls=       722 time=           3.55 %=  2.2
