
 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> Constraint potential parameters read from file congeom.dat
 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)@comp34.ch.
                 Created on  5/28/12 at 10:32:57 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
 fetchz> Using constraint potential for initial interpolation in each cycle
         with absolute distance change tolerance         0.30000
         extra distance before turning on constraint potential         0.17500
         constraint spring constant=       10.00000
         image distance spring constant=        1.00000
         repulsion factor between unconstrained atoms=      100.00000
         repulsion cutoff will be the minimum of         1.55000 and the shortest distance in the end points
         fraction for restoring true potential=        0.99000
         maximum separation of atoms in sequence for constraint=   218
         minimum separation of atoms in sequence for repulsion=     0
         maximum optimization steps for constrained potential=  300001
         initial # images for constrained potential, maximum, check interval=       3      75      25
         number of interpolation attempts and initial image increment=       2      12
         RMS gradient per image tolerance for constrained potential=        0.01000
         maximum optimization steps for constrained/real potential=      25
         maximum steps for relaxation after adding a new atom before backtrack=     200
         maximum number of constraints per atom=     6
         maximum energy per image for convergence during constraint potential phase=        0.1000000000
         interval for checking repulsive interactions=    10
         multiple of cutoff for repulsion neighbour list=        2.0000000000
         adding terms for constraint internal minima
         Minimum and Maximum image separations:         0.10000       10.00000
 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> Number of updates in qci=   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=    -394.5890829     RMS force=    0.8668942108E-06
 OPTIM> Final energy  =    -401.3454376     RMS force=    0.9309026839E-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 from interp function and dist, power=     3

 initialise> Interpolation metric value for minima 1 and 2 is      26.72756013    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     15604.    
 decide> The unconnected minima in the chain and their distances are:
     2       24.96     1 
 

 tryconnect> Interpolation for minima 1_S and 2_F using 3 initial images  (interp attempt #1)  ...
 intlbfgs> Maximum number of steps for constraint potential phase is 300001
 intlbfgs> Total number of atoms moving less than threshold=    90
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    122 fraction=    0.990000 images=     4 time=       0.1
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    147 steps, energy/image=    -387.3548792     RMS=.6235614534     images=   4
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   29.47     Attempts, images and iterations=     0     8   280
 lbfgs> Final DNEB force constant     0.6507276371    
 Double-ended search iterations= 280 RMS= 0.1597 Dev= 3.75% S= 28.67 time= 3.36
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         27
 DNEB run yielded 1 true transition state(s) time=   4.73

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     988 steps. Energy=    -394.5890829       time=       3.48
 Minus side of path:                     915 steps. Energy=    -393.5316147       time=       3.25

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -394.5890829  3.1498         -391.4392777  2.0923         -393.5316147   9.757   9.002  22.679   6.394
        Known (#1)                                              *NEW* (Placed in 3)
 checkperc> Increasing con cutoff atoms    54   55 from     0.12762E-01 to     0.13156E-01 ref=     1.5336    
 checkperc> Increasing con cutoff atoms   111  112 from     0.65702E-02 to     0.98701E-02 ref=    0.96688    
 checkperc> Increasing con cutoff atoms   114  116 from     0.59669E-02 to     0.69823E-02 ref=     1.3394    
 checkperc> Increasing con cutoff atoms   114  118 from     0.36285E-01 to     0.47180E-01 ref=     2.4726    
 checkperc> Increasing con cutoff atoms   115  118 from     0.90405E-01 to     0.95002E-01 ref=     2.8239    
 checkperc> Increasing con cutoff atoms   117  118 from     0.18686E-01 to     0.18763E-01 ref=     2.1119    
 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=     8399.7    
 decide> The unconnected minima in the chain and their distances are:
     2       20.31     3 
 

 tryconnect> Interpolation for minima 2_F and 3_S using 3 initial images  (interp attempt #1)  ...
 intlbfgs> Maximum number of steps for constraint potential phase is 300001
 intlbfgs> Total number of atoms moving less than threshold=    95
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    104 fraction=    0.990000 images=     4 time=       0.1
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    129 steps, energy/image=    -389.2000526     RMS=.6160758606     images=   4
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      2     3 dist=   23.93     Attempts, images and iterations=     0     7   245
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 245 RMS= 0.2806 Dev= 2.09% S= 23.77 time= 2.56
 Following    2 images are candidates for TS:    3    7  
 Failed to converge to TS (number of iterations):        251
 bfgsts> WARNING *** initial eigenvalue is positive - increase NEBK?
 Converged to TS (number of iterations):         86
 DNEB run yielded 1 true transition state(s) time=  28.74

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     920 steps. Energy=    -393.5316147       time=       2.66
 Minus side of path:                    1103 steps. Energy=    -396.2688547       time=       3.49

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -393.5316147 0.72101         -392.8106089  3.4582         -396.2688547  24.721  20.121   4.738  30.603
        Known (#3)                                              *NEW* (Placed in 4)
 checkperc> Increasing con cutoff atoms    25   26 from     0.19092E-02 to     0.19342E-02 ref=     1.2337    
 checkperc> Increasing con cutoff atoms    25   29 from     0.13779E-01 to     0.16249E-01 ref=     2.4463    
 checkperc> Increasing con cutoff atoms    27   29 from     0.33634E-02 to     0.53019E-02 ref=     1.4536    
 checkperc> Increasing con cutoff atoms    27   34 from     0.54168E-01 to     0.69963E-01 ref=     2.4623    
 checkperc> Increasing con cutoff atoms    55   57 from     0.38766E-01 to     0.40166E-01 ref=     2.5798    
 checkperc> Increasing con cutoff atoms    55   60 from     0.41155E-01 to     0.41357E-01 ref=     2.5130    
 checkperc> Increasing con cutoff atoms    96   99 from     0.76815E-02 to     0.78451E-02 ref=     2.2606    
 checkperc> Increasing con cutoff atoms   111  112 from     0.98701E-02 to     0.10839E-01 ref=    0.96688    
 checkperc> Increasing con cutoff atoms   132  135 from     0.46211E-01 to     0.46617E-01 ref=     2.4437    
 checkperc> Increasing con cutoff atoms   135  143 from     0.33423E-01 to     0.35174E-01 ref=     2.5262    
 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=     652.75    
 decide> The unconnected minima in the chain and their distances are:
     2        8.67     4 
 

 tryconnect> Interpolation for minima 2_F and 4_S using 3 initial images  (interp attempt #1)  ...
 intlbfgs> Maximum number of steps for constraint potential phase is 300001
 intlbfgs> Total number of atoms moving less than threshold=   131
 intlbfgs> Freezing    130 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     46 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     71 steps, energy/image=    -389.9845800     RMS=.6741206733     images=   3
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      2     4 dist=   12.64     Attempts, images and iterations=     0     3   105
 lbfgs> Final DNEB force constant      5.846792891    
 Double-ended search iterations= 105 RMS= 0.3926 Dev= 0.20% S= 9.54 time= 0.48
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):        108
 DNEB run yielded 1 true transition state(s) time=   8.26

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1112 steps. Energy=    -401.3454376       time=       3.43
 Minus side of path:                     791 steps. Energy=    -394.6708445       time=       2.19

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -401.3454376  6.7095         -394.6359786 0.34866E-01     -394.6708445  13.374  12.388   8.365  17.335
        Known (#2)                                              *NEW* (Placed in 5)
 checkperc> Increasing con cutoff atoms    14   16 from     0.20851E-01 to     0.22095E-01 ref=     2.5967    
 Unconnected minimum 5 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     1305.5    
 decide> The unconnected minima in the chain and their distances are:
     2        8.67     4 
 

 tryconnect> Interpolation for minima 2_F and 4_S using 15 initial images  (interp attempt #2)  ...
 intlbfgs> Maximum number of steps for constraint potential phase is 300001
 intlbfgs> Total number of atoms moving less than threshold=   131
 intlbfgs> Freezing    130 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     30 fraction=    0.990000 images=    15 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     55 steps, energy/image=    -395.3329519     RMS=.6381974286     images=  15
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      2     4 dist=   13.67     Attempts, images and iterations=     3    23   805
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 805 RMS= 0.0823 Dev= 4.44% S= 15.16 time= 28.10
 Following    3 images are candidates for TS:    6   20   22  
 Converged to TS (number of iterations):         16
 Converged to TS (number of iterations):         14
 Converged to TS (number of iterations):         16
 DNEB run yielded 3 true transition state(s) time=   7.60

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     813 steps. Energy=    -401.3454376       time=       2.01
 Minus side of path:                     804 steps. Energy=    -401.6605666       time=       1.95

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -401.3454376  4.7124         -396.6330266  5.0275         -401.6605666   6.559   5.694  36.980   3.921
        Known (#2)                                              *NEW* (Placed in 6)
 checkperc> Increasing con cutoff atoms    38   42 from     0.67666E-01 to     0.67701E-01 ref=     4.4565    
 Unconnected minimum 6 found its way to F set.

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     760 steps. Energy=    -396.2627584       time=       1.71
 Minus side of path:                     840 steps. Energy=    -401.6605666       time=       2.12

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -396.2627584 0.75032         -395.5124341  6.1481         -401.6605666   7.049   6.334   3.554  40.801
        *NEW* (Placed in 7)                                     Known (#6)
 checkperc> Increasing con cutoff atoms    55   57 from     0.40166E-01 to     0.44341E-01 ref=     2.5798    
 checkperc> Increasing con cutoff atoms    55   60 from     0.41357E-01 to     0.45257E-01 ref=     2.5130    
 checkperc> Increasing con cutoff atoms    56   57 from     0.53752E-02 to     0.59239E-02 ref=     1.5242    
 checkperc> Increasing con cutoff atoms    96   99 from     0.78451E-02 to     0.79028E-02 ref=     2.2606    
 checkperc> Increasing con cutoff atoms   109  111 from     0.36462E-01 to     0.37838E-01 ref=     2.3908    
 checkperc> Increasing con cutoff atoms   122  123 from     0.66351E-02 to     0.67697E-02 ref=     2.3875    
 checkperc> Increasing con cutoff atoms   126  127 from     0.34631E-01 to     0.34933E-01 ref=     2.6982    
 checkperc> Increasing con cutoff atoms   126  129 from     0.40764E-01 to     0.41267E-01 ref=     4.0389    
 Unconnected minimum 7 found its way to F set.

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     780 steps. Energy=    -396.2688547       time=       2.10
 Minus side of path:                     768 steps. Energy=    -396.2627584       time=       2.02

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -396.2688547  1.2127         -395.0561138  1.2066         -396.2627584   3.118   2.077  12.248  11.838
        Known (#4)                                              Known (#7)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -394.5890829  3.1498        -391.4392777  2.0923        -393.5316147   9.757   9.002  22.679   6.394
   2     -393.5316147 0.72101        -392.8106089  3.4582        -396.2688547  24.721  20.121   4.738  30.603
   6     -396.2688547  1.2127        -395.0561138  1.2066        -396.2627584   3.118   2.077  12.248  11.838
   5     -396.2627584 0.75032        -395.5124341  6.1481        -401.6605666   7.049   6.334   3.554  40.801
   4     -401.6605666  5.0275        -396.6330266  4.7124        -401.3454376   6.559   5.694  36.980   3.921

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

 Elapsed time=                               115.91
 OPTIM> # of energy calls=                          8 time=           0.01 %=  0.0
 OPTIM> # of energy+gradient calls=             41116 time=          59.84 %= 51.6
 OPTIM> # of energy+gradient+Hessian calls=       517 time=           2.64 %=  2.3
