
 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 10:35:38 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=    -381.7669886     RMS force=    0.9837765615E-06
 OPTIM> Final energy  =    -386.9073905     RMS force=    0.8744481453E-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      39.02818602    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     58904.    
 decide> The unconnected minima in the chain and their distances are:
     2       38.87     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=    22
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    205 fraction=    0.990000 images=     4 time=       0.3
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    230 steps, energy/image=    -375.7061741     RMS=1.384543976     images=   5
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   41.00     Attempts, images and iterations=     0    12   420
 lbfgs> Final DNEB force constant     0.1659964797    
 Double-ended search iterations= 420 RMS= 0.0447 Dev= 2.12% S= 42.40 time= 6.39
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         31
 DNEB run yielded 1 true transition state(s) time=   4.04

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1131 steps. Energy=    -384.4607947       time=       3.05
 Minus side of path:                    1016 steps. Energy=    -381.7659382       time=       2.64

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.4607947  2.9162         -381.5445660 0.22137         -381.7659382  29.991  27.856   2.391  60.632
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 checkperc> Increasing con cutoff atoms    38   47 from     0.13393     to     0.16088     ref=     5.6336    
 checkperc> Increasing con cutoff atoms    39   42 from     0.76667E-02 to     0.77047E-02 ref=     3.6267    
 checkperc> Increasing con cutoff atoms    39   46 from     0.64601E-02 to     0.82253E-02 ref=     4.5147    
 checkperc> Increasing con cutoff atoms    93  105 from     0.87648E-02 to     0.90789E-02 ref=     1.5278    
 checkperc> Increasing con cutoff atoms   120  124 from     0.35062E-02 to     0.37165E-02 ref=     1.3813    
 checkperc> Increasing con cutoff atoms   123  128 from     0.16460E-02 to     0.16849E-02 ref=     1.3867    
 checkperc> Increasing con cutoff atoms   123  129 from     0.56665E-02 to     0.57821E-02 ref=     2.4259    
 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=     18937.    
 decide> The unconnected minima in the chain and their distances are:
     2       26.63     3     4        0.76     1 
 

 tryconnect> Interpolation for minima 2_F and 3_U 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=    41
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    108 fraction=    0.990000 images=     3 time=       0.2
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    133 steps, energy/image=    -305.7019321     RMS=27.95901851     images=   3
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      2     3 dist=   33.10     Attempts, images and iterations=     0     9   315
 lbfgs> Final DNEB force constant     0.4624599827    
 Double-ended search iterations= 315 RMS= 0.0271 Dev= 2.05% S= 27.92 time= 3.59
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         79
 DNEB run yielded 1 true transition state(s) time=   7.28

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1011 steps. Energy=    -386.2069067       time=       4.11
 Minus side of path:                    1022 steps. Energy=    -386.9073905       time=       3.59

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.2069067 0.39047         -385.8164362  1.0910         -386.9073905  20.257  17.288   1.843  78.680
        *NEW* (Placed in 5)                                     Known (#2)
 checkperc> Increasing con cutoff atoms    38   40 from     0.20123E-01 to     0.23544E-01 ref=     2.5675    
 checkperc> Increasing con cutoff atoms    39   46 from     0.82253E-02 to     0.84977E-02 ref=     4.5147    
 Unconnected minimum 5 found its way to F set.

 tryconnect> Interpolation for minima 1_S and 4_U 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=   145
 intlbfgs> Freezing    130 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     16 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     41 steps, energy/image=    -377.9438776     RMS=.2692965123E-01 images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      1     4 dist=  0.9644     Attempts, images and iterations=     0     2    70
 lbfgs> Final DNEB force constant      6.768393620    
 Double-ended search iterations= 70 RMS= 0.0189 Dev= 0.30% S= 0.76 time= 0.18
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         12
 DNEB run yielded 1 true transition state(s) time=   3.79

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     947 steps. Energy=    -381.7659382       time=       2.21
 Minus side of path:                     946 steps. Energy=    -381.7669886       time=       2.10

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.7659382 0.26998E-02     -381.7632384 0.37502E-02     -381.7669886   0.761   0.757   5.502  26.353
        Known (#4)                                              Known (#1)
 Unconnected minimum 4 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     3074.3    
 decide> The unconnected minima in the chain and their distances are:
     5       14.53     3 
 

 tryconnect> Interpolation for minima 3_S and 5_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=    76
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     75 fraction=    0.990000 images=     3 time=       0.1
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    100 steps, energy/image=    -376.0529514     RMS=5.987938278     images=   3
 intlbfgs> First  minimum number      3
 intlbfgs> Second minimum number      5
 intlbfgs> DNEB for minima      3     5 dist=   20.50     Attempts, images and iterations=     0     6   210
 lbfgs> Final DNEB force constant      3.100679103    
 Double-ended search iterations= 210 RMS= 0.0612 Dev= 1.13% S= 14.77 time= 1.55
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         17
 DNEB run yielded 1 true transition state(s) time=   3.44

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1004 steps. Energy=    -386.2069067       time=       2.36
 Minus side of path:                     940 steps. Energy=    -384.9563440       time=       2.12

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.2069067  1.5966         -384.6103521 0.34599         -384.9563440   3.181   2.942  15.650   9.265
        Known (#5)                                              *NEW* (Placed in 6)
 Unconnected minimum 6 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 6 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     2776.6    
 decide> The unconnected minima in the chain and their distances are:
     6       14.04     3 
 

 tryconnect> Interpolation for minima 3_S and 6_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=    78
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     69 fraction=    0.990000 images=     3 time=       0.1
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     94 steps, energy/image=    -375.8320335     RMS=6.541324627     images=   3
 intlbfgs> First  minimum number      3
 intlbfgs> Second minimum number      6
 intlbfgs> DNEB for minima      3     6 dist=   19.58     Attempts, images and iterations=     0     5   175
 lbfgs> Final DNEB force constant      3.957339570    
 Double-ended search iterations= 175 RMS= 0.0252 Dev= 0.29% S= 14.08 time= 1.08
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         22
 DNEB run yielded 1 true transition state(s) time=   4.00

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1028 steps. Energy=    -384.9563440       time=       3.99
 Minus side of path:                     943 steps. Energy=    -384.4607947       time=       3.48

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.9563440 0.49729         -384.4590587 0.17360E-02     -384.4607947  14.142  14.042   2.266  63.995
        Known (#6)                                              Known (#3)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   3     -381.7669886 0.37502E-02    -381.7632384 0.26998E-02    -381.7659382   0.761   0.757   5.502  26.353
   1     -381.7659382 0.22137        -381.5445660  2.9162        -384.4607947  29.991  27.856   2.391  60.632
   5     -384.4607947 0.17360E-02    -384.4590587 0.49729        -384.9563440  14.142  14.042   2.266  63.995
   4     -384.9563440 0.34599        -384.6103521  1.5966        -386.2069067   3.181   2.942  15.650   9.265
   2     -386.2069067 0.39047        -385.8164362  1.0910        -386.9073905  20.257  17.288   1.843  78.680

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

 Elapsed time=                                66.57
 OPTIM> # of energy calls=                         10 time=           0.01 %=  0.0
 OPTIM> # of energy+gradient calls=             25673 time=          31.20 %= 46.9
 OPTIM> # of energy+gradient+Hessian calls=       161 time=           0.73 %=  1.1
