
 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)@comp35.ch.
                 Created on  5/28/12 at 10:33:34 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=    -377.6518882     RMS force=    0.9126844213E-06
 OPTIM> Final energy  =    -381.9953018     RMS force=    0.9302122287E-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      13.68058560    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     2561.3    
 decide> The unconnected minima in the chain and their distances are:
     2       13.67     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=    87
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     84 fraction=    0.990000 images=     3 time=       0.1
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    109 steps, energy/image=    -369.7495932     RMS=.8294051275     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   16.54     Attempts, images and iterations=     0     4   140
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 140 RMS= 0.4034 Dev= 2.84% S= 14.56 time= 0.78
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         26
 DNEB run yielded 1 true transition state(s) time=   4.58

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     919 steps. Energy=    -377.6518882       time=       2.72
 Minus side of path:                     928 steps. Energy=    -379.7352272       time=       3.06

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -377.6518882  2.1752         -375.4766666  4.2586         -379.7352272   8.715   7.668   3.297  43.981
        Known (#1)                                              *NEW* (Placed in 3)
 checkperc> Increasing con cutoff atoms    29   33 from     0.24294E-01 to     0.25940E-01 ref=     2.5627    
 checkperc> Increasing con cutoff atoms    31   32 from     0.54707E-02 to     0.56987E-02 ref=    0.96683    
 checkperc> Increasing con cutoff atoms    31   34 from     0.98748E-01 to     0.11767     ref=     3.0899    
 checkperc> Increasing con cutoff atoms    33   34 from     0.48388E-01 to     0.52608E-01 ref=     3.8758    
 checkperc> Increasing con cutoff atoms    38   40 from     0.20123E-01 to     0.20162E-01 ref=     2.5675    
 checkperc> Increasing con cutoff atoms    55   57 from     0.38766E-01 to     0.67486E-01 ref=     2.5798    
 checkperc> Increasing con cutoff atoms    55   60 from     0.41155E-01 to     0.66943E-01 ref=     2.5130    
 checkperc> Increasing con cutoff atoms    62   63 from     0.49763E-02 to     0.52872E-02 ref=    0.98236    
 checkperc> Increasing con cutoff atoms    84   86 from     0.35522E-01 to     0.39850E-01 ref=     2.0803    
 checkperc> Increasing con cutoff atoms    85   86 from     0.10915E-01 to     0.12051E-01 ref=     1.0469    
 checkperc> Increasing con cutoff atoms    87   88 from     0.20299E-01 to     0.25639E-01 ref=     1.6892    
 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=     2006.4    
 decide> The unconnected minima in the chain and their distances are:
     2       12.60     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=   109
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     51 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     76 steps, energy/image=    -346.0356779     RMS=15.55146138     images=   3
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      2     3 dist=   19.97     Attempts, images and iterations=     0     5   175
 lbfgs> Final DNEB force constant      6.446089162    
 Double-ended search iterations= 175 RMS= 1.9735 Dev= 1.12% S= 13.09 time= 1.27
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         51
 DNEB run yielded 1 true transition state(s) time=   5.13

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     910 steps. Energy=    -381.0468764       time=       2.12
 Minus side of path:                     924 steps. Energy=    -381.0682154       time=       2.21

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.0468764 0.72299         -380.3238877 0.74433         -381.0682154  12.551  12.265   4.584  31.632
        *NEW* (Placed in 4)                                     *NEW* (Placed in 5)
 checkperc> Increasing con cutoff atoms     3    9 from     0.78927E-01 to     0.78996E-01 ref=     2.4232    
 checkperc> Increasing con cutoff atoms    30   33 from     0.13861E-02 to     0.14714E-02 ref=     1.5223    
 checkperc> Increasing con cutoff atoms    38   40 from     0.20162E-01 to     0.20425E-01 ref=     2.5675    
 checkperc> Increasing con cutoff atoms    56   58 from     0.18229E-01 to     0.19797E-01 ref=     2.3865    
 checkperc> Increasing con cutoff atoms    60   62 from     0.38635E-02 to     0.53917E-02 ref=     1.3353    
 checkperc> Increasing con cutoff atoms    29   35 from     0.16666E-01 to     0.21579E-01 ref=     2.4050    
 checkperc> Increasing con cutoff atoms    30   34 from     0.27459E-01 to     0.29288E-01 ref=     2.5472    
 checkperc> Increasing con cutoff atoms    38   40 from     0.20425E-01 to     0.20962E-01 ref=     2.5675    
 checkperc> Increasing con cutoff atoms    72   75 from     0.67402E-01 to     0.68160E-01 ref=     2.8163    
 checkperc> Increasing con cutoff atoms    84   87 from     0.47655E-01 to     0.48039E-01 ref=     2.0673    
 checkperc> Increasing con cutoff atoms    86   88 from     0.26847E-01 to     0.27291E-01 ref=     1.7022    
 checkperc> Increasing con cutoff atoms   110  113 from     0.35448E-02 to     0.36886E-02 ref=     1.5239    
 checkperc> Increasing con cutoff atoms   137  138 from     0.95575E-02 to     0.96267E-02 ref=     1.5258    
 checkperc> Increasing con cutoff atoms   137  139 from     0.50023E-01 to     0.50629E-01 ref=     2.4704    
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     1886.6    
 decide> The unconnected minima in the chain and their distances are:
     2        7.31     5     4       11.42     3 
 

 tryconnect> Interpolation for minima 2_F and 5_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=   130
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     22 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     47 steps, energy/image=    -376.1479622     RMS=.4306794584     images=   3
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      5
 intlbfgs> DNEB for minima      2     5 dist=   9.958     Attempts, images and iterations=     0     2    70
 lbfgs> Final DNEB force constant      8.227024748    
 Double-ended search iterations= 70 RMS= 0.2220 Dev= 0.35% S= 7.48 time= 0.20
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         36
 DNEB run yielded 1 true transition state(s) time=   4.61

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     960 steps. Energy=    -381.0682154       time=       2.96
 Minus side of path:                     920 steps. Energy=    -381.9953018       time=       2.64

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.0682154  1.2025         -379.8656787  2.1296         -381.9953018   9.606   7.308   6.548  22.145
        Known (#5)                                              Known (#2)
 Unconnected minimum 5 found its way to F set.

 tryconnect> Interpolation for minima 3_S and 4_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=   115
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     31 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     56 steps, energy/image=    -362.5342219     RMS=8.709777624     images=   3
 intlbfgs> First  minimum number      3
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      3     4 dist=   17.75     Attempts, images and iterations=     0     5   175
 lbfgs> Final DNEB force constant      4.362966876    
 Double-ended search iterations= 175 RMS= 0.6767 Dev= 1.76% S= 11.92 time= 1.23
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         60
 DNEB run yielded 1 true transition state(s) time=   7.16

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     981 steps. Energy=    -381.4802082       time=       3.18
 Minus side of path:                     890 steps. Energy=    -379.7352272       time=       2.28

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.4802082  3.1375         -378.3426718  1.3926         -379.7352272   9.709   6.292   8.198  17.687
        *NEW* (Placed in 6)                                     Known (#3)
 checkperc> Increasing con cutoff atoms    38   52 from     0.39493E-01 to     0.40733E-01 ref=     2.4103    
 checkperc> Increasing con cutoff atoms    38   53 from     0.77078E-01 to     0.82519E-01 ref=     2.4918    
 checkperc> Increasing con cutoff atoms    50   53 from     0.16819E-01 to     0.17844E-01 ref=     1.9979    
 checkperc> Increasing con cutoff atoms    51   52 from     0.13589E-01 to     0.15055E-01 ref=     2.2496    
 checkperc> Increasing con cutoff atoms    51   54 from     0.48609E-01 to     0.50864E-01 ref=     2.7964    
 checkperc> Increasing con cutoff atoms    58   59 from     0.10143E-01 to     0.14842E-01 ref=     2.1536    
 checkperc> Increasing con cutoff atoms    71   72 from     0.39186E-02 to     0.41683E-02 ref=     1.2354    
 checkperc> Increasing con cutoff atoms    81   82 from     0.10275E-01 to     0.10661E-01 ref=     1.5298    
 checkperc> Increasing con cutoff atoms    84   86 from     0.39850E-01 to     0.40599E-01 ref=     2.0803    
 Unconnected minimum 6 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 6 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     1530.4    
 decide> The unconnected minima in the chain and their distances are:
     5       11.51     6 
 

 tryconnect> Interpolation for minima 5_F and 6_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=   113
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     33 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     58 steps, energy/image=    -359.1812994     RMS=12.49375500     images=   3
 intlbfgs> First  minimum number      5
 intlbfgs> Second minimum number      6
 intlbfgs> DNEB for minima      5     6 dist=   17.38     Attempts, images and iterations=     0     5   175
 lbfgs> Final DNEB force constant      4.810170981    
 Double-ended search iterations= 175 RMS= 1.2227 Dev= 0.90% S= 11.66 time= 1.22
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         27
 DNEB run yielded 1 true transition state(s) time=   3.49

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     933 steps. Energy=    -381.4802082       time=       2.25
 Minus side of path:                     917 steps. Energy=    -381.0682154       time=       2.16

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -381.4802082  1.3909         -380.0893099 0.97891         -381.0682154  12.182  11.512   3.518  41.216
        Known (#6)                                              Known (#5)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -377.6518882  2.1752        -375.4766666  4.2586        -379.7352272   8.715   7.668   3.297  43.981
   4     -379.7352272  1.3926        -378.3426718  3.1375        -381.4802082   9.709   6.292   8.198  17.687
   5     -381.4802082  1.3909        -380.0893099 0.97891        -381.0682154  12.182  11.512   3.518  41.216
   3     -381.0682154  1.2025        -379.8656787  2.1296        -381.9953018   9.606   7.308   6.548  22.145

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

 Elapsed time=                                56.37
 OPTIM> # of energy calls=                         10 time=           0.01 %=  0.0
 OPTIM> # of energy+gradient calls=             17745 time=          24.33 %= 43.2
 OPTIM> # of energy+gradient+Hessian calls=       200 time=           0.97 %=  1.7
