
 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 10:34:49 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=    -386.9073905     RMS force=    0.8744481453E-06
 OPTIM> Final energy  =    -386.2083399     RMS force=    0.9212818411E-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      17.36563396    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     5034.1    
 decide> The unconnected minima in the chain and their distances are:
     2       17.12     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=    56
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    103 fraction=    0.990000 images=     3 time=       0.2
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    128 steps, energy/image=    -377.7787789     RMS=1.003942921     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   22.84     Attempts, images and iterations=     0     6   210
 lbfgs> Final DNEB force constant      2.098661666    
 Double-ended search iterations= 210 RMS= 0.2258 Dev= 1.44% S= 18.09 time= 1.57
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         59
 DNEB run yielded 1 true transition state(s) time=   6.09

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1024 steps. Energy=    -386.9073905       time=       3.77
 Minus side of path:                    1013 steps. Energy=    -386.2069067       time=       3.28

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.9073905  1.0910         -385.8164362 0.39047         -386.2069067  20.257  17.288   1.843  78.685
        Known (#1)                                              *NEW* (Placed in 3)
 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=     345.24    
 decide> The unconnected minima in the chain and their distances are:
     2        7.01     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=   139
 intlbfgs> Freezing    130 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     29 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     54 steps, energy/image=    -381.3648205     RMS=.3832114184     images=   3
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      2     3 dist=   8.733     Attempts, images and iterations=     0     2    70
 lbfgs> Final DNEB force constant      6.768393620    
 Double-ended search iterations= 70 RMS= 0.7406 Dev= 0.70% S= 7.46 time= 0.18
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):        183
 DNEB run yielded 1 true transition state(s) time=  24.43

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1239 steps. Energy=    -386.2069067       time=       4.96
 Minus side of path:                     998 steps. Energy=    -385.0925330       time=       2.44

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.2069067  1.2270         -384.9799329 0.11260         -385.0925330  31.883  29.249   1.949  74.410
        Known (#3)                                              *NEW* (Placed in 4)
 checkperc> Increasing con cutoff atoms    38   40 from     0.28646E-01 to     0.46264E-01 ref=     2.5590    
 checkperc> Increasing con cutoff atoms    38   42 from     0.78441E-01 to     0.23242     ref=     4.4497    
 checkperc> Increasing con cutoff atoms    39   40 from     0.23498E-02 to     0.40611E-02 ref=     1.5253    
 checkperc> Increasing con cutoff atoms    39   43 from     0.37511E-01 to     0.44291E-01 ref=     3.2676    
 checkperc> Increasing con cutoff atoms    39   44 from     0.13835E-01 to     0.31253E-01 ref=     2.5376    
 checkperc> Increasing con cutoff atoms    39   45 from     0.65297E-02 to     0.18717E-01 ref=     3.6163    
 checkperc> Increasing con cutoff atoms    39   46 from     0.93853E-02 to     0.22318E-01 ref=     4.5177    
 checkperc> Increasing con cutoff atoms    39   48 from     0.36608E-01 to     0.41570E-01 ref=     4.6107    
 checkperc> Increasing con cutoff atoms    39   49 from     0.27837E-01 to     0.28472E-01 ref=     5.2730    
 checkperc> Increasing con cutoff atoms    40   42 from     0.21966E-02 to     0.33606E-02 ref=     2.1257    
 checkperc> Increasing con cutoff atoms    40   44 from     0.10485E-02 to     0.26283E-02 ref=     1.3812    
 checkperc> Increasing con cutoff atoms    40   45 from     0.32756E-02 to     0.51203E-02 ref=     2.1588    
 checkperc> Increasing con cutoff atoms    40   46 from     0.53434E-02 to     0.60061E-02 ref=     3.1089    
 checkperc> Increasing con cutoff atoms    41   44 from     0.24474E-02 to     0.32994E-02 ref=     2.2654    
 checkperc> Increasing con cutoff atoms    41   45 from     0.13437E-02 to     0.18204E-02 ref=     2.2384    
 checkperc> Increasing con cutoff atoms    60   61 from     0.31170E-02 to     0.31255E-02 ref=     1.2352    
 checkperc> Increasing con cutoff atoms    60   64 from     0.24213E-01 to     0.30735E-01 ref=     2.4536    
 checkperc> Increasing con cutoff atoms    61   64 from     0.61979E-01 to     0.78653E-01 ref=     2.8023    
 checkperc> Increasing con cutoff atoms    62   64 from     0.44247E-02 to     0.53085E-02 ref=     1.4566    
 checkperc> Increasing con cutoff atoms    62   71 from     0.77625E-01 to     0.99619E-01 ref=     2.4573    
 checkperc> Increasing con cutoff atoms    72   74 from     0.24935E-01 to     0.25418E-01 ref=     3.1030    
 checkperc> Increasing con cutoff atoms    74   75 from     0.18200E-01 to     0.19293E-01 ref=     2.1090    
 checkperc> Increasing con cutoff atoms    94   95 from     0.59775E-02 to     0.64333E-02 ref=     1.5268    
 checkperc> Increasing con cutoff atoms    94  105 from     0.63044E-01 to     0.69349E-01 ref=     2.5319    
 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      2 steps with      1 missing connections, weight=     690.49    
 decide> The unconnected minima in the chain and their distances are:
     2        7.01     3 
 

 tryconnect> Interpolation for minima 2_F and 3_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=   139
 intlbfgs> Freezing    130 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     34 fraction=    0.990000 images=    15 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     59 steps, energy/image=    -381.9412937     RMS=.2337687487     images=  15
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      2     3 dist=   10.17     Attempts, images and iterations=     3    23   805
 lbfgs> Final DNEB force constant     0.7984714498E-01
 Double-ended search iterations= 805 RMS= 0.0177 Dev= 4.36% S= 10.57 time= 23.47
 Following    1 images are candidates for TS:   13  
 Converged to TS (number of iterations):         13
 DNEB run yielded 1 true transition state(s) time=   4.58

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1027 steps. Energy=    -386.2083399       time=       2.55
 Minus side of path:                    1004 steps. Energy=    -386.2069067       time=       2.63

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.2083399  2.8989         -383.3094846  2.8974         -386.2069067   8.071   7.010  23.275   6.230
        Known (#2)                                              Known (#3)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -386.9073905  1.0910        -385.8164362 0.39047        -386.2069067  20.257  17.288   1.843  78.685
   3     -386.2069067  2.8974        -383.3094846  2.8989        -386.2083399   8.071   7.010  23.275   6.230

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

 Elapsed time=                                80.97
 OPTIM> # of energy calls=                          6 time=           0.01 %=  0.0
 OPTIM> # of energy+gradient calls=             30900 time=          37.72 %= 46.6
 OPTIM> # of energy+gradient+Hessian calls=       255 time=           1.33 %=  1.6
