
 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 10:29:35 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=    -405.8944151     RMS force=    0.9788626174E-06
 OPTIM> Final energy  =    -403.4480819     RMS force=    0.9034371829E-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      9.650347830    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     901.43    
 decide> The unconnected minima in the chain and their distances are:
     2        9.65     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=   124
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     27 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     52 steps, energy/image=    -386.4007252     RMS=10.52631863     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   19.86     Attempts, images and iterations=     0     5   175
 lbfgs> Final DNEB force constant      8.638375985    
 Double-ended search iterations= 175 RMS= 0.0400 Dev= 0.72% S= 9.69 time= 1.33
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         83
 DNEB run yielded 1 true transition state(s) time=   7.75

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     739 steps. Energy=    -406.2752359       time=       1.74
 Minus side of path:                     654 steps. Energy=    -405.8944151       time=       1.77

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -406.2752359 0.49250         -405.7827371 0.11168         -405.8944151   7.691   7.430   4.329  33.496
        *NEW* (Placed in 3)                                     Known (#1)
 checkperc> Increasing con cutoff atoms    15   21 from     0.98794E-02 to     0.99902E-02 ref=     3.1121    
 checkperc> Increasing con cutoff atoms    15   22 from     0.12880E-01 to     0.13125E-01 ref=     3.4441    
 checkperc> Increasing con cutoff atoms    15   23 from     0.17820E-01 to     0.18295E-01 ref=     3.6665    
 checkperc> Increasing con cutoff atoms    15   24 from     0.16308E-01 to     0.17213E-01 ref=     4.0177    
 checkperc> Increasing con cutoff atoms    19   24 from     0.22224E-01 to     0.22311E-01 ref=     4.4252    
 checkperc> Increasing con cutoff atoms    20   22 from     0.12391E-01 to     0.12401E-01 ref=     2.3787    
 checkperc> Increasing con cutoff atoms    20   24 from     0.15256E-01 to     0.15334E-01 ref=     3.5774    
 checkperc> Increasing con cutoff atoms    23   24 from     0.22309E-02 to     0.23918E-02 ref=     1.3926    
 checkperc> Increasing con cutoff atoms    30   31 from     0.44130E-02 to     0.44203E-02 ref=     1.4256    
 checkperc> Increasing con cutoff atoms    38   42 from     0.62465E-01 to     0.72766E-01 ref=     4.4537    
 checkperc> Increasing con cutoff atoms    41   44 from     0.18691E-02 to     0.21341E-02 ref=     2.2651    
 checkperc> Increasing con cutoff atoms    42   46 from     0.16835E-02 to     0.21089E-02 ref=     2.0734    
 checkperc> Increasing con cutoff atoms    43   48 from     0.51992E-03 to     0.60205E-03 ref=     1.3870    
 checkperc> Increasing con cutoff atoms    43   49 from     0.22541E-02 to     0.24274E-02 ref=     2.4277    
 checkperc> Increasing con cutoff atoms    51   53 from     0.15986E-01 to     0.16375E-01 ref=     3.1086    
 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=     1734.1    
 decide> The unconnected minima in the chain and their distances are:
     2       12.00     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=   117
 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=    -395.8595292     RMS=2.486409028     images=   3
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      2     3 dist=   18.08     Attempts, images and iterations=     0     5   175
 lbfgs> Final DNEB force constant      3.957339570    
 Double-ended search iterations= 175 RMS= 0.0792 Dev= 1.00% S= 12.23 time= 1.35
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         52
 DNEB run yielded 1 true transition state(s) time=   4.56

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     928 steps. Energy=    -405.8944151       time=       3.18
 Minus side of path:                     795 steps. Energy=    -403.9573236       time=       2.50

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -405.8944151  2.7517         -403.1427632 0.81456         -403.9573236  23.080  21.919   5.404  26.833
        Known (#1)                                              *NEW* (Placed in 4)
 checkperc> Increasing con cutoff atoms    45   46 from     0.27750E-02 to     0.29203E-02 ref=    0.98247    
 checkperc> Increasing con cutoff atoms    50   53 from     0.15114E-01 to     0.16004E-01 ref=     1.9971    
 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      1 steps with      1 missing connections, weight=     1802.9    
 decide> The unconnected minima in the chain and their distances are:
     2        9.65     1 
 

 tryconnect> Interpolation for minima 1_S and 2_F 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=   124
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     22 fraction=    0.990000 images=    15 time=       0.1
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     47 steps, energy/image=    -399.0429350     RMS=.3398565465     images=  15
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   18.30     Attempts, images and iterations=     3    23   805
 lbfgs> Final DNEB force constant     0.5621229993    
 Double-ended search iterations= 805 RMS= 0.0141 Dev= 4.64% S= 10.74 time= 28.57
 Following    1 images are candidates for TS:   22  
 Converged to TS (number of iterations):         12
 DNEB run yielded 1 true transition state(s) time=   2.41

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     913 steps. Energy=    -405.8944151       time=       2.42
 Minus side of path:                     789 steps. Energy=    -403.4480819       time=       1.86

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -405.8944151  2.4903         -403.4041140 0.43968E-01     -403.4480819   9.753   9.651   5.700  25.439
        Known (#1)                                              Known (#2)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   3     -405.8944151  2.4903        -403.4041140 0.43968E-01    -403.4480819   9.753   9.651   5.700  25.439

 Number of TS in the path       =      1
 Number of cycles               =      3

 Elapsed time=                                60.55
 OPTIM> # of energy calls=                          6 time=           0.01 %=  0.0
 OPTIM> # of energy+gradient calls=             28263 time=          41.65 %= 68.8
 OPTIM> # of energy+gradient+Hessian calls=       147 time=           0.74 %=  1.2
