
 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     79
 keyword> Local permutational alignment: alignment threshold=        1.00000
 keyword> Local permutational alignment: alignment cutoff=           5.00000
 keyword> Number of groups of permutable atoms=     8
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)@comp33.ch.
                 Created on  5/28/12 at 12: 6:24 by user: wales       

            Maximum number of ATOMS:     25140, and RESidues:       14000
            Current HEAP size:         2048000, and STACK size:    500000

 RDTITL> *
 RDTITL> No title read.

      ***** LEVEL  1 WARNING FROM <RDTITL> *****
      ***** Title expected.
      ******************************************
      BOMLEV (  0) IS NOT REACHED. WRNLEV IS  5

  
 CHARMM>    BOMLev -5
 MISCOM> Setting BOMLev < -2 is NOT a good idea.
 Parameter: TOP <- "toph19_eef1_bs360.inp"
 Parameter: PAR <- "param19_eef1_bs360.inp"
  
 CHARMM>    WRNLEV -1
  
 CHARMM>    PRNLEV 2
 Parameter: 0 <- "/HOME/BS360/C31A2-SAT39/TOPPAR"
 VOPEN> Attempting to open::/home/bs360/c31a2-sat39/toppar/toph19_eef1_bs360.inp::
 OPNLGU> Unit  1 opened for READONLY access to /home/bs360/c31a2-sat39/toppar/toph19_eef1_bs360.inp
 MAINIO> Residue topology file being read from unit   1.
 TITLE> * TOPOLOGY FILE FOR PROTEINS USING EXPLICIT HYDROGEN ATOMS: VERSION 19
 TITLE> * S TRYGUBENKO: ASN, GLN AND TYR DIHEDRALS AND CTER IMPROPER WERE
 TITLE> * SYMMETRIZED TO ENSURE THAT ROTAMERS OF THESE RESIDUES HAVE THE SAME
 TITLE> * ENERGIES AND GEOMETRIES. VISIT HTTP://WWW.TRYGUB.COM/CHARMM/ROTAMERS/
 TITLE> * FOR MORE INFORMATION. UNSUPPORTED. USE THIS FILE AT YOUR OWN RISK.
 TITLE> * MODIFICATIONS ARE MARKED WITH SAT AND DAE.
 TITLE> * ALSO, TOPOLOGY FOR D-PROLINE (DPR) RESIDUE WAS ADDED.
 TITLE> * * T. LAZARIDIS: HERE THE IONIC SIDECHAINS AND TERMINI ARE NEUTRALIZED
 TITLE> * ALSO, A NEW ATOM TYPE HAS BEEN ADDED, CR, FOR 4-BONDED CARBON IN
 TITLE> * AROMATICS AND ARGININE. MODIFICATIONS ARE MARKED BY TL
 TITLE> *
 VCLOSE: Closing unit    1 with status "KEEP"
 VOPEN> Attempting to open::/home/bs360/c31a2-sat39/toppar/param19_eef1_bs360.inp::
 OPNLGU> Unit  2 opened for READONLY access to /home/bs360/c31a2-sat39/toppar/param19_eef1_bs360.inp

          PARAMETER FILE BEING READ FROM UNIT  2
 TITLE> * - PARAMETER FILE PARAM19 * S TRYGUBENKO: ASN, GLN AND TYR DIHEDRALS AND CTER IMPROPER WERE
 TITLE> * SYMMETRIZED TO ENSURE THAT ROTAMERS OF THESE RESIDUES HAVE THE SAME
 TITLE> * ENERGIES AND GEOMETRIES. VISIT HTTP://WWW.TRYGUB.COM/CHARMM/ROTAMERS/
 TITLE> * FOR MORE INFORMATION. UNSUPPORTED. USE THIS FILE AT YOUR OWN RISK.
 TITLE> * MODIFICATIONS ARE MARKED WITH SAT AND DAE.
 TITLE> * * PEPTIDE GEOMETRY FROM RAMACHANDRAN ET AL BBA 359:298 (1974)
 TITLE> * TORSIONS FROM HAGLER ET AL JACS 98:4600 (1976)
 TITLE> * JORGENSEN NONBOND PARAMETERS JACS 103:3976-3985 WITH 1-4 RC=1.80/0.1
 TITLE> *
 VCLOSE: Closing unit    2 with status "KEEP"
 MAINIO> Sequence information being read from unit   5.
 RDTITL> *

          RESIDUE SEQUENCE --     7 RESIDUES
          GLY ASN ASN GLN GLN ASN TYR 
 THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE
 THE PATCH 'CTER' WILL BE USED FOR THE LAST  RESIDUE
 GENPSF> Segment   1 has been generated. Its identifier is SEG1.
 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.
 PSFSUM> Summary of the structure file counters :
         Number of segments      =        1   Number of residues   =        7
         Number of atoms         =       79   Number of groups     =       33
         Number of bonds         =       79   Number of angles     =      113
         Number of dihedrals     =       48   Number of impropers  =       37
         Number of cross-terms   =        0
         Number of HB acceptors  =       14   Number of HB donors  =       20
         Number of NB exclusions =        3   Total charge =    0.00000
 VOPEN> Attempting to open::input.crd::
 OPNLGU> Unit 20 opened for READONLY access to input.crd
          SPATIAL COORDINATES BEING READ FROM UNIT 20
 TITLE> 79
 VCLOSE: Closing unit   20 with status "KEEP"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      GROUps   RDIElec  SWITch   VGROup   VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 15.000 CTEXNB =999.000 CTONNB =  7.000 CTOFNB =  9.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  1.000
 NBXMOD =      5
 There are        0 atom  pairs and        0 atom  exclusions.
 There are        0 group pairs and        0 group exclusions.
 <MAKINB> with mode   5 found    195 exclusions and    129 interactions(1-4)
 VOPEN> Attempting to open::/home/bs360/c31a2-sat39/toppar/solvpar.inp::
 OPNLGU> Unit 30 opened for READONLY access to /home/bs360/c31a2-sat39/toppar/solvpar.inp
 NBOND           79
 NTHETA          113
 NPHI           48

chsetdihe> number of internal coordinates for segment    1
 chsetdihe> NPHIPSI           14
 chsetdihe> NOMEGAC            6
 chsetdihe> NSIDECHAIN           15
 chsetdihe> NCHIRAL            6

chsetdihe> total number of internal coordinates
 chsetdihe> NPHIPSITOT=            14
 chsetdihe> NOMEGACTOT=             6
 chsetdihe> NSIDECHAINTOT=            15
 chsetdihe> NCHIRALTOT=             6

 chsetdihe>            29  twistable dihedrals identified
chsetdihe> SEG-NR, NSEGATOMS :    1      79

 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>  237 Cartesian coordinates will be optimised for   79 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
 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> 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=    -290.9123533     RMS force=    0.7818240378E-06
 OPTIM> Final energy  =    -289.7570772     RMS force=    0.9074071206E-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 is D^3

 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     2128.4    
 decide> The unconnected minima in the chain and their distances are:
     2       12.86     1 
 

 tryconnect> 105-iteration DNEB run for minima 1_S and 2_F using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      27.85962590    
 Double-ended search iterations= 105 RMS= 32.2834 Dev= 66.02% S= 44.30 time= 0.18
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         44
 DNEB run yielded 1 true transition state(s) time=   0.96

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     616 steps. Energy=    -290.5964147       time=       0.52
 Minus side of path:                     531 steps. Energy=    -290.5516891       time=       0.44

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -290.5964147  2.2623         -288.3340806  2.2176         -290.5516891  11.453   8.238   5.397  14.638
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 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=     1857.9    
 decide> The unconnected minima in the chain and their distances are:
     2       12.21     3     4        3.37     1 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 3_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      27.85962590    
 Double-ended search iterations= 164 RMS= 28.7924 Dev= 6.31% S= 46.38 time= 0.29
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         83
 DNEB run yielded 1 true transition state(s) time=   1.45

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     496 steps. Energy=    -291.7066672       time=       0.41
 Minus side of path:                     484 steps. Energy=    -288.6742464       time=       0.39

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -291.7066672  4.6272         -287.0794742  1.5948         -288.6742464   9.502   5.955   7.181  11.001
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 4_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      9.070294785    
 Double-ended search iterations= 70 RMS= 0.2722 Dev= 0.26% S= 3.38 time= 0.08
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         13
 DNEB run yielded 1 true transition state(s) time=   0.54

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     489 steps. Energy=    -290.5516891       time=       0.38
 Minus side of path:                     526 steps. Energy=    -290.9123533       time=       0.41

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -290.5516891 0.29009E-01     -290.5226801 0.38967         -290.9123533   3.545   3.367   3.056  25.854
        Known (#4)                                              Known (#1)
 Unconnected minimum 4 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     1907.1    
 decide> The unconnected minima in the chain and their distances are:
     2       12.40     4 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 4_S using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      27.85962590    
 Double-ended search iterations= 138 RMS= 37.3062 Dev= 31.67% S= 56.47 time= 0.23
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         78
 DNEB run yielded 1 true transition state(s) time=   1.38

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     562 steps. Energy=    -282.8608255       time=       0.44
 Minus side of path:                     576 steps. Energy=    -287.6091133       time=       0.47

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -282.8608255 0.50180         -282.3590261  5.2501         -287.6091133  15.747  15.071   4.173  18.932
        *NEW* (Placed in 7)                                     *NEW* (Placed in 8)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 8 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     3639.4    
 decide> The unconnected minima in the chain and their distances are:
     2       12.21     3 
 

 tryconnect> 805-iteration DNEB run for minima 2_F and 3_S using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      6.446089162    
 Double-ended search iterations= 805 RMS= 0.2832 Dev= 3.15% S= 21.31 time= 9.98
 Following    2 images are candidates for TS:    6   12  
 Converged to TS (number of iterations):         23
 Converged to TS (number of iterations):         28
 DNEB run yielded 2 true transition state(s) time=   1.37

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     514 steps. Energy=    -289.7570772       time=       0.40
 Minus side of path:                     491 steps. Energy=    -286.0883813       time=       0.38

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -289.7570772  6.2442         -283.5128914  2.5755         -286.0883813   8.875   7.533  12.399   6.372
        Known (#2)                                              *NEW* (Placed in 9)
 Unconnected minimum 9 found its way to F set.

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     507 steps. Energy=    -286.8064550       time=       0.40
 Minus side of path:                     503 steps. Energy=    -291.0875651       time=       0.39

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -286.8064550  3.0399         -283.7665614  7.3210         -291.0875651  12.084   6.465   5.947  13.283
        *NEW* (Placed in 10)                                    *NEW* (Placed in 11)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 11 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     1653.7    
 decide> The unconnected minima in the chain and their distances are:
     2       11.48    11    11        5.20     3 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 11_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.446089162    
 Double-ended search iterations= 105 RMS= 1.0659 Dev= 1.07% S= 12.83 time= 0.17
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         86
 DNEB run yielded 1 true transition state(s) time=   1.37

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     485 steps. Energy=    -287.0136992       time=       0.38
 Minus side of path:                     616 steps. Energy=    -291.0875651       time=       0.52

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -287.0136992 0.10212         -286.9115832  4.1760         -291.0875651  14.859  14.448   3.193  24.741
        *NEW* (Placed in 12)                                    Known (#11)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 3_S and 11_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      19.79931599    
 Double-ended search iterations= 129 RMS= 5.4196 Dev= 39.76% S= 5.78 time= 0.14
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         19
 DNEB run yielded 1 true transition state(s) time=   0.55

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     453 steps. Energy=    -290.5964147       time=       0.34
 Minus side of path:                     478 steps. Energy=    -291.0875651       time=       0.37

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -290.5964147 0.35611E-01     -290.5608035 0.52676         -291.0875651   5.357   5.205   8.122   9.726
        Known (#3)                                              Known (#11)
 Unconnected minimum 11 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 12 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     1030.9    
 decide> The unconnected minima in the chain and their distances are:
     9       10.10    12 
 

 tryconnect> 105-iteration DNEB run for minima 9_F and 12_S using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      7.835261665    
 Double-ended search iterations= 105 RMS= 0.6459 Dev= 0.59% S= 10.46 time= 0.17
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         20
 DNEB run yielded 1 true transition state(s) time=   0.63

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     603 steps. Energy=    -291.0875651       time=       0.50
 Minus side of path:                     487 steps. Energy=    -286.0883813       time=       0.38

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -291.0875651  8.5678         -282.5198103  3.5686         -286.0883813  15.052  13.403   8.594   9.193
        Known (#11)                                             Known (#9)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   3     -290.9123533 0.38967        -290.5226801 0.29009E-01    -290.5516891   3.545   3.367   3.056  25.854
   1     -290.5516891  2.2176        -288.3340806  2.2623        -290.5964147  11.453   8.238   5.397  14.638
   8     -290.5964147 0.35611E-01    -290.5608035 0.52676        -291.0875651   5.357   5.205   8.122   9.726
   9     -291.0875651  8.5678        -282.5198103  3.5686        -286.0883813  15.052  13.403   8.594   9.193
   5     -286.0883813  2.5755        -283.5128914  6.2442        -289.7570772   8.875   7.533  12.399   6.372

 Number of TS in the path       =      5
 Number of cycles               =      6

 Elapsed time=                                27.59
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             35334 time=          18.10 %= 65.6
 OPTIM> # of energy+gradient+Hessian calls=       394 time=           0.40 %=  1.5
