
 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 12:16:26 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


 natintsetup, NATOMS           79
 cartres            7
 KeyInt>> Using natural internal coordinates. # of coords =        231
 KeyInt>> Parameter file for internal coordinates is naturals-noH.par                                                                                    
 KeyInt>> KD, NNZ are         44      2388
 KeyInt>> Back transform convergence (for interpolation)     0.1000000000E-07
 KeyInt>> Back transform convergence criterion (except for interpolation)     0.1000000000E-03
 KeyInt>> Using internal coordinates for interpolation.
 KeyInt>> Choosing internal or Cartesian coordinates for interpolation, based on max energy.
 KeyInt>> Permuting endpoint atoms to minimise torsion distance
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -287.4599974     RMS force=    0.8514778919E-06
 OPTIM> Final energy  =    -288.8590457     RMS force=    0.9299205492E-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=     825.66    
 decide> The unconnected minima in the chain and their distances are:
     2        9.38     1 
 

 tryconnect> 70-iteration DNEB run for minima 1_S and 2_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 2.4235 Dev= 1.12% S= 11.66 time= 0.11
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         30
 DNEB run yielded 1 true transition state(s) time=   0.73

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     509 steps. Energy=    -293.7003601       time=       0.41
 Minus side of path:                     485 steps. Energy=    -288.8590457       time=       0.39

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -293.7003601  7.7850         -285.9153269  2.9437         -288.8590457   7.683   6.880   3.343  23.635
        *NEW* (Placed in 3)                                     Known (#2)
 Unconnected minimum 3 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 3 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     1381.0    
 decide> The unconnected minima in the chain and their distances are:
     3       11.14     1 
 

 tryconnect> 105-iteration DNEB run for minima 1_S and 3_F using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.4504 Dev= 0.27% S= 14.17 time= 0.21
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         64
 DNEB run yielded 1 true transition state(s) time=   1.26

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     535 steps. Energy=    -292.0136734       time=       0.44
 Minus side of path:                     469 steps. Energy=    -290.2862866       time=       0.39

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -292.0136734  3.3538         -288.6599136  1.6264         -290.2862866  15.865  13.957   4.136  19.100
        *NEW* (Placed in 4)                                     *NEW* (Placed in 5)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     1651.3    
 decide> The unconnected minima in the chain and their distances are:
     2        9.38     1 
 

 tryconnect> 735-iteration DNEB run for minima 1_S and 2_F using 21 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      2.429463211    
 Double-ended search iterations= 735 RMS= 1.7705 Dev= 5.77% S= 24.97 time= 8.73
 Following    4 images are candidates for TS:    3   10   17   21  
 Converged to TS (number of iterations):         52
 Converged to TS (number of iterations):         26
 Converged to TS (number of iterations):         21
 Converged to TS (number of iterations):         12
 DNEB run yielded 4 true transition state(s) time=   2.91

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     489 steps. Energy=    -291.7173474       time=       0.40
 Minus side of path:                     475 steps. Energy=    -290.9141828       time=       0.38

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -291.7173474 0.97457         -290.7427804 0.17140         -290.9141828   5.992   5.411   2.708  29.177
        *NEW* (Placed in 6)                                     *NEW* (Placed in 7)
 Connection established between members of the U set.

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     522 steps. Energy=    -293.9151787       time=       0.42
 Minus side of path:                     498 steps. Energy=    -290.9141828       time=       0.40

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -293.9151787  4.5634         -289.3517489  1.5624         -290.9141828  13.411  10.328   3.686  21.431
        *NEW* (Placed in 8)                                     Known (#7)
 Connection established between members of the U set.

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     516 steps. Energy=    -293.7846098       time=       0.41
 Minus side of path:                     516 steps. Energy=    -290.7149131       time=       0.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -293.7846098  6.0024         -287.7822165  2.9327         -290.7149131  12.561   9.587   3.119  25.328
        *NEW* (Placed in 9)                                     *NEW* (Placed in 10)
 Connection established between members of the U set.

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     474 steps. Energy=    -288.8590457       time=       0.37
 Minus side of path:                     467 steps. Energy=    -291.2678816       time=       0.37

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -288.8590457 0.12108         -288.7379659  2.5299         -291.2678816   4.570   4.342   2.324  33.993
        Known (#2)                                              *NEW* (Placed in 11)
 Unconnected minimum 11 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 11 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      3 missing connections, weight=     1030.1    
 decide> The unconnected minima in the chain and their distances are:
    11        5.19    10     9        5.80     8     7        8.86     1 
 

 tryconnect> 70-iteration DNEB run for minima 10_U and 11_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1132 Dev= 0.02% S= 5.21 time= 0.11
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         17
 DNEB run yielded 1 true transition state(s) time=   0.56

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     504 steps. Energy=    -290.7149131       time=       0.41
 Minus side of path:                     468 steps. Energy=    -291.2678816       time=       0.37

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -290.7149131 0.44448         -290.2704366 0.99745         -291.2678816   5.637   5.189   3.682  21.456
        Known (#10)                                             Known (#11)
 Unconnected minimum 10 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 8_U and 9_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2534 Dev= 0.18% S= 5.92 time= 0.11
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         14
 DNEB run yielded 1 true transition state(s) time=   0.49

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     490 steps. Energy=    -293.9151787       time=       0.39
 Minus side of path:                     464 steps. Energy=    -293.7846098       time=       0.36

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -293.9151787 0.31831         -293.5968677 0.18774         -293.7846098   6.017   5.799   8.218   9.613
        Known (#8)                                              Known (#9)
 Unconnected minimum 8 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 7_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 1.5650 Dev= 0.33% S= 9.13 time= 0.11
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         39
 DNEB run yielded 1 true transition state(s) time=   0.85

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     472 steps. Energy=    -287.4599974       time=       0.37
 Minus side of path:                     563 steps. Energy=    -291.7173474       time=       0.49

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -287.4599974 0.44204         -287.0179599  4.6994         -291.7173474  14.024  11.067   3.652  21.631
        Known (#1)                                              Known (#6)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   9     -287.4599974 0.44204        -287.0179599  4.6994        -291.7173474  14.024  11.067   3.652  21.631
   3     -291.7173474 0.97457        -290.7427804 0.17140        -290.9141828   5.992   5.411   2.708  29.177
   4     -290.9141828  1.5624        -289.3517489  4.5634        -293.9151787  13.411  10.328   3.686  21.431
   8     -293.9151787 0.31831        -293.5968677 0.18774        -293.7846098   6.017   5.799   8.218   9.613
   5     -293.7846098  6.0024        -287.7822165  2.9327        -290.7149131  12.561   9.587   3.119  25.328
   7     -290.7149131 0.44448        -290.2704366 0.99745        -291.2678816   5.637   5.189   3.682  21.456
   6     -291.2678816  2.5299        -288.7379659 0.12108        -288.8590457   4.570   4.342   2.324  33.993

 Number of TS in the path       =      7
 Number of cycles               =      4

 Elapsed time=                                23.92
 OPTIM> # of energy calls=                         64 time=           0.03 %=  0.1
 OPTIM> # of energy+gradient calls=             30110 time=          16.14 %= 67.5
 OPTIM> # of energy+gradient+Hessian calls=       275 time=           0.30 %=  1.2
