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 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
 ###############################################################
 User: maly  Run date: 26/ 5/2020 Run time: 12:08:26 


 Please reference: Collaborative Computational Project, Number 4. 2011.
 "Overview of the CCP4 suite and current developments". Acta Cryst. D67, 235-242.
 as well as any specific reference in the program write-up.


 $TEXT:Reference1: $$ Primary reference $$ 
   "Overview of refinement procedures within REFMAC5: utilizing data from different sources"
   O.Kovalevskiy, R.A.Nicholls, F.Long, G.N.Murshudov,(2018) 
   Acta Crystallogr. D74, 492-505

 $$
 $SUMMARY :Reference1:  $$ Refmac: $$
 :TEXT:Reference1: $$

 $TEXT:Reference1: $$ Primary reference for EM $$ 
   "Current approaches for the fitting and refinement of atomic models into cryo-EM maps using CCP-EM
   R.A. Nicholls, M. Tykac, O.Kovalevskiy, G.N.Murshudov,(2018) 
   Acta Crystallogr. D74, 215-227

 $$
 $SUMMARY :Reference2:  $$ Refmac: $$
 :TEXT:Reference1: $$

 $TEXT:Reference1: $$ Secondary reference $$ 
   "REFMAC5 for the refinement of macromolecular crystal structures:"
   G.N.Murshudov, P.Skubak, A.A.Lebedev, N.S.Pannu, R.A.Steiner, R.A.Nicholls, M.D.Winn, F.Long and A.A.Vagin,(2011) 
   Acta Crystallogr. D67, 355-367

 $$
 $SUMMARY :Reference3:  $$ Refmac: $$
 :TEXT:Reference1: $$

 $TEXT:Reference2: $$ Secondary reference $$ 
   "Refinement of Macromolecular Structures by the  Maximum-Likelihood Method:"
   G.N. Murshudov, A.A.Vagin and E.J.Dodson,(1997)
   Acta Crystallogr. D53, 240-255
   EU  Validation contract: BIO2CT-92-0524

 $$
 $SUMMARY :Reference4:  $$ Refmac: $$
 :TEXT:Reference2: $$

  Data line--- make     check NONE
  Data line--- refi     type REST reso 42.68 1.10     resi MLKF     meth CGMAT     bref MIXED
  Data line--- scal     type SIMP     LSSC     ANISO     EXPE
  Data line--- solvent YES
  Data line--- bins 11
  Data line--- ncyc 10
  Data line--- monitor MEDIum
  Data line--- free 0
  Data line--- END

 OPENED INPUT MTZ FILE 
 Logical Name: HKLIN   Filename: EP_R.mtz 

 LABIN FP=FP SIGFP=SIGFP FREE=FREE

    ****                     Input and Default parameters#                      ****


Input coordinate file.  Logical name - XYZIN actual file name  - EP_R00_1-15A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - EP_R00_1-10A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - EP_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - EP_R00_1-10A.mtz

Cell from mtz :    45.203    73.097    52.573    90.000   109.248    90.000
Space group from mtz: number -    4; name - P 1 21 1

  Refinement type                        : Restrained

    ****                           Makecif parameters                           ****

Dictionary files for restraints : /protein2/ccp4/ccp4-7.0/ccp4-7.0/lib/data/monomers/mon*cif
Parameters for new entry and VDW: /protein2/ccp4/ccp4-7.0/ccp4-7.0/lib/data/monomers/ener_lib.cif
    Program will rely on residue and atom names. No checking
    If this option is used then monomers should be checked carefully before using
    Hydrogens will be restored in their riding positions
    Links between monomers will be checked. Only those links present in the coordinate file will be used
    Standard sugar links will be analysed and used
    For new ligands "ideal restraint" values will be taken from the energetic libary ener_lib.cif
    Symmetry related links will be analysed and used
    Cis peptides will be found and used automatically


  Residual                               : Rice Maximum Likelihood for Fs

    ****                    Least-square scaling parameters                     ****

Overall scale
Overall B value
Overall anisotropic B with tr(B) = 0.0
Constant bulk solvent in non protein region
Probe radii for non-ions     1.200
Probe radii for ions         0.800
Shrinkage of the mask  by    0.800


    ****                 Map sharpening parameters and methods                  ****

No map sharpening will be performed

  Method of minimisation                 : Sparse Matrix
  Experimental sigmas used for weighting
  Number of Bins and width:    11       0.0751
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    42.6836  1.1000
  Estimated number of reflections :     189100
  Free R exclusion - flag equals:     0
  Auto weighting. An attempt
  Refinement cycles       :    10
  Scaling type                           :
          Wilson scaling type with Guassians

  Estimation of D/Sigma in resolution bins
  using  free set of reflns with experimental sigmas
  using  free set of reflns with experimental sigmas

  Scaling and SigmaA resln:    42.6836  1.1000

  Damping factors:     1.0000  1.0000  1.0000


    ****                    Geometry restraints and weights                     ****


                                              Sigma:
 Bonding distances
          Weight =  1.00

 Bond angles
          Weight =  1.00

 Planar groups (all and main chain)
          WEIGHT= 1.00 1.00

 Chiral centers
          Weight= 1.00

 NON-BONDED CONTACTS
          Overall weight                          =  1.00
          Sigma for simple VDW                    =  0.20
          Sigma for VDW trhough torsion angle     =  0.20
          Sigma for HBOND                         =  0.20
          Sigma for metal-ion                     =  0.20
          Sigma for DUMMY and other atom          =  0.30
          Distance for donor-accepetor = vdw1+vdw2+(-0.30)
          Distance for acceptor - H    = vdw1+     ( 0.10)
          VDW distance through torsion = vdw1+vdw2+(-0.30)
          Distance for DUMMY-others    = vdw1+vdw2+(-0.70)

 TORSION ANGLES
          Weight= 1.00

 THERMAL FACTORS
          Weight= 1.00
     Main chain bond (1-2 neighbour)          1.5A**2
     Main chain angle (1-3 neighbour)         2.0A**2
     Side chain bond                          3.0A**2
     Side chain angle                         4.5A**2

 RESTRAINTS AGAINST EXCESSIVE SHIFTS
     Positional parameters                   0.00A
     Thermal parameters                      0.00A
     Occupancy parameters                    0.00

 RADIUS OF CONFIDENCE
     Positional parameters 0.00A
     Thermal parameters    0.00A**2
     Occupancy parameters  0.00

Monitoring style is "MEDIUM". Complete information will be printed out in the
first and last cycle. In all other cycles minimum information will be printed out
Sigma cutoffs for printing out outliers
If deviation of restraint parameter > alpha*sigma then information will be printed out
Distance outliers      10.000
Angle outliers         10.000
Torsion outliers       10.000
Chiral volume outliers 10.000
Plane outliers         10.000
Non-bonding outliers   10.000
B value  outliers      10.000
Rigid bond outliers    10.000
Sphericity outliers    10.000
---------------------------------------------------------------

 Input file :EP_R00_1-15A.pdb
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      5.51
 _lib_update       11/07/18
  ------------------------------
  NUMBER OF MONOMERS IN THE LIBRARY          : 24624
                with complete description    : 24624
  NUMBER OF MODIFICATIONS                    :    70
  NUMBER OF LINKS                            :    77
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )
  Number of atoms    :    2459
  Number of residues :     330
  Number of chains   :       1
  I am reading library. Please wait.
                mon_lib.cif
  --------------------------------
  --- title of input coord file ---

  PDB_code:xxxx
  PDB_name:----
  PDB_date:26-MAY-20
  --------------------------------
  ATTENTION: atom:CE   LYS                63  AAA  is missing in the structure
  ATTENTION: atom:NZ   LYS                63  AAA  is missing in the structure
  ATTENTION: atom:CD   LYS                68  AAA  is missing in the structure
  ATTENTION: atom:CE   LYS                68  AAA  is missing in the structure
  ATTENTION: atom:NZ   LYS                68  AAA  is missing in the structure
  ATTENTION: atom:CE   LYS               110  AAA  is missing in the structure
  ATTENTION: atom:NZ   LYS               110  AAA  is missing in the structure
  ATTENTION: atom:NZ   LYS               142  AAA  is missing in the structure
  ATTENTION: atom:NZ   LYS               149  AAA  is missing in the structure
  ATTENTION: atom:CG   LYS               191  AAA  is missing in the structure
  ATTENTION: atom:CD   LYS               191  AAA  is missing in the structure
  ATTENTION: atom:CE   LYS               191  AAA  is missing in the structure
  ATTENTION: atom:NZ   LYS               191  AAA  is missing in the structure
  ATTENTION: atom:NZ   LYS               243  AAA  is missing in the structure
  ATTENTION: atom:OXT  ALA               328  AAA  is missing in the structure
  Number of chains                  :       1
  Total number of monomers          :     330
  Number of atoms                   :    4853
  Number of missing atoms           :       7
  Number of rebuilt atoms           :    2344
  Number of unknown atoms           :       0
  Number of deleted atoms           :       0

_ccp4_form_factor.scat_method    'Sum of Gaussians'
_ccp4_form_factor.scat_data_source  X-ray


 loop_
     _atom_type_symbol
     _atom_type_scat_Cromer_Mann_a1
     _atom_type_scat_Cromer_Mann_b1
     _atom_type_scat_Cromer_Mann_a2
     _atom_type_scat_Cromer_Mann_b2
     _atom_type_scat_Cromer_Mann_a3
     _atom_type_scat_Cromer_Mann_b3
     _atom_type_scat_Cromer_Mann_a4
     _atom_type_scat_Cromer_Mann_b4
     _atom_type_scat_Cromer_Mann_c


  N     12.2220   0.0057   3.1346   9.8933   2.0141  28.9975   1.1672   0.5826 -11.5379
  H      0.4930  10.5109   0.3229  26.1257   0.1402   3.1424   0.0408  57.7997   0.0030
  C      2.3103  20.8439   1.0201  10.2075   1.5888   0.5687   0.8651  51.6512   0.2156
  O      3.0487  13.2771   2.2870   5.7011   1.5464   0.3239   0.8671  32.9089   0.2508
  S      6.9054   1.4679   5.2035  22.2151   1.4379   0.2536   1.5863  56.1720   1.0317


 Number of distances         :           0
 Number of angles            :           0
 Number of torsions          :           0
 Number of planes            :           0
 Number of chirals           :           0
 Number of intervals         :           0
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
                        Standard  External       All
                Bonds:      4719         0      4719
               Angles:      8613         0      8613
              Chirals:       376         0       376
               Planes:       786         0       786
             Torsions:      2619         0      2619
            Intervals:         0         0         0
--------------------------------------------------------------------------------


  Number of harmonic restraints       =            0
  Number of atoms in special position =            0
 -----------------------------------------------------


    ****                           Info from mtz file                           ****

FreeR flag                            0
Number of "free" reflections       6521
Number of   all  reflections     130515
--------------------------------------------------------------------------------
 Number of reflections in file     149916
 Number of reflections read         130515

   Current auto weighting coefficient =    5.2497382    

 mode : HKRF


######  TLS Group Definitions ######



     CGMAT cycle number =      1

    ****                              VDW outliers                              ****

VDW deviations from the ideal >10.000Sigma or dist <  1.000 will be monitored

A    328 ALA C   . - A    329 SER H   B mod.= 0.870 id.= 2.950 dev= -2.08 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.50
 Grid spacing to be used        :   132  216  154
 Maximuum H,K,L                 :    42   67   48
 Minimum acceptable grid spacing:    88  143  103
 Limits of asymmetric unit      : 1.00 1.00 0.50
 Grid spacing to be used        :   132  216  154
 Maximuum H,K,L                 :    42   67   48
 Minimum acceptable grid spacing:    88  143  103
 Weight matrix   2.35695280E-02
 Actual weight    5.2497382      is applied to the X-ray term
Norm of X_ray positional gradient                80.9
Norm of Geom. positional gradient                103.
Norm of X_ray B-factor gradient                  100.
Norm of Geom. B-factor gradient                 0.173E+04
Product of X_ray and Geom posit. gradients      0.854E+07
 Cosine of angle between them                       0.073
Product of X_ray and Geom B-fact gradients      0.380E+08
 Cosine of angle between them                       0.013


Residuals: XRAY=     0.2538E+07 GEOM=     0.2693E+05 TOTAL=     0.2565E+07
 function value    2564659.5    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2533     0.015     0.013
Bond distances: others                         2186     0.038     0.017
Bond angles  : refined atoms                   3498     1.870     1.637
Bond angles  : others                          5115     2.560     1.563
Torsion angles, period  1. refined              363     7.065     5.000
Torsion angles, period  2. refined               86    29.874    25.000
Torsion angles, period  3. refined              342    10.535    15.000
Torsion angles, period  4. refined                1    15.881    15.000
Chiral centres: refined atoms                   376     0.094     0.200
Planar groups: refined atoms                   2955     0.014     0.020
Planar groups: others                           524     0.027     0.020
VDW repulsions: refined_atoms                   435     0.238     0.200
VDW repulsions.others                          1899     0.230     0.200
VDW; torsion: refined_atoms                    1286     0.173     0.200
VDW; torsion.others                            1073     0.080     0.200
HBOND: refined_atoms                             39     0.120     0.200
VDW repulsions: symmetry: refined_atoms           2     0.091     0.200
VDW repulsions: symmetry: others                 29     0.138     0.200
HBOND: symmetry: refined_atoms                    2     0.030     0.200
M. chain bond B values: refined atoms          1369     1.687     1.339
M. chain bond B values: others                 1368     1.688  8716.139
M. chain angle B values: refined atoms         1719     1.952     2.030
M. chain angle B values: others                1720     1.952    11.472
S. chain bond B values: refined atoms          1164     2.088     1.462
S. chain bond B values: others                 1164     2.087**********
S. chain angle B values: refined atoms         1765     2.322     2.140
S. chain angle B values: others                1765     2.321     2.139
Long range B values: refined atoms             2682     2.321    16.147
Long range B values: others                    2683     2.321    16.148
Rigid bond restraints                          2533    15.025     3.000
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0394, B  =   -0.0001
Partial structure    1: scale =     0.3300, B  =   99.9913
Overall anisotropic scale factors
   B11 =   0.00 B22 =   0.00 B33 =  -0.00 B12 =   0.00 B13 =  -0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------

    ****                Things for loggraph, R factor and others                ****


$TABLE: Cycle    1. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle    1.  v. resln :N:1,6,7,11,12:
:Cycle    1.  and  v. resln :N:1,4,5,9,10:
:Cycle    1. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.038    3503  99.51   353.3   322.9  0.28  0.30     185   336.9   316.5  0.27  0.28
 0.113    6230  99.26   231.2   185.2  0.28  0.28     330   229.0   185.6  0.30  0.30
 0.188    7965  98.68   146.3   127.5  0.29  0.28     417   142.5   129.6  0.33  0.32
 0.263    9396  98.29   102.3    92.5  0.33  0.31     496   101.7    91.4  0.35  0.33
 0.338   10577  97.64    61.8    60.1  0.40  0.38     553    62.0    59.8  0.45  0.43
 0.413   11568  96.93    44.3    46.6  0.51  0.49     608    45.2    45.7  0.49  0.47
 0.489   12448  96.26    33.8    38.0  0.63  0.62     668    34.3    37.8  0.59  0.58
 0.564   13313  95.55    26.2    32.1  0.78  0.77     677    26.3    32.5  0.78  0.76
 0.639   14052  94.92    21.7    28.8  0.93  0.92     758    21.8    28.2  0.89  0.88
 0.714   14662  94.07    18.2    26.6  1.08  1.09     839    18.3    24.8  0.99  1.01
 0.789   14997  90.83    15.4    23.6  1.19  1.22     715    15.5    23.0  1.11  1.12
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle    1. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle    1. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0381   3261   0.817    242   0.704   3503   0.809  1.097  0.9138  0.9268  0.8053  0.7818
  0.1132   5984   0.789    246   0.663   6230   0.784  1.098  0.8920  0.9025  0.8196  0.8567
  0.1883   7729   0.751    236   0.622   7965   0.748  0.986  0.8573  0.8748  0.7270  0.7999
  0.2633   9148   0.680    248   0.557   9396   0.677  0.874  0.8227  0.8359  0.7304  0.7671
  0.3384  10327   0.486    250   0.465  10577   0.486  0.643  0.6692  0.7045  0.5780  0.6978
  0.4135  11315   0.369    253   0.371  11568   0.369  0.466  0.5975  0.5938  0.6468  0.6516
  0.4886  12199   0.213    249   0.224  12448   0.213  0.275  0.3716  0.3864  0.5705  0.5698
  0.5637  13057   0.133    256   0.154  13313   0.134  0.122  0.2892  0.2829  0.4058  0.4577
  0.6387  13806   0.025    246   0.027  14052   0.025  0.018  0.0579  0.0663  0.3027  0.3537
  0.7138  14414   0.006    248   0.006  14662   0.006  0.004  0.0121  0.0136  0.2323  0.2056
  0.7889  14783   0.003    242   0.003  15025   0.003  0.002  0.0055  0.0067  0.2110  0.1394
 $$
Resolution limits                    =     42.684     1.100
Number of used reflections           =     118739
Percentage observed                  =    95.7653
Percentage of free reflections       =     5.0004
Overall R factor                     =     0.4393
Free R factor                        =     0.4463
Average Fourier shell correlation    =     0.4027
AverageFree Fourier shell correlation=     0.3943
Overall weighted R factor            =     0.3917
Free weighted R factor               =     0.3978
Overall weighted R2 factor           =     0.3762
Free weighted R2 factor              =     0.3681
Average correlation coefficient      =     0.5040
Overall correlation coefficient      =     0.8767
Free correlation coefficient         =     0.8696
Cruickshanks DPI for coordinate error=     0.0796
DPI based on free R factor           =     0.0729
Overall figure of merit              =     0.2894
ML based su of positional parameters =     0.2070
ML based su of thermal parameters    =    13.6316
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    483402.06       26925.135       2564659.5      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   4.35461216E-02
 Actual weight    5.2497382      is applied to the X-ray term


 function value    2422884.8    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2533     0.012     0.013
Bond distances: others                         2186     0.020     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0507, B  =    4.0843
Partial structure    1: scale =     0.5065, B  =   35.3079
Overall anisotropic scale factors
   B11 =   0.67 B22 =   0.31 B33 =  -0.93 B12 =  -0.00 B13 =   0.25 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2668
Free R factor                        =     0.2988
Average Fourier shell correlation    =     0.4495
AverageFree Fourier shell correlation=     0.4392
Average correlation coefficient      =     0.5827
Overall figure of merit              =     0.3156
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    458054.13       18220.484       2422884.8       2564659.5    


     CGMAT cycle number =      3

 Weight matrix   9.15014148E-02
 Actual weight    5.2497382      is applied to the X-ray term


 function value    2506741.0    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2533     0.013     0.013
Bond distances: others                         2186     0.010     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0497, B  =    0.8384
Partial structure    1: scale =     0.5069, B  =   39.5078
Overall anisotropic scale factors
   B11 =   1.70 B22 =   0.24 B33 =  -1.72 B12 =  -0.00 B13 =   0.29 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2540
Free R factor                        =     0.2832
Average Fourier shell correlation    =     0.5187
AverageFree Fourier shell correlation=     0.5044
Average correlation coefficient      =     0.6174
Overall figure of merit              =     0.3708
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02


 fvalues    472581.88       11800.407       2605159.0       2422884.8    

 fvalues    472581.88       11800.407       2524650.3       2492731.8    
 fvalues    472581.88       11800.407       2524650.3       2492731.8    


     CGMAT cycle number =      4

 Weight matrix   0.11306729    
 Actual weight    5.2497382      is applied to the X-ray term


 function value    2498388.0    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2533     0.013     0.013
Bond distances: others                         2186     0.009     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0496, B  =    0.5929
Partial structure    1: scale =     0.5075, B  =   40.2847
Overall anisotropic scale factors
   B11 =   1.85 B22 =   0.22 B33 =  -1.83 B12 =  -0.00 B13 =   0.31 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2479
Free R factor                        =     0.2811
Average Fourier shell correlation    =     0.5337
AverageFree Fourier shell correlation=     0.5184
Average correlation coefficient      =     0.6299
Overall figure of merit              =     0.3893
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02


 fvalues    473663.00       11713.531       2528601.8       2492731.8    

 fvalues    473663.00       11713.531       2512974.5       2498320.3    
 fvalues    473663.00       11713.531       2512974.5       2498320.3    


     CGMAT cycle number =      5

 Weight matrix   0.11288510    
 Actual weight    5.2497382      is applied to the X-ray term


 function value    2504881.5    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2533     0.013     0.013
Bond distances: others                         2186     0.009     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0495, B  =    0.5214
Partial structure    1: scale =     0.5079, B  =   40.4798
Overall anisotropic scale factors
   B11 =   1.91 B22 =   0.21 B33 =  -1.88 B12 =  -0.00 B13 =   0.32 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2467
Free R factor                        =     0.2805
Average Fourier shell correlation    =     0.5358
AverageFree Fourier shell correlation=     0.5200
Average correlation coefficient      =     0.6316
Overall figure of merit              =     0.3891
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03


 fvalues    474892.34       11805.940       2517535.0       2498320.3    

 fvalues    474892.34       11805.940       2511779.5       2504866.5    
 fvalues    474892.34       11805.940       2511779.5       2504866.5    


     CGMAT cycle number =      6

 Weight matrix   0.11243441    
 Actual weight    5.2497382      is applied to the X-ray term


 function value    2508267.8    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2533     0.013     0.013
Bond distances: others                         2186     0.008     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0495, B  =    0.4910
Partial structure    1: scale =     0.5078, B  =   40.5345
Overall anisotropic scale factors
   B11 =   1.93 B22 =   0.20 B33 =  -1.90 B12 =  -0.00 B13 =   0.32 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2464
Free R factor                        =     0.2803
Average Fourier shell correlation    =     0.5364
AverageFree Fourier shell correlation=     0.5205
Average correlation coefficient      =     0.6321
Overall figure of merit              =     0.3887
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03


 fvalues    475574.03       11866.373       2513993.5       2504866.5    

 fvalues    475574.03       11866.373       2511030.8       2508505.5    
 fvalues    475574.03       11866.373       2511030.8       2508505.5    


     CGMAT cycle number =      7

 Weight matrix   0.11215776    
 Actual weight    5.2497382      is applied to the X-ray term


 function value    2510139.8    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2533     0.013     0.013
Bond distances: others                         2186     0.008     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0495, B  =    0.4736
Partial structure    1: scale =     0.5078, B  =   40.5280
Overall anisotropic scale factors
   B11 =   1.95 B22 =   0.20 B33 =  -1.91 B12 =  -0.00 B13 =   0.32 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2462
Free R factor                        =     0.2803
Average Fourier shell correlation    =     0.5367
AverageFree Fourier shell correlation=     0.5207
Average correlation coefficient      =     0.6323
Overall figure of merit              =     0.3885
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05


 fvalues    475884.41       11897.201       2511425.0       2508505.5    

 fvalues    475884.41       11897.201       2511383.5       2510165.8    
 fvalues    475884.41       11897.201       2511383.5       2510165.8    


     CGMAT cycle number =      8

 Weight matrix   0.11220273    
 Actual weight    5.2497382      is applied to the X-ray term


 function value    2510604.5    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2533     0.013     0.013
Bond distances: others                         2186     0.008     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0495, B  =    0.4708
Partial structure    1: scale =     0.5079, B  =   40.5527
Overall anisotropic scale factors
   B11 =   1.95 B22 =   0.20 B33 =  -1.91 B12 =  -0.00 B13 =   0.32 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2462
Free R factor                        =     0.2803
Average Fourier shell correlation    =     0.5368
AverageFree Fourier shell correlation=     0.5208
Average correlation coefficient      =     0.6323
Overall figure of merit              =     0.3885
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    475959.56       11911.252       2511548.3       2510165.8    

 fvalues    475959.56       11911.252       2510750.0       2510574.3    
 fvalues    475959.56       11911.252       2510750.0       2510574.3    


     CGMAT cycle number =      9

 Weight matrix   0.11222804    
 Actual weight    5.2497382      is applied to the X-ray term


 function value    2510800.3    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2533     0.013     0.013
Bond distances: others                         2186     0.008     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0495, B  =    0.4687
Partial structure    1: scale =     0.5079, B  =   40.5563
Overall anisotropic scale factors
   B11 =   1.95 B22 =   0.20 B33 =  -1.91 B12 =  -0.00 B13 =   0.32 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2461
Free R factor                        =     0.2802
Average Fourier shell correlation    =     0.5369
AverageFree Fourier shell correlation=     0.5209
Average correlation coefficient      =     0.6324
Overall figure of merit              =     0.3885
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    476014.50       11915.131       2511184.8       2510574.3    

 fvalues    476014.50       11915.131       2511186.0       2510866.8    
 fvalues    476014.50       11915.131       2511186.0       2510866.8    


     CGMAT cycle number =     10

    ****                              VDW outliers                              ****

VDW deviations from the ideal >10.000Sigma or dist <  1.000 will be monitored

A    328 ALA C   . - A    329 SER H   B mod.= 0.981 id.= 2.950 dev= -1.97 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.50
 Grid spacing to be used        :   132  216  154
 Maximuum H,K,L                 :    42   67   48
 Minimum acceptable grid spacing:    88  143  103
 Limits of asymmetric unit      : 1.00 1.00 0.50
 Grid spacing to be used        :   132  216  154
 Maximuum H,K,L                 :    42   67   48
 Minimum acceptable grid spacing:    88  143  103
 Weight matrix   0.11227922    
 Actual weight    5.2497382      is applied to the X-ray term
Norm of X_ray positional gradient                95.1
Norm of Geom. positional gradient                52.3
Norm of X_ray B-factor gradient                  115.
Norm of Geom. B-factor gradient                  205.
Product of X_ray and Geom posit. gradients     -0.489E+08
 Cosine of angle between them                      -0.705
Product of X_ray and Geom B-fact gradients     -0.577E+07
 Cosine of angle between them                      -0.014


Residuals: XRAY=     0.2499E+07 GEOM=     0.1192E+05 TOTAL=     0.2511E+07
 function value    2510500.5    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2533     0.013     0.013
Bond distances: others                         2186     0.008     0.017
Bond angles  : refined atoms                   3498     1.739     1.637
Bond angles  : others                          5115     1.611     1.563
Torsion angles, period  1. refined              363     7.117     5.000
Torsion angles, period  2. refined               86    29.752    25.000
Torsion angles, period  3. refined              342    10.487    15.000
Torsion angles, period  4. refined                1    15.707    15.000
Chiral centres: refined atoms                   376     0.082     0.200
Planar groups: refined atoms                   2955     0.011     0.020
Planar groups: others                           524     0.006     0.020
VDW repulsions: refined_atoms                   421     0.235     0.200
VDW repulsions.others                          1903     0.203     0.200
VDW; torsion: refined_atoms                    1271     0.170     0.200
VDW; torsion.others                            1089     0.080     0.200
HBOND: refined_atoms                             42     0.108     0.200
VDW repulsions: symmetry: refined_atoms           2     0.083     0.200
VDW repulsions: symmetry: others                 28     0.146     0.200
HBOND: symmetry: refined_atoms                    3     0.036     0.200
M. chain bond B values: refined atoms          1369     1.725     1.517
M. chain bond B values: others                 1368     1.727  9781.912
M. chain angle B values: refined atoms         1719     2.069     2.296
M. chain angle B values: others                1720     2.069    12.948
S. chain bond B values: refined atoms          1164     2.213     1.644
S. chain bond B values: others                 1164     2.213**********
S. chain angle B values: refined atoms         1765     2.432     2.413
S. chain angle B values: others                1765     2.432     2.412
Long range B values: refined atoms             2661     2.457    18.248
Long range B values: others                    2662     2.457    23.916
Rigid bond restraints                          2533     7.834     3.000
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0495, B  =    0.4730
Partial structure    1: scale =     0.5080, B  =   40.5696
Overall anisotropic scale factors
   B11 =   1.95 B22 =   0.20 B33 =  -1.91 B12 =  -0.00 B13 =   0.32 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------

    ****                Things for loggraph, R factor and others                ****


$TABLE: Cycle   10. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   10.  v. resln :N:1,6,7,11,12:
:Cycle   10.  and  v. resln :N:1,4,5,9,10:
:Cycle   10. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.038    3503  99.51   281.6   287.0  0.22  0.24     185   268.5   284.1  0.23  0.24
 0.113    6230  99.26   184.3   172.4  0.22  0.22     330   182.5   173.1  0.25  0.25
 0.188    7965  98.68   116.6   111.8  0.21  0.19     417   113.5   113.0  0.28  0.26
 0.263    9396  98.29    81.5    75.9  0.20  0.18     496    81.1    75.8  0.25  0.23
 0.338   10577  97.64    49.3    45.2  0.21  0.19     553    49.4    46.6  0.26  0.25
 0.413   11568  96.93    35.3    31.9  0.24  0.22     608    36.0    32.4  0.29  0.28
 0.489   12448  96.26    26.9    24.1  0.29  0.28     668    27.3    24.7  0.31  0.30
 0.564   13313  95.55    20.9    19.0  0.35  0.36     677    20.9    19.0  0.35  0.35
 0.639   14052  94.92    17.3    15.5  0.38  0.39     758    17.4    15.7  0.37  0.38
 0.714   14662  94.07    14.5    13.1  0.42  0.43     839    14.5    12.8  0.42  0.43
 0.789   14997  90.83    12.3    10.7  0.43  0.45     715    12.4    10.8  0.44  0.45
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle   10. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   10. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0381   3261   0.891    242   0.802   3503   0.885  0.942  0.9444  0.9518  0.8717  0.8563
  0.1132   5984   0.831    246   0.707   6230   0.826  1.000  0.9191  0.9279  0.8463  0.8829
  0.1883   7729   0.803    236   0.649   7965   0.798  0.999  0.9077  0.9308  0.7959  0.8867
  0.2633   9148   0.774    248   0.612   9396   0.770  1.010  0.9180  0.9338  0.8396  0.9053
  0.3384  10327   0.725    250   0.603  10577   0.722  0.980  0.9030  0.9263  0.8043  0.8930
  0.4135  11315   0.646    253   0.559  11568   0.644  0.936  0.8775  0.9047  0.7696  0.8555
  0.4886  12199   0.550    249   0.431  12448   0.547  0.819  0.8421  0.8608  0.7010  0.7733
  0.5637  13057   0.141    256   0.132  13313   0.141  0.170  0.3942  0.4154  0.5651  0.6040
  0.6387  13806   0.027    246   0.020  14052   0.027  0.018  0.0818  0.1075  0.4688  0.4661
  0.7138  14414   0.007    248   0.005  14662   0.007  0.004  0.0164  0.0199  0.3468  0.2870
  0.7889  14783   0.003    242   0.002  15025   0.003  0.002  0.0078  0.0091  0.2212  0.2161
 $$
Resolution limits                    =     42.684     1.100
Number of used reflections           =     118739
Percentage observed                  =    95.7653
Percentage of free reflections       =     5.0004
Overall R factor                     =     0.2461
Free R factor                        =     0.2803
Average Fourier shell correlation    =     0.5369
AverageFree Fourier shell correlation=     0.5209
Overall weighted R factor            =     0.2326
Free weighted R factor               =     0.2659
Overall weighted R2 factor           =     0.2989
Free weighted R2 factor              =     0.2849
Average correlation coefficient      =     0.6324
Overall correlation coefficient      =     0.9521
Free correlation coefficient         =     0.9414
Cruickshanks DPI for coordinate error=     0.0446
DPI based on free R factor           =     0.0458
Overall figure of merit              =     0.3885
ML based su of positional parameters =     0.0948
ML based su of thermal parameters    =     5.4978
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    475944.44       11916.870       2510500.5       2510866.8    

    ****                              VDW outliers                              ****

VDW deviations from the ideal >10.000Sigma or dist <  1.000 will be monitored

A    328 ALA C   . - A    329 SER H   B mod.= 0.981 id.= 2.950 dev= -1.97 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 LABOUT FREE=FREE FP=FP SIGFP=SIGFP FC=FC PHIC=PHIC FC_ALL=FC_ALL PHIC_ALL=PHIC_ALL FWT=FWT PHWT=PHWT DELFWT=DELFWT PHDELWT=PHDELWT FOM=FOM FC_ALL_LS=FC_ALL_LS PHIC_ALL_LS=PHIC_ALL_LS

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: EP_R00_1-10A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2533     0.013     0.013
Bond distances: others                         2186     0.008     0.017
Bond angles  : refined atoms                   3498     1.740     1.637
Bond angles  : others                          5115     1.611     1.563
Torsion angles, period  1. refined              363     7.117     5.000
Torsion angles, period  2. refined               86    29.752    25.000
Torsion angles, period  3. refined              342    10.487    15.000
Torsion angles, period  4. refined                1    15.710    15.000
Chiral centres: refined atoms                   376     0.082     0.200
Planar groups: refined atoms                   2955     0.011     0.020
Planar groups: others                           524     0.006     0.020
VDW repulsions: refined_atoms                   421     0.235     0.200
VDW repulsions.others                          1903     0.203     0.200
VDW; torsion: refined_atoms                    1271     0.170     0.200
VDW; torsion.others                            1089     0.080     0.200
HBOND: refined_atoms                             42     0.108     0.200
VDW repulsions: symmetry: refined_atoms           2     0.083     0.200
VDW repulsions: symmetry: others                 28     0.146     0.200
HBOND: symmetry: refined_atoms                    3     0.036     0.200
M. chain bond B values: refined atoms          1369     1.726     1.517
M. chain bond B values: others                 1368     1.728  9782.428
M. chain angle B values: refined atoms         1719     2.069     2.296
M. chain angle B values: others                1720     2.069    12.949
S. chain bond B values: refined atoms          1164     2.213     1.644
S. chain bond B values: others                 1164     2.213**********
S. chain angle B values: refined atoms         1765     2.432     2.413
S. chain angle B values: others                1765     2.432     2.413
Long range B values: refined atoms             2661     2.457    18.249
Long range B values: others                    2662     2.457    23.917
Rigid bond restraints                          2533     7.842     3.000
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0495, B  =    0.4721
Partial structure    1: scale =     0.5081, B  =   40.5769
Overall anisotropic scale factors
   B11 =   1.95 B22 =   0.20 B33 =  -1.91 B12 =  -0.00 B13 =   0.32 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------

    ****                Things for loggraph, R factor and others                ****


$TABLE: Cycle   11. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   11.  v. resln :N:1,6,7,11,12:
:Cycle   11.  and  v. resln :N:1,4,5,9,10:
:Cycle   11. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.038    3503  99.51   281.6   287.0  0.22  0.24     185   268.5   284.1  0.23  0.24
 0.113    6230  99.26   184.3   172.4  0.22  0.22     330   182.5   173.1  0.25  0.25
 0.188    7965  98.68   116.6   111.8  0.21  0.19     417   113.5   113.0  0.28  0.26
 0.263    9396  98.29    81.5    75.9  0.20  0.18     496    81.1    75.8  0.25  0.23
 0.338   10577  97.64    49.3    45.2  0.21  0.19     553    49.4    46.6  0.26  0.25
 0.413   11568  96.93    35.3    31.9  0.24  0.22     608    36.0    32.4  0.29  0.28
 0.489   12448  96.26    26.9    24.1  0.29  0.28     668    27.3    24.8  0.31  0.30
 0.564   13313  95.55    20.9    19.0  0.35  0.36     677    20.9    19.0  0.35  0.35
 0.639   14052  94.92    17.3    15.5  0.38  0.39     758    17.4    15.7  0.37  0.38
 0.714   14662  94.07    14.5    13.1  0.42  0.43     839    14.5    12.8  0.42  0.43
 0.789   14997  90.83    12.3    10.7  0.43  0.44     715    12.4    10.8  0.44  0.45
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle   11. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   11. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0381   3261   0.891    242   0.802   3503   0.885  0.942  0.9444  0.9518  0.8717  0.8562
  0.1132   5984   0.831    246   0.707   6230   0.826  1.000  0.9191  0.9279  0.8463  0.8829
  0.1883   7729   0.803    236   0.649   7965   0.798  0.999  0.9077  0.9308  0.7959  0.8867
  0.2633   9148   0.774    248   0.612   9396   0.770  1.010  0.9180  0.9338  0.8396  0.9054
  0.3384  10327   0.725    250   0.603  10577   0.722  0.980  0.9030  0.9263  0.8043  0.8930
  0.4135  11315   0.646    253   0.559  11568   0.644  0.936  0.8776  0.9047  0.7697  0.8555
  0.4886  12199   0.550    249   0.431  12448   0.547  0.819  0.8422  0.8609  0.7010  0.7734
  0.5637  13057   0.141    256   0.132  13313   0.141  0.170  0.3942  0.4154  0.5651  0.6041
  0.6387  13806   0.027    246   0.020  14052   0.027  0.018  0.0819  0.1076  0.4690  0.4661
  0.7138  14414   0.007    248   0.005  14662   0.007  0.004  0.0164  0.0199  0.3471  0.2868
  0.7889  14783   0.003    242   0.002  15025   0.003  0.002  0.0078  0.0091  0.2216  0.2159
 $$
Resolution limits                    =     42.684     1.100
Number of used reflections           =     118739
Percentage observed                  =    95.7653
Percentage of free reflections       =     5.0004
Overall R factor                     =     0.2461
Free R factor                        =     0.2803
Average Fourier shell correlation    =     0.5369
AverageFree Fourier shell correlation=     0.5209
Overall weighted R factor            =     0.2326
Free weighted R factor               =     0.2659
Overall weighted R2 factor           =     0.2989
Free weighted R2 factor              =     0.2849
Average correlation coefficient      =     0.6324
Overall correlation coefficient      =     0.9521
Free correlation coefficient         =     0.9414
Cruickshanks DPI for coordinate error=     0.0446
DPI based on free R factor           =     0.0458
Overall figure of merit              =     0.3885
ML based su of positional parameters =     0.0948
ML based su of thermal parameters    =     5.4978
-----------------------------------------------------------------------------
  Time in seconds: CPU =       141.30
             Elapsed =         256.00

    ****           Things for loggraph, R factor and others vs cycle            ****


$TABLE: Rfactor analysis, stats vs cycle  :
$GRAPHS: vs cycle :N:1,2,3:
:FOM vs cycle :N:1,4:
:-LL vs cycle :N:1,5:
:-LLfree vs cycle :N:1,6:
:Geometry vs cycle:N:1,7,8,9,10,11:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.4393   0.4463   0.289      483402.   25622.8   0.0149  1.112   1.870  1.154   0.094
       1   0.2668   0.2988   0.316      458054.   24342.0   0.0122  0.893   1.751  1.073   0.084
       2   0.2540   0.2832   0.371      475250.   25338.5   0.0133  0.933   1.728  1.056   0.079
       3   0.2479   0.2811   0.389      473676.   25393.8   0.0131  0.934   1.720  1.056   0.080
       4   0.2467   0.2805   0.389      474895.   25473.5   0.0131  0.938   1.731  1.064   0.081
       5   0.2464   0.2803   0.389      475529.   25511.1   0.0131  0.941   1.736  1.067   0.081
       6   0.2462   0.2803   0.388      475879.   25531.4   0.0131  0.942   1.738  1.069   0.082
       7   0.2462   0.2803   0.388      475965.   25536.3   0.0131  0.942   1.739  1.069   0.082
       8   0.2461   0.2802   0.388      476002.   25538.6   0.0131  0.943   1.739  1.070   0.082
       9   0.2461   0.2803   0.388      475944.   25536.0   0.0131  0.943   1.739  1.070   0.082
      10   0.2461   0.2803   0.388      475962.   25537.1   0.0131  0.943   1.740  1.070   0.082
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.4393   0.2461
             R free    0.4463   0.2803
     Rms BondLength    0.0149   0.0131
      Rms BondAngle    1.8695   1.7397
     Rms ChirVolume    0.0944   0.0817
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:     177.4s System:    0.8s Elapsed:     2:58