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 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
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 User: maly  Run date: 26/ 5/2020 Run time: 11:43:38 


 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.

<!--SUMMARY_END--></FONT></B>
 $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 1.30     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_1-35A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - EP_R00_1-30A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - EP_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - EP_R00_1-30A.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       0.0538
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    42.6836  1.3000
  Estimated number of reflections :     114513
  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  1.3000

  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_1-35A.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       3945
Number of   all  reflections      79246
--------------------------------------------------------------------------------
 Number of reflections in file     149916
 Number of reflections read          79246

   Current auto weighting coefficient =    5.7496905    

 mode : HKRF


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


     CGMAT cycle number =      1

    ****                Large deviation of atoms from planarity                 ****

Deviations from the planarity >10.000Sigma will be monitored
Atom: A    130 PHE HE1   deviation=   0.22 sigma.=   0.02

    ****                              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.= 0.923 id.= 2.950 dev= -2.03 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        :   120  192  140
 Maximuum H,K,L                 :    35   57   41
 Minimum acceptable grid spacing:    77  124   89
 Limits of asymmetric unit      : 1.00 1.00 0.50
 Grid spacing to be used        :   120  192  140
 Maximuum H,K,L                 :    35   57   41
 Minimum acceptable grid spacing:    77  124   89
 Weight matrix   0.32041740    
 Actual weight    5.7496905      is applied to the X-ray term
Norm of X_ray positional gradient                51.4
Norm of Geom. positional gradient                97.4
Norm of X_ray B-factor gradient                  45.8
Norm of Geom. B-factor gradient                 0.162E+04
Product of X_ray and Geom posit. gradients     -0.325E+08
 Cosine of angle between them                      -0.465
Product of X_ray and Geom B-fact gradients     -0.104E+08
 Cosine of angle between them                      -0.008


Residuals: XRAY=     0.1765E+07 GEOM=     0.2243E+05 TOTAL=     0.1787E+07
 function value    1787076.4    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2533     0.014     0.013
Bond distances: others                         2186     0.038     0.017
Bond angles  : refined atoms                   3498     1.781     1.637
Bond angles  : others                          5115     2.544     1.563
Torsion angles, period  1. refined              363     6.926     5.000
Torsion angles, period  2. refined               86    29.561    25.000
Torsion angles, period  3. refined              342    10.477    15.000
Torsion angles, period  4. refined                1    15.565    15.000
Chiral centres: refined atoms                   376     0.091     0.200
Planar groups: refined atoms                   2955     0.013     0.020
Planar groups: others                           524     0.026     0.020
VDW repulsions: refined_atoms                   431     0.242     0.200
VDW repulsions.others                          1932     0.227     0.200
VDW; torsion: refined_atoms                    1297     0.172     0.200
VDW; torsion.others                            1073     0.080     0.200
HBOND: refined_atoms                             42     0.124     0.200
VDW repulsions: symmetry: refined_atoms           2     0.073     0.200
VDW repulsions: symmetry: others                 25     0.150     0.200
HBOND: symmetry: refined_atoms                    3     0.040     0.200
M. chain bond B values: refined atoms          1369     1.986     1.375
M. chain bond B values: others                 1368     1.989  8446.378
M. chain angle B values: refined atoms         1719     2.265     2.079
M. chain angle B values: others                1720     2.264    11.294
S. chain bond B values: refined atoms          1164     2.491     1.485
S. chain bond B values: others                 1164     2.491**********
S. chain angle B values: refined atoms         1765     2.707     2.179
S. chain angle B values: others                1765     2.705     2.178
Long range B values: refined atoms             2691     2.643    16.544
Long range B values: others                    2692     2.643    16.545
Rigid bond restraints                          2533     4.001     3.000
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0477, B  =    0.0370
Partial structure    1: scale =     0.5009, B  =   37.4979
Overall anisotropic scale factors
   B11 =  -0.26 B22 =   0.03 B33 =   0.51 B12 =   0.00 B13 =  -0.59 B23 =   0.00
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle    1. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle    1. <Rfactor> v. resln :N:1,6,7,11,12:
:Cycle    1. <Fobs> and <Fc> v. resln :N:1,4,5,9,10:
:Cycle    1. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.027    2145  99.56   280.3   300.5  0.21  0.23     113   271.3   288.0  0.20  0.21
 0.081    3797  99.48   264.3   239.6  0.21  0.21     202   253.3   242.8  0.26  0.26
 0.135    4871  99.07   156.0   151.6  0.20  0.19     256   153.6   152.0  0.25  0.24
 0.189    5703  98.73   119.8   116.4  0.21  0.19     299   120.6   120.3  0.27  0.26
 0.242    6496  98.37    98.3    92.8  0.19  0.18     342    92.6    89.3  0.27  0.24
 0.296    7089  97.95    66.3    63.1  0.17  0.15     373    68.3    64.3  0.24  0.22
 0.350    7664  97.60    47.8    45.4  0.18  0.16     401    48.1    46.9  0.26  0.24
 0.404    8203  97.13    38.1    36.0  0.20  0.18     432    38.9    36.6  0.28  0.26
 0.457    8668  96.34    31.1    29.0  0.24  0.23     458    31.5    29.4  0.30  0.29
 0.511    9074  96.04    25.7    24.0  0.31  0.31     485    26.3    24.4  0.30  0.30
 0.565    9584  95.59    21.5    20.5  0.37  0.37     485    21.6    20.3  0.37  0.37
$$

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

 $TABLE: Cycle    1. FSC and  Fom(<cos(DelPhi)>-acentric, centric, overall v resln:
 $GRAPHS:Cycle    1. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0274   1971   0.887    174   0.763   2145   0.877  0.913  0.9527  0.9562  0.9065  0.8785
  0.0812   3624   0.854    173   0.750   3797   0.849  1.020  0.9242  0.9384  0.8504  0.8934
  0.1349   4696   0.851    175   0.743   4871   0.847  0.972  0.9239  0.9356  0.8428  0.8905
  0.1886   5530   0.821    173   0.677   5703   0.816  0.971  0.9076  0.9230  0.7929  0.8840
  0.2424   6317   0.831    179   0.687   6496   0.827  0.986  0.9019  0.9298  0.8078  0.9038
  0.2961   6916   0.835    173   0.733   7089   0.832  0.971  0.9171  0.9344  0.8531  0.9262
  0.3499   7488   0.811    176   0.705   7664   0.809  0.934  0.8911  0.9148  0.7859  0.9175
  0.4036   8021   0.777    182   0.685   8203   0.775  0.904  0.8679  0.8855  0.7936  0.8965
  0.4574   8490   0.722    178   0.610   8668   0.719  0.851  0.8118  0.8326  0.7397  0.8456
  0.5111   8890   0.683    184   0.561   9074   0.680  0.768  0.7771  0.7677  0.6998  0.7201
  0.5648   9424   0.522    181   0.443   9605   0.521  0.596  0.6216  0.6121  0.5452  0.5931
 $$
Resolution limits                    =     42.684     1.300
Number of used reflections           =      73315
Percentage observed                  =    97.3690
Percentage of free reflections       =     4.9856
Overall R factor                     =     0.2124
Free R factor                        =     0.2600
Average Fourier shell correlation    =     0.8516
AverageFree Fourier shell correlation=     0.8411
Overall weighted R factor            =     0.2035
Free weighted R factor               =     0.2466
Overall weighted R2 factor           =     0.2766
Free weighted R2 factor              =     0.2744
Average correlation coefficient      =     0.8326
Overall correlation coefficient      =     0.9513
Free correlation coefficient         =     0.9362
Cruickshanks DPI for coordinate error=     0.0621
DPI based on free R factor           =     0.0635
Overall figure of merit              =     0.7519
ML based su of positional parameters =     0.0588
ML based su of thermal parameters    =     3.2770
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    306912.16       22426.527       1787076.4      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.30479789    
 Actual weight    5.7496905      is applied to the X-ray term


 function value    1785432.0    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2533     0.014     0.013
Bond distances: others                         2186     0.019     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0476, B  =   -0.0961
Partial structure    1: scale =     0.5030, B  =   37.6320
Overall anisotropic scale factors
   B11 =  -0.19 B22 =   0.04 B33 =   0.48 B12 =   0.00 B13 =  -0.64 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2118
Free R factor                        =     0.2592
Average Fourier shell correlation    =     0.8388
AverageFree Fourier shell correlation=     0.8282
Average correlation coefficient      =     0.8377
Overall figure of merit              =     0.7325
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    308052.91       14223.127       1785432.0       1787076.4    


     CGMAT cycle number =      3

 Weight matrix   0.29934651    
 Actual weight    5.7496905      is applied to the X-ray term


 function value    1789289.3    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2533     0.014     0.013
Bond distances: others                         2186     0.010     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0476, B  =   -0.1519
Partial structure    1: scale =     0.5036, B  =   37.6444
Overall anisotropic scale factors
   B11 =  -0.10 B22 =   0.05 B33 =   0.43 B12 =   0.00 B13 =  -0.68 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2116
Free R factor                        =     0.2591
Average Fourier shell correlation    =     0.8383
AverageFree Fourier shell correlation=     0.8275
Average correlation coefficient      =     0.8387
Overall figure of merit              =     0.7282
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02


 fvalues    309143.19       12213.794       1794999.8       1785432.0    

 fvalues    309143.19       12213.794       1792340.1       1789691.4    
 fvalues    309143.19       12213.794       1792340.1       1789691.4    


     CGMAT cycle number =      4

 Weight matrix   0.27157807    
 Actual weight    5.2269912      is applied to the X-ray term


 function value    1629050.5    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2533     0.014     0.013
Bond distances: others                         2186     0.009     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0476, B  =   -0.1652
Partial structure    1: scale =     0.5039, B  =   37.6418
Overall anisotropic scale factors
   B11 =  -0.07 B22 =   0.05 B33 =   0.41 B12 =   0.00 B13 =  -0.70 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2115
Free R factor                        =     0.2591
Average Fourier shell correlation    =     0.8392
AverageFree Fourier shell correlation=     0.8282
Average correlation coefficient      =     0.8391
Overall figure of merit              =     0.7279
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    309353.38       12063.158       1629050.5       1789691.4    


     CGMAT cycle number =      5

 Weight matrix   0.24345002    
 Actual weight    4.7518101      is applied to the X-ray term


 function value    1484743.0    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2533     0.014     0.013
Bond distances: others                         2186     0.007     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0476, B  =   -0.1871
Partial structure    1: scale =     0.5037, B  =   37.5747
Overall anisotropic scale factors
   B11 =  -0.03 B22 =   0.05 B33 =   0.39 B12 =   0.00 B13 =  -0.72 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2116
Free R factor                        =     0.2590
Average Fourier shell correlation    =     0.8364
AverageFree Fourier shell correlation=     0.8255
Average correlation coefficient      =     0.8394
Overall figure of merit              =     0.7227
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    309972.75       11811.319       1484743.0       1629050.5    


     CGMAT cycle number =      6

 Weight matrix   0.24446356    
 Actual weight    4.7518101      is applied to the X-ray term


 function value    1486223.0    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2533     0.014     0.013
Bond distances: others                         2186     0.005     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0476, B  =   -0.2003
Partial structure    1: scale =     0.5037, B  =   37.5437
Overall anisotropic scale factors
   B11 =   0.02 B22 =   0.05 B33 =   0.36 B12 =   0.00 B13 =  -0.74 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2116
Free R factor                        =     0.2590
Average Fourier shell correlation    =     0.8402
AverageFree Fourier shell correlation=     0.8291
Average correlation coefficient      =     0.8395
Overall figure of merit              =     0.7252
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03


 fvalues    310437.06       11572.483       1489466.9       1484743.0    

 fvalues    310437.06       11572.483       1488323.6       1486710.5    
 fvalues    310437.06       11572.483       1488323.6       1486710.5    


     CGMAT cycle number =      7

 Weight matrix   0.24164169    
 Actual weight    4.7518101      is applied to the X-ray term


 function value    1487610.9    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2533     0.014     0.013
Bond distances: others                         2186     0.005     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0476, B  =   -0.2045
Partial structure    1: scale =     0.5036, B  =   37.5310
Overall anisotropic scale factors
   B11 =   0.03 B22 =   0.05 B33 =   0.35 B12 =   0.00 B13 =  -0.75 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2117
Free R factor                        =     0.2590
Average Fourier shell correlation    =     0.8365
AverageFree Fourier shell correlation=     0.8254
Average correlation coefficient      =     0.8395
Overall figure of merit              =     0.7200
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05


 fvalues    310726.16       11529.844       1488890.8       1486710.5    

 fvalues    310726.16       11529.844       1488357.3       1488041.5    
 fvalues    310726.16       11529.844       1488357.3       1488041.5    


     CGMAT cycle number =      8

 Weight matrix   0.24135482    
 Actual weight    4.7518101      is applied to the X-ray term


 function value    1488104.8    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2533     0.014     0.013
Bond distances: others                         2186     0.005     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0476, B  =   -0.2073
Partial structure    1: scale =     0.5036, B  =   37.5295
Overall anisotropic scale factors
   B11 =   0.04 B22 =   0.05 B33 =   0.35 B12 =   0.00 B13 =  -0.75 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2117
Free R factor                        =     0.2590
Average Fourier shell correlation    =     0.8363
AverageFree Fourier shell correlation=     0.8251
Average correlation coefficient      =     0.8396
Overall figure of merit              =     0.7194
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    310743.59       11512.577       1488492.1       1488041.5    

 fvalues    310743.59       11512.577       1488267.1       1488107.1    
 fvalues    310743.59       11512.577       1488267.1       1488107.1    


     CGMAT cycle number =      9

 Weight matrix   0.24132177    
 Actual weight    4.7518101      is applied to the X-ray term


 function value    1488177.1    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2533     0.014     0.013
Bond distances: others                         2186     0.005     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0476, B  =   -0.2070
Partial structure    1: scale =     0.5036, B  =   37.5300
Overall anisotropic scale factors
   B11 =   0.04 B22 =   0.05 B33 =   0.35 B12 =   0.00 B13 =  -0.75 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2117
Free R factor                        =     0.2590
Average Fourier shell correlation    =     0.8363
AverageFree Fourier shell correlation=     0.8252
Average correlation coefficient      =     0.8396
Overall figure of merit              =     0.7194
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    310758.78       11506.475       1488774.5       1488107.1    

 fvalues    310758.78       11506.475       1488705.3       1488173.3    
 fvalues    310758.78       11506.475       1488705.3       1488173.3    


     CGMAT cycle number =     10

 Limits of asymmetric unit      : 1.00 1.00 0.50
 Grid spacing to be used        :   120  192  140
 Maximuum H,K,L                 :    35   57   41
 Minimum acceptable grid spacing:    77  124   89
 Limits of asymmetric unit      : 1.00 1.00 0.50
 Grid spacing to be used        :   120  192  140
 Maximuum H,K,L                 :    35   57   41
 Minimum acceptable grid spacing:    77  124   89
 Weight matrix   0.24130410    
 Actual weight    4.7518101      is applied to the X-ray term
Norm of X_ray positional gradient                44.3
Norm of Geom. positional gradient                48.6
Norm of X_ray B-factor gradient                  38.9
Norm of Geom. B-factor gradient                  53.9
Product of X_ray and Geom posit. gradients     -0.288E+08
 Cosine of angle between them                      -0.961
Product of X_ray and Geom B-fact gradients     -0.102E+08
 Cosine of angle between them                      -0.287


Residuals: XRAY=     0.1477E+07 GEOM=     0.1150E+05 TOTAL=     0.1488E+07
 function value    1488187.0    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2533     0.014     0.013
Bond distances: others                         2186     0.005     0.017
Bond angles  : refined atoms                   3498     1.761     1.637
Bond angles  : others                          5115     1.603     1.563
Torsion angles, period  1. refined              363     6.915     5.000
Torsion angles, period  2. refined               86    29.575    25.000
Torsion angles, period  3. refined              342    10.434    15.000
Torsion angles, period  4. refined                1    15.271    15.000
Chiral centres: refined atoms                   376     0.090     0.200
Planar groups: refined atoms                   2955     0.012     0.020
Planar groups: others                           524     0.004     0.020
VDW repulsions: refined_atoms                   433     0.240     0.200
VDW repulsions.others                          1901     0.204     0.200
VDW; torsion: refined_atoms                    1301     0.172     0.200
VDW; torsion.others                            1094     0.085     0.200
HBOND: refined_atoms                             39     0.124     0.200
VDW repulsions: symmetry: refined_atoms           2     0.074     0.200
VDW repulsions: symmetry: others                 24     0.148     0.200
HBOND: symmetry: refined_atoms                    3     0.036     0.200
M. chain bond B values: refined atoms          1369     1.935     1.361
M. chain bond B values: others                 1368     1.939  8308.949
M. chain angle B values: refined atoms         1719     2.234     2.060
M. chain angle B values: others                1720     2.233    11.226
S. chain bond B values: refined atoms          1164     2.445     1.477
S. chain bond B values: others                 1164     2.445**********
S. chain angle B values: refined atoms         1765     2.701     2.165
S. chain angle B values: others                1765     2.700     2.164
Long range B values: refined atoms             2692     2.643    16.434
Long range B values: others                    2693     2.642    16.434
Rigid bond restraints                          2533     3.865     3.000
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0476, B  =   -0.2063
Partial structure    1: scale =     0.5036, B  =   37.5318
Overall anisotropic scale factors
   B11 =   0.04 B22 =   0.05 B33 =   0.35 B12 =   0.00 B13 =  -0.75 B23 =   0.00
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle   10. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   10. <Rfactor> v. resln :N:1,6,7,11,12:
:Cycle   10. <Fobs> and <Fc> v. resln :N:1,4,5,9,10:
:Cycle   10. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.027    2145  99.56   280.4   300.5  0.21  0.23     113   271.4   288.2  0.20  0.21
 0.081    3797  99.48   264.4   239.7  0.21  0.21     202   253.5   242.7  0.26  0.26
 0.135    4871  99.07   156.0   151.6  0.21  0.20     256   153.6   151.8  0.24  0.24
 0.189    5703  98.73   119.8   116.4  0.21  0.19     299   120.7   120.4  0.27  0.25
 0.242    6496  98.37    98.4    93.0  0.19  0.18     342    92.7    89.5  0.27  0.24
 0.296    7089  97.95    66.3    63.2  0.17  0.15     373    68.3    64.4  0.23  0.22
 0.350    7664  97.60    47.8    45.5  0.18  0.16     401    48.1    46.9  0.26  0.24
 0.404    8203  97.13    38.1    36.0  0.20  0.19     432    38.9    36.5  0.28  0.26
 0.457    8668  96.34    31.2    29.1  0.24  0.23     458    31.5    29.5  0.30  0.29
 0.511    9074  96.04    25.7    24.1  0.30  0.30     485    26.3    24.4  0.30  0.30
 0.565    9584  95.59    21.5    20.4  0.36  0.36     485    21.6    20.3  0.37  0.37
$$

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

 $TABLE: Cycle   10. FSC and  Fom(<cos(DelPhi)>-acentric, centric, overall v resln:
 $GRAPHS:Cycle   10. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0274   1971   0.912    174   0.796   2145   0.903  0.919  0.9600  0.9630  0.9066  0.8764
  0.0812   3624   0.858    173   0.755   3797   0.854  1.020  0.9258  0.9402  0.8499  0.8927
  0.1349   4696   0.856    175   0.752   4871   0.852  0.972  0.9255  0.9369  0.8426  0.8893
  0.1886   5530   0.829    173   0.688   5703   0.825  0.971  0.9126  0.9272  0.7973  0.8851
  0.2424   6317   0.836    179   0.697   6496   0.833  0.986  0.9055  0.9328  0.8108  0.9048
  0.2961   6916   0.837    173   0.740   7089   0.834  0.971  0.9195  0.9364  0.8547  0.9255
  0.3499   7488   0.810    176   0.705   7664   0.808  0.934  0.8933  0.9171  0.7890  0.9163
  0.4036   8021   0.748    182   0.671   8203   0.746  0.900  0.8606  0.8781  0.7898  0.8935
  0.4574   8490   0.700    178   0.597   8668   0.698  0.848  0.8109  0.8321  0.7390  0.8477
  0.5111   8890   0.609    184   0.498   9074   0.606  0.730  0.7474  0.7425  0.7040  0.7443
  0.5648   9424   0.367    181   0.337   9605   0.366  0.486  0.5199  0.5150  0.5452  0.6253
 $$
Resolution limits                    =     42.684     1.300
Number of used reflections           =      73315
Percentage observed                  =    97.3690
Percentage of free reflections       =     4.9856
Overall R factor                     =     0.2117
Free R factor                        =     0.2590
Average Fourier shell correlation    =     0.8363
AverageFree Fourier shell correlation=     0.8252
Overall weighted R factor            =     0.2031
Free weighted R factor               =     0.2457
Overall weighted R2 factor           =     0.2790
Free weighted R2 factor              =     0.2740
Average correlation coefficient      =     0.8396
Overall correlation coefficient      =     0.9510
Free correlation coefficient         =     0.9364
Cruickshanks DPI for coordinate error=     0.0619
DPI based on free R factor           =     0.0633
Overall figure of merit              =     0.7194
ML based su of positional parameters =     0.0615
ML based su of thermal parameters    =     3.5056
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    310762.41       11503.996       1488498.1       1488173.3    

 fvalues    310762.41       11503.996       1488647.5       1488187.9    
 fvalues    310762.41       11503.996       1488647.5       1488187.9    

 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_1-30A.mtz 


-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2533     0.014     0.013
Bond distances: others                         2186     0.005     0.017
Bond angles  : refined atoms                   3498     1.761     1.637
Bond angles  : others                          5115     1.603     1.563
Torsion angles, period  1. refined              363     6.915     5.000
Torsion angles, period  2. refined               86    29.575    25.000
Torsion angles, period  3. refined              342    10.434    15.000
Torsion angles, period  4. refined                1    15.271    15.000
Chiral centres: refined atoms                   376     0.090     0.200
Planar groups: refined atoms                   2955     0.012     0.020
Planar groups: others                           524     0.004     0.020
VDW repulsions: refined_atoms                   433     0.240     0.200
VDW repulsions.others                          1901     0.204     0.200
VDW; torsion: refined_atoms                    1301     0.172     0.200
VDW; torsion.others                            1094     0.085     0.200
HBOND: refined_atoms                             39     0.124     0.200
VDW repulsions: symmetry: refined_atoms           2     0.074     0.200
VDW repulsions: symmetry: others                 24     0.148     0.200
HBOND: symmetry: refined_atoms                    3     0.036     0.200
M. chain bond B values: refined atoms          1369     1.935     1.361
M. chain bond B values: others                 1368     1.939  8308.760
M. chain angle B values: refined atoms         1719     2.234     2.060
M. chain angle B values: others                1720     2.233    11.226
S. chain bond B values: refined atoms          1164     2.445     1.477
S. chain bond B values: others                 1164     2.444**********
S. chain angle B values: refined atoms         1765     2.701     2.165
S. chain angle B values: others                1765     2.700     2.164
Long range B values: refined atoms             2692     2.643    16.433
Long range B values: others                    2693     2.642    16.434
Rigid bond restraints                          2533     3.864     3.000
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0476, B  =   -0.2081
Partial structure    1: scale =     0.5036, B  =   37.5278
Overall anisotropic scale factors
   B11 =   0.04 B22 =   0.05 B33 =   0.35 B12 =   0.00 B13 =  -0.75 B23 =   0.00
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle   11. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   11. <Rfactor> v. resln :N:1,6,7,11,12:
:Cycle   11. <Fobs> and <Fc> v. resln :N:1,4,5,9,10:
:Cycle   11. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.027    2145  99.56   280.5   300.5  0.21  0.23     113   271.4   288.2  0.20  0.21
 0.081    3797  99.48   264.5   239.7  0.21  0.21     202   253.5   242.7  0.26  0.26
 0.135    4871  99.07   156.1   151.6  0.21  0.20     256   153.7   151.8  0.24  0.24
 0.189    5703  98.73   119.9   116.5  0.21  0.19     299   120.7   120.4  0.27  0.25
 0.242    6496  98.37    98.4    93.0  0.19  0.18     342    92.7    89.5  0.27  0.24
 0.296    7089  97.95    66.3    63.2  0.17  0.15     373    68.3    64.4  0.23  0.22
 0.350    7664  97.60    47.8    45.5  0.18  0.16     401    48.2    46.9  0.26  0.24
 0.404    8203  97.13    38.1    36.0  0.20  0.19     432    38.9    36.5  0.28  0.26
 0.457    8668  96.34    31.2    29.1  0.24  0.23     458    31.5    29.5  0.30  0.29
 0.511    9074  96.04    25.7    24.1  0.30  0.30     485    26.3    24.5  0.30  0.30
 0.565    9584  95.59    21.5    20.4  0.36  0.36     485    21.6    20.3  0.37  0.37
$$

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

 $TABLE: Cycle   11. FSC and  Fom(<cos(DelPhi)>-acentric, centric, overall v resln:
 $GRAPHS:Cycle   11. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0274   1971   0.912    174   0.796   2145   0.903  0.919  0.9600  0.9630  0.9066  0.8764
  0.0812   3624   0.858    173   0.755   3797   0.854  1.020  0.9258  0.9402  0.8499  0.8927
  0.1349   4696   0.856    175   0.752   4871   0.852  0.972  0.9255  0.9369  0.8426  0.8893
  0.1886   5530   0.829    173   0.688   5703   0.825  0.971  0.9125  0.9272  0.7973  0.8851
  0.2424   6317   0.836    179   0.697   6496   0.833  0.986  0.9055  0.9328  0.8108  0.9048
  0.2961   6916   0.837    173   0.740   7089   0.834  0.971  0.9195  0.9364  0.8547  0.9255
  0.3499   7488   0.810    176   0.705   7664   0.808  0.934  0.8933  0.9171  0.7890  0.9163
  0.4036   8021   0.748    182   0.671   8203   0.746  0.900  0.8606  0.8781  0.7899  0.8936
  0.4574   8490   0.700    178   0.597   8668   0.698  0.848  0.8109  0.8321  0.7390  0.8478
  0.5111   8890   0.609    184   0.498   9074   0.606  0.730  0.7474  0.7425  0.7041  0.7443
  0.5648   9424   0.367    181   0.337   9605   0.366  0.486  0.5200  0.5151  0.5452  0.6253
 $$
Resolution limits                    =     42.684     1.300
Number of used reflections           =      73315
Percentage observed                  =    97.3690
Percentage of free reflections       =     4.9856
Overall R factor                     =     0.2117
Free R factor                        =     0.2590
Average Fourier shell correlation    =     0.8363
AverageFree Fourier shell correlation=     0.8252
Overall weighted R factor            =     0.2031
Free weighted R factor               =     0.2457
Overall weighted R2 factor           =     0.2789
Free weighted R2 factor              =     0.2740
Average correlation coefficient      =     0.8396
Overall correlation coefficient      =     0.9510
Free correlation coefficient         =     0.9364
Cruickshanks DPI for coordinate error=     0.0619
DPI based on free R factor           =     0.0633
Overall figure of merit              =     0.7194
ML based su of positional parameters =     0.0615
ML based su of thermal parameters    =     3.5056
-----------------------------------------------------------------------------
  Time in seconds: CPU =        74.45
             Elapsed =           0.00

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


$TABLE: Rfactor analysis, stats vs cycle  :
$GRAPHS:<Rfactor> 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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2124   0.2600   0.752      306912.   16603.7   0.0139  1.052   1.781  1.096   0.091
       1   0.2118   0.2592   0.733      308053.   16670.2   0.0137  1.034   1.776  1.093   0.091
       2   0.2116   0.2591   0.728      309073.   16727.3   0.0138  1.043   1.778  1.095   0.092
       3   0.2115   0.2591   0.728      309353.   16743.7   0.0139  1.045   1.779  1.096   0.092
       4   0.2116   0.2590   0.723      309973.   16775.5   0.0138  1.038   1.774  1.093   0.091
       5   0.2116   0.2590   0.725      310334.   16796.2   0.0136  1.023   1.764  1.087   0.090
       6   0.2117   0.2590   0.720      310636.   16810.7   0.0135  1.020   1.762  1.086   0.090
       7   0.2117   0.2590   0.719      310743.   16815.8   0.0135  1.019   1.762  1.085   0.090
       8   0.2117   0.2590   0.719      310760.   16816.7   0.0135  1.019   1.761  1.085   0.090
       9   0.2117   0.2590   0.719      310762.   16816.9   0.0135  1.019   1.761  1.085   0.090
      10   0.2117   0.2590   0.719      310777.   16817.6   0.0135  1.018   1.761  1.085   0.090
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2124   0.2117
             R free    0.2600   0.2590
     Rms BondLength    0.0139   0.0135
      Rms BondAngle    1.7806   1.7612
     Rms ChirVolume    0.0907   0.0900
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created
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 Refmac:  End of Refmac_5.8.0258   
Times: User:     109.1s System:    0.5s Elapsed:     1:49  
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