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 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
 ###############################################################
 User: malyma  Run date: 12/ 3/2021 Run time: 11:01:51 


 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 47.32 2.10     resi MLKF     meth CGMAT     bref MIXED
  Data line--- scal     type SIMP     LSSC     ANISO     EXPE
  Data line--- solvent YES
  Data line--- bins 5
  Data line--- ncyc 10
  Data line--- weight matrix 0.0600
  Data line--- monitor MEDIum
  Data line--- free 0
  Data line--- END

 OPENED INPUT MTZ FILE 
 Logical Name: HKLIN   Filename: poli67_1-9A.mtz 

 LABIN FP=F_XDSdataset SIGFP=SIGF_XDSdataset FREE=FreeR_flag

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


Input coordinate file.  Logical name - XYZIN actual file name  - poli_webinar_R00_2-30A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - poli_webinar_R00_2-10A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - poli67_1-9A.mtz
Output reflection file. Logical name - HKLOUT actual file name - poli_webinar_R00_2-10A.mtz

Cell from mtz :    58.265    79.758    94.643    90.000    90.000    90.000
Space group from mtz: number -   19; name - P 21 21 21

  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:     5       0.0454
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    47.3245  2.1000
  Estimated number of reflections :      34260
  Free R exclusion - flag equals:     0
  Weighting by comparison of trace of matrix
  Weighting parameters   :     0.0600
  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:    47.3245  2.1000

  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 :poli_webinar_R00_2-30A.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    :    2286
  Number of residues :     307
  Number of chains   :       3
  I am reading library. Please wait.
                mon_lib.cif
  --------------------------------
  --- title of input coord file ---

  PDB_code:xxxx
  PDB_name:----
  PDB_date:24-OCT-17
  --------------------------------
  ATTENTION: atom:OXT  ASN                69  AAA  is missing in the structure
  ATTENTION: atom:OXT  ARG               164  AAA  is missing in the structure
  ATTENTION: atom:OXT  PRO                36  BBB  is missing in the structure
  ATTENTION: atom:OXT  THR                70  BBB  is missing in the structure
  ATTENTION: atom:OXT  ASN               153  BBB  is missing in the structure
  Number of chains                  :       3
  Total number of monomers          :     307
  Number of atoms                   :    4696
  Number of missing atoms           :       5
  Number of rebuilt atoms           :    2331
  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:      4485         0      4485
               Angles:      8175         0      8175
              Chirals:       284         0       284
               Planes:       646         0       646
             Torsions:      2321         0      2321
            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       1283
Number of   all  reflections      26407
--------------------------------------------------------------------------------
 Number of reflections in file      35470
 Number of reflections read          26407

   Current auto weighting coefficient =    7.7495594    

 mode : HKRF


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


     CGMAT cycle number =      1

 Limits of asymmetric unit      : 1.00 1.00 0.25
 Grid spacing to be used        :   108  144  168
 Maximuum H,K,L                 :    28   39   46
 Minimum acceptable grid spacing:    68   94  111
 Limits of asymmetric unit      : 1.00 1.00 0.25
 Grid spacing to be used        :   108  144  168
 Maximuum H,K,L                 :    28   39   46
 Minimum acceptable grid spacing:    68   94  111
 Weight matrix   5.99999987E-02
 Actual weight    21.494122      is applied to the X-ray term
Norm of X_ray positional gradient                36.2
Norm of Geom. positional gradient                75.1
Norm of X_ray B-factor gradient                  41.8
Norm of Geom. B-factor gradient                  27.7
Product of X_ray and Geom posit. gradients     -0.119E+08
 Cosine of angle between them                      -0.326
Product of X_ray and Geom B-fact gradients     -0.383E+07
 Cosine of angle between them                      -0.738


Residuals: XRAY=     0.2273E+07 GEOM=     0.1677E+05 TOTAL=     0.2290E+07
 function value    2289806.5    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.012     0.013
Bond distances: others                         2201     0.034     0.017
Bond angles  : refined atoms                   3054     1.809     1.648
Bond angles  : others                          5121     2.241     1.582
Torsion angles, period  1. refined              265     7.195     5.000
Torsion angles, period  2. refined              135    32.808    22.370
Torsion angles, period  3. refined              475    19.799    15.000
Torsion angles, period  4. refined               19    19.641    15.000
Chiral centres: refined atoms                   284     0.079     0.200
Planar groups: refined atoms                   2462     0.009     0.020
Planar groups: others                           467     0.013     0.020
VDW repulsions: refined_atoms                   508     0.221     0.200
VDW repulsions.others                          1889     0.212     0.200
VDW; torsion: refined_atoms                    1091     0.171     0.200
VDW; torsion.others                            1036     0.078     0.200
HBOND: refined_atoms                             50     0.175     0.200
HBOND.others                                      1     0.002     0.200
VDW repulsions: symmetry: refined_atoms          11     0.187     0.200
VDW repulsions: symmetry: others                 25     0.269     0.200
HBOND: symmetry: refined_atoms                    2     0.147     0.200
M. chain bond B values: refined atoms          1075     7.318     7.057
M. chain bond B values: others                 1074     7.295     7.048
M. chain angle B values: refined atoms         1335     9.833    10.526
M. chain angle B values: others                1336     9.833    10.536
S. chain bond B values: refined atoms          1209     8.646     7.896
S. chain bond B values: others                 1207     8.644     7.887
S. chain angle B values: refined atoms         1719    12.333    11.486
S. chain angle B values: others                1719    12.328    11.486
Long range B values: refined atoms             2586    14.558    79.591
Long range B values: others                    2585    14.563    79.562
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.5429, B  =    0.3074
Partial structure    1: scale =     0.3830, B  =   55.4240
Overall anisotropic scale factors
   B11 =   5.61 B22 =  -1.82 B33 =  -3.79 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. <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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.023    2431  99.41   273.3   272.9  0.21  0.22     116   255.0   256.7  0.33  0.33
 0.068    4157  99.86   172.5   161.6  0.19  0.19     220   173.5   161.8  0.25  0.25
 0.114    5265  99.71    67.1    62.2  0.24  0.21     282    65.6    62.8  0.33  0.30
 0.159    6203  99.89    32.5    31.8  0.33  0.29     319    34.4    34.5  0.37  0.33
 0.204    7017  99.95    21.8    16.8  0.43  0.43     344    21.2    15.9  0.44  0.44
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0231   1864   0.810    567   0.741   2431   0.794  0.910  0.9036  0.9425  0.8434  0.9266
  0.0683   3575   0.833    582   0.742   4157   0.821  0.996  0.9196  0.9383  0.8529  0.9272
  0.1136   4683   0.755    582   0.676   5265   0.746  0.947  0.8513  0.8934  0.7498  0.8975
  0.1589   5624   0.576    579   0.532   6203   0.572  0.738  0.7326  0.7299  0.7359  0.8241
  0.2041   6433   0.234    589   0.211   7022   0.232  0.356  0.3114  0.3235  0.6841  0.6379
 $$
Resolution limits                    =     47.324     2.100
Number of used reflections           =      25078
Percentage observed                  =    99.8107
Percentage of free reflections       =     4.8598
Overall R factor                     =     0.2362
Free R factor                        =     0.3127
Average Fourier shell correlation    =     0.7056
AverageFree Fourier shell correlation=     0.6933
Overall weighted R factor            =     0.2136
Free weighted R factor               =     0.2925
Overall weighted R2 factor           =     0.2314
Free weighted R2 factor              =     0.3199
Average correlation coefficient      =     0.8144
Overall correlation coefficient      =     0.9589
Free correlation coefficient         =     0.9151
Cruickshanks DPI for coordinate error=     0.1911
DPI based on free R factor           =     0.2017
Overall figure of merit              =     0.5761
ML based su of positional parameters =     0.2646
ML based su of thermal parameters    =    11.7351
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Not converging with gamma equal    0.0000000    
 Trying gamma equal   5.24999984E-02
 Gamma decreased to   4.19999994E-02
 fvalues    105751.59       16769.105       2289806.5      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   6.00000024E-02
 Actual weight    20.046167      is applied to the X-ray term


 function value    2125792.0    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.013     0.013
Bond distances: others                         2201     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.5421, B  =   -0.2031
Partial structure    1: scale =     0.3855, B  =   55.7098
Overall anisotropic scale factors
   B11 =   5.44 B22 =  -1.74 B33 =  -3.69 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2347
Free R factor                        =     0.3103
Average Fourier shell correlation    =     0.7134
AverageFree Fourier shell correlation=     0.7006
Average correlation coefficient      =     0.8168
Overall figure of merit              =     0.5814
-----------------------------------------------------------------------------
 Trying gamma equal   4.19999994E-02
 Gamma decreased to   3.24545428E-02
 fvalues    105481.47       11292.817       2125792.0       2289806.5    


     CGMAT cycle number =      3

 Weight matrix   5.99999949E-02
 Actual weight    19.815968      is applied to the X-ray term


 function value    2100893.0    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.013     0.013
Bond distances: others                         2201     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.5410, B  =   -0.0820
Partial structure    1: scale =     0.3858, B  =   55.2225
Overall anisotropic scale factors
   B11 =   5.38 B22 =  -1.71 B33 =  -3.67 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2337
Free R factor                        =     0.3099
Average Fourier shell correlation    =     0.7168
AverageFree Fourier shell correlation=     0.7034
Average correlation coefficient      =     0.8174
Overall figure of merit              =     0.5836
-----------------------------------------------------------------------------
 Trying gamma equal   3.24545428E-02
 Gamma decreased to   2.37768572E-02
 fvalues    105440.20       11493.605       2100893.0       2125792.0    


     CGMAT cycle number =      4

 Weight matrix   5.99999949E-02
 Actual weight    19.639538      is applied to the X-ray term


 function value    2081741.8    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.013     0.013
Bond distances: others                         2201     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.5409, B  =   -0.0953
Partial structure    1: scale =     0.3865, B  =   55.0854
Overall anisotropic scale factors
   B11 =   5.32 B22 =  -1.68 B33 =  -3.64 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2331
Free R factor                        =     0.3102
Average Fourier shell correlation    =     0.7197
AverageFree Fourier shell correlation=     0.7056
Average correlation coefficient      =     0.8181
Overall figure of merit              =     0.5853
-----------------------------------------------------------------------------
 Trying gamma equal   2.37768572E-02
 Gamma decreased to   1.58880539E-02
 fvalues    105407.59       11585.377       2081741.8       2100893.0    


     CGMAT cycle number =      5

 Weight matrix   5.99999987E-02
 Actual weight    19.642035      is applied to the X-ray term


 function value    2082244.3    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.013     0.013
Bond distances: others                         2201     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.5396, B  =   -0.1309
Partial structure    1: scale =     0.3866, B  =   54.7974
Overall anisotropic scale factors
   B11 =   5.29 B22 =  -1.67 B33 =  -3.62 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2327
Free R factor                        =     0.3102
Average Fourier shell correlation    =     0.7211
AverageFree Fourier shell correlation=     0.7066
Average correlation coefficient      =     0.8186
Overall figure of merit              =     0.5860
-----------------------------------------------------------------------------
 Trying gamma equal   1.58880539E-02
 Gamma decreased to   8.71641375E-03


 fvalues    105421.70       11642.236       2082427.6       2081741.8    

 fvalues    105421.70       11642.236       2082348.4       2082339.0    
 fvalues    105421.70       11642.236       2082348.4       2082339.0    


     CGMAT cycle number =      6

 Weight matrix   5.99999987E-02
 Actual weight    19.684803      is applied to the X-ray term


 function value    2087166.0    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.013     0.013
Bond distances: others                         2201     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.5385, B  =   -0.0969
Partial structure    1: scale =     0.3868, B  =   54.7708
Overall anisotropic scale factors
   B11 =   5.28 B22 =  -1.66 B33 =  -3.62 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2327
Free R factor                        =     0.3102
Average Fourier shell correlation    =     0.7215
AverageFree Fourier shell correlation=     0.7069
Average correlation coefficient      =     0.8187
Overall figure of merit              =     0.5861
-----------------------------------------------------------------------------
 Trying gamma equal   8.71641375E-03
 Gamma decreased to   2.19674082E-03


 fvalues    105445.26       11656.633       2087251.1       2082339.0    
 fvalues    105445.26       11656.633       2087251.1       2087325.8    


     CGMAT cycle number =      7

 Weight matrix   5.99999987E-02
 Actual weight    19.659233      is applied to the X-ray term


 function value    2084436.5    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.013     0.013
Bond distances: others                         2201     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.5383, B  =   -0.0941
Partial structure    1: scale =     0.3868, B  =   54.6915
Overall anisotropic scale factors
   B11 =   5.28 B22 =  -1.65 B33 =  -3.62 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2325
Free R factor                        =     0.3096
Average Fourier shell correlation    =     0.7215
AverageFree Fourier shell correlation=     0.7070
Average correlation coefficient      =     0.8189
Overall figure of merit              =     0.5861
-----------------------------------------------------------------------------
 Trying gamma equal   2.19674082E-03
 Not converging with gamma equal   2.19674082E-03
 Trying gamma equal   3.33133601E-02
 Gamma decreased to   2.70900354E-02
 fvalues    105434.32       11678.619       2084436.5       2087325.8    


     CGMAT cycle number =      8

 Weight matrix   5.99999987E-02
 Actual weight    19.658400      is applied to the X-ray term


 function value    2084109.6    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.013     0.013
Bond distances: others                         2201     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.5392, B  =   -0.0854
Partial structure    1: scale =     0.3869, B  =   54.5989
Overall anisotropic scale factors
   B11 =   5.26 B22 =  -1.64 B33 =  -3.62 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2324
Free R factor                        =     0.3098
Average Fourier shell correlation    =     0.7213
AverageFree Fourier shell correlation=     0.7067
Average correlation coefficient      =     0.8191
Overall figure of merit              =     0.5859
-----------------------------------------------------------------------------
 Trying gamma equal   2.70900354E-02
 Gamma decreased to   2.14324687E-02
 fvalues    105421.18       11698.009       2084109.6       2084436.5    


     CGMAT cycle number =      9

 Weight matrix   5.99999949E-02
 Actual weight    19.660833      is applied to the X-ray term


 function value    2084109.4    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.013     0.013
Bond distances: others                         2201     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.5396, B  =   -0.0727
Partial structure    1: scale =     0.3869, B  =   54.6647
Overall anisotropic scale factors
   B11 =   5.26 B22 =  -1.63 B33 =  -3.62 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2323
Free R factor                        =     0.3096
Average Fourier shell correlation    =     0.7213
AverageFree Fourier shell correlation=     0.7067
Average correlation coefficient      =     0.8193
Overall figure of merit              =     0.5858
-----------------------------------------------------------------------------
 Trying gamma equal   2.14324687E-02
 Gamma decreased to   1.62892267E-02
 fvalues    105407.10       11717.873       2084109.4       2084109.6    


     CGMAT cycle number =     10

 Limits of asymmetric unit      : 1.00 1.00 0.25
 Grid spacing to be used        :   108  144  168
 Maximuum H,K,L                 :    28   39   46
 Minimum acceptable grid spacing:    68   94  111
 Limits of asymmetric unit      : 1.00 1.00 0.25
 Grid spacing to be used        :   108  144  168
 Maximuum H,K,L                 :    28   39   46
 Minimum acceptable grid spacing:    68   94  111
 Weight matrix   5.99999987E-02
 Actual weight    19.855537      is applied to the X-ray term
Norm of X_ray positional gradient                32.4
Norm of Geom. positional gradient                32.0
Norm of X_ray B-factor gradient                  32.0
Norm of Geom. B-factor gradient                  32.0
Product of X_ray and Geom posit. gradients     -0.139E+08
 Cosine of angle between them                      -0.997
Product of X_ray and Geom B-fact gradients     -0.456E+07
 Cosine of angle between them                      -0.992


Residuals: XRAY=     0.2093E+07 GEOM=     0.1174E+05 TOTAL=     0.2105E+07
 function value    2105002.3    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.013     0.013
Bond distances: others                         2201     0.001     0.017
Bond angles  : refined atoms                   3054     1.955     1.648
Bond angles  : others                          5121     1.402     1.582
Torsion angles, period  1. refined              265     7.605     5.000
Torsion angles, period  2. refined              135    32.858    22.370
Torsion angles, period  3. refined              475    20.532    15.000
Torsion angles, period  4. refined               19    20.538    15.000
Chiral centres: refined atoms                   284     0.087     0.200
Planar groups: refined atoms                   2462     0.010     0.020
Planar groups: others                           467     0.001     0.020
VDW repulsions: refined_atoms                   536     0.232     0.200
VDW repulsions.others                          2035     0.195     0.200
VDW; torsion: refined_atoms                    1098     0.174     0.200
VDW; torsion.others                            1106     0.091     0.200
HBOND: refined_atoms                             55     0.197     0.200
VDW repulsions: symmetry: refined_atoms          11     0.213     0.200
VDW repulsions: symmetry: others                 32     0.235     0.200
HBOND: symmetry: refined_atoms                    2     0.150     0.200
M. chain bond B values: refined atoms          1075     7.855     6.990
M. chain bond B values: others                 1074     7.809     6.980
M. chain angle B values: refined atoms         1335     9.996    10.430
M. chain angle B values: others                1336    10.000    10.439
S. chain bond B values: refined atoms          1209     9.170     7.790
S. chain bond B values: others                 1207     9.173     7.782
S. chain angle B values: refined atoms         1719    12.694    11.348
S. chain angle B values: others                1719    12.688    11.348
Long range B values: refined atoms             2616    14.605    79.948
Long range B values: others                    2616    14.615    79.992
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.5401, B  =   -0.0866
Partial structure    1: scale =     0.3873, B  =   54.6587
Overall anisotropic scale factors
   B11 =   5.25 B22 =  -1.62 B33 =  -3.62 B12 =   0.00 B13 =   0.00 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.023    2431  99.41   273.8   272.6  0.20  0.21     116   255.4   255.7  0.32  0.33
 0.068    4157  99.86   172.9   162.1  0.19  0.18     220   173.8   161.7  0.25  0.24
 0.114    5265  99.71    67.2    62.9  0.24  0.21     282    65.8    63.2  0.33  0.30
 0.159    6203  99.89    32.6    31.9  0.33  0.29     319    34.4    34.6  0.37  0.33
 0.204    7017  99.95    21.8    16.7  0.42  0.42     344    21.2    15.8  0.43  0.42
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0231   1864   0.829    567   0.756   2431   0.812  0.920  0.9065  0.9470  0.8467  0.9300
  0.0683   3575   0.834    582   0.744   4157   0.821  0.997  0.9191  0.9397  0.8524  0.9313
  0.1136   4683   0.768    582   0.691   5265   0.759  0.954  0.8575  0.8991  0.7611  0.8984
  0.1589   5624   0.569    579   0.527   6203   0.565  0.734  0.7359  0.7326  0.7290  0.8238
  0.2041   6433   0.248    589   0.227   7022   0.246  0.377  0.3405  0.3583  0.6939  0.6519
 $$
Resolution limits                    =     47.324     2.100
Number of used reflections           =      25078
Percentage observed                  =    99.8107
Percentage of free reflections       =     4.8598
Overall R factor                     =     0.2322
Free R factor                        =     0.3099
Average Fourier shell correlation    =     0.7179
AverageFree Fourier shell correlation=     0.7034
Overall weighted R factor            =     0.2095
Free weighted R factor               =     0.2886
Overall weighted R2 factor           =     0.2271
Free weighted R2 factor              =     0.3169
Average correlation coefficient      =     0.8195
Overall correlation coefficient      =     0.9607
Free correlation coefficient         =     0.9163
Cruickshanks DPI for coordinate error=     0.1879
DPI based on free R factor           =     0.1999
Overall figure of merit              =     0.5829
ML based su of positional parameters =     0.2540
ML based su of thermal parameters    =    11.3040
-----------------------------------------------------------------------------
 Trying gamma equal   1.62892267E-02
 Gamma decreased to   1.16135515E-02


 fvalues    105398.14       11738.990       2104553.8       2084109.4    

 fvalues    105398.14       11738.990       2104382.8       2104475.8    
 fvalues    105398.14       11738.990       2104382.8       2104475.8    

 LABOUT FreeR_flag=FreeR_flag F_XDSdataset=F_XDSdataset SIGF_XDSdataset=SIGF_XDSdataset 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: poli_webinar_R00_2-10A.mtz 


-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.013     0.013
Bond distances: others                         2201     0.001     0.017
Bond angles  : refined atoms                   3054     1.957     1.648
Bond angles  : others                          5121     1.402     1.582
Torsion angles, period  1. refined              265     7.613     5.000
Torsion angles, period  2. refined              135    32.879    22.370
Torsion angles, period  3. refined              475    20.558    15.000
Torsion angles, period  4. refined               19    20.604    15.000
Chiral centres: refined atoms                   284     0.087     0.200
Planar groups: refined atoms                   2462     0.010     0.020
Planar groups: others                           467     0.001     0.020
VDW repulsions: refined_atoms                   540     0.232     0.200
VDW repulsions.others                          2038     0.195     0.200
VDW; torsion: refined_atoms                    1099     0.174     0.200
VDW; torsion.others                            1104     0.091     0.200
HBOND: refined_atoms                             55     0.197     0.200
VDW repulsions: symmetry: refined_atoms          11     0.214     0.200
VDW repulsions: symmetry: others                 32     0.235     0.200
HBOND: symmetry: refined_atoms                    2     0.150     0.200
M. chain bond B values: refined atoms          1075     7.863     6.990
M. chain bond B values: others                 1074     7.818     6.980
M. chain angle B values: refined atoms         1335    10.001    10.430
M. chain angle B values: others                1336    10.005    10.439
S. chain bond B values: refined atoms          1209     9.181     7.791
S. chain bond B values: others                 1207     9.184     7.783
S. chain angle B values: refined atoms         1719    12.703    11.348
S. chain angle B values: others                1719    12.698    11.348
Long range B values: refined atoms             2621    14.601    80.066
Long range B values: others                    2621    14.612    80.109
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.5396, B  =   -0.0650
Partial structure    1: scale =     0.3875, B  =   54.7456
Overall anisotropic scale factors
   B11 =   5.24 B22 =  -1.62 B33 =  -3.62 B12 =   0.00 B13 =   0.00 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.023    2431  99.41   273.9   272.6  0.20  0.21     116   255.5   255.6  0.32  0.33
 0.068    4157  99.86   172.9   162.0  0.19  0.18     220   173.9   161.6  0.25  0.24
 0.114    5265  99.71    67.2    62.8  0.24  0.21     282    65.8    63.1  0.33  0.30
 0.159    6203  99.89    32.6    31.9  0.33  0.29     319    34.5    34.6  0.37  0.33
 0.204    7017  99.95    21.8    16.7  0.42  0.42     344    21.3    15.8  0.43  0.42
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0231   1864   0.829    567   0.756   2431   0.812  0.920  0.9063  0.9470  0.8467  0.9301
  0.0683   3575   0.834    582   0.744   4157   0.821  0.997  0.9191  0.9396  0.8525  0.9313
  0.1136   4683   0.767    582   0.691   5265   0.759  0.954  0.8574  0.8991  0.7614  0.8986
  0.1589   5624   0.570    579   0.528   6203   0.566  0.736  0.7362  0.7329  0.7293  0.8239
  0.2041   6433   0.257    589   0.236   7022   0.255  0.387  0.3526  0.3709  0.6945  0.6517
 $$
Resolution limits                    =     47.324     2.100
Number of used reflections           =      25078
Percentage observed                  =    99.8107
Percentage of free reflections       =     4.8598
Overall R factor                     =     0.2321
Free R factor                        =     0.3098
Average Fourier shell correlation    =     0.7214
AverageFree Fourier shell correlation=     0.7067
Overall weighted R factor            =     0.2094
Free weighted R factor               =     0.2886
Overall weighted R2 factor           =     0.2270
Free weighted R2 factor              =     0.3168
Average correlation coefficient      =     0.8195
Overall correlation coefficient      =     0.9608
Free correlation coefficient         =     0.9163
Cruickshanks DPI for coordinate error=     0.1878
DPI based on free R factor           =     0.1998
Overall figure of merit              =     0.5856
ML based su of positional parameters =     0.2540
ML based su of thermal parameters    =    11.3040
-----------------------------------------------------------------------------
  Time in seconds: CPU =        27.57
             Elapsed =         128.00

    ****           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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2362   0.3127   0.576      105752.    5544.4   0.0118  0.830   1.809  1.081   0.079
       1   0.2347   0.3103   0.581      105481.    5541.9   0.0130  0.902   1.884  1.127   0.082
       2   0.2337   0.3099   0.584      105440.    5541.9   0.0128  0.886   1.915  1.143   0.084
       3   0.2331   0.3102   0.585      105408.    5541.9   0.0128  0.885   1.930  1.149   0.085
       4   0.2327   0.3102   0.586      105417.    5542.9   0.0127  0.880   1.941  1.154   0.086
       5   0.2327   0.3102   0.586      105437.    5544.0   0.0127  0.880   1.942  1.155   0.086
       6   0.2325   0.3096   0.586      105434.    5544.0   0.0127  0.880   1.946  1.156   0.086
       7   0.2324   0.3098   0.586      105421.    5543.8   0.0127  0.879   1.948  1.157   0.086
       8   0.2323   0.3096   0.586      105407.    5543.0   0.0127  0.879   1.951  1.158   0.086
       9   0.2322   0.3099   0.583      105425.    5544.2   0.0127  0.879   1.955  1.160   0.087
      10   0.2321   0.3098   0.586      105408.    5543.5   0.0127  0.880   1.957  1.161   0.087
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2362   0.2321
             R free    0.3127   0.3098
     Rms BondLength    0.0118   0.0127
      Rms BondAngle    1.8085   1.9570
     Rms ChirVolume    0.0787   0.0866
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
 Refmac:  End of Refmac_5.8.0258   
Times: User:      60.8s System:    0.2s Elapsed:     1:01  
</pre>
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