# Date 2007-11-30 Time 22:48:34 PST -0800 (1196491714.68 s)
#phil __OFF__

Command line arguments: "1yfr.mtz" "1yfr.pdb" "twin_law=h,l,-k"

HOST = rosie.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 17187

-------------------------------------------------------------------------------
  PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography
  User: phzwart
-------------------------------------------------------------------------------

              phenix.refine: Macromolecular Structure Refinement

-------------------------------------------------------------------------------
Phenix developers include:
  Paul Adams, Pavel Afonine, Vicent Chen, Ian Davis, Kreshna Gopal,
  Ralf Grosse-Kunstleve, Li-Wei Hung, Robert Immormino, Tom Ioerger,
  Airlie McCoy, Erik McKee, Nigel Moriarty, Reetal Pai, Randy Read,
  Jane Richardson, David Richardson, Tod Romo, Jim Sacchettini,
  Nicholas Sauter, Jacob Smith, Laurent Storoni, Tom Terwilliger,
  Peter Zwart
Phenix home page:
  http://www.phenix-online.org/
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Phenix components are copyrighted by:
  - Lawrence Berkeley National Laboratory
  - Los Alamos National Laboratory
  - University of Cambridge
  - Duke University
  - Texas Agricultural Experiment Station &
    Texas Engineering Experiment Station
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Major third-party components of Phenix include:
    Python, wxwidgets, wxPython, Boost, SCons, Clipper,
    CCP4 Monomer Library, CCP4 I/O libraries, PyCifRW, FFTPACK, L-BFGS
  Enter phenix.acknowledgments for details.
-------------------------------------------------------------------------------

Processing inputs. This may take a minute or two.

Command line parameter definitions:
  refinement.twinning.twin_law = h,l,-k

Working crystal symmetry after inspecting all inputs:
  Unit cell: (173.602, 73.926, 73.976, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

1yfr.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 7350
  Number of models: 1
  Model: 0
    Number of conformers: 1
    Conformer: " "
      Number of atoms: 7350
      Number of chains: 3
        Number of residues, atoms: 448, 3641
          Classifications: {'peptide': 448}
          Link IDs: {'PTRANS': 19, 'TRANS': 428}
          Chain breaks: 1
        Number of residues, atoms: 448, 3641
          Classifications: {'peptide': 448}
          Link IDs: {'PTRANS': 19, 'TRANS': 428}
          Chain breaks: 1
        Number of residues, atoms: 8, 68
          Unusual residues: {' MG': 6, 'ATP': 2}
          Classifications: {'undetermined': 8}
          Link IDs: {None: 7}
  Time building chain proxies: 4.28, per 1000 atoms: 0.58


================================== X-ray data =================================

F-obs:
  1yfr.mtz:FOBS_X,SIGFOBS_X

R-free flags:
  1yfr.mtz:R-free-flags

Miller array info: 1yfr.mtz:FOBS_X,SIGFOBS_X
Observation type: xray.amplitude
Type of data: double, size=49362
Type of sigmas: double, size=49362
Number of Miller indices: 49362
Anomalous flag: False
Unit cell: (173.602, 73.926, 73.976, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 4514
Resolution range: 33.3963 2.15004
Completeness in resolution range: 0.938423
Completeness with d_max=infinity: 0.938067

Number of F-obs in resolution range:                   49362
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  33.3963
                             d_min =   2.1500

Miller array info: 1yfr.mtz:R-free-flags
Observation type: None
Type of data: int, size=49362
Type of sigmas: None
Number of Miller indices: 49362
Anomalous flag: False
Unit cell: (173.602, 73.926, 73.976, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 4514
Resolution range: 33.3963 2.15004
Completeness in resolution range: 0.938423
Completeness with d_max=infinity: 0.938067

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 33.4003 -  4.6284 [4958/5535]  4430   528  10.6%
  bin  2:  4.6284 -  3.6752 [4798/5338]  4326   472   9.8%
  bin  3:  3.6752 -  3.2111 [5058/5272]  4549   509  10.1%
  bin  4:  3.2111 -  2.9177 [5204/5260]  4711   493   9.5%
  bin  5:  2.9177 -  2.7086 [5182/5241]  4639   543  10.5%
  bin  6:  2.7086 -  2.5490 [5098/5170]  4604   494   9.7%
  bin  7:  2.5490 -  2.4214 [5159/5243]  4608   551  10.7%
  bin  8:  2.4214 -  2.3160 [5092/5176]  4603   489   9.6%
  bin  9:  2.3160 -  2.2269 [4055/5170]  3662   393   9.7%
  bin 10:  2.2269 -  2.1500 [4758/5196]  4265   493  10.4%
                                overall 44397  4965  10.1%

No array of experimental phases found.


========================== Anomalous scatterer groups =========================

All atoms refined with f_prime=0 and f_double_prime=0.

========================== Set up restraints manager ==========================

  Number of disulfides: simple=0, symmetry=0
  Time building geometry restraints manager: 0.35 seconds
  Histogram of bond lengths:
        1.19 -     1.33: 1476
        1.33 -     1.46: 2247
        1.46 -     1.59: 3746
        1.59 -     1.72: 9
        1.72 -     1.85: 38
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " C5  ATP  2500 " - " C4  ATP  2500 " 1.490  1.394  0.096 2.50e+03 2.29e+01
  " C5  ATP  1500 " - " C4  ATP  1500 " 1.490  1.395  0.095 2.50e+03 2.24e+01
  " CG  MET A 220 " - " SD  MET A 220 " 1.803  1.710  0.093 1.60e+03 1.39e+01
  " SD  MET A 327 " - " CE  MET A 327 " 1.791  1.715  0.076 1.60e+03 9.33e+00
  " SD  MET A 220 " - " CE  MET A 220 " 1.791  1.723  0.068 1.60e+03 7.42e+00
  ... (remaining 7511 not shown)
  Histogram of nonbonded interaction distances:
        1.69 -     2.33: 10
        2.33 -     2.97: 4060
        2.97 -     3.62: 11422
        3.62 -     4.26: 19558
        4.26 -     4.90: 30546
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw
  " OE1 GLU A 191 " - " O3* ATP  1500 "  1.689 3.040
  " ND1 HIS A  87 " - " N1  ATP  1500 "  1.694 3.200
  " CD  GLU A 191 " - " O3* ATP  1500 "  1.839 3.270
  " OE2 GLU B 191 " - " O3G ATP  2500 "  1.904 3.040
  " CE1 HIS A  87 " - " N1  ATP  1500 "  1.972 3.340
  ... (remaining 65591 not shown)
  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.59: 2474
       33.59 -    67.17: 272
       67.17 -   100.76: 56
      100.76 -   134.35: 2
      134.35 -   167.93: 2
  Dihedral angle restraints sorted by residual:
  " O2A ATP  1500 "
  " PA  ATP  1500 "
  " O5* ATP  1500 "
  " C5* ATP  1500 "
      ideal   model   delta periodicty    weight residual
      60.00 -132.06 -167.93     1       2.50e-03 7.05e+01
  " O2A ATP  2500 "
  " PA  ATP  2500 "
  " O5* ATP  2500 "
  " C5* ATP  2500 "
      ideal   model   delta periodicty    weight residual
      60.00 -132.09 -167.91     1       2.50e-03 7.05e+01
  " PB  ATP  2500 "
  " PA  ATP  2500 "
  " O3A ATP  2500 "
  " O2A ATP  2500 "
      ideal   model   delta periodicty    weight residual
      59.99  -66.10  126.09     1       2.50e-03 3.97e+01
  ... (remaining 2803 not shown)

==================== Fixing bad ADP in input model (if any) ===================


============================== Scattering factors =============================


                ----------X-ray scattering dictionary----------                

Number of scattering types: 6
  Type Number    sf(0)   Gaussians
   S      24     15.96       2
   P       6     14.95       2
   Mg      6     11.95       2
   O    1376      7.97       2
   N    1240      6.97       2
   C    4698      5.97       2
  sf(0) = scattering factor at diffraction angle 0.


====================== Modifying start model if requested =====================


==================== Fixing bad ADP in input model (if any) ===================


================== Extract refinement strategy and selections =================

individual_sites       = True
rigid_body             = False
individual_adp         = True
group_adp              = False
tls                    = False
individual_occupancies = False
group_occupancies      = False
group_anomalous        = False
size = 7350

n_use            =  7350
n_use_u_iso      =  7350
n_use_u_aniso    =  0
n_grad_site      =  0
n_grad_u_iso     =  0
n_grad_u_aniso   =  0
n_grad_occupancy =  0
n_grad_fp        =  0
n_grad_fdp       =  0
n_anisotropic_flag =  0
total number of scatterers =  7350

==================== Process input NCS or/and find new NCS ====================

Using existing and finding new NCS is disabled.
Use refinement.main.ncs=true to activate it.
Look at refinement.ncs for more NCS related parameters.

=================== Write initial parameters into .eff file ===================

Writing effective parameters to file:
  /net/cci-filer1/vol1/home/phzwart/Users/swairjo/1YFR/1yfr_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/home/phzwart/Users/swairjo/1YFR/1yfr_refine_001.geo

CPU time processing inputs: 11.27


============================ Non-default parameters ===========================

A complete record of all parameters was written to the .eff file above.
Below are only the non-defaults.

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 173.602005 73.9260025 73.97599792 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/home/phzwart/Users/swairjo/1YFR/1yfr.pdb"
    }
    xray_data {
      file_name = "1yfr.mtz"
      labels = "FOBS_X,SIGFOBS_X"
      r_free_flags {
        file_name = "1yfr.mtz"
        label = "R-free-flags"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "1yfr_refine"
    serial = 1
  }
  twinning {
    twin_law = "h,l,-k"
  }
}
#phil __OFF__


============================= ml refinement start =============================


   ----------structure factors based statistics (before refinement)----------  


                         ----------X-ray data----------                        

|--(resolution: 2.15 - 33.40 A; n_refl. = 49362)------------------------------|
|                                                                             |
| r_work= 0.2064   r_free= 0.2156   ksol= 0.00   Bsol= 0.00   scale= 0.857    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   None A                  |
| x-ray target function (twin_lsq_f) for work reflections: 0.379290           |
| twin fraction: 0.30  twin operator: h,-l,k                                  |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 33.4003 -  5.8263 0.98   2220  251 0.2711 0.2568        None        None|
|  2:  5.8263 -  4.6284 0.98   2210  277 0.2123 0.2253        None        None|
|  3:  4.6284 -  4.0445 0.98   2102  223 0.1651 0.1639        None        None|
|  4:  4.0445 -  3.6752 0.98   2224  249 0.1745 0.1790        None        None|
|  5:  3.6752 -  3.4121 0.98   2243  247 0.1731 0.1777        None        None|
|  6:  3.4121 -  3.2111 0.98   2306  262 0.1814 0.1979        None        None|
|  7:  3.2111 -  3.0504 0.98   2377  251 0.1789 0.1796        None        None|
|  8:  3.0504 -  2.9177 0.98   2334  242 0.1926 0.2235        None        None|
|  9:  2.9177 -  2.8054 0.98   2316  284 0.1877 0.2067        None        None|
| 10:  2.8054 -  2.7086 0.98   2323  259 0.1905 0.2183        None        None|
| 11:  2.7086 -  2.6240 0.98   2311  245 0.2026 0.2229        None        None|
| 12:  2.6240 -  2.5490 0.98   2293  249 0.2026 0.2213        None        None|
| 13:  2.5490 -  2.4819 0.98   2319  268 0.2101 0.2218        None        None|
| 14:  2.4819 -  2.4214 0.98   2289  283 0.2132 0.2125        None        None|
| 15:  2.4214 -  2.3664 0.98   2301  241 0.2102 0.2111        None        None|
| 16:  2.3664 -  2.3160 0.98   2302  248 0.2133 0.2227        None        None|
| 17:  2.3160 -  2.2697 0.98   1987  202 0.2388 0.2803        None        None|
| 18:  2.2697 -  2.2269 0.98   1675  191 0.3926 0.4124        None        None|
| 19:  2.2269 -  2.1871 0.98   1985  233 0.2848 0.2835        None        None|
| 20:  2.1871 -  2.1500 0.98   2280  260 0.2149 0.2338        None        None|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 33.4003 -  5.8263  2220   251  0.90  15.94   None     0.80      50339.86|
|  2:  5.8263 -  4.6284  2210   277  0.91  15.51   None     0.83      36326.22|
|  3:  4.6284 -  4.0445  2102   223  0.93  14.32   None     0.89      35372.40|
|  4:  4.0445 -  3.6752  2224   249  0.88  19.37   None     0.94      29732.46|
|  5:  3.6752 -  3.4121  2243   247  0.89  18.00   None     0.96      23871.02|
|  6:  3.4121 -  3.2111  2306   262  0.85  21.93   None     0.96      19648.34|
|  7:  3.2111 -  3.0504  2377   251  0.86  21.75   None     0.95      16476.83|
|  8:  3.0504 -  2.9177  2334   242  0.85  22.96   None     0.93      13576.70|
|  9:  2.9177 -  2.8054  2316   284  0.82  25.42   None     0.91      11425.54|
| 10:  2.8054 -  2.7086  2323   259  0.83  24.49   None     0.89       9824.17|
| 11:  2.7086 -  2.6240  2311   245  0.82  25.23   None     0.89       8539.23|
| 12:  2.6240 -  2.5490  2293   249  0.84  24.19   None     0.89       7186.28|
| 13:  2.5490 -  2.4819  2319   268  0.84  23.39   None     0.88       5836.25|
| 14:  2.4819 -  2.4214  2289   283  0.84  23.44   None     0.87       4763.23|
| 15:  2.4214 -  2.3664  2301   241  0.83  24.34   None     0.87       4511.23|
| 16:  2.3664 -  2.3160  2302   248  0.80  28.16   None     0.89       5407.15|
| 17:  2.3160 -  2.2697  1987   202  0.69  36.61   None     0.92       7387.93|
| 18:  2.2697 -  2.2269  1675   191  0.75  32.17   None     0.93       9041.86|
| 19:  2.2269 -  2.1871  1985   233  0.70  35.84   None     0.88       6016.84|
| 20:  2.1871 -  2.1500  2280   260  0.79  28.77   None     0.86       3147.06|
|alpha:            min =        0.60 max =            0.96 mean =         0.90|
|beta:             min =     2777.49 max =        77616.08 mean =     15637.48|
|figures of merit: min =        0.00 max =            1.00 mean =         0.84|
|phase err.(work): min =        0.00 max =           89.78 mean =        23.72|
|phase err.(test): min =        0.00 max =           89.95 mean =        23.02|
|-----------------------------------------------------------------------------|

============================== Outliers rejection =============================


====================== Target weights (before refinement) =====================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.375862              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.192   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.051920              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 84.032   (deg)                 |
|-----------------------------------------------------------------------------|


        ----------Initial model statistics (before refinement)----------       

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.010:  5663 |   0.000 -   1.062:  8033 |  1.689 -  2.010:        6 |
| 0.010 - 0.019:  1346 |   1.062 -   2.124:  1505 |  2.010 -  2.331:        4 |
| 0.019 - 0.029:   362 |   2.124 -   3.186:   348 |  2.331 -  2.652:      170 |
| 0.029 - 0.038:    87 |   3.186 -   4.248:   127 |  2.652 -  2.973:     3890 |
| 0.038 - 0.048:    38 |   4.248 -   5.310:    70 |  2.973 -  3.294:     5088 |
| 0.048 - 0.057:    11 |   5.310 -   6.372:    19 |  3.294 -  3.616:     6334 |
| 0.057 - 0.067:     3 |   6.372 -   7.434:    10 |  3.616 -  3.937:     9822 |
| 0.067 - 0.077:     3 |   7.434 -   8.495:     8 |  3.937 -  4.258:     9736 |
| 0.077 - 0.086:     0 |   8.495 -   9.557:    10 |  4.258 -  4.579:    13625 |
| 0.086 - 0.096:     3 |   9.557 -  10.619:     6 |  4.579 -  4.900:    16921 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     7516 |   0.010    0.096  0.000 |       0.186 |              |
|     angle |    10136 |   1.166   10.619  0.000 |       0.240 |              |
| chirality |     1058 |   0.086    0.458  0.000 |       0.184 |        0.106 |
| planarity |     1306 |   0.005    0.030  0.000 |       0.323 |              |
|  dihedral |     2806 |  21.666  167.934  0.000 |       1.211 |              |
| nonbonded |     7516 |   4.117    4.900  1.689 |       0.204 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics--------------------------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 7350   0      6.00    60.00   34.73    None  None   None       |
|    all(noH): 7350   0      6.00    60.00   34.73    None  None   None       |
|    Sol.    : 0      0      None    None    None     None  None   None       |
|    Mac.    : 7350   0      6.00    60.00   34.73    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     6.000 -  11.400:   30   |   5:    33.000 -  38.400: 1580        |
|      1:    11.400 -  16.800:  110   |   6:    38.400 -  43.800: 1205        |
|      2:    16.800 -  22.200:  440   |   7:    43.800 -  49.200:  857        |
|      3:    22.200 -  27.600: 1135   |   8:    49.200 -  54.600:  285        |
|      4:    27.600 -  33.000: 1550   |   9:    54.600 -  60.000:  158        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

|-Occupancies statistics------------------------------------------------------|
| occupancies: max = 1.00   min = 1.00   number of occupancies < 0.1 = 0      |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 1 OF 3 *************************

|--(resolution: 2.15 - 33.40 A; n_refl. = 49362)------------------------------|
|                                                                             |
| r_work= 0.2064   r_free= 0.2156   ksol= 0.00   Bsol= 0.00   scale= 0.857    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   None A                  |
| x-ray target function (twin_lsq_f) for work reflections: 0.379290           |
| twin fraction: 0.30  twin operator: h,-l,k                                  |
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 2.15 - 33.40 A; n_refl. = 49362)------------------------------|
|                                                                             |
| r_work= 0.1821   r_free= 0.1912   ksol= 0.15   Bsol= 22.55   scale= 0.841   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.91,0.79,1.12,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   None A                  |
| x-ray target function (twin_lsq_f) for work reflections: 0.238415           |
| twin fraction: 0.28  twin operator: h,-l,k                                  |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.197652              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.116   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.070636              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 98.517   (deg)                 |
|-----------------------------------------------------------------------------|


================================ xyz refinement ===============================

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1821      final r-factor (work) = 0.1708          |
| start r-factor (free) = 0.1912      final r-factor (free) = 0.1911          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 0.4873 = 3.20 * 0.50 * 0.2384 + 1.00 * 0.1061                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 0.3691 = 3.20 * 0.50 * 0.1863 + 1.00 * 0.0711                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


                 ----------Individual ADP refinement----------                 

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1708      final r-factor (work) = 0.1642          |
| start r-factor (free) = 0.1911      final r-factor (free) = 0.1910          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.0144 = 0.07 * 1.00 * 0.1863 + 1.00 * 0.0013                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.0129 = 0.07 * 1.00 * 0.1693 + 1.00 * 0.0010                               |
|-----------------------------------------------------------------------------|
| number of iterations = 11      |    number of function evaluations = 12     |
|-----------------------------------------------------------------------------|

|-ADP statistics--------------------------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 7350   0      11.07   72.13   35.94    None  None   None       |
|    all(noH): 7350   0      11.07   72.13   35.94    None  None   None       |
|    Sol.    : 0      0      None    None    None     None  None   None       |
|    Mac.    : 7350   0      11.07   72.13   35.94    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    11.072 -  17.178:   33   |   5:    41.600 -  47.706: 1067        |
|      1:    17.178 -  23.284:  468   |   6:    47.706 -  53.812:  545        |
|      2:    23.284 -  29.389: 1407   |   7:    53.812 -  59.917:  183        |
|      3:    29.389 -  35.495: 1836   |   8:    59.917 -  66.023:   67        |
|      4:    35.495 -  41.600: 1728   |   9:    66.023 -  72.128:   16        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


*********************** REFINEMENT MACRO_CYCLE 2 OF 3 *************************

|--(resolution: 2.15 - 33.40 A; n_refl. = 49362)------------------------------|
|                                                                             |
| r_work= 0.1642   r_free= 0.1910   ksol= 0.15   Bsol= 22.55   scale= 0.841   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.91,0.79,1.12,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   None A                  |
| x-ray target function (twin_lsq_f) for work reflections: 0.169309           |
| twin fraction: 0.28  twin operator: h,-l,k                                  |
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 2.15 - 33.40 A; n_refl. = 49362)------------------------------|
|                                                                             |
| r_work= 0.1645   r_free= 0.1910   ksol= 0.16   Bsol= 23.35   scale= 0.856   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.42,1.10,1.32,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   None A                  |
| x-ray target function (twin_lsq_f) for work reflections: 0.169087           |
| twin fraction: 0.29  twin operator: h,-l,k                                  |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.557964              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 122.264  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.075026              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 172.516  (deg)                 |
|-----------------------------------------------------------------------------|


================================ xyz refinement ===============================

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1645      final r-factor (work) = 0.1544          |
| start r-factor (free) = 0.1910      final r-factor (free) = 0.1914          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 0.7947 = 8.56 * 0.50 * 0.1691 + 1.00 * 0.0711                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 0.7142 = 8.56 * 0.50 * 0.1440 + 1.00 * 0.0980                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


                 ----------Individual ADP refinement----------                 

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1544      final r-factor (work) = 0.1534          |
| start r-factor (free) = 0.1914      final r-factor (free) = 0.1916          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.0118 = 0.08 * 1.00 * 0.1440 + 1.00 * 0.0009                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.0116 = 0.08 * 1.00 * 0.1424 + 1.00 * 0.0009                               |
|-----------------------------------------------------------------------------|
| number of iterations = 12      |    number of function evaluations = 13     |
|-----------------------------------------------------------------------------|

|-ADP statistics--------------------------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 7350   0      12.27   73.42   36.52    None  None   None       |
|    all(noH): 7350   0      12.27   73.42   36.52    None  None   None       |
|    Sol.    : 0      0      None    None    None     None  None   None       |
|    Mac.    : 7350   0      12.27   73.42   36.52    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    12.267 -  18.383:   46   |   5:    42.845 -  48.961: 1029        |
|      1:    18.383 -  24.498:  604   |   6:    48.961 -  55.077:  483        |
|      2:    24.498 -  30.614: 1497   |   7:    55.077 -  61.192:  153        |
|      3:    30.614 -  36.730: 1818   |   8:    61.192 -  67.308:   71        |
|      4:    36.730 -  42.845: 1631   |   9:    67.308 -  73.423:   18        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


*********************** REFINEMENT MACRO_CYCLE 3 OF 3 *************************

|--(resolution: 2.15 - 33.40 A; n_refl. = 49362)------------------------------|
|                                                                             |
| r_work= 0.1534   r_free= 0.1916   ksol= 0.16   Bsol= 23.35   scale= 0.856   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.42,1.10,1.32,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   None A                  |
| x-ray target function (twin_lsq_f) for work reflections: 0.142407           |
| twin fraction: 0.29  twin operator: h,-l,k                                  |
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 2.15 - 33.40 A; n_refl. = 49362)------------------------------|
|                                                                             |
| r_work= 0.1533   r_free= 0.1913   ksol= 0.16   Bsol= 24.07   scale= 0.858   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.21,1.38,0.84,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   None A                  |
| x-ray target function (twin_lsq_f) for work reflections: 0.142317           |
| twin fraction: 0.30  twin operator: h,-l,k                                  |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.151507              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 149.044  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.077146              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 176.282  (deg)                 |
|-----------------------------------------------------------------------------|


================================ xyz refinement ===============================

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1533      final r-factor (work) = 0.1548          |
| start r-factor (free) = 0.1913      final r-factor (free) = 0.1919          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 0.5357 = 6.15 * 0.50 * 0.1423 + 1.00 * 0.0980                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 0.5223 = 6.15 * 0.50 * 0.1454 + 1.00 * 0.0751                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


                 ----------Individual ADP refinement----------                 

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1548      final r-factor (work) = 0.1543          |
| start r-factor (free) = 0.1919      final r-factor (free) = 0.1918          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.0121 = 0.08 * 1.00 * 0.1454 + 1.00 * 0.0009                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.0121 = 0.08 * 1.00 * 0.1445 + 1.00 * 0.0010                               |
|-----------------------------------------------------------------------------|
| number of iterations = 9       |    number of function evaluations = 11     |
|-----------------------------------------------------------------------------|

|-ADP statistics--------------------------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 7350   0      12.11   74.22   36.71    None  None   None       |
|    all(noH): 7350   0      12.11   74.22   36.71    None  None   None       |
|    Sol.    : 0      0      None    None    None     None  None   None       |
|    Mac.    : 7350   0      12.11   74.22   36.71    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    12.111 -  18.322:   41   |   5:    43.167 -  49.378: 1048        |
|      1:    18.322 -  24.533:  596   |   6:    49.378 -  55.589:  454        |
|      2:    24.533 -  30.745: 1522   |   7:    55.589 -  61.800:  161        |
|      3:    30.745 -  36.956: 1822   |   8:    61.800 -  68.012:   72        |
|      4:    36.956 -  43.167: 1614   |   9:    68.012 -  74.223:   20        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


                         ----------X-ray data----------                        

|--(resolution: 2.15 - 33.40 A; n_refl. = 49362)------------------------------|
|                                                                             |
| r_work= 0.1543   r_free= 0.1918   ksol= 0.16   Bsol= 24.07   scale= 0.858   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.21,1.38,0.84,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   None A                  |
| x-ray target function (twin_lsq_f) for work reflections: 0.144471           |
| twin fraction: 0.30  twin operator: h,-l,k                                  |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 33.4003 -  5.8263 0.98   2220  251 0.1116 0.1511        None        None|
|  2:  5.8263 -  4.6284 0.98   2210  277 0.1037 0.1500        None        None|
|  3:  4.6284 -  4.0445 0.98   2102  223 0.1089 0.1360        None        None|
|  4:  4.0445 -  3.6752 0.98   2224  249 0.1225 0.1620        None        None|
|  5:  3.6752 -  3.4121 0.98   2243  247 0.1320 0.1683        None        None|
|  6:  3.4121 -  3.2111 0.98   2306  262 0.1505 0.1984        None        None|
|  7:  3.2111 -  3.0504 0.98   2377  251 0.1613 0.1903        None        None|
|  8:  3.0504 -  2.9177 0.98   2334  242 0.1694 0.2157        None        None|
|  9:  2.9177 -  2.8054 0.98   2316  284 0.1772 0.2215        None        None|
| 10:  2.8054 -  2.7086 0.98   2323  259 0.1800 0.2217        None        None|
| 11:  2.7086 -  2.6240 0.98   2311  245 0.1846 0.2405        None        None|
| 12:  2.6240 -  2.5490 0.98   2293  249 0.1900 0.2196        None        None|
| 13:  2.5490 -  2.4819 0.98   2319  268 0.1946 0.2334        None        None|
| 14:  2.4819 -  2.4214 0.98   2289  283 0.2005 0.2320        None        None|
| 15:  2.4214 -  2.3664 0.98   2301  241 0.2076 0.2179        None        None|
| 16:  2.3664 -  2.3160 0.98   2302  248 0.2063 0.2366        None        None|
| 17:  2.3160 -  2.2697 0.98   1987  202 0.2175 0.2585        None        None|
| 18:  2.2697 -  2.2269 0.98   1675  191 0.3762 0.4176        None        None|
| 19:  2.2269 -  2.1871 0.98   1985  233 0.2438 0.2671        None        None|
| 20:  2.1871 -  2.1500 0.98   2280  260 0.2199 0.2504        None        None|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 33.4003 -  5.8263  2220   251  0.90  15.94   None     0.80      50339.86|
|  2:  5.8263 -  4.6284  2210   277  0.91  15.51   None     0.83      36326.22|
|  3:  4.6284 -  4.0445  2102   223  0.93  14.32   None     0.89      35372.40|
|  4:  4.0445 -  3.6752  2224   249  0.88  19.37   None     0.94      29732.46|
|  5:  3.6752 -  3.4121  2243   247  0.89  18.00   None     0.96      23871.02|
|  6:  3.4121 -  3.2111  2306   262  0.85  21.93   None     0.96      19648.34|
|  7:  3.2111 -  3.0504  2377   251  0.86  21.75   None     0.95      16476.83|
|  8:  3.0504 -  2.9177  2334   242  0.85  22.96   None     0.93      13576.70|
|  9:  2.9177 -  2.8054  2316   284  0.82  25.42   None     0.91      11425.54|
| 10:  2.8054 -  2.7086  2323   259  0.83  24.49   None     0.89       9824.17|
| 11:  2.7086 -  2.6240  2311   245  0.82  25.23   None     0.89       8539.23|
| 12:  2.6240 -  2.5490  2293   249  0.84  24.19   None     0.89       7186.28|
| 13:  2.5490 -  2.4819  2319   268  0.84  23.39   None     0.88       5836.25|
| 14:  2.4819 -  2.4214  2289   283  0.84  23.44   None     0.87       4763.23|
| 15:  2.4214 -  2.3664  2301   241  0.83  24.34   None     0.87       4511.23|
| 16:  2.3664 -  2.3160  2302   248  0.80  28.16   None     0.89       5407.15|
| 17:  2.3160 -  2.2697  1987   202  0.69  36.61   None     0.92       7387.93|
| 18:  2.2697 -  2.2269  1675   191  0.75  32.17   None     0.93       9041.86|
| 19:  2.2269 -  2.1871  1985   233  0.70  35.84   None     0.88       6016.84|
| 20:  2.1871 -  2.1500  2280   260  0.79  28.77   None     0.86       3147.06|
|alpha:            min =        0.60 max =            0.96 mean =         0.90|
|beta:             min =     2777.49 max =        77616.08 mean =     15637.48|
|figures of merit: min =        0.00 max =            1.00 mean =         0.84|
|phase err.(work): min =        0.00 max =           89.78 mean =        23.72|
|phase err.(test): min =        0.00 max =           89.95 mean =        23.02|
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 2.15 - 33.40 A; n_refl. = 49362)------------------------------|
|                                                                             |
| r_work= 0.1544   r_free= 0.1920   ksol= 0.17   Bsol= 24.65   scale= 0.860   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.52,1.67,0.80,0.00,0.00,0.00); trace/3= -0.02                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   None A                  |
| x-ray target function (twin_lsq_f) for work reflections: 0.144594           |
| twin fraction: 0.30  twin operator: h,-l,k                                  |
|-----------------------------------------------------------------------------|

                         ----------X-ray data----------                        

|--(resolution: 2.15 - 33.40 A; n_refl. = 49362)------------------------------|
|                                                                             |
| r_work= 0.1544   r_free= 0.1920   ksol= 0.17   Bsol= 24.65   scale= 0.860   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.52,1.67,0.80,0.00,0.00,0.00); trace/3= -0.02                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   None A                  |
| x-ray target function (twin_lsq_f) for work reflections: 0.144594           |
| twin fraction: 0.30  twin operator: h,-l,k                                  |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 33.4003 -  5.8263 0.98   2220  251 0.1117 0.1514        None        None|
|  2:  5.8263 -  4.6284 0.98   2210  277 0.1048 0.1512        None        None|
|  3:  4.6284 -  4.0445 0.98   2102  223 0.1093 0.1361        None        None|
|  4:  4.0445 -  3.6752 0.98   2224  249 0.1226 0.1620        None        None|
|  5:  3.6752 -  3.4121 0.98   2243  247 0.1312 0.1673        None        None|
|  6:  3.4121 -  3.2111 0.98   2306  262 0.1498 0.1980        None        None|
|  7:  3.2111 -  3.0504 0.98   2377  251 0.1610 0.1905        None        None|
|  8:  3.0504 -  2.9177 0.98   2334  242 0.1694 0.2161        None        None|
|  9:  2.9177 -  2.8054 0.98   2316  284 0.1771 0.2216        None        None|
| 10:  2.8054 -  2.7086 0.98   2323  259 0.1808 0.2219        None        None|
| 11:  2.7086 -  2.6240 0.98   2311  245 0.1853 0.2408        None        None|
| 12:  2.6240 -  2.5490 0.98   2293  249 0.1905 0.2214        None        None|
| 13:  2.5490 -  2.4819 0.98   2319  268 0.1951 0.2337        None        None|
| 14:  2.4819 -  2.4214 0.98   2289  283 0.2009 0.2327        None        None|
| 15:  2.4214 -  2.3664 0.98   2301  241 0.2076 0.2182        None        None|
| 16:  2.3664 -  2.3160 0.98   2302  248 0.2058 0.2363        None        None|
| 17:  2.3160 -  2.2697 0.98   1987  202 0.2181 0.2598        None        None|
| 18:  2.2697 -  2.2269 0.98   1675  191 0.3736 0.4158        None        None|
| 19:  2.2269 -  2.1871 0.98   1985  233 0.2456 0.2694        None        None|
| 20:  2.1871 -  2.1500 0.98   2280  260 0.2188 0.2490        None        None|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 33.4003 -  5.8263  2220   251  0.90  15.94   None     0.80      50339.86|
|  2:  5.8263 -  4.6284  2210   277  0.91  15.51   None     0.83      36326.22|
|  3:  4.6284 -  4.0445  2102   223  0.93  14.32   None     0.89      35372.40|
|  4:  4.0445 -  3.6752  2224   249  0.88  19.37   None     0.94      29732.46|
|  5:  3.6752 -  3.4121  2243   247  0.89  18.00   None     0.96      23871.02|
|  6:  3.4121 -  3.2111  2306   262  0.85  21.93   None     0.96      19648.34|
|  7:  3.2111 -  3.0504  2377   251  0.86  21.75   None     0.95      16476.83|
|  8:  3.0504 -  2.9177  2334   242  0.85  22.96   None     0.93      13576.70|
|  9:  2.9177 -  2.8054  2316   284  0.82  25.42   None     0.91      11425.54|
| 10:  2.8054 -  2.7086  2323   259  0.83  24.49   None     0.89       9824.17|
| 11:  2.7086 -  2.6240  2311   245  0.82  25.23   None     0.89       8539.23|
| 12:  2.6240 -  2.5490  2293   249  0.84  24.19   None     0.89       7186.28|
| 13:  2.5490 -  2.4819  2319   268  0.84  23.39   None     0.88       5836.25|
| 14:  2.4819 -  2.4214  2289   283  0.84  23.44   None     0.87       4763.23|
| 15:  2.4214 -  2.3664  2301   241  0.83  24.34   None     0.87       4511.23|
| 16:  2.3664 -  2.3160  2302   248  0.80  28.16   None     0.89       5407.15|
| 17:  2.3160 -  2.2697  1987   202  0.69  36.61   None     0.92       7387.93|
| 18:  2.2697 -  2.2269  1675   191  0.75  32.17   None     0.93       9041.86|
| 19:  2.2269 -  2.1871  1985   233  0.70  35.84   None     0.88       6016.84|
| 20:  2.1871 -  2.1500  2280   260  0.79  28.77   None     0.86       3147.06|
|alpha:            min =        0.60 max =            0.96 mean =         0.90|
|beta:             min =     2777.49 max =        77616.08 mean =     15637.48|
|figures of merit: min =        0.00 max =            1.00 mean =         0.84|
|phase err.(work): min =        0.00 max =           89.78 mean =        23.72|
|phase err.(test): min =        0.00 max =           89.95 mean =        23.02|
|-----------------------------------------------------------------------------|

|-ADP statistics--------------------------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 7350   0      11.96   74.07   36.56    None  None   None       |
|    all(noH): 7350   0      11.96   74.07   36.56    None  None   None       |
|    Sol.    : 0      0      None    None    None     None  None   None       |
|    Mac.    : 7350   0      11.96   74.07   36.56    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    11.959 -  18.170:   41   |   5:    43.014 -  49.226: 1048        |
|      1:    18.170 -  24.381:  596   |   6:    49.226 -  55.437:  454        |
|      2:    24.381 -  30.592: 1522   |   7:    55.437 -  61.648:  161        |
|      3:    30.592 -  36.803: 1822   |   8:    61.648 -  67.859:   72        |
|      4:    36.803 -  43.014: 1614   |   9:    67.859 -  74.070:   20        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


================= overall refinement statistics: step by step =================

****************** REFINEMENT STATISTICS STEP BY STEP ******************
leading digit, like 1_, means number of macro-cycle                     
0    : statistics at the very beginning when nothing is done yet        
1_bss: bulk solvent correction and/or (anisotropic) scaling             
1_xyz: refinement of coordinates                                        
1_adp: refinement of ADPs (Atomic Displacement Parameters)              
------------------------------------------------------------------------
 R-factors, x-ray target values and norm of gradient of x-ray target
 stage     r-work r-free  xray_target_w  xray_target_t
   0    :  0.2064 0.2156   3.792899e-01   3.924333e-01
   1_bss:  0.1821 0.1912   2.384148e-01   2.544101e-01
   1_xyz:  0.1708 0.1911   1.863496e-01   2.469057e-01
   1_adp:  0.1642 0.1910   1.693086e-01   2.435288e-01
   2_bss:  0.1645 0.1910   1.690866e-01   2.422477e-01
   2_xyz:  0.1544 0.1914   1.440066e-01   2.395198e-01
   2_adp:  0.1534 0.1916   1.424069e-01   2.406670e-01
   3_bss:  0.1533 0.1913   1.423174e-01   2.397912e-01
   3_xyz:  0.1548 0.1919   1.453992e-01   2.405802e-01
   3_adp:  0.1543 0.1918   1.444711e-01   2.401041e-01
   3_bss:  0.1544 0.1920   1.445937e-01   2.409003e-01
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.154  22.548  -1.908   0.787   1.121   0.000   0.000   0.000
   1_xyz:  0.154  22.548  -1.908   0.787   1.121   0.000   0.000   0.000
   1_adp:  0.154  22.548  -1.908   0.787   1.121   0.000   0.000   0.000
   2_bss:  0.162  23.352  -2.421   1.101   1.320   0.000   0.000   0.000
   2_xyz:  0.162  23.352  -2.421   1.101   1.320   0.000   0.000   0.000
   2_adp:  0.162  23.352  -2.421   1.101   1.320   0.000   0.000   0.000
   3_bss:  0.165  24.073  -2.213   1.378   0.835   0.000   0.000   0.000
   3_xyz:  0.165  24.073  -2.213   1.378   0.835   0.000   0.000   0.000
   3_adp:  0.165  24.073  -2.213   1.378   0.835   0.000   0.000   0.000
   3_bss:  0.165  24.649  -2.520   1.674   0.800   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  23.089 0.8433  0.8961    15575.025
   1_bss:  23.089 0.8433  0.8961    15575.025
   1_xyz:  23.089 0.8433  0.8961    15575.025
   1_adp:  23.089 0.8433  0.8961    15575.025
   2_bss:  23.089 0.8433  0.8961    15575.025
   2_xyz:  23.089 0.8433  0.8961    15575.025
   2_adp:  23.089 0.8433  0.8961    15575.025
   3_bss:  23.089 0.8433  0.8961    15575.025
   3_xyz:  23.089 0.8433  0.8961    15575.025
   3_adp:  23.089 0.8433  0.8961    15575.025
   3_bss:  23.089 0.8433  0.8961    15575.025
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.166  0.010  0.086 21.666  0.005  4.117   1.0607e-01
   1_bss:   1.166  0.010  0.086 21.666  0.005  4.117   1.0607e-01
   1_xyz:   0.863  0.006  0.050 20.487  0.003  4.119   7.1139e-02
   1_adp:   0.863  0.006  0.050 20.487  0.003  4.119   7.1139e-02
   2_bss:   0.863  0.006  0.050 20.487  0.003  4.119   7.1139e-02
   2_xyz:   1.121  0.009  0.063 20.909  0.004  4.119   9.7963e-02
   2_adp:   1.121  0.009  0.063 20.909  0.004  4.119   9.7963e-02
   3_bss:   1.121  0.009  0.063 20.909  0.004  4.119   9.7963e-02
   3_xyz:   0.889  0.006  0.051 20.436  0.003  4.120   7.5089e-02
   3_adp:   0.889  0.006  0.051 20.436  0.003  4.120   7.5089e-02
   3_bss:   0.889  0.006  0.051 20.436  0.003  4.120   7.5089e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  10.619  0.096  0.458167.934  0.030  1.689   6.6267e-02
   1_bss:  10.619  0.096  0.458167.934  0.030  1.689   6.6267e-02
   1_xyz:   7.994  0.034  0.196144.834  0.028  2.264   2.4729e-02
   1_adp:   7.994  0.034  0.196144.834  0.028  2.264   2.4729e-02
   2_bss:   7.994  0.034  0.196144.834  0.028  2.264   2.4729e-02
   2_xyz:   9.395  0.047  0.290148.734  0.052  2.123   3.7081e-02
   2_adp:   9.395  0.047  0.290148.734  0.052  2.123   3.7081e-02
   3_bss:   9.395  0.047  0.290148.734  0.052  2.123   3.7081e-02
   3_xyz:   7.713  0.042  0.249147.422  0.034  2.329   2.4888e-02
   3_adp:   7.713  0.042  0.249147.422  0.034  2.329   2.4888e-02
   3_bss:   7.713  0.042  0.249147.422  0.034  2.329   2.4888e-02
------------------------------------------------------------------------
 stage      b_max   b_min   b_ave
   0    :   60.00    6.00   34.73
   1_bss:   61.60    7.60   36.33
   1_xyz:   61.60    7.60   36.33
   1_adp:   72.13   11.07   35.94
   2_bss:   72.77   11.72   36.59
   2_xyz:   72.77   11.72   36.59
   2_adp:   73.42   12.27   36.52
   3_bss:   73.48   12.33   36.58
   3_xyz:   73.48   12.33   36.58
   3_adp:   74.22   12.11   36.71
   3_bss:   74.07   11.96   36.56
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.010    0.004    0.095
   1_adp:    1.010    0.004    0.095
   2_bss:    1.010    0.004    0.095
   2_xyz:    0.953    0.007    0.168
   2_adp:    0.953    0.007    0.168
   3_bss:    0.953    0.007    0.168
   3_xyz:    0.995    0.011    0.177
   3_adp:    0.995    0.011    0.177
   3_bss:    0.995    0.011    0.177
------------------------------------------------------------------------

CPU time actual refinement: 349.31


============================== Exporting results ==============================

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/home/phzwart/Users/swairjo/1YFR/1yfr_refine_001.pdb
n_use            =  7350
n_use_u_iso      =  7350
n_use_u_aniso    =  0
n_grad_site      =  0
n_grad_u_iso     =  7350
n_grad_u_aniso   =  0
n_grad_occupancy =  0
n_grad_fp        =  0
n_grad_fdp       =  0
n_anisotropic_flag =  0
total number of scatterers =  7350

Writing 2mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/home/phzwart/Users/swairjo/1YFR/1yfr_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/home/phzwart/Users/swairjo/1YFR/1yfr_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/home/phzwart/Users/swairjo/1YFR/1yfr_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/home/phzwart/Users/swairjo/1YFR/1yfr_refine_002.def


=============================== Detailed timings ==============================

Pure refinement (no I/O, processing, etc)= 349.19 
  Macro-tasks:
    individual site refinement   = 132.63 
    weights calculation          = 66.37  
    collect and process          = 5.27   
    model show statistics        = 0.16   
    TOTAL for macro-tasks        = 204.43 
  Micro-tasks:
    mask                            = 0.00   
    f_calc                          = 0.00   
    alpha_beta                      = 0.00   
    target                          = 0.01   
    gradients_wrt_atomic_parameters = 83.13  
    fmodel                         = 0.00   
    r_factors                      = 0.00   
    phase_errors                   = 0.00   
    foms                           = 0.00   
    TOTAL for micro-tasks          = 83.14  
NUMBER OF MASK CALCS=  1
Time per interpreted Python bytecode instruction: 5.483 micro seconds
Total CPU time: 6.33 minutes
from_scatterers_fft:    182 calls, 72.04 s
gradients_fft:          133 calls, 69.20 s

=========================== phenix.refine: finished ===========================

# Date 2007-11-30 Time 22:54:54 PST -0800 (1196492094.93 s)
Start R-work = 0.2064, R-free = 0.2156 (no bulk solvent and anisotropic scale)
Final R-work = 0.1553, R-free = 0.1935 (no bulk solvent and anisotropic scale)

Start R-work = 0.1821, R-free = 0.1912
Final R-work = 0.1544, R-free = 0.1920