# Date 2007-12-02 Time 10:27:53 PST -0800 (1196620073.66 s)
#phil __OFF__

Command line arguments: "pdb1yfs_refine_003.def" "ordered_solvent=True" "twin_law=h,l,-k" "--overwrite"

HOST = rosie.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 21075

-------------------------------------------------------------------------------
  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.main.ordered_solvent = True

  refinement.twinning.twin_law = h,l,-k

Working crystal symmetry after inspecting all inputs:
  Unit cell: (173.026, 73.868, 73.999, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/home/phzwart/Users/swairjo/1YFS/pdb1yfs_refine_002.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 7693
  Number of models: 1
  Model: 0
    Number of conformers: 1
    Conformer: " "
      Number of atoms: 7693
      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: 401, 411
          Inner-chain residues flagged as termini: ['ALA, ,2500, ,    ']
          Classifications: {'water': 399, 'peptide': 2}
          Modifications used: {'COO': 2}
          Link IDs: {None: 399, 'TRANS': 1}
          Chain breaks: 1
  Time building chain proxies: 4.33, per 1000 atoms: 0.56


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

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

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

Miller array info: 1yfs.mtz:FOBS_X,SIGFOBS_X
Observation type: xray.amplitude
Type of data: double, size=57744
Type of sigmas: double, size=57744
Number of Miller indices: 57744
Anomalous flag: False
Unit cell: (173.026, 73.868, 73.999, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 5502
Resolution range: 36.934 2.08
Completeness in resolution range: 0.998616
Completeness with d_max=infinity: 0.998358

Number of F-obs in resolution range:                   57744
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  36.9340
                             d_min =   2.0800

Miller array info: 1yfs.mtz:R-free-flags
Observation type: None
Type of data: int, size=57744
Type of sigmas: None
Number of Miller indices: 57744
Anomalous flag: False
Unit cell: (173.026, 73.868, 73.999, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 5502
Resolution range: 36.934 2.08
Completeness in resolution range: 0.998616
Completeness with d_max=infinity: 0.998358

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 36.9398 -  4.4788 [6018/6088]  5396   622  10.3%
  bin  2:  4.4788 -  3.5559 [5846/5854]  5266   580   9.9%
  bin  3:  3.5559 -  3.1067 [5795/5797]  5177   618  10.7%
  bin  4:  3.1067 -  2.8227 [5765/5765]  5196   569   9.9%
  bin  5:  2.8227 -  2.6205 [5732/5732]  5144   588  10.3%
  bin  6:  2.6205 -  2.4660 [5712/5712]  5174   538   9.4%
  bin  7:  2.4660 -  2.3425 [5757/5757]  5152   605  10.5%
  bin  8:  2.3425 -  2.2406 [5662/5662]  5103   559   9.9%
  bin  9:  2.2406 -  2.1543 [5750/5750]  5176   574  10.0%
  bin 10:  2.1543 -  2.0800 [5707/5707]  5156   551   9.7%
                                overall 51940  5804  10.1%

========================== 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:
        1.21 -     1.34: 2329
        1.34 -     1.47: 1689
        1.47 -     1.59: 3402
        1.59 -     1.72: 0
        1.72 -     1.85: 40
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " N   ARG A  85 " - " CA  ARG A  85 " 1.458  1.488 -0.030 2.77e+03 2.48e+00
  " CA  VAL A 294 " - " C   VAL A 294 " 1.525  1.558 -0.033 2.27e+03 2.44e+00
  " CG1 ILE B 295 " - " CD1 ILE B 295 " 1.513  1.453  0.060 6.57e+02 2.35e+00
  " CA  SER A 172 " - " C   SER A 172 " 1.525  1.494  0.031 2.27e+03 2.20e+00
  " CG  GLU B 349 " - " CD  GLU B 349 " 1.516  1.553 -0.037 1.60e+03 2.20e+00
  ... (remaining 7455 not shown)
  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 1199
        2.75 -     3.29: 8720
        3.29 -     3.83: 15253
        3.83 -     4.36: 19321
        4.36 -     4.90: 28994
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw
  " OD2 ASP A 398 " - " O   HOH   337 "  2.218 3.040
  " ND2 ASN B 159 " - " O   HOH    12 "  2.318 3.120
  " NH2 ARG B  69 " - " O   HOH   330 "  2.325 3.120
  " O   ILE A 344 " - " O   HOH    11 "  2.336 3.040
  " O   HOH   212 " - " O   HOH   383 "  2.348 3.040
  ... (remaining 73482 not shown)
  Histogram of dihedral angle deviations from ideal:
        0.01 -    17.82: 2217
       17.82 -    35.64: 338
       35.64 -    53.46: 150
       53.46 -    71.28: 49
       71.28 -    89.09: 28
  Dihedral angle restraints sorted by residual:
  " N   PRO B 330 "
  " CA  PRO B 330 "
  " CB  PRO B 330 "
  " CG  PRO B 330 "
      ideal   model   delta periodicty    weight residual
     -25.00   36.75   58.25     3       4.44e-03 1.51e+01
  " CA  PRO B 168 "
  " CB  PRO B 168 "
  " CG  PRO B 168 "
  " CD  PRO B 168 "
      ideal   model   delta periodicty    weight residual
      35.00  -26.84  -58.16     3       4.44e-03 1.50e+01
  " CA  HIS A 272 "
  " CB  HIS A 272 "
  " CG  HIS A 272 "
  " ND1 HIS A 272 "
      ideal   model   delta periodicty    weight residual
      90.00 -166.96   76.96     2       2.50e-03 1.48e+01
  ... (remaining 2779 not shown)

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


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


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

Number of scattering types: 4
  Type Number    sf(0)   Gaussians
   S      24     15.96       2
   O    1753      7.97       2
   N    1232      6.97       2
   C    4684      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 = 7693

n_use            =  7693
n_use_u_iso      =  7693
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 =  7693

==================== 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/1YFS/pdb1yfs_refine_003.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/home/phzwart/Users/swairjo/1YFS/pdb1yfs_refine_003.geo

CPU time processing inputs: 11.73


============================ 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 = 173.026001 73.86799622 73.99900055 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/home/phzwart/Users/swairjo/1YFS/pdb1yfs_refine_002.pdb"
    }
    xray_data {
      file_name = "1yfs.mtz"
      labels = "FOBS_X,SIGFOBS_X"
      r_free_flags {
        file_name = "1yfs.mtz"
        label = "R-free-flags"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "pdb1yfs_refine"
    serial = 3
  }
  main {
    ordered_solvent = True
    random_seed = 2864671
  }
  alpha_beta {
    interpolation = False
  }
  twinning {
    twin_law = "h,l,-k"
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.08 - 36.93 A; n_refl. = 57744)------------------------------|
|                                                                             |
| r_work= 0.1700   r_free= 0.2010   ksol= 0.00   Bsol= 0.00   scale= 0.929    |
|                                                                             |
| 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: 0.575058           |
| twin fraction: 0.23  twin operator: h,-l,k                                  |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 36.9398 -  5.6396 0.98   2732  323 0.3911 0.3467        None        None|
|  2:  5.6396 -  4.4788 0.98   2664  299 0.1764 0.2168        None        None|
|  3:  4.4788 -  3.9134 0.98   2643  280 0.1279 0.1493        None        None|
|  4:  3.9134 -  3.5559 0.98   2623  300 0.1323 0.1670        None        None|
|  5:  3.5559 -  3.3012 0.98   2586  320 0.1407 0.1725        None        None|
|  6:  3.3012 -  3.1067 0.98   2591  298 0.1469 0.1774        None        None|
|  7:  3.1067 -  2.9512 0.98   2603  271 0.1409 0.1741        None        None|
|  8:  2.9512 -  2.8227 0.98   2593  298 0.1420 0.1646        None        None|
|  9:  2.8227 -  2.7141 0.98   2588  282 0.1489 0.1994        None        None|
| 10:  2.7141 -  2.6205 0.98   2556  306 0.1414 0.1848        None        None|
| 11:  2.6205 -  2.5386 0.98   2592  270 0.1464 0.1919        None        None|
| 12:  2.5386 -  2.4660 0.98   2582  268 0.1513 0.1964        None        None|
| 13:  2.4660 -  2.4011 0.98   2581  305 0.1524 0.1968        None        None|
| 14:  2.4011 -  2.3425 0.98   2571  300 0.1492 0.1852        None        None|
| 15:  2.3425 -  2.2893 0.98   2564  301 0.1576 0.2059        None        None|
| 16:  2.2893 -  2.2406 0.98   2539  258 0.1566 0.2177        None        None|
| 17:  2.2406 -  2.1958 0.98   2612  283 0.1505 0.1777        None        None|
| 18:  2.1958 -  2.1543 0.98   2564  291 0.1455 0.2008        None        None|
| 19:  2.1543 -  2.1159 0.98   2563  246 0.1656 0.2123        None        None|
| 20:  2.1159 -  2.0800 0.98   2593  305 0.1509 0.1918        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: 36.9398 -  5.6396  2732   323  0.88  17.30   None     0.74      59495.49|
|  2:  5.6396 -  4.4788  2664   299  0.89  17.10   None     0.83      44720.58|
|  3:  4.4788 -  3.9134  2643   280  0.90  16.63   None     0.93      52337.61|
|  4:  3.9134 -  3.5559  2623   300  0.92  14.72   None     0.98      42386.69|
|  5:  3.5559 -  3.3012  2586   320  0.91  16.30   None     0.97      32197.66|
|  6:  3.3012 -  3.1067  2591   298  0.90  17.07   None     0.96      26631.95|
|  7:  3.1067 -  2.9512  2603   271  0.91  17.11   None     0.94      23085.07|
|  8:  2.9512 -  2.8227  2593   298  0.91  16.54   None     0.93      19526.71|
|  9:  2.8227 -  2.7141  2588   282  0.89  19.00   None     0.91      16213.34|
| 10:  2.7141 -  2.6205  2556   306  0.90  17.48   None     0.90      13942.62|
| 11:  2.6205 -  2.5386  2592   270  0.88  20.03   None     0.89      12946.75|
| 12:  2.5386 -  2.4660  2582   268  0.87  20.83   None     0.89      12804.10|
| 13:  2.4660 -  2.4011  2581   305  0.85  22.32   None     0.90      12862.15|
| 14:  2.4011 -  2.3425  2571   300  0.84  23.63   None     0.91      12425.78|
| 15:  2.3425 -  2.2893  2564   301  0.85  22.53   None     0.92      11455.61|
| 16:  2.2893 -  2.2406  2539   258  0.86  22.15   None     0.92      10408.66|
| 17:  2.2406 -  2.1958  2612   283  0.85  22.78   None     0.93       9762.92|
| 18:  2.1958 -  2.1543  2564   291  0.85  23.17   None     0.94       9432.49|
| 19:  2.1543 -  2.1159  2563   246  0.86  22.64   None     0.94       8592.19|
| 20:  2.1159 -  2.0800  2593   305  0.86  21.88   None     0.94       7205.45|
|alpha:            min =        0.43 max =            0.98 mean =         0.91|
|beta:             min =     6895.63 max =       128401.90 mean =     22376.58|
|figures of merit: min =        0.01 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.50 mean =        19.49|
|phase err.(test): min =        0.00 max =           89.94 mean =        18.95|
|-----------------------------------------------------------------------------|

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


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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.375679              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 108.714  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.047295              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 101.599  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.006:  4577 |   0.000 -   0.844:  7109 |  2.218 -  2.486:       55 |
| 0.006 - 0.012:  1968 |   0.844 -   1.689:  1986 |  2.486 -  2.754:     1144 |
| 0.012 - 0.018:   597 |   1.689 -   2.533:   616 |  2.754 -  3.022:     4137 |
| 0.018 - 0.024:   198 |   2.533 -   3.378:   200 |  3.022 -  3.291:     4583 |
| 0.024 - 0.030:    77 |   3.378 -   4.222:    73 |  3.291 -  3.559:     5975 |
| 0.030 - 0.036:    32 |   4.222 -   5.066:    29 |  3.559 -  3.827:     9278 |
| 0.036 - 0.042:     4 |   5.066 -   5.911:    18 |  3.827 -  4.095:     8542 |
| 0.042 - 0.048:     2 |   5.911 -   6.755:     7 |  4.095 -  4.364:    10779 |
| 0.048 - 0.054:     2 |   6.755 -   7.600:     4 |  4.364 -  4.632:    13309 |
| 0.054 - 0.060:     3 |   7.600 -   8.444:     2 |  4.632 -  4.900:    15685 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     7460 |   0.008    0.060  0.000 |       0.123 |              |
|     angle |    10044 |   1.054    8.444  0.000 |       0.220 |              |
| chirality |     1052 |   0.068    0.260  0.000 |       0.115 |        0.084 |
| planarity |     1306 |   0.005    0.037  0.000 |       0.153 |              |
|  dihedral |     2782 |  18.920   89.095  0.006 |       1.245 |              |
| nonbonded |     7460 |   4.109    4.900  2.218 |       0.153 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics--------------------------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 7693   0      2.68    77.16   22.72    None  None   None       |
|    all(noH): 7693   0      2.68    77.16   22.72    None  None   None       |
|    Sol.    : 399    0      8.68    42.48   25.46    None  None   None       |
|    Mac.    : 7294   0      2.68    77.16   22.57    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:     2.680 -  10.128:  106   |   5:    39.920 -  47.368:  181        |
|      1:    10.128 -  17.576: 2141   |   6:    47.368 -  54.816:   90        |
|      2:    17.576 -  25.024: 3150   |   7:    54.816 -  62.264:   68        |
|      3:    25.024 -  32.472: 1423   |   8:    62.264 -  69.712:   15        |
|      4:    32.472 -  39.920:  517   |   9:    69.712 -  77.160:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 2.08 - 36.93 A; n_refl. = 57744)------------------------------|
|                                                                             |
| r_work= 0.1700   r_free= 0.2010   ksol= 0.00   Bsol= 0.00   scale= 0.929    |
|                                                                             |
| 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: 0.575058           |
| twin fraction: 0.23  twin operator: h,-l,k                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.08 - 36.93 A; n_refl. = 57744)------------------------------|
|                                                                             |
| r_work= 0.1362   r_free= 0.1722   ksol= 0.23   Bsol= 26.77   scale= 0.911   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.62,0.95,0.66,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   None A                  |
| x-ray target function (twin_lsq_f) for work reflections: 0.182934           |
| twin fraction: 0.23  twin operator: h,-l,k                                  |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.542693              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 114.784  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.052613              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 114.220  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1362      final r-factor (work) = 0.1262          |
| start r-factor (free) = 0.1722      final r-factor (free) = 0.1617          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 0.5908 = 5.54 * 0.50 * 0.1829 + 1.00 * 0.0838                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 0.4703 = 5.54 * 0.50 * 0.1427 + 1.00 * 0.0749                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1262      final r-factor (work) = 0.1276          |
| start r-factor (free) = 0.1617      final r-factor (free) = 0.1606          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.0093 = 0.05 * 1.00 * 0.1427 + 1.00 * 0.0018                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.0086 = 0.05 * 1.00 * 0.1441 + 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     : 7693   0      7.02    66.36   22.65    None  None   None       |
|    all(noH): 7693   0      7.02    66.36   22.65    None  None   None       |
|    Sol.    : 399    0      9.85    46.75   24.55    None  None   None       |
|    Mac.    : 7294   0      7.02    66.36   22.55    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:     7.022 -  12.956:  367   |   5:    36.690 -  42.623:  230        |
|      1:    12.956 -  18.889: 2386   |   6:    42.623 -  48.556:   91        |
|      2:    18.889 -  24.823: 2771   |   7:    48.556 -  54.490:   51        |
|      3:    24.823 -  30.756: 1171   |   8:    54.490 -  60.423:   60        |
|      4:    30.756 -  36.690:  542   |   9:    60.423 -  66.357:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|--(resolution: 2.08 - 36.93 A; n_refl. = 57744)------------------------------|
|                                                                             |
| r_work= 0.1276   r_free= 0.1606   ksol= 0.23   Bsol= 26.77   scale= 0.911   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.62,0.95,0.66,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   None A                  |
| x-ray target function (twin_lsq_f) for work reflections: 0.144145           |
| twin fraction: 0.23  twin operator: h,-l,k                                  |
|-----------------------------------------------------------------------------|

================== ordered solvent: location/analysis/update ==================

Start model:
  number           = 399    
  b_iso_min        = 9.85    (limit = 1.00)
  b_iso_max        = 46.75   (limit = 50.00)
  b_iso_mean       = 24.55               
  occupancy_min    = 1.00    (limit = 0.10)
  occupancy_max    = 1.00    (limit = 1.20)
  dist_sol_mol_min = 2.15    (limit = 1.80)
  dist_sol_mol_max = 5.05    (limit = 6.00)
Peak search:
   maximum allowed number of peaks:           7294
   number of peaks from mFobs-DFmodel map:  606
Filter by distance & map next to the model:
   mapped sites are within: 0.082 - 5.937 
   number of sites selected in [dist_min= 1.80, dist_max= 6.00]: 62 from: 606
   mapped sites are within: 1.818 - 5.937 
2Fo-Fc map selection:
  number           = 348    
  b_iso_min        = 9.85    (limit = 1.00)
  b_iso_max        = 42.22   (limit = 50.00)
  b_iso_mean       = 22.96               
  occupancy_min    = 1.00    (limit = 0.10)
  occupancy_max    = 1.00    (limit = 1.20)
  dist_sol_mol_min = 2.11    (limit = 1.80)
  dist_sol_mol_max = 4.22    (limit = 6.00)

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

|--(resolution: 2.08 - 36.93 A; n_refl. = 57744)------------------------------|
|                                                                             |
| r_work= 0.1293   r_free= 0.1587   ksol= 0.23   Bsol= 26.84   scale= 0.915   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.65,1.24,0.40,0.00,0.00,0.00); trace/3= -0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   None A                  |
| x-ray target function (twin_lsq_f) for work reflections: 0.150389           |
| twin fraction: 0.27  twin operator: h,-l,k                                  |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.716364              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 136.927  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.055776              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 152.973  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1293      final r-factor (work) = 0.1263          |
| start r-factor (free) = 0.1587      final r-factor (free) = 0.1564          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 0.4295 = 4.72 * 0.50 * 0.1504 + 1.00 * 0.0749                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 0.4041 = 4.72 * 0.50 * 0.1426 + 1.00 * 0.0679                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1263      final r-factor (work) = 0.1255          |
| start r-factor (free) = 0.1564      final r-factor (free) = 0.1561          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.0089 = 0.06 * 1.00 * 0.1426 + 1.00 * 0.0010                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.0088 = 0.06 * 1.00 * 0.1405 + 1.00 * 0.0009                               |
|-----------------------------------------------------------------------------|
| number of iterations = 10      |    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     : 7642   0      6.94    66.39   22.68    None  None   None       |
|    all(noH): 7642   0      6.94    66.39   22.68    None  None   None       |
|    Sol.    : 348    0      10.09   41.95   22.98    None  None   None       |
|    Mac.    : 7294   0      6.94    66.39   22.66    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:     6.938 -  12.883:  343   |   5:    36.663 -  42.608:  232        |
|      1:    12.883 -  18.828: 2306   |   6:    42.608 -  48.553:   90        |
|      2:    18.828 -  24.773: 2820   |   7:    48.553 -  54.498:   53        |
|      3:    24.773 -  30.718: 1193   |   8:    54.498 -  60.443:   69        |
|      4:    30.718 -  36.663:  514   |   9:    60.443 -  66.389:   22        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|--(resolution: 2.08 - 36.93 A; n_refl. = 57744)------------------------------|
|                                                                             |
| r_work= 0.1255   r_free= 0.1561   ksol= 0.23   Bsol= 26.84   scale= 0.915   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.65,1.24,0.40,0.00,0.00,0.00); trace/3= -0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   None A                  |
| x-ray target function (twin_lsq_f) for work reflections: 0.140532           |
| twin fraction: 0.27  twin operator: h,-l,k                                  |
|-----------------------------------------------------------------------------|

================== ordered solvent: location/analysis/update ==================

Start model:
  number           = 348    
  b_iso_min        = 10.09   (limit = 1.00)
  b_iso_max        = 41.95   (limit = 50.00)
  b_iso_mean       = 22.98               
  occupancy_min    = 1.00    (limit = 0.10)
  occupancy_max    = 1.00    (limit = 1.20)
  dist_sol_mol_min = 2.18    (limit = 1.80)
  dist_sol_mol_max = 4.18    (limit = 6.00)
Peak search:
   maximum allowed number of peaks:           7294
   number of peaks from mFobs-DFmodel map:  633
Filter by distance & map next to the model:
   mapped sites are within: 0.086 - 5.378 
   number of sites selected in [dist_min= 1.80, dist_max= 6.00]: 74 from: 633
   mapped sites are within: 1.801 - 5.378 
2Fo-Fc map selection:
  number           = 341    
  b_iso_min        = 10.09   (limit = 1.00)
  b_iso_max        = 38.61   (limit = 50.00)
  b_iso_mean       = 22.67               
  occupancy_min    = 1.00    (limit = 0.10)
  occupancy_max    = 1.00    (limit = 1.20)
  dist_sol_mol_min = 2.18    (limit = 1.80)
  dist_sol_mol_max = 4.18    (limit = 6.00)

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

|--(resolution: 2.08 - 36.93 A; n_refl. = 57744)------------------------------|
|                                                                             |
| r_work= 0.1267   r_free= 0.1565   ksol= 0.23   Bsol= 30.22   scale= 0.916   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.53,1.44,0.10,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   None A                  |
| x-ray target function (twin_lsq_f) for work reflections: 0.143917           |
| twin fraction: 0.28  twin operator: h,-l,k                                  |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.193545              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 128.253  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.058385              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 158.258  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1267      final r-factor (work) = 0.1247          |
| start r-factor (free) = 0.1565      final r-factor (free) = 0.1555          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 0.4418 = 5.19 * 0.50 * 0.1439 + 1.00 * 0.0681                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 0.4287 = 5.19 * 0.50 * 0.1381 + 1.00 * 0.0702                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1247      final r-factor (work) = 0.1241          |
| start r-factor (free) = 0.1555      final r-factor (free) = 0.1551          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.0090 = 0.06 * 1.00 * 0.1381 + 1.00 * 0.0009                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.0090 = 0.06 * 1.00 * 0.1368 + 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     : 7635   0      7.16    66.75   22.68    None  None   None       |
|    all(noH): 7635   0      7.16    66.75   22.68    None  None   None       |
|    Sol.    : 341    0      10.00   42.36   22.78    None  None   None       |
|    Mac.    : 7294   0      7.16    66.75   22.67    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:     7.164 -  13.122:  409   |   5:    36.957 -  42.916:  216        |
|      1:    13.122 -  19.081: 2390   |   6:    42.916 -  48.875:   92        |
|      2:    19.081 -  25.040: 2748   |   7:    48.875 -  54.834:   61        |
|      3:    25.040 -  30.999: 1139   |   8:    54.834 -  60.792:   63        |
|      4:    30.999 -  36.957:  499   |   9:    60.792 -  66.751:   18        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= ordered solvent: final clean up =======================

Start model:
  number           = 341    
  b_iso_min        = 10.00   (limit = 1.00)
  b_iso_max        = 42.36   (limit = 50.00)
  b_iso_mean       = 22.78               
  occupancy_min    = 1.00    (limit = 0.10)
  occupancy_max    = 1.00    (limit = 1.20)
  dist_sol_mol_min = 2.15    (limit = 1.80)
  dist_sol_mol_max = 4.19    (limit = 6.00)
2Fo-Fc map selection:
  number           = 330    
  b_iso_min        = 10.00   (limit = 1.00)
  b_iso_max        = 42.36   (limit = 50.00)
  b_iso_mean       = 22.55               
  occupancy_min    = 1.00    (limit = 0.10)
  occupancy_max    = 1.00    (limit = 1.20)
  dist_sol_mol_min = 2.15    (limit = 1.80)
  dist_sol_mol_max = 4.19    (limit = 6.00)

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

|--(resolution: 2.08 - 36.93 A; n_refl. = 57744)------------------------------|
|                                                                             |
| r_work= 0.1251   r_free= 0.1561   ksol= 0.23   Bsol= 30.22   scale= 0.916   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.53,1.44,0.10,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   None A                  |
| x-ray target function (twin_lsq_f) for work reflections: 0.139573           |
| twin fraction: 0.28  twin operator: h,-l,k                                  |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 36.9398 -  5.6396 0.98   2732  323 0.1075 0.1309        None        None|
|  2:  5.6396 -  4.4788 0.98   2664  299 0.0953 0.1342        None        None|
|  3:  4.4788 -  3.9134 0.98   2643  280 0.0851 0.1176        None        None|
|  4:  3.9134 -  3.5559 0.98   2623  300 0.1045 0.1412        None        None|
|  5:  3.5559 -  3.3012 0.98   2586  320 0.1175 0.1554        None        None|
|  6:  3.3012 -  3.1067 0.98   2591  298 0.1265 0.1594        None        None|
|  7:  3.1067 -  2.9512 0.98   2603  271 0.1280 0.1641        None        None|
|  8:  2.9512 -  2.8227 0.98   2593  298 0.1351 0.1581        None        None|
|  9:  2.8227 -  2.7141 0.98   2588  282 0.1385 0.1640        None        None|
| 10:  2.7141 -  2.6205 0.98   2556  306 0.1382 0.1694        None        None|
| 11:  2.6205 -  2.5386 0.98   2592  270 0.1428 0.1726        None        None|
| 12:  2.5386 -  2.4660 0.98   2582  268 0.1482 0.1823        None        None|
| 13:  2.4660 -  2.4011 0.98   2581  305 0.1467 0.1701        None        None|
| 14:  2.4011 -  2.3425 0.98   2571  300 0.1471 0.1729        None        None|
| 15:  2.3425 -  2.2893 0.98   2564  301 0.1512 0.1878        None        None|
| 16:  2.2893 -  2.2406 0.98   2539  258 0.1548 0.2020        None        None|
| 17:  2.2406 -  2.1958 0.98   2612  283 0.1551 0.1670        None        None|
| 18:  2.1958 -  2.1543 0.98   2564  291 0.1574 0.1821        None        None|
| 19:  2.1543 -  2.1159 0.98   2563  246 0.1680 0.1897        None        None|
| 20:  2.1159 -  2.0800 0.98   2593  305 0.1712 0.1887        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: 36.9398 -  5.6396  2732   323  0.88  17.30   None     0.74      59495.49|
|  2:  5.6396 -  4.4788  2664   299  0.89  17.10   None     0.83      44720.58|
|  3:  4.4788 -  3.9134  2643   280  0.90  16.63   None     0.93      52337.61|
|  4:  3.9134 -  3.5559  2623   300  0.92  14.72   None     0.98      42386.69|
|  5:  3.5559 -  3.3012  2586   320  0.91  16.30   None     0.97      32197.66|
|  6:  3.3012 -  3.1067  2591   298  0.90  17.07   None     0.96      26631.95|
|  7:  3.1067 -  2.9512  2603   271  0.91  17.11   None     0.94      23085.07|
|  8:  2.9512 -  2.8227  2593   298  0.91  16.54   None     0.93      19526.71|
|  9:  2.8227 -  2.7141  2588   282  0.89  19.00   None     0.91      16213.34|
| 10:  2.7141 -  2.6205  2556   306  0.90  17.48   None     0.90      13942.62|
| 11:  2.6205 -  2.5386  2592   270  0.88  20.03   None     0.89      12946.75|
| 12:  2.5386 -  2.4660  2582   268  0.87  20.83   None     0.89      12804.10|
| 13:  2.4660 -  2.4011  2581   305  0.85  22.32   None     0.90      12862.15|
| 14:  2.4011 -  2.3425  2571   300  0.84  23.63   None     0.91      12425.78|
| 15:  2.3425 -  2.2893  2564   301  0.85  22.53   None     0.92      11455.61|
| 16:  2.2893 -  2.2406  2539   258  0.86  22.15   None     0.92      10408.66|
| 17:  2.2406 -  2.1958  2612   283  0.85  22.78   None     0.93       9762.92|
| 18:  2.1958 -  2.1543  2564   291  0.85  23.17   None     0.94       9432.49|
| 19:  2.1543 -  2.1159  2563   246  0.86  22.64   None     0.94       8592.19|
| 20:  2.1159 -  2.0800  2593   305  0.86  21.88   None     0.94       7205.45|
|alpha:            min =        0.43 max =            0.98 mean =         0.91|
|beta:             min =     6895.63 max =       128401.90 mean =     22376.58|
|figures of merit: min =        0.01 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.50 mean =        19.49|
|phase err.(test): min =        0.00 max =           89.94 mean =        18.95|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.08 - 36.93 A; n_refl. = 57744)------------------------------|
|                                                                             |
| r_work= 0.1250   r_free= 0.1560   ksol= 0.23   Bsol= 30.67   scale= 0.916   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.55,1.71,-0.16,0.00,-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: 0.139513           |
| twin fraction: 0.28  twin operator: h,-l,k                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.08 - 36.93 A; n_refl. = 57744)------------------------------|
|                                                                             |
| r_work= 0.1250   r_free= 0.1560   ksol= 0.23   Bsol= 30.67   scale= 0.916   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.55,1.71,-0.16,0.00,-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: 0.139513           |
| twin fraction: 0.28  twin operator: h,-l,k                                  |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 36.9398 -  5.6396 0.98   2732  323 0.1078 0.1312        None        None|
|  2:  5.6396 -  4.4788 0.98   2664  299 0.0959 0.1349        None        None|
|  3:  4.4788 -  3.9134 0.98   2643  280 0.0853 0.1178        None        None|
|  4:  3.9134 -  3.5559 0.98   2623  300 0.1043 0.1407        None        None|
|  5:  3.5559 -  3.3012 0.98   2586  320 0.1172 0.1549        None        None|
|  6:  3.3012 -  3.1067 0.98   2591  298 0.1262 0.1590        None        None|
|  7:  3.1067 -  2.9512 0.98   2603  271 0.1278 0.1642        None        None|
|  8:  2.9512 -  2.8227 0.98   2593  298 0.1350 0.1577        None        None|
|  9:  2.8227 -  2.7141 0.98   2588  282 0.1383 0.1643        None        None|
| 10:  2.7141 -  2.6205 0.98   2556  306 0.1386 0.1697        None        None|
| 11:  2.6205 -  2.5386 0.98   2592  270 0.1430 0.1728        None        None|
| 12:  2.5386 -  2.4660 0.98   2582  268 0.1481 0.1822        None        None|
| 13:  2.4660 -  2.4011 0.98   2581  305 0.1469 0.1700        None        None|
| 14:  2.4011 -  2.3425 0.98   2571  300 0.1470 0.1726        None        None|
| 15:  2.3425 -  2.2893 0.98   2564  301 0.1508 0.1873        None        None|
| 16:  2.2893 -  2.2406 0.98   2539  258 0.1543 0.2014        None        None|
| 17:  2.2406 -  2.1958 0.98   2612  283 0.1544 0.1670        None        None|
| 18:  2.1958 -  2.1543 0.98   2564  291 0.1566 0.1818        None        None|
| 19:  2.1543 -  2.1159 0.98   2563  246 0.1673 0.1881        None        None|
| 20:  2.1159 -  2.0800 0.98   2593  305 0.1702 0.1879        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: 36.9398 -  5.6396  2732   323  0.88  17.30   None     0.74      59495.49|
|  2:  5.6396 -  4.4788  2664   299  0.89  17.10   None     0.83      44720.58|
|  3:  4.4788 -  3.9134  2643   280  0.90  16.63   None     0.93      52337.61|
|  4:  3.9134 -  3.5559  2623   300  0.92  14.72   None     0.98      42386.69|
|  5:  3.5559 -  3.3012  2586   320  0.91  16.30   None     0.97      32197.66|
|  6:  3.3012 -  3.1067  2591   298  0.90  17.07   None     0.96      26631.95|
|  7:  3.1067 -  2.9512  2603   271  0.91  17.11   None     0.94      23085.07|
|  8:  2.9512 -  2.8227  2593   298  0.91  16.54   None     0.93      19526.71|
|  9:  2.8227 -  2.7141  2588   282  0.89  19.00   None     0.91      16213.34|
| 10:  2.7141 -  2.6205  2556   306  0.90  17.48   None     0.90      13942.62|
| 11:  2.6205 -  2.5386  2592   270  0.88  20.03   None     0.89      12946.75|
| 12:  2.5386 -  2.4660  2582   268  0.87  20.83   None     0.89      12804.10|
| 13:  2.4660 -  2.4011  2581   305  0.85  22.32   None     0.90      12862.15|
| 14:  2.4011 -  2.3425  2571   300  0.84  23.63   None     0.91      12425.78|
| 15:  2.3425 -  2.2893  2564   301  0.85  22.53   None     0.92      11455.61|
| 16:  2.2893 -  2.2406  2539   258  0.86  22.15   None     0.92      10408.66|
| 17:  2.2406 -  2.1958  2612   283  0.85  22.78   None     0.93       9762.92|
| 18:  2.1958 -  2.1543  2564   291  0.85  23.17   None     0.94       9432.49|
| 19:  2.1543 -  2.1159  2563   246  0.86  22.64   None     0.94       8592.19|
| 20:  2.1159 -  2.0800  2593   305  0.86  21.88   None     0.94       7205.45|
|alpha:            min =        0.43 max =            0.98 mean =         0.91|
|beta:             min =     6895.63 max =       128401.90 mean =     22376.58|
|figures of merit: min =        0.01 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.50 mean =        19.49|
|phase err.(test): min =        0.00 max =           89.94 mean =        18.95|
|-----------------------------------------------------------------------------|

|-ADP statistics--------------------------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 7624   0      7.08    66.67   22.58    None  None   None       |
|    all(noH): 7624   0      7.08    66.67   22.58    None  None   None       |
|    Sol.    : 330    0      9.92    42.27   22.47    None  None   None       |
|    Mac.    : 7294   0      7.08    66.67   22.59    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:     7.079 -  13.037:  409   |   5:    36.872 -  42.831:  215        |
|      1:    13.037 -  18.996: 2390   |   6:    42.831 -  48.790:   92        |
|      2:    18.996 -  24.955: 2745   |   7:    48.790 -  54.749:   61        |
|      3:    24.955 -  30.914: 1135   |   8:    54.749 -  60.707:   63        |
|      4:    30.914 -  36.872:  496   |   9:    60.707 -  66.666:   18        |
|                               =>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)              
1_wat: ordered solvent update (add / remove)                            
------------------------------------------------------------------------
 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    :  0.1700 0.2010   5.750585e-01   5.277777e-01
   1_bss:  0.1362 0.1722   1.829342e-01   2.881764e-01
   1_xyz:  0.1262 0.1617   1.426783e-01   2.517336e-01
   1_adp:  0.1276 0.1606   1.441454e-01   2.468805e-01
   2_bss:  0.1293 0.1587   1.503889e-01   2.391521e-01
   2_xyz:  0.1263 0.1564   1.425646e-01   2.311909e-01
   2_adp:  0.1255 0.1561   1.405321e-01   2.302115e-01
   3_bss:  0.1267 0.1565   1.439169e-01   2.325321e-01
   3_xyz:  0.1247 0.1555   1.380889e-01   2.296996e-01
   3_adp:  0.1241 0.1551   1.367879e-01   2.276623e-01
   3_bss:  0.1250 0.1560   1.395125e-01   2.304974e-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:  0.230  26.771  -1.617   0.954   0.664   0.000   0.000   0.000
   1_xyz:  0.230  26.771  -1.617   0.954   0.664   0.000   0.000   0.000
   1_adp:  0.230  26.771  -1.617   0.954   0.664   0.000   0.000   0.000
   2_bss:  0.232  26.841  -1.648   1.245   0.403   0.000   0.000   0.000
   2_xyz:  0.232  26.841  -1.648   1.245   0.403   0.000   0.000   0.000
   2_adp:  0.232  26.841  -1.648   1.245   0.403   0.000   0.000   0.000
   3_bss:  0.233  30.222  -1.535   1.439   0.096   0.000   0.000   0.000
   3_xyz:  0.233  30.222  -1.535   1.439   0.096   0.000   0.000   0.000
   3_adp:  0.233  30.222  -1.535   1.439   0.096   0.000   0.000   0.000
   3_bss:  0.232  30.669  -1.552   1.710  -0.157   0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  19.002 0.8846  0.9121    22289.912
   1_bss:  19.002 0.8846  0.9121    22289.912
   1_xyz:  19.002 0.8846  0.9121    22289.912
   1_adp:  19.002 0.8846  0.9121    22289.912
   2_bss:  19.002 0.8846  0.9121    22289.912
   2_xyz:  19.002 0.8846  0.9121    22289.912
   2_adp:  19.002 0.8846  0.9121    22289.912
   3_bss:  19.002 0.8846  0.9121    22289.912
   3_xyz:  19.002 0.8846  0.9121    22289.912
   3_adp:  19.002 0.8846  0.9121    22289.912
   3_bss:  19.002 0.8846  0.9121    22289.912
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.054  0.008  0.068 18.920  0.005  4.109   8.3778e-02
   1_bss:   1.054  0.008  0.068 18.920  0.005  4.109   8.3778e-02
   1_xyz:   0.970  0.007  0.061 18.582  0.004  4.110   7.4878e-02
   1_adp:   0.970  0.007  0.061 18.582  0.004  4.110   7.4878e-02
   2_bss:   0.970  0.007  0.061 18.582  0.004  4.112   7.4888e-02
   2_xyz:   0.890  0.006  0.057 18.397  0.004  4.113   6.7885e-02
   2_adp:   0.890  0.006  0.057 18.397  0.004  4.113   6.7885e-02
   3_bss:   0.890  0.006  0.057 18.397  0.004  4.112   6.8112e-02
   3_xyz:   0.919  0.006  0.058 18.372  0.004  4.112   7.0163e-02
   3_adp:   0.919  0.006  0.058 18.372  0.004  4.112   7.0163e-02
   3_bss:   0.919  0.006  0.058 18.372  0.004  4.113   7.0126e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   8.444  0.060  0.260 89.095  0.037  2.218   3.4861e-02
   1_bss:   8.444  0.060  0.260 89.095  0.037  2.218   3.4861e-02
   1_xyz:   7.144  0.052  0.227 89.127  0.041  2.151   2.8722e-02
   1_adp:   7.144  0.052  0.227 89.127  0.041  2.151   2.8722e-02
   2_bss:   7.144  0.052  0.227 89.127  0.041  2.113   2.8790e-02
   2_xyz:   6.792  0.051  0.218 88.622  0.035  2.184   3.1009e-02
   2_adp:   6.792  0.051  0.218 88.622  0.035  2.184   3.1009e-02
   3_bss:   6.792  0.051  0.218 88.622  0.035  2.092   3.1051e-02
   3_xyz:   7.514  0.048  0.224 88.815  0.036  2.148   2.2966e-02
   3_adp:   7.514  0.048  0.224 88.815  0.036  2.148   2.2966e-02
   3_bss:   7.514  0.048  0.224 88.815  0.036  2.148   2.2970e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  77.16   2.68  22.72  77.16   2.68  22.57  42.48   8.68  25.46
   1_bss:  77.24   2.76  22.80  77.24   2.76  22.65  42.56   8.76  25.55
   1_xyz:  77.24   2.76  22.80  77.24   2.76  22.65  42.56   8.76  25.55
   1_adp:  66.36   7.02  22.65  66.36   7.02  22.55  46.75   9.85  24.55
   2_bss:  66.47   7.14  22.68  66.47   7.14  22.66  42.33   9.97  23.08
   2_xyz:  66.47   7.14  22.68  66.47   7.14  22.66  42.33   9.97  23.08
   2_adp:  66.39   6.94  22.68  66.39   6.94  22.66  41.95  10.09  22.98
   3_bss:  66.33   6.87  22.60  66.33   6.87  22.60  38.55  10.03  22.60
   3_xyz:  66.33   6.87  22.60  66.33   6.87  22.60  38.55  10.03  22.60
   3_adp:  66.75   7.16  22.68  66.75   7.16  22.67  42.36  10.00  22.78
   3_bss:  66.67   7.08  22.58  66.67   7.08  22.59  42.27   9.92  22.47
------------------------------------------------------------------------
 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:    0.503    0.006    0.097
   1_adp:    0.503    0.006    0.097
   2_bss:    0.392    0.006    0.093
   2_xyz:    0.758    0.006    0.128
   2_adp:    0.758    0.006    0.128
   3_bss:    0.758    0.006    0.128
   3_xyz:    1.089    0.007    0.144
   3_adp:    1.089    0.007    0.144
   3_bss:    1.089    0.007    0.144
------------------------------------------------------------------------
 stage  number of ordered solvent
     0    :              399
     1_bss:              399
     1_xyz:              399
     1_adp:              399
     2_bss:              348
     2_xyz:              348
     2_adp:              348
     3_bss:              341
     3_xyz:              341
     3_adp:              341
     3_bss:              330
------------------------------------------------------------------------

CPU time actual refinement: 483.45


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/home/phzwart/Users/swairjo/1YFS/pdb1yfs_refine_003.pdb
n_use            =  7624
n_use_u_iso      =  7624
n_use_u_aniso    =  0
n_grad_site      =  0
n_grad_u_iso     =  7624
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 =  7624

Writing 2mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/home/phzwart/Users/swairjo/1YFS/pdb1yfs_refine_003_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/home/phzwart/Users/swairjo/1YFS/pdb1yfs_refine_003_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/home/phzwart/Users/swairjo/1YFS/pdb1yfs_refine_003_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/home/phzwart/Users/swairjo/1YFS/pdb1yfs_refine_004.def


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

Pure refinement (no I/O, processing, etc)= 483.28 
  Macro-tasks:
    individual site refinement   = 151.83 
    weights calculation          = 68.54  
    collect and process          = 8.54   
    model show statistics        = 0.19   
    TOTAL for macro-tasks        = 229.10 
  Micro-tasks:
    mask                            = 0.00   
    f_calc                          = 0.00   
    alpha_beta                      = 0.00   
    target                          = 0.03   
    gradients_wrt_atomic_parameters = 95.97  
    fmodel                         = 0.00   
    r_factors                      = 0.00   
    phase_errors                   = 0.00   
    foms                           = 0.00   
    TOTAL for micro-tasks          = 96.00  
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 5.587 micro seconds
Total CPU time: 8.63 minutes
from_scatterers_fft:    216 calls, 78.79 s
gradients_fft:          161 calls, 78.25 s

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

# Date 2007-12-02 Time 10:36:31 PST -0800 (1196620591.44 s)
Start R-work = 0.1700, R-free = 0.2010 (no bulk solvent and anisotropic scale)
Final R-work = 0.1261, R-free = 0.1566 (no bulk solvent and anisotropic scale)

Start R-work = 0.1362, R-free = 0.1722
Final R-work = 0.1250, R-free = 0.1560