# Date 2008-01-16 Time 04:42:59 PST -0800 (1200487379.98 s)
#phil __OFF__

Command line arguments: "../427.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 3469
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 427

-------------------------------------------------------------------------------
  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.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.5475, 46.93, 88.1178, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 2.75, per 1000 atoms: 0.97


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

F-obs:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA

R-free flags:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 46.93, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.962 1.98077
Completeness in resolution range: 0.948758
Completeness with d_max=infinity: 0.945826

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9620
                             d_min =   1.9808

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 46.93, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.962 1.98077
Completeness in resolution range: 0.948758
Completeness with d_max=infinity: 0.945826

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9625 -  4.2381 [2176/2203]  1956   220  10.1%
  bin  2:  4.2381 -  3.3767 [2067/2083]  1861   206  10.0%
  bin  3:  3.3767 -  2.9536 [2063/2082]  1859   204   9.9%
  bin  4:  2.9536 -  2.6852 [2041/2071]  1834   207  10.1%
  bin  5:  2.6852 -  2.4937 [2006/2025]  1807   199   9.9%
  bin  6:  2.4937 -  2.3473 [2026/2051]  1822   204  10.1%
  bin  7:  2.3473 -  2.2301 [2015/2049]  1819   196   9.7%
  bin  8:  2.2301 -  2.1333 [1983/2013]  1776   207  10.4%
  bin  9:  2.1333 -  2.0514 [1980/2022]  1790   190   9.6%
  bin 10:  2.0514 -  1.9808 [1232/2048]  1106   126  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_427/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.12 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.47 -     2.16: 12
        2.16 -     2.84: 1033
        2.84 -     3.53: 4365
        3.53 -     4.21: 9252
        4.21 -     4.90: 13532
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.469 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.634 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.779 3.040 -x+1,y+1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.841 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28189 not shown)
  Histogram of dihedral angle deviations from ideal:
        0.01 -    17.19: 754
       17.19 -    34.36: 62
       34.36 -    51.54: 27
       51.54 -    68.71: 23
       68.71 -    85.89: 4
  Dihedral angle restraints sorted by residual:
  " CA  PHE A 192 "
  " CB  PHE A 192 "
  " CG  PHE A 192 "
  " CD1 PHE A 192 "
      ideal   model   delta periodicty    weight residual
      90.00    7.91   82.09     2       2.50e-03 1.68e+01
  " N   PRO A  54 "
  " CG  PRO A  54 "
  " CD  PRO A  54 "
  " CB  PRO A  54 "
      ideal   model   delta periodicty    weight residual
      30.00  -27.17   57.17     3       4.44e-03 1.45e+01
  " N   PRO A 280 "
  " CA  PRO A 280 "
  " CB  PRO A 280 "
  " CG  PRO A 280 "
      ideal   model   delta periodicty    weight residual
     -25.00   38.44   56.56     3       4.44e-03 1.42e+01
  ... (remaining 867 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      13     15.96       2
   O     902      7.97       2
   N     437      6.97       2
   C    1471      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 = True
group_occupancies      = False
group_anomalous        = False
size = 2823

n_use            =  2823
n_use_u_iso      =  2823
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 =  2823

==================== 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/tmp/phzwart/tassos/noshake/run_427/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_427/model_refine_001.geo

CPU time processing inputs: 7.63


============================ 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 = 69.5475 46.93 88.1178 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3494   r_free= 0.3445   ksol= 0.00   Bsol= 0.00   scale= 0.953    |
|                                                                             |
| 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:   0.43 A                  |
| x-ray target function (ml) for work reflections: 6.107718                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9625 -  4.7269 0.99   1411  156 0.2858 0.2858      6.3797      6.3168|
|  2:  4.7269 -  3.7717 0.99   1353  152 0.2702 0.2898      6.4934      6.5593|
|  3:  3.7717 -  3.3007 0.99   1324  147 0.3205 0.2833      6.4571      6.3937|
|  4:  3.3007 -  3.0016 0.99   1329  141 0.3280 0.3669       6.305      6.3744|
|  5:  3.0016 -  2.7879 0.99   1308  152 0.3600 0.3085      6.1701      6.1025|
|  6:  2.7879 -  2.6245 0.99   1310  141 0.3683 0.4140      6.0782      6.0764|
|  7:  2.6245 -  2.4937 0.99   1282  147 0.3632 0.3195      6.0467      5.9513|
|  8:  2.4937 -  2.3856 0.98   1291  145 0.4030 0.3604      6.0737      5.9978|
|  9:  2.3856 -  2.2941 0.98   1308  140 0.3873 0.3808      5.9613      6.0055|
| 10:  2.2941 -  2.2152 0.98   1296  142 0.4064 0.4046       6.002      5.9226|
| 11:  2.2152 -  2.1461 0.99   1272  148 0.4081 0.4005      5.9134      5.9081|
| 12:  2.1461 -  2.0849 0.97   1274  137 0.4098 0.3997      5.8453      5.9326|
| 13:  2.0849 -  2.0302 0.98   1282  138 0.4199 0.4462      5.7878      5.7675|
| 14:  2.0302 -  1.9808 0.46    590   73 0.3614 0.3410       5.716      5.5984|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9625 -  4.7269  1411   156  0.80  25.50   0.86     0.81      42563.71|
|  2:  4.7269 -  3.7717  1353   152  0.82  23.95   0.97     0.90      54151.95|
|  3:  3.7717 -  3.3007  1324   147  0.77  28.98   0.96     0.91      54549.11|
|  4:  3.3007 -  3.0016  1329   141  0.73  32.47   0.97     0.87      48134.06|
|  5:  3.0016 -  2.7879  1308   152  0.68  37.56   0.98     0.84      38954.06|
|  6:  2.7879 -  2.6245  1310   141  0.66  38.82   0.97     0.83      34271.13|
|  7:  2.6245 -  2.4937  1282   147  0.68  37.63   0.99     0.85      30362.11|
|  8:  2.4937 -  2.3856  1291   145  0.68  37.74   0.97     0.86      26750.27|
|  9:  2.3856 -  2.2941  1308   140  0.67  38.08   1.00     0.87      25542.18|
| 10:  2.2941 -  2.2152  1296   142  0.65  40.02   1.02     0.86      24643.00|
| 11:  2.2152 -  2.1461  1272   148  0.62  42.37   1.00     0.89      26063.22|
| 12:  2.1461 -  2.0849  1274   137  0.61  43.23   1.01     0.88      24468.42|
| 13:  2.0849 -  2.0302  1282   138  0.58  45.82   1.00     0.84      22407.27|
| 14:  2.0302 -  1.9808   590    73  0.59  45.19   1.05     0.73      18815.85|
|alpha:            min =        0.73 max =            0.91 mean =         0.86|
|beta:             min =    18815.85 max =        54549.11 mean =     34505.01|
|figures of merit: min =        0.00 max =            1.00 mean =         0.69|
|phase err.(work): min =        0.00 max =           89.96 mean =        36.47|
|phase err.(test): min =        0.00 max =           89.67 mean =        36.34|
|-----------------------------------------------------------------------------|

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

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 0
total                    = 0

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.574956              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.389   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.698692              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.252   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.469 -  1.812:        4 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.812 -  2.155:        8 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.155 -  2.498:       25 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.498 -  2.841:     1008 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.841 -  3.185:     1944 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.185 -  3.528:     2421 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.528 -  3.871:     4622 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.871 -  4.214:     4630 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.214 -  4.557:     6113 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.557 -  4.900:     7419 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.010    0.070  0.000 |       0.254 |              |
|     angle |     3299 |   1.822    9.874  0.001 |       1.000 |              |
| chirality |      348 |   0.101    0.314  0.000 |       0.257 |        0.172 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.113    4.900  1.469 |       0.307 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.943)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    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:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

|-Occupancies statistics------------------------------------------------------|
| occupancies: max = 1.00   min = 0.30   number of occupancies < 0.1 = 0      |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 1 OF 5 *************************

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3494   r_free= 0.3445   ksol= 0.00   Bsol= 0.00   scale= 0.953    |
|                                                                             |
| 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:   0.43 A                  |
| x-ray target function (ml) for work reflections: 6.107718                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3332   r_free= 0.3292   ksol= 0.32   Bsol= 45.12   scale= 0.973   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.34,-3.03,4.41,-0.00,0.00,0.00); trace/3= -0.32                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 6.081145                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.086039              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.150   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.403941              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.973   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3332      final r-factor (work) = 0.2218          |
| start r-factor (free) = 0.3292      final r-factor (free) = 0.2455          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.5584 = 3.09 * 0.50 * 6.0833 + 1.00 * 0.1718                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.0787 = 3.09 * 0.50 * 5.8365 + 1.00 * 0.0729                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2218      final r-factor (work) = 0.2055          |
| start r-factor (free) = 0.2455      final r-factor (free) = 0.2503          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3645 = 0.40 * 1.00 * 5.8365 + 1.00 * 0.0069                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4058 = 0.40 * 1.00 * 5.6520 + 1.00 * 0.1228                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 9      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.943)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.83  16.64    None  None   None       |
|    all(noH): 2823   0      0.00    101.83  16.64    None  None   None       |
|    Sol.    : 438    0      5.76    63.33   37.44    None  None   None       |
|    Mac.    : 2385   0      0.00    101.83  12.82    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:     0.000 -  10.183:  954   |   5:    50.915 -  61.098:   62        |
|      1:    10.183 -  20.366: 1222   |   6:    61.098 -  71.282:    4        |
|      2:    20.366 -  30.549:  270   |   7:    71.282 -  81.465:    0        |
|      3:    30.549 -  40.732:  170   |   8:    81.465 -  91.648:    0        |
|      4:    40.732 -  50.915:  140   |   9:    91.648 - 101.831:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2055 r_free = 0.2503             target_work(ml) = 5.659         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2051 r_free = 0.2504             target_work(ml) = 5.659         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 2 OF 5 *************************

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2051   r_free= 0.2504   ksol= 0.32   Bsol= 45.12   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.34,-3.03,4.41,-0.00,0.00,0.00); trace/3= -0.32                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.658733                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2022   r_free= 0.2485   ksol= 0.33   Bsol= 57.29   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.12,-2.76,0.93,-0.00,0.00,0.00); trace/3= -1.65                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.651149                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.318631              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.159   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.781554              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.707   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2022      final r-factor (work) = 0.1398          |
| start r-factor (free) = 0.2485      final r-factor (free) = 0.1810          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.2820 = 4.32 * 0.50 * 5.6541 + 1.00 * 0.0729                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.9373 = 4.32 * 0.50 * 5.4976 + 1.00 * 0.0662                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1398      final r-factor (work) = 0.1273          |
| start r-factor (free) = 0.1810      final r-factor (free) = 0.1743          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3659 = 0.78 * 1.00 * 5.4976 + 1.00 * 0.0693                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1324 = 0.78 * 1.00 * 5.2742 + 1.00 * 0.0103                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.943)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.54   17.41    None  None   None       |
|    all(noH): 2823   0      0.00    86.54   17.41    None  None   None       |
|    Sol.    : 438    0      5.96    86.54   41.41    None  None   None       |
|    Mac.    : 2385   0      0.00    83.88   13.01    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:     0.000 -   8.654:  733   |   5:    43.271 -  51.925:  112        |
|      1:     8.654 -  17.308: 1290   |   6:    51.925 -  60.579:   85        |
|      2:    17.308 -  25.962:  299   |   7:    60.579 -  69.233:   48        |
|      3:    25.962 -  34.616:  133   |   8:    69.233 -  77.887:   13        |
|      4:    34.616 -  43.271:  104   |   9:    77.887 -  86.541:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1273 r_free = 0.1743             target_work(ml) = 5.251         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1273 r_free = 0.1742             target_work(ml) = 5.251         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 3 OF 5 *************************

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1273   r_free= 0.1742   ksol= 0.33   Bsol= 57.29   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.12,-2.76,0.93,-0.00,0.00,0.00); trace/3= -1.65                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.250706                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1269   r_free= 0.1730   ksol= 0.33   Bsol= 62.85   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.85,-2.31,0.03,-0.00,0.00,0.00); trace/3= -1.71                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.246537                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.012046              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 111.164  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.317315              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 124.399  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1269      final r-factor (work) = 0.1151          |
| start r-factor (free) = 0.1730      final r-factor (free) = 0.1612          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0081 = 3.01 * 0.50 * 5.2734 + 1.00 * 0.0662                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9102 = 3.01 * 0.50 * 5.2081 + 1.00 * 0.0666                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1151      final r-factor (work) = 0.1135          |
| start r-factor (free) = 0.1612      final r-factor (free) = 0.1584          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6629 = 0.32 * 1.00 * 5.2081 + 1.00 * 0.0102                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6477 = 0.32 * 1.00 * 5.1641 + 1.00 * 0.0090                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.943)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.07   16.89    None  None   None       |
|    all(noH): 2823   0      0.00    85.07   16.89    None  None   None       |
|    Sol.    : 438    0      0.00    82.46   39.65    None  None   None       |
|    Mac.    : 2385   0      0.95    85.07   12.71    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:     0.000 -   8.508:  715   |   5:    42.537 -  51.045:   91        |
|      1:     8.508 -  17.015: 1321   |   6:    51.045 -  59.552:   82        |
|      2:    17.015 -  25.522:  303   |   7:    59.552 -  68.060:   39        |
|      3:    25.522 -  34.030:  128   |   8:    68.060 -  76.567:   16        |
|      4:    34.030 -  42.537:  123   |   9:    76.567 -  85.074:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1135 r_free = 0.1584             target_work(ml) = 5.157         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1134 r_free = 0.1584             target_work(ml) = 5.156         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 4 OF 5 *************************

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1134   r_free= 0.1584   ksol= 0.33   Bsol= 62.85   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.85,-2.31,0.03,-0.00,0.00,0.00); trace/3= -1.71                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.156101                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1133   r_free= 0.1584   ksol= 0.33   Bsol= 56.88   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.62,-2.06,-0.15,-0.00,-0.00,-0.00); trace/3= -1.61                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.155794                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.236344              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 143.931  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.140936              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 138.309  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1133      final r-factor (work) = 0.1091          |
| start r-factor (free) = 0.1584      final r-factor (free) = 0.1566          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.4225 = 3.24 * 0.50 * 5.1638 + 1.00 * 0.0666                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.3922 = 3.24 * 0.50 * 5.1396 + 1.00 * 0.0755                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1091      final r-factor (work) = 0.1102          |
| start r-factor (free) = 0.1566      final r-factor (free) = 0.1558          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7333 = 0.14 * 1.00 * 5.1396 + 1.00 * 0.0090                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7314 = 0.14 * 1.00 * 5.1397 + 1.00 * 0.0071                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.943)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.05    78.84   16.18    None  None   None       |
|    all(noH): 2823   0      1.05    78.84   16.18    None  None   None       |
|    Sol.    : 438    0      1.05    75.32   36.63    None  None   None       |
|    Mac.    : 2385   0      1.87    78.84   12.42    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:     1.051 -   8.831:  786   |   5:    39.948 -  47.727:   94        |
|      1:     8.831 -  16.610: 1252   |   6:    47.727 -  55.507:   76        |
|      2:    16.610 -  24.389:  297   |   7:    55.507 -  63.286:   26        |
|      3:    24.389 -  32.169:  136   |   8:    63.286 -  71.066:   12        |
|      4:    32.169 -  39.948:  139   |   9:    71.066 -  78.845:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1102 r_free = 0.1558             target_work(ml) = 5.137         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1101 r_free = 0.1556             target_work(ml) = 5.136         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 5 OF 5 *************************

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1101   r_free= 0.1556   ksol= 0.33   Bsol= 56.88   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.62,-2.06,-0.15,-0.00,-0.00,-0.00); trace/3= -1.61                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.136136                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1101   r_free= 0.1556   ksol= 0.33   Bsol= 56.88   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.58,-2.00,-0.21,-0.00,-0.00,-0.00); trace/3= -1.60                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.136111                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.461814              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 161.973  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.517093              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 159.634  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1101      final r-factor (work) = 0.1142          |
| start r-factor (free) = 0.1556      final r-factor (free) = 0.1572          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8318 = 1.46 * 0.50 * 5.1392 + 1.00 * 0.0755                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8210 = 1.46 * 0.50 * 5.1541 + 1.00 * 0.0539                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1142      final r-factor (work) = 0.1128          |
| start r-factor (free) = 0.1572      final r-factor (free) = 0.1582          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6722 = 0.52 * 1.00 * 5.1541 + 1.00 * 0.0070                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6728 = 0.52 * 1.00 * 5.1518 + 1.00 * 0.0088                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.943)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.76    84.25   16.47    None  None   None       |
|    all(noH): 2823   0      0.76    84.25   16.47    None  None   None       |
|    Sol.    : 438    0      1.37    79.16   38.61    None  None   None       |
|    Mac.    : 2385   0      0.76    84.25   12.40    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:     0.763 -   9.112:  931   |   5:    42.509 -  50.858:  100        |
|      1:     9.112 -  17.461: 1173   |   6:    50.858 -  59.207:   77        |
|      2:    17.461 -  25.810:  249   |   7:    59.207 -  67.556:   30        |
|      3:    25.810 -  34.159:  127   |   8:    67.556 -  75.905:   12        |
|      4:    34.159 -  42.509:  120   |   9:    75.905 -  84.254:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1128 r_free = 0.1582             target_work(ml) = 5.156         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1127 r_free = 0.1582             target_work(ml) = 5.156         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1127   r_free= 0.1582   ksol= 0.33   Bsol= 56.88   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.58,-2.00,-0.21,-0.00,-0.00,-0.00); trace/3= -1.60                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.156351                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9625 -  4.7269 0.99   1411  156 0.1044 0.1329      5.4407      5.5792|
|  2:  4.7269 -  3.7717 0.99   1353  152 0.0879 0.1085      5.4586      5.6187|
|  3:  3.7717 -  3.3007 0.99   1324  147 0.1067 0.1542      5.4754      5.8532|
|  4:  3.3007 -  3.0016 0.99   1329  141 0.1196 0.1546      5.4348      5.5915|
|  5:  3.0016 -  2.7879 0.99   1308  152 0.1316 0.1580       5.316      5.4935|
|  6:  2.7879 -  2.6245 0.99   1310  141 0.1248 0.2036      5.2146       5.513|
|  7:  2.6245 -  2.4937 0.99   1282  147 0.1284 0.1650      5.1858       5.336|
|  8:  2.4937 -  2.3856 0.98   1291  145 0.1140 0.1686       5.079      5.3147|
|  9:  2.3856 -  2.2941 0.98   1308  140 0.1191 0.1930      5.0322        5.37|
| 10:  2.2941 -  2.2152 0.98   1296  142 0.1134 0.1646      4.9553      5.1461|
| 11:  2.2152 -  2.1461 0.99   1272  148 0.1144 0.1853      4.9346      5.3019|
| 12:  2.1461 -  2.0849 0.97   1274  137 0.1171 0.1583      4.8996      5.1563|
| 13:  2.0849 -  2.0302 0.98   1282  138 0.1087 0.1810      4.7809      5.0314|
| 14:  2.0302 -  1.9808 0.46    590   73 0.0905 0.1685      4.6273      4.9342|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9625 -  4.7269  1411   156  0.93   9.84   0.97     0.94       8031.31|
|  2:  4.7269 -  3.7717  1353   152  0.95   8.06   1.01     0.99       9331.29|
|  3:  3.7717 -  3.3007  1324   147  0.93  11.31   1.02     1.01      10185.44|
|  4:  3.3007 -  3.0016  1329   141  0.92  13.20   1.00     0.99       9882.31|
|  5:  3.0016 -  2.7879  1308   152  0.91  15.46   0.99     0.96       8060.78|
|  6:  2.7879 -  2.6245  1310   141  0.89  16.54   0.97     0.95       7087.95|
|  7:  2.6245 -  2.4937  1282   147  0.91  15.63   0.98     0.95       6352.57|
|  8:  2.4937 -  2.3856  1291   145  0.91  15.19   0.99     0.96       5516.09|
|  9:  2.3856 -  2.2941  1308   140  0.91  15.68   0.99     0.95       5000.18|
| 10:  2.2941 -  2.2152  1296   142  0.90  15.76   0.99     0.95       4326.05|
| 11:  2.2152 -  2.1461  1272   148  0.90  16.35   0.98     0.95       4405.44|
| 12:  2.1461 -  2.0849  1274   137  0.91  15.80   0.99     0.98       4097.10|
| 13:  2.0849 -  2.0302  1282   138  0.90  16.45   0.98     0.96       3390.84|
| 14:  2.0302 -  1.9808   590    73  0.93  13.05   0.96     0.92       2398.64|
|alpha:            min =        0.92 max =            1.01 mean =         0.96|
|beta:             min =     2398.64 max =        10185.44 mean =      6489.11|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.78 mean =        14.15|
|phase err.(test): min =        0.00 max =           89.93 mean =        13.74|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1127   r_free= 0.1582   ksol= 0.32   Bsol= 56.86   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.40,-1.82,-0.08,-0.00,-0.00,-0.00); trace/3= -1.43                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.156346                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1127   r_free= 0.1582   ksol= 0.32   Bsol= 56.86   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.40,-1.82,-0.08,-0.00,-0.00,-0.00); trace/3= -1.43                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.156346                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9625 -  4.7269 0.99   1411  156 0.1043 0.1329      5.4401      5.5793|
|  2:  4.7269 -  3.7717 0.99   1353  152 0.0880 0.1085      5.4591      5.6191|
|  3:  3.7717 -  3.3007 0.99   1324  147 0.1067 0.1542      5.4755      5.8532|
|  4:  3.3007 -  3.0016 0.99   1329  141 0.1196 0.1546      5.4347      5.5916|
|  5:  3.0016 -  2.7879 0.99   1308  152 0.1316 0.1579      5.3159       5.493|
|  6:  2.7879 -  2.6245 0.99   1310  141 0.1248 0.2036      5.2146      5.5131|
|  7:  2.6245 -  2.4937 0.99   1282  147 0.1284 0.1650      5.1858      5.3359|
|  8:  2.4937 -  2.3856 0.98   1291  145 0.1140 0.1685      5.0792      5.3146|
|  9:  2.3856 -  2.2941 0.98   1308  140 0.1191 0.1931      5.0322      5.3699|
| 10:  2.2941 -  2.2152 0.98   1296  142 0.1134 0.1646      4.9553      5.1458|
| 11:  2.2152 -  2.1461 0.99   1272  148 0.1144 0.1852      4.9345      5.3016|
| 12:  2.1461 -  2.0849 0.97   1274  137 0.1171 0.1582      4.8995      5.1561|
| 13:  2.0849 -  2.0302 0.98   1282  138 0.1087 0.1812      4.7809      5.0319|
| 14:  2.0302 -  1.9808 0.46    590   73 0.0905 0.1685      4.6277      4.9342|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9625 -  4.7269  1411   156  0.93   9.83   0.97     0.94       8020.80|
|  2:  4.7269 -  3.7717  1353   152  0.95   8.06   1.01     0.99       9332.66|
|  3:  3.7717 -  3.3007  1324   147  0.93  11.32   1.02     1.02      10190.49|
|  4:  3.3007 -  3.0016  1329   141  0.92  13.20   1.01     0.99       9880.35|
|  5:  3.0016 -  2.7879  1308   152  0.91  15.46   0.99     0.97       8060.27|
|  6:  2.7879 -  2.6245  1310   141  0.89  16.54   0.98     0.95       7085.77|
|  7:  2.6245 -  2.4937  1282   147  0.91  15.63   0.99     0.95       6352.57|
|  8:  2.4937 -  2.3856  1291   145  0.91  15.20   1.00     0.97       5517.38|
|  9:  2.3856 -  2.2941  1308   140  0.91  15.68   1.00     0.96       5000.52|
| 10:  2.2941 -  2.2152  1296   142  0.90  15.76   1.00     0.96       4324.14|
| 11:  2.2152 -  2.1461  1272   148  0.90  16.34   0.99     0.96       4402.01|
| 12:  2.1461 -  2.0849  1274   137  0.91  15.79   1.00     0.99       4095.95|
| 13:  2.0849 -  2.0302  1282   138  0.90  16.46   0.99     0.97       3391.47|
| 14:  2.0302 -  1.9808   590    73  0.93  13.06   0.97     0.93       2400.33|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2400.33 max =        10190.49 mean =      6488.16|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.61 mean =        14.15|
|phase err.(test): min =        0.00 max =           89.93 mean =        13.74|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.943)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.74    84.23   16.44    None  None   None       |
|    all(noH): 2823   0      0.74    84.23   16.44    None  None   None       |
|    Sol.    : 438    0      1.35    79.14   38.58    None  None   None       |
|    Mac.    : 2385   0      0.74    84.23   12.38    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:     0.737 -   9.086:  931   |   5:    42.483 -  50.832:  100        |
|      1:     9.086 -  17.435: 1173   |   6:    50.832 -  59.181:   77        |
|      2:    17.435 -  25.785:  249   |   7:    59.181 -  67.530:   30        |
|      3:    25.785 -  34.134:  127   |   8:    67.530 -  75.880:   12        |
|      4:    34.134 -  42.483:  120   |   9:    75.880 -  84.229:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


========== residual map mFobs-DFmodel: highest peaks and deepst holes =========


                           ----------peaks----------                           

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 279         
Filter by distance & map next to the model:
   mapped sites are within: 0.500 - 5.321
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 272 from: 279
   mapped sites are within: 0.709 - 5.321

peak=    5.361 closest distance to " O   HOH Z 113 " =    2.193
peak=    5.265 closest distance to " CB  GLN A 223 " =    1.434
peak=    5.181 closest distance to " CB  ARG A 275 " =    0.932
peak=    5.151 closest distance to " CG  PRO A  54 " =    1.387
peak=    4.970 closest distance to " CZ  PHE A 218 " =    1.080
peak=    4.751 closest distance to " O   HOH Z 142 " =    1.695
peak=    4.743 closest distance to " CB  PRO A  54 " =    1.005
peak=    4.725 closest distance to " O   HOH Z 126 " =    1.835
peak=    4.721 closest distance to " NE2 GLN A  11 " =    1.089
peak=    4.660 closest distance to " CB  GLN A 183 " =    1.231
peak=    4.626 closest distance to " CG  PRO A 198 " =    1.302
peak=    4.618 closest distance to " O   HOH Z  78 " =    1.778
peak=    4.535 closest distance to " O   HOH Z 232 " =    2.375
peak=    4.516 closest distance to " CB  ARG A  79 " =    1.406
peak=    4.488 closest distance to " CG  PRO A 213 " =    1.237
peak=    4.449 closest distance to " CB  ARG A 190 " =    1.681
peak=    4.448 closest distance to " CG  PRO A  90 " =    1.269
peak=    4.426 closest distance to " O   HOH Z 287 " =    2.074
peak=    4.412 closest distance to " CA  TYR A  30 " =    0.966
peak=    4.402 closest distance to " O   HOH Z 298 " =    1.852
peak=    4.345 closest distance to " O   HOH Z 188 " =    2.942
peak=    4.316 closest distance to " O   HOH Z 303 " =    2.113
peak=    4.314 closest distance to " CB  GLU A 152 " =    1.160
peak=    4.307 closest distance to " CG2 VAL A 257 " =    0.842
peak=    4.290 closest distance to " O   HOH Z  19 " =    2.397
peak=    4.284 closest distance to " ND2 ASN A 187 " =    1.483
peak=    4.275 closest distance to " O   HOH Z 369 " =    2.300
peak=    4.269 closest distance to " CA  ARG A  36 " =    1.052
peak=    4.268 closest distance to " CD2 TRP A 179 " =    1.311
peak=    4.264 closest distance to " CE  LYS A  76 " =    0.880
peak=    4.235 closest distance to " CG  PRO A 243 " =    1.061
peak=    4.221 closest distance to " CB  SER A  63 " =    1.159
peak=    4.213 closest distance to " CB  VAL A 265 " =    1.217
peak=    4.194 closest distance to " O   HOH Z 423 " =    1.925
peak=    4.187 closest distance to " O   HOH Z  15 " =    2.143
peak=    4.171 closest distance to " C   PRO A 198 " =    1.518
peak=    4.165 closest distance to " ND2 ASN A 249 " =    0.895
peak=    4.159 closest distance to " O   HOH Z 427 " =    3.015
peak=    4.144 closest distance to " O   HOH Z 158 " =    3.086
peak=    4.121 closest distance to " CB  ASN A 148 " =    1.469
peak=    4.117 closest distance to " CB  ASN A  39 " =    0.915
peak=    4.092 closest distance to " CB  ARG A  79 " =    0.939
peak=    4.071 closest distance to " O   HOH Z 313 " =    2.073
peak=    4.056 closest distance to " CA  ASN A 215 " =    1.045
peak=    4.044 closest distance to " CB  LEU A 228 " =    1.089
peak=    4.034 closest distance to " O   HOH Z 272 " =    1.873
peak=    4.025 closest distance to " O   HOH Z 250 " =    1.463
peak=    4.014 closest distance to " O   HOH Z 180 " =    2.176
peak=    4.011 closest distance to " CB  GLU A  46 " =    1.004
peak=    3.988 closest distance to " O   HOH Z 316 " =    3.150
peak=    3.968 closest distance to " O   HOH Z 406 " =    1.641
peak=    3.949 closest distance to " CB  TRP A 266 " =    1.012
peak=    3.934 closest distance to " O   HOH Z 392 " =    2.861
peak=    3.919 closest distance to " CA  ARG A 195 " =    1.224
peak=    3.913 closest distance to " O   HOH Z 346 " =    1.711
peak=    3.909 closest distance to " O   ASN A  74 " =    1.357
peak=    3.905 closest distance to " CB  ASN A 142 " =    1.048
peak=    3.903 closest distance to " O   HOH Z 402 " =    1.380
peak=    3.899 closest distance to " O   HOH Z 234 " =    3.748
peak=    3.897 closest distance to " O   HOH Z  40 " =    1.798
peak=    3.897 closest distance to " CB  GLU A 277 " =    3.637
peak=    3.879 closest distance to " O  BHOH Z 338 " =    2.330
peak=    3.860 closest distance to " N   ASN A  39 " =    1.230
peak=    3.858 closest distance to " CZ3 TRP A 266 " =    1.120
peak=    3.855 closest distance to " O  BHOH Z  74 " =    1.169
peak=    3.845 closest distance to " CG2 ILE A 120 " =    1.189
peak=    3.842 closest distance to " CD  ARG A 269 " =    0.914
peak=    3.839 closest distance to " NH1AARG A 145 " =    1.305
peak=    3.837 closest distance to " CD  ARG A 159 " =    0.732
peak=    3.833 closest distance to " CA  THR A 264 " =    0.924
peak=    3.833 closest distance to " CZ  PHE A  38 " =    1.216
peak=    3.829 closest distance to " NZ  LYS A 117 " =    3.208
peak=    3.826 closest distance to " CB  VAL A 202 " =    1.570
peak=    3.820 closest distance to " O   SER A  87 " =    2.258
peak=    3.813 closest distance to " O   HOH Z  63 " =    1.973
peak=    3.799 closest distance to " CB  GLU A 128 " =    0.915
peak=    3.792 closest distance to " CB  ASN A 110 " =    1.084
peak=    3.788 closest distance to " CB  THR A  31 " =    1.555
peak=    3.770 closest distance to " CD  LYS A 166 " =    1.211
peak=    3.746 closest distance to " O   HOH Z  97 " =    2.415
peak=    3.721 closest distance to " O   HOH Z 389 " =    1.826
peak=    3.697 closest distance to " CG  LEU A 167 " =    1.255
peak=    3.695 closest distance to " O   HOH Z  61 " =    1.681
peak=    3.695 closest distance to " O   HOH Z 214 " =    2.211
peak=    3.692 closest distance to " N   ARG A 156 " =    1.377
peak=    3.686 closest distance to " O   THR A 220 " =    1.228
peak=    3.676 closest distance to " CG  GLU A  37 " =    0.912
peak=    3.669 closest distance to " O   HOH Z 126 " =    1.556
peak=    3.661 closest distance to " O   HOH Z 209 " =    2.258
peak=    3.658 closest distance to " O   HOH Z 421 " =    2.038
peak=    3.657 closest distance to " N   TYR A 116 " =    1.563
peak=    3.656 closest distance to " O   HOH Z 265 " =    2.138
peak=    3.655 closest distance to " O   HOH Z 353 " =    2.649
peak=    3.645 closest distance to " O   HOH Z  43 " =    1.856
peak=    3.642 closest distance to " O   HOH Z  21 " =    1.840
peak=    3.633 closest distance to " CG  MET A 185 " =    1.095
peak=    3.622 closest distance to " O   HOH Z 411 " =    3.914
peak=    3.613 closest distance to " OD1 ASN A  69 " =    2.541
peak=    3.612 closest distance to " CA  SER A  87 " =    1.017
peak=    3.612 closest distance to " CD2 LEU A 297 " =    0.918
peak=    3.608 closest distance to " CB  ALA A 291 " =    1.082
peak=    3.605 closest distance to " O   HOH Z 403 " =    1.549
peak=    3.604 closest distance to " O   HOH Z 185 " =    1.856
peak=    3.600 closest distance to " O   HOH Z 368 " =    3.626
peak=    3.598 closest distance to " O   HOH Z 128 " =    2.057
peak=    3.596 closest distance to " CB  PRO A  90 " =    1.087
peak=    3.593 closest distance to " CB  ALA A 114 " =    1.079
peak=    3.592 closest distance to " O   HOH Z 132 " =    2.997
peak=    3.582 closest distance to " O   HOH Z 359 " =    1.552
peak=    3.569 closest distance to " OG BSER A 164 " =    2.340
peak=    3.568 closest distance to " CG2 ILE A 239 " =    0.716
peak=    3.568 closest distance to " O   HOH Z  10 " =    1.751
peak=    3.566 closest distance to " O   HOH Z 327 " =    1.521
peak=    3.564 closest distance to " CB  TYR A 169 " =    0.709
peak=    3.560 closest distance to " CG  ARG A  66 " =    2.422
peak=    3.546 closest distance to " O   HOH Z 291 " =    1.553
peak=    3.545 closest distance to " CB  ASN A 187 " =    1.049
peak=    3.544 closest distance to " O   HOH Z  88 " =    3.076
peak=    3.529 closest distance to " CA  ALA A 160 " =    0.915
peak=    3.528 closest distance to " CB  PHE A 204 " =    0.720
peak=    3.526 closest distance to " CD1 LEU A  96 " =    0.713
peak=    3.521 closest distance to " CD1 ILE A 199 " =    1.047
peak=    3.511 closest distance to " CB  ASP A 140 " =    1.093
peak=    3.508 closest distance to " CG  GLN A  11 " =    1.867
peak=    3.501 closest distance to " N   PHE A 130 " =    1.211
peak=    3.496 closest distance to " O   HOH Z 248 " =    1.572
peak=    3.492 closest distance to " CG2AVAL A  72 " =    1.630
peak=    3.491 closest distance to " CG1 VAL A 153 " =    1.011
peak=    3.490 closest distance to " CA  ILE A 234 " =    0.972
peak=    3.488 closest distance to " CB  LEU A  83 " =    0.748
peak=    3.482 closest distance to " O   HOH Z 419 " =    2.125
peak=    3.481 closest distance to " CE1 TYR A 186 " =    1.336
peak=    3.481 closest distance to " O   HOH Z  88 " =    2.594
peak=    3.479 closest distance to " O   HOH Z  44 " =    1.797
peak=    3.464 closest distance to " CA  ALA A  51 " =    0.909
peak=    3.463 closest distance to " O   HOH Z 280 " =    2.968
peak=    3.461 closest distance to " O   HOH Z 337 " =    3.601
peak=    3.456 closest distance to " CA  MET A 105 " =    1.013
peak=    3.453 closest distance to " CD1 LEU A 300 " =    1.170
peak=    3.452 closest distance to " O   THR A 182 " =    1.381
peak=    3.451 closest distance to " NE2 HIS A 207 " =    1.157
peak=    3.446 closest distance to " OG1 THR A 264 " =    0.735
peak=    3.444 closest distance to " O   HOH Z 394 " =    4.004
peak=    3.444 closest distance to " O   HOH Z 172 " =    3.467
peak=    3.442 closest distance to " O   HOH Z 261 " =    1.966
peak=    3.437 closest distance to " O   HOH Z 368 " =    2.121
peak=    3.433 closest distance to " CB  ASN A 215 " =    1.167
peak=    3.432 closest distance to " CA  ASN A 217 " =    1.229
peak=    3.428 closest distance to " O   HOH Z 371 " =    2.928
peak=    3.426 closest distance to " O   HOH Z 285 " =    2.401
peak=    3.421 closest distance to " CB  SER A   3 " =    1.252
peak=    3.421 closest distance to " CB  ASP A 191 " =    1.246
peak=    3.413 closest distance to " CA  ASN A 127 " =    1.128
peak=    3.409 closest distance to " O   HOH Z 148 " =    3.480
peak=    3.409 closest distance to " CA  ALA A 154 " =    0.998
peak=    3.401 closest distance to " O   HOH Z 325 " =    2.440
peak=    3.397 closest distance to " NZ  LYS A  48 " =    1.149
peak=    3.392 closest distance to " CA  TYR A 116 " =    1.412
peak=    3.387 closest distance to " O   ALA A 165 " =    1.602
peak=    3.386 closest distance to " CZ2 TRP A 179 " =    1.803
peak=    3.380 closest distance to " CG AARG A 275 " =    1.085
peak=    3.374 closest distance to " CB  ILE A 120 " =    1.235
peak=    3.370 closest distance to " CB  SER A 212 " =    1.222
peak=    3.370 closest distance to " CB  ALA A 248 " =    1.309
peak=    3.362 closest distance to " O   HOH Z 365 " =    2.849
peak=    3.360 closest distance to " CG1 ILE A  49 " =    1.571
peak=    3.359 closest distance to " CB  ALA A 242 " =    0.880
peak=    3.359 closest distance to " O   HOH Z 294 " =    1.522
peak=    3.358 closest distance to " O   HOH Z 417 " =    3.338
peak=    3.355 closest distance to " CB  GLN A  89 " =    1.333
peak=    3.354 closest distance to " O   HOH Z 128 " =    2.194
peak=    3.351 closest distance to " CG1 ILE A  33 " =    1.237
peak=    3.351 closest distance to " O   HOH Z 245 " =    1.338
peak=    3.343 closest distance to " O   HOH Z  97 " =    1.999
peak=    3.343 closest distance to " O   HOH Z   1 " =    1.923
peak=    3.342 closest distance to " OG BSER A  99 " =    2.335
peak=    3.339 closest distance to " N   HIS A 108 " =    1.888
peak=    3.338 closest distance to " OD2 ASP A 286 " =    3.181
peak=    3.338 closest distance to " CA  ALA A 158 " =    1.345
peak=    3.334 closest distance to " O   HOH Z  59 " =    2.091
peak=    3.333 closest distance to " CB  SER A 210 " =    0.806
peak=    3.330 closest distance to " O   HOH Z 273 " =    2.819
peak=    3.329 closest distance to " CB  MET A  47 " =    1.037
peak=    3.328 closest distance to " O   HOH Z 234 " =    1.956
peak=    3.327 closest distance to " O   HOH Z   9 " =    2.092
peak=    3.320 closest distance to " O   HOH Z 371 " =    1.663
peak=    3.318 closest distance to " CA  VAL A 125 " =    1.088
peak=    3.316 closest distance to " O   HOH Z 106 " =    4.179
peak=    3.316 closest distance to " CB  TYR A 116 " =    0.742
peak=    3.312 closest distance to " O   HOH Z 171 " =    4.012
peak=    3.312 closest distance to " O   HOH Z 173 " =    1.874
peak=    3.309 closest distance to " CA  ASP A 162 " =    1.051
peak=    3.308 closest distance to " CA  ASP A 124 " =    0.720
peak=    3.308 closest distance to " O   HOH Z 422 " =    2.647
peak=    3.306 closest distance to " CB  GLN A  88 " =    1.164
peak=    3.306 closest distance to " O   HOH Z 203 " =    1.676
peak=    3.296 closest distance to " CA  ARG A 139 " =    0.947
peak=    3.293 closest distance to " N   ASP A 162 " =    1.092
peak=    3.292 closest distance to " CD1 LEU A 281 " =    1.001
peak=    3.290 closest distance to " CD1AILE A 234 " =    0.995
peak=    3.287 closest distance to " CB  SER A  26 " =    1.785
peak=    3.283 closest distance to " CG2 ILE A  20 " =    1.216
peak=    3.275 closest distance to " CD1 LEU A 228 " =    2.034
peak=    3.272 closest distance to " O   ALA A   1 " =    1.671
peak=    3.270 closest distance to " CB  LYS A 117 " =    1.201
peak=    3.263 closest distance to " O   HOH Z  80 " =    2.188
peak=    3.258 closest distance to " OG  SER A  22 " =    2.615
peak=    3.257 closest distance to " CB  ASN A 173 " =    1.048
peak=    3.253 closest distance to " OG  SER A  28 " =    1.517
peak=    3.251 closest distance to " O   HOH Z 163 " =    1.873
peak=    3.244 closest distance to " NH2BARG A 145 " =    2.151
peak=    3.243 closest distance to " CG  LYS A  76 " =    0.888
peak=    3.241 closest distance to " O   HOH Z 299 " =    4.337
peak=    3.241 closest distance to " O   HOH Z 251 " =    1.590
peak=    3.238 closest distance to " O   HOH Z 258 " =    2.155
peak=    3.233 closest distance to " O   HOH Z 383 " =    1.933
peak=    3.232 closest distance to " O   HOH Z 234 " =    2.221
peak=    3.230 closest distance to " CB  ALA A 227 " =    1.155
peak=    3.224 closest distance to " O   HOH Z  88 " =    2.581
peak=    3.224 closest distance to " O   HOH Z 147 " =    1.853
peak=    3.223 closest distance to " O   HOH Z 187 " =    2.288
peak=    3.222 closest distance to " N   TYR A 247 " =    1.300
peak=    3.222 closest distance to " CA  ARG A 159 " =    1.263
peak=    3.221 closest distance to " O   HOH Z  80 " =    1.705
peak=    3.215 closest distance to " O   HOH Z 425 " =    1.951
peak=    3.207 closest distance to " O   TYR A 116 " =    1.517
peak=    3.203 closest distance to " O   HOH Z 188 " =    1.929
peak=    3.197 closest distance to " O   HOH Z 336 " =    1.602
peak=    3.195 closest distance to " CG  ARG A 138 " =    1.266
peak=    3.193 closest distance to " OE2 GLU A  53 " =    1.361
peak=    3.191 closest distance to " OG BSER A 134 " =    2.925
peak=    3.191 closest distance to " CD  ARG A  66 " =    2.462
peak=    3.191 closest distance to " O   HOH Z  44 " =    3.046
peak=    3.188 closest distance to " O   HOH Z 344 " =    3.157
peak=    3.187 closest distance to " CB  TRP A 179 " =    1.402
peak=    3.185 closest distance to " CG  MET A 113 " =    0.997
peak=    3.184 closest distance to " O   HOH Z 233 " =    1.748
peak=    3.182 closest distance to " CB  SER A 141 " =    1.003
peak=    3.180 closest distance to " O   GLN A 278 " =    1.275
peak=    3.178 closest distance to " CA  GLN A  94 " =    0.776
peak=    3.173 closest distance to " CA  THR A 221 " =    1.019
peak=    3.168 closest distance to " CB  HIS A 108 " =    0.822
peak=    3.165 closest distance to " CG2 VAL A 197 " =    1.085
peak=    3.160 closest distance to " O   HOH Z 371 " =    3.230
peak=    3.156 closest distance to " CA  ASP A 140 " =    1.170
peak=    3.156 closest distance to " OD1 ASP A 171 " =    1.380
peak=    3.154 closest distance to " N   GLY A  98 " =    1.069
peak=    3.152 closest distance to " CB  GLN A 205 " =    1.076
peak=    3.147 closest distance to " O   HOH Z 305 " =    3.580
peak=    3.146 closest distance to " N   ASN A 127 " =    1.237
peak=    3.146 closest distance to " CB  ARG A 156 " =    1.167
peak=    3.136 closest distance to " O   HOH Z 227 " =    1.421
peak=    3.126 closest distance to " O   HOH Z 213 " =    1.965
peak=    3.120 closest distance to " O   HOH Z 426 " =    1.963
peak=    3.118 closest distance to " CB  PRO A 243 " =    1.340
peak=    3.111 closest distance to " CA  ARG A 102 " =    1.129
peak=    3.111 closest distance to " CD1 LEU A 261 " =    1.207
peak=    3.105 closest distance to " O   SER A 164 " =    1.387
peak=    3.098 closest distance to " O   HOH Z 407 " =    2.558
peak=    3.093 closest distance to " CG2 THR A 220 " =    0.723
peak=    3.090 closest distance to " O   HOH Z  62 " =    2.105
peak=    3.081 closest distance to " O   HOH Z  48 " =    1.493
peak=    3.079 closest distance to " O   HOH Z 430 " =    5.321
peak=    3.077 closest distance to " CD2 LEU A   5 " =    1.151
peak=    3.071 closest distance to " O   HOH Z 433 " =    1.816
peak=    3.069 closest distance to " O   HOH Z  88 " =    1.875
peak=    3.068 closest distance to " N   VAL A 265 " =    1.331
peak=    3.066 closest distance to " CB  GLN A 103 " =    0.806
peak=    3.063 closest distance to " CB  LEU A 300 " =    0.942
peak=    3.048 closest distance to " CA  ILE A 106 " =    0.792
peak=    3.045 closest distance to " O   HOH Z   1 " =    2.068
peak=    3.013 closest distance to " CA  GLU A  46 " =    1.060

                           ----------holes----------                           

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 178         
Filter by distance & map next to the model:
   mapped sites are within: 0.788 - 5.709
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 178 from: 178
   mapped sites are within: 0.788 - 5.709

peak=   -4.842 closest distance to " CD  GLN A  58 " =    1.002
peak=   -4.794 closest distance to " CD  ARG A  14 " =    3.418
peak=   -4.428 closest distance to " O   HOH Z 231 " =    2.272
peak=   -4.376 closest distance to " CD  ARG A 156 " =    2.103
peak=   -4.366 closest distance to " CG1 VAL A 112 " =    2.897
peak=   -4.351 closest distance to " O   PRO A 198 " =    1.239
peak=   -4.339 closest distance to " CD2 PHE A 192 " =    2.072
peak=   -4.281 closest distance to " C   HIS A 108 " =    1.082
peak=   -4.255 closest distance to " CG1 VAL A 112 " =    2.646
peak=   -4.202 closest distance to " O   HOH Z 266 " =    5.549
peak=   -4.202 closest distance to " O   HOH Z 198 " =    1.539
peak=   -4.188 closest distance to " OG BSER A 134 " =    1.315
peak=   -4.173 closest distance to " O   VAL A  67 " =    2.610
peak=   -4.143 closest distance to " CB  PRO A 243 " =    2.722
peak=   -4.115 closest distance to " CD2 TYR A 293 " =    1.967
peak=   -4.107 closest distance to " O   HOH Z 377 " =    2.124
peak=   -4.101 closest distance to " CZ3 TRP A 179 " =    1.197
peak=   -4.005 closest distance to " CA  VAL A  67 " =    2.928
peak=   -3.987 closest distance to " N   ALA A  43 " =    2.566
peak=   -3.987 closest distance to " O   HOH Z  73 " =    2.451
peak=   -3.968 closest distance to " CE  MET A 105 " =    2.407
peak=   -3.963 closest distance to " CG  GLN A 223 " =    2.073
peak=   -3.887 closest distance to " O   HOH Z 372 " =    2.290
peak=   -3.884 closest distance to " CE2 TYR A  30 " =    2.760
peak=   -3.857 closest distance to " OXT GLY A 302 " =    2.858
peak=   -3.834 closest distance to " CB  ALA A 161 " =    2.574
peak=   -3.833 closest distance to " CG2 ILE A  49 " =    2.776
peak=   -3.833 closest distance to " OG  SER A  97 " =    2.287
peak=   -3.826 closest distance to " O   HOH Z 185 " =    2.344
peak=   -3.822 closest distance to " CE2 PHE A  61 " =    2.633
peak=   -3.809 closest distance to " O   HOH Z 351 " =    1.441
peak=   -3.807 closest distance to " O   HOH Z 290 " =    1.173
peak=   -3.774 closest distance to " CE BMET A  47 " =    1.404
peak=   -3.756 closest distance to " CG  ARG A 269 " =    2.349
peak=   -3.756 closest distance to " O   HOH Z 394 " =    1.522
peak=   -3.731 closest distance to " ND2 ASN A  45 " =    1.772
peak=   -3.710 closest distance to " ND2 ASN A 249 " =    2.385
peak=   -3.708 closest distance to " CB  ALA A  43 " =    2.543
peak=   -3.707 closest distance to " CG2 ILE A 263 " =    2.310
peak=   -3.702 closest distance to " O   SER A 210 " =    2.068
peak=   -3.699 closest distance to " CB  ASN A  39 " =    2.317
peak=   -3.692 closest distance to " O   HOH Z 357 " =    2.067
peak=   -3.690 closest distance to " CG  PHE A 283 " =    2.655
peak=   -3.687 closest distance to " O   HOH Z 196 " =    2.033
peak=   -3.666 closest distance to " CG  ARG A  66 " =    2.430
peak=   -3.664 closest distance to " CB  ALA A 248 " =    2.308
peak=   -3.647 closest distance to " CA  ASP A 298 " =    1.095
peak=   -3.638 closest distance to " ND2 ASN A  45 " =    1.104
peak=   -3.619 closest distance to " OD2 ASP A 191 " =    1.419
peak=   -3.603 closest distance to " CA  GLY A 241 " =    2.369
peak=   -3.589 closest distance to " CA  GLY A 241 " =    3.309
peak=   -3.589 closest distance to " NH2AARG A 275 " =    5.230
peak=   -3.586 closest distance to " OD1 ASN A 148 " =    1.434
peak=   -3.579 closest distance to " CZ  PHE A 155 " =    1.100
peak=   -3.565 closest distance to " NE2 GLN A 278 " =    1.728
peak=   -3.563 closest distance to " N   ALA A 248 " =    1.645
peak=   -3.562 closest distance to " CD1 LEU A 101 " =    2.384
peak=   -3.558 closest distance to " O   PRO A 163 " =    2.038
peak=   -3.551 closest distance to " OD1 ASP A 171 " =    1.565
peak=   -3.542 closest distance to " O   HOH Z 389 " =    1.986
peak=   -3.537 closest distance to " NE2 GLN A 194 " =    1.928
peak=   -3.536 closest distance to " CD1 PHE A  59 " =    2.052
peak=   -3.526 closest distance to " CA  GLY A 203 " =    2.347
peak=   -3.520 closest distance to " CB  ALA A 291 " =    2.302
peak=   -3.518 closest distance to " CG1 VAL A 250 " =    2.660
peak=   -3.515 closest distance to " O   HOH Z 211 " =    1.510
peak=   -3.512 closest distance to " O   HOH Z  10 " =    1.475
peak=   -3.505 closest distance to " CB  ALA A 129 " =    2.459
peak=   -3.501 closest distance to " CD1 LEU A 255 " =    2.783
peak=   -3.500 closest distance to " O   HOH Z 114 " =    3.107
peak=   -3.497 closest distance to " O   HOH Z 174 " =    2.618
peak=   -3.497 closest distance to " O   ALA A  10 " =    1.687
peak=   -3.488 closest distance to " O   SER A  95 " =    1.633
peak=   -3.481 closest distance to " CG  GLN A  11 " =    1.734
peak=   -3.477 closest distance to " O   HOH Z 407 " =    2.956
peak=   -3.461 closest distance to " CG  HIS A  86 " =    1.111
peak=   -3.458 closest distance to " O   HOH Z 102 " =    1.572
peak=   -3.453 closest distance to " CD  GLU A 236 " =    1.096
peak=   -3.451 closest distance to " CG2 THR A 178 " =    2.389
peak=   -3.450 closest distance to " O   HOH Z 166 " =    1.948
peak=   -3.449 closest distance to " CZ  TYR A 169 " =    1.782
peak=   -3.448 closest distance to " CG  GLU A 277 " =    1.251
peak=   -3.420 closest distance to " CG  ASP A 132 " =    2.301
peak=   -3.412 closest distance to " CG  LYS A 193 " =    2.698
peak=   -3.406 closest distance to " C   LEU A 143 " =    1.000
peak=   -3.404 closest distance to " CD  ARG A  79 " =    1.162
peak=   -3.401 closest distance to " CD1 ILE A 239 " =    2.384
peak=   -3.399 closest distance to " O   HOH Z 429 " =    1.989
peak=   -3.399 closest distance to " ND2 ASN A 187 " =    1.511
peak=   -3.398 closest distance to " O   HOH Z  38 " =    1.630
peak=   -3.397 closest distance to " ND2 ASN A  60 " =    1.299
peak=   -3.396 closest distance to " NE2 GLN A  88 " =    1.863
peak=   -3.389 closest distance to " O   HOH Z  15 " =    1.527
peak=   -3.386 closest distance to " O   PHE A 218 " =    1.510
peak=   -3.383 closest distance to " NH2 ARG A  79 " =    1.514
peak=   -3.382 closest distance to " CE3 TRP A 150 " =    2.222
peak=   -3.380 closest distance to " CB  ALA A 291 " =    2.207
peak=   -3.379 closest distance to " O   HOH Z  37 " =    1.788
peak=   -3.372 closest distance to " O   HOH Z 216 " =    1.396
peak=   -3.366 closest distance to " CD  PRO A 243 " =    2.116
peak=   -3.365 closest distance to " N   THR A  52 " =    1.693
peak=   -3.355 closest distance to " CB  TRP A  85 " =    2.497
peak=   -3.355 closest distance to " O   HOH Z 313 " =    1.869
peak=   -3.333 closest distance to " O   HOH Z   6 " =    2.305
peak=   -3.329 closest distance to " O   HOH Z  51 " =    1.832
peak=   -3.326 closest distance to " CG  LEU A  83 " =    1.974
peak=   -3.325 closest distance to " O   HOH Z 348 " =    2.204
peak=   -3.317 closest distance to " CG1 VAL A 125 " =    1.816
peak=   -3.313 closest distance to " O   HOH Z  71 " =    2.308
peak=   -3.309 closest distance to " OE1 GLN A  88 " =    1.104
peak=   -3.309 closest distance to " O   ALA A 161 " =    1.697
peak=   -3.305 closest distance to " OH  TYR A 247 " =    2.069
peak=   -3.295 closest distance to " O   HOH Z  63 " =    1.716
peak=   -3.293 closest distance to " CA  ILE A 263 " =    1.104
peak=   -3.287 closest distance to " CD  ARG A 139 " =    1.664
peak=   -3.278 closest distance to " O   HOH Z 353 " =    2.196
peak=   -3.275 closest distance to " O   ILE A 106 " =    1.881
peak=   -3.273 closest distance to " O   HOH Z  60 " =    1.800
peak=   -3.271 closest distance to " O   HOH Z 174 " =    3.847
peak=   -3.270 closest distance to " O   VAL A 189 " =    1.647
peak=   -3.269 closest distance to " CG  TRP A 266 " =    1.955
peak=   -3.268 closest distance to " O   ASN A 252 " =    1.373
peak=   -3.264 closest distance to " O   HOH Z 134 " =    3.309
peak=   -3.253 closest distance to " O   HOH Z 421 " =    3.208
peak=   -3.246 closest distance to " O   HOH Z 177 " =    1.759
peak=   -3.246 closest distance to " CE3 TRP A 274 " =    2.408
peak=   -3.245 closest distance to " C   MET A 188 " =    1.316
peak=   -3.241 closest distance to " CD  GLN A  88 " =    1.184
peak=   -3.241 closest distance to " C   SER A 206 " =    1.594
peak=   -3.233 closest distance to " O   ARG A 145 " =    1.543
peak=   -3.228 closest distance to " O   VAL A 174 " =    2.103
peak=   -3.222 closest distance to " O   HOH Z 253 " =    3.897
peak=   -3.219 closest distance to " O   TRP A  70 " =    1.451
peak=   -3.207 closest distance to " O   HOH Z 200 " =    4.696
peak=   -3.206 closest distance to " O   HOH Z 139 " =    5.193
peak=   -3.202 closest distance to " O   HOH Z 171 " =    1.949
peak=   -3.198 closest distance to " O   HOH Z 191 " =    5.709
peak=   -3.185 closest distance to " OE2 GLU A 152 " =    1.334
peak=   -3.180 closest distance to " CG1AVAL A  41 " =    2.649
peak=   -3.180 closest distance to " O   HOH Z 368 " =    1.764
peak=   -3.174 closest distance to " O   HOH Z 119 " =    2.341
peak=   -3.174 closest distance to " O   TYR A 247 " =    2.788
peak=   -3.174 closest distance to " CG  ASP A 231 " =    0.788
peak=   -3.173 closest distance to " O   HOH Z 285 " =    1.619
peak=   -3.170 closest distance to " O   HOH Z  52 " =    1.498
peak=   -3.166 closest distance to " CB  ASP A 286 " =    1.766
peak=   -3.162 closest distance to " O   HOH Z   6 " =    1.436
peak=   -3.160 closest distance to " O   HOH Z 113 " =    1.892
peak=   -3.159 closest distance to " CB  ALA A 100 " =    2.214
peak=   -3.159 closest distance to " CG1 VAL A  67 " =    3.139
peak=   -3.158 closest distance to " CA  SER A 135 " =    1.284
peak=   -3.156 closest distance to " O   HOH Z 298 " =    2.606
peak=   -3.151 closest distance to " O   SER A 135 " =    1.456
peak=   -3.147 closest distance to " C   GLY A 262 " =    2.004
peak=   -3.130 closest distance to " CG1BVAL A  41 " =    2.786
peak=   -3.126 closest distance to " CG  GLN A 103 " =    2.426
peak=   -3.124 closest distance to " CG1 VAL A 197 " =    2.227
peak=   -3.123 closest distance to " CB  ALA A  10 " =    2.314
peak=   -3.121 closest distance to " O   HOH Z 283 " =    5.589
peak=   -3.117 closest distance to " CZ  PHE A  38 " =    2.043
peak=   -3.115 closest distance to " OD2 ASP A  50 " =    2.086
peak=   -3.113 closest distance to " O   ALA A 292 " =    2.038
peak=   -3.091 closest distance to " N   MET A 188 " =    1.991
peak=   -3.090 closest distance to " O   HOH Z 110 " =    1.404
peak=   -3.088 closest distance to " CD  PRO A 213 " =    2.163
peak=   -3.088 closest distance to " O   GLU A 152 " =    1.306
peak=   -3.087 closest distance to " CD1 ILE A 199 " =    2.466
peak=   -3.086 closest distance to " O   HOH Z  13 " =    1.769
peak=   -3.083 closest distance to " O   ALA A  51 " =    1.283
peak=   -3.081 closest distance to " CD1 LEU A   5 " =    2.478
peak=   -3.077 closest distance to " CD2 HIS A 207 " =    2.318
peak=   -3.069 closest distance to " O   HOH Z 216 " =    1.456
peak=   -3.061 closest distance to " CA  GLY A 241 " =    2.866
peak=   -3.061 closest distance to " O   HOH Z 128 " =    2.574
peak=   -3.057 closest distance to " O   ALA A 227 " =    1.572
peak=   -3.056 closest distance to " O   ALA A  34 " =    2.308
peak=   -3.046 closest distance to " OG BSER A 134 " =    1.826
peak=   -3.032 closest distance to " CA  GLY A  57 " =    2.110

================= 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_occ: refinement of individual occupancies                             
------------------------------------------------------------------------
 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    :  0.3494 0.3445   6.107718e+00   6.086537e+00
   1_bss:  0.3332 0.3292   6.081145e+00   6.056589e+00
   1_xyz:  0.2218 0.2455   5.706039e+00   5.787041e+00
   1_adp:  0.2055 0.2503   5.659196e+00   5.807032e+00
   1_occ:  0.2051 0.2504   5.658733e+00   5.807671e+00
   2_bss:  0.2022 0.2485   5.651149e+00   5.803722e+00
   2_xyz:  0.1398 0.1810   5.319753e+00   5.517575e+00
   2_adp:  0.1273 0.1743   5.251221e+00   5.475118e+00
   2_occ:  0.1273 0.1742   5.250706e+00   5.474639e+00
   3_bss:  0.1269 0.1730   5.246537e+00   5.468626e+00
   3_xyz:  0.1151 0.1612   5.169536e+00   5.406349e+00
   3_adp:  0.1135 0.1584   5.156610e+00   5.391173e+00
   3_occ:  0.1134 0.1584   5.156101e+00   5.390956e+00
   4_bss:  0.1133 0.1584   5.155794e+00   5.391036e+00
   4_xyz:  0.1091 0.1566   5.133964e+00   5.383738e+00
   4_adp:  0.1102 0.1558   5.136995e+00   5.379103e+00
   4_occ:  0.1101 0.1556   5.136136e+00   5.378732e+00
   5_bss:  0.1101 0.1556   5.136111e+00   5.378739e+00
   5_xyz:  0.1142 0.1572   5.160052e+00   5.389147e+00
   5_adp:  0.1128 0.1582   5.156371e+00   5.394788e+00
   5_occ:  0.1127 0.1582   5.156351e+00   5.394966e+00
   5_bss:  0.1127 0.1582   5.156346e+00   5.394946e+00
------------------------------------------------------------------------
 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:  0.317  45.119  -2.341  -3.031   4.405  -0.000   0.000   0.000
   1_xyz:  0.317  45.119  -2.341  -3.031   4.405  -0.000   0.000   0.000
   1_adp:  0.317  45.119  -2.341  -3.031   4.405  -0.000   0.000   0.000
   1_occ:  0.317  45.119  -2.341  -3.031   4.405  -0.000   0.000   0.000
   2_bss:  0.328  57.289  -3.117  -2.756   0.931  -0.000   0.000   0.000
   2_xyz:  0.328  57.289  -3.117  -2.756   0.931  -0.000   0.000   0.000
   2_adp:  0.328  57.289  -3.117  -2.756   0.931  -0.000   0.000   0.000
   2_occ:  0.328  57.289  -3.117  -2.756   0.931  -0.000   0.000   0.000
   3_bss:  0.331  62.852  -2.846  -2.310   0.033  -0.000   0.000   0.000
   3_xyz:  0.331  62.852  -2.846  -2.310   0.033  -0.000   0.000   0.000
   3_adp:  0.331  62.852  -2.846  -2.310   0.033  -0.000   0.000   0.000
   3_occ:  0.331  62.852  -2.846  -2.310   0.033  -0.000   0.000   0.000
   4_bss:  0.325  56.882  -2.621  -2.058  -0.153  -0.000  -0.000  -0.000
   4_xyz:  0.325  56.882  -2.621  -2.058  -0.153  -0.000  -0.000  -0.000
   4_adp:  0.325  56.882  -2.621  -2.058  -0.153  -0.000  -0.000  -0.000
   4_occ:  0.325  56.882  -2.621  -2.058  -0.153  -0.000  -0.000  -0.000
   5_bss:  0.325  56.882  -2.583  -2.002  -0.208  -0.000  -0.000  -0.000
   5_xyz:  0.325  56.882  -2.583  -2.002  -0.208  -0.000  -0.000  -0.000
   5_adp:  0.325  56.882  -2.583  -2.002  -0.208  -0.000  -0.000  -0.000
   5_occ:  0.325  56.882  -2.583  -2.002  -0.208  -0.000  -0.000  -0.000
   5_bss:  0.322  56.856  -2.403  -1.819  -0.076  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  36.454 0.6875  0.8582    34501.285
   1_bss:  34.864 0.7043  0.8711    30747.306
   1_xyz:  23.973 0.8233  0.9789    15464.198
   1_adp:  24.689 0.8153  0.9710    16190.928
   1_occ:  24.736 0.8148  0.9702    16215.718
   2_bss:  24.328 0.8194  0.9323    15978.248
   2_xyz:  17.210 0.8870  0.9757     8372.965
   2_adp:  16.152 0.8965  0.9728     7717.132
   2_occ:  16.139 0.8965  0.9728     7707.501
   3_bss:  15.986 0.8979  0.9717     7591.204
   3_xyz:  14.521 0.9104  0.9765     6619.205
   3_adp:  14.181 0.9135  0.9699     6450.444
   3_occ:  14.177 0.9135  0.9698     6445.175
   4_bss:  14.175 0.9135  0.9733     6444.472
   4_xyz:  13.961 0.9153  0.9761     6350.117
   4_adp:  13.859 0.9163  0.9724     6338.944
   4_occ:  13.845 0.9164  0.9724     6329.684
   5_bss:  13.845 0.9164  0.9729     6329.905
   5_xyz:  13.994 0.9155  0.9710     6447.267
   5_adp:  14.108 0.9145  0.9644     6486.974
   5_occ:  14.110 0.9145  0.9643     6488.022
   5_bss:  14.111 0.9145  0.9690     6487.070
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.113   1.7176e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.113   1.7176e-01
   1_xyz:   1.137  0.008  0.073 15.034  0.005  4.111   7.2913e-02
   1_adp:   1.137  0.008  0.073 15.034  0.005  4.111   7.2913e-02
   1_occ:   1.137  0.008  0.073 15.034  0.005  4.111   7.2913e-02
   2_bss:   1.137  0.008  0.073 15.034  0.005  4.111   7.2913e-02
   2_xyz:   1.060  0.009  0.078 15.101  0.004  4.125   6.6211e-02
   2_adp:   1.060  0.009  0.078 15.101  0.004  4.125   6.6211e-02
   2_occ:   1.060  0.009  0.078 15.101  0.004  4.125   6.6211e-02
   3_bss:   1.060  0.009  0.078 15.101  0.004  4.125   6.6211e-02
   3_xyz:   1.051  0.009  0.079 14.871  0.004  4.112   6.6641e-02
   3_adp:   1.051  0.009  0.079 14.871  0.004  4.112   6.6641e-02
   3_occ:   1.051  0.009  0.079 14.871  0.004  4.112   6.6641e-02
   4_bss:   1.051  0.009  0.079 14.871  0.004  4.112   6.6641e-02
   4_xyz:   1.121  0.010  0.085 14.900  0.004  4.115   7.5519e-02
   4_adp:   1.121  0.010  0.085 14.900  0.004  4.115   7.5519e-02
   4_occ:   1.121  0.010  0.085 14.900  0.004  4.115   7.5519e-02
   5_bss:   1.121  0.010  0.085 14.900  0.004  4.115   7.5519e-02
   5_xyz:   0.937  0.007  0.074 14.493  0.004  4.114   5.3868e-02
   5_adp:   0.937  0.007  0.074 14.493  0.004  4.114   5.3868e-02
   5_occ:   0.937  0.007  0.074 14.493  0.004  4.114   5.3868e-02
   5_bss:   0.937  0.007  0.074 14.493  0.004  4.114   5.3868e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.469   2.4206e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.469   2.4206e-01
   1_xyz:   8.310  0.046  0.295 82.518  0.038  2.175   7.6055e-02
   1_adp:   8.310  0.046  0.295 82.518  0.038  2.175   7.6055e-02
   1_occ:   8.310  0.046  0.295 82.518  0.038  2.175   7.6055e-02
   2_bss:   8.310  0.046  0.295 82.518  0.038  2.175   7.6055e-02
   2_xyz:   7.075  0.045  0.268 85.630  0.035  2.266   7.3478e-02
   2_adp:   7.075  0.045  0.268 85.630  0.035  2.266   7.3478e-02
   2_occ:   7.075  0.045  0.268 85.630  0.035  2.266   7.3478e-02
   3_bss:   7.075  0.045  0.268 85.630  0.035  2.266   7.3478e-02
   3_xyz:   7.119  0.051  0.260 82.266  0.037  2.364   5.4428e-02
   3_adp:   7.119  0.051  0.260 82.266  0.037  2.364   5.4428e-02
   3_occ:   7.119  0.051  0.260 82.266  0.037  2.364   5.4428e-02
   4_bss:   7.119  0.051  0.260 82.266  0.037  2.364   5.4428e-02
   4_xyz:   7.391  0.057  0.294 82.673  0.036  2.280   5.9240e-02
   4_adp:   7.391  0.057  0.294 82.673  0.036  2.280   5.9240e-02
   4_occ:   7.391  0.057  0.294 82.673  0.036  2.280   5.9240e-02
   5_bss:   7.391  0.057  0.294 82.673  0.036  2.280   5.9240e-02
   5_xyz:   6.378  0.045  0.226 82.328  0.037  2.377   3.2480e-02
   5_adp:   6.378  0.045  0.226 82.328  0.037  2.377   3.2480e-02
   5_occ:   6.378  0.045  0.226 82.328  0.037  2.377   3.2480e-02
   5_bss:   6.378  0.045  0.226 82.328  0.037  2.377   3.2480e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_bss:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_xyz:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_adp: 101.83   0.00  16.64 101.83   0.00  12.82  63.33   5.76  37.44
   1_occ: 101.83   0.00  16.64 101.83   0.00  12.82  63.33   5.76  37.44
   2_bss: 101.83   0.00  16.64 101.83   0.00  12.82  63.33   5.76  37.44
   2_xyz: 101.83   0.00  16.64 101.83   0.00  12.82  63.33   5.76  37.44
   2_adp:  86.54   0.00  17.41  83.88   0.00  13.01  86.54   5.96  41.41
   2_occ:  86.54   0.00  17.41  83.88   0.00  13.01  86.54   5.96  41.41
   3_bss:  86.54   0.00  17.41  83.88   0.00  13.01  86.54   5.96  41.41
   3_xyz:  86.54   0.00  17.41  83.88   0.00  13.01  86.54   5.96  41.41
   3_adp:  85.07   0.00  16.89  85.07   0.95  12.71  82.46   0.00  39.65
   3_occ:  85.07   0.00  16.89  85.07   0.95  12.71  82.46   0.00  39.65
   4_bss:  85.07   0.00  16.89  85.07   0.95  12.71  82.46   0.00  39.65
   4_xyz:  85.07   0.00  16.89  85.07   0.95  12.71  82.46   0.00  39.65
   4_adp:  78.84   1.05  16.18  78.84   1.87  12.42  75.32   1.05  36.63
   4_occ:  78.84   1.05  16.18  78.84   1.87  12.42  75.32   1.05  36.63
   5_bss:  78.84   1.05  16.18  78.84   1.87  12.42  75.32   1.05  36.63
   5_xyz:  78.84   1.05  16.18  78.84   1.87  12.42  75.32   1.05  36.63
   5_adp:  84.25   0.76  16.47  84.25   0.76  12.40  79.16   1.37  38.61
   5_occ:  84.25   0.76  16.47  84.25   0.76  12.40  79.16   1.37  38.61
   5_bss:  84.23   0.74  16.44  84.23   0.74  12.38  79.14   1.35  38.58
------------------------------------------------------------------------
 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:    1.596    0.010    0.274
   1_adp:    1.596    0.010    0.274
   1_occ:    1.596    0.010    0.274
   2_bss:    1.596    0.010    0.274
   2_xyz:    1.068    0.036    0.401
   2_adp:    1.068    0.036    0.401
   2_occ:    1.068    0.036    0.401
   3_bss:    1.068    0.036    0.401
   3_xyz:    1.035    0.037    0.423
   3_adp:    1.035    0.037    0.423
   3_occ:    1.035    0.037    0.423
   4_bss:    1.035    0.037    0.423
   4_xyz:    1.306    0.036    0.440
   4_adp:    1.306    0.036    0.440
   4_occ:    1.306    0.036    0.440
   5_bss:    1.306    0.036    0.440
   5_xyz:    1.446    0.028    0.442
   5_adp:    1.446    0.028    0.442
   5_occ:    1.446    0.028    0.442
   5_bss:    1.446    0.028    0.442
------------------------------------------------------------------------

CPU time actual refinement: 273.51


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_427/model_refine_001.pdb
n_use            =  2823
n_use_u_iso      =  2823
n_use_u_aniso    =  0
n_grad_site      =  0
n_grad_u_iso     =  0
n_grad_u_aniso   =  0
n_grad_occupancy =  106
n_grad_fp        =  0
n_grad_fdp       =  0
n_anisotropic_flag =  0
total number of scatterers =  2823

Writing 2mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_427/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_427/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_427/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_427/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 273.39 
  Macro-tasks:
    bulk solvent and scale       = 29.98  
    individual site refinement   = 118.32 
    weights calculation          = 24.05  
    collect and process          = 5.45   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 177.89 
  Micro-tasks:
    mask                            = 0.99   
    f_calc                          = 87.65  
    alpha_beta                      = 6.68   
    target                          = 0.95   
    gradients_wrt_atomic_parameters = 96.74  
    fmodel                         = 5.62   
    r_factors                      = 0.18   
    phase_errors                   = 9.17   
    foms                           = 0.23   
    TOTAL for micro-tasks          = 208.21 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 3.821 micro seconds
Total CPU time: 4.74 minutes
from_scatterers_fft:    659 calls, 87.39 s
gradients_fft:          604 calls, 84.58 s

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

# Date 2008-01-16 Time 04:47:45 PST -0800 (1200487665.14 s)
Start R-work = 0.3494, R-free = 0.3445 (no bulk solvent and anisotropic scale)
Final R-work = 0.1350, R-free = 0.1759 (no bulk solvent and anisotropic scale)

Start R-work = 0.3332, R-free = 0.3292
Final R-work = 0.1127, R-free = 0.1582