# Date 2008-01-16 Time 05:32:12 PST -0800 (1200490332.24 s)
#phil __OFF__

Command line arguments: "../776.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 22925
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 776

-------------------------------------------------------------------------------
  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: (70.6012, 46.6953, 86.822, 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: 2.81, per 1000 atoms: 1.00


================================== 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: (70.6012, 46.6953, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0689 1.99223
Completeness in resolution range: 0.969512
Completeness with d_max=infinity: 0.966499

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0689
                             d_min =   1.9922

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: (70.6012, 46.6953, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0689 1.99223
Completeness in resolution range: 0.969512
Completeness with d_max=infinity: 0.966499

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0694 -  4.2628 [2118/2142]  1905   213  10.1%
  bin  2:  4.2628 -  3.3962 [2037/2057]  1834   203  10.0%
  bin  3:  3.3962 -  2.9707 [2013/2032]  1813   200   9.9%
  bin  4:  2.9707 -  2.7007 [2001/2031]  1801   200  10.0%
  bin  5:  2.7007 -  2.5081 [1986/2005]  1786   200  10.1%
  bin  6:  2.5081 -  2.3608 [1957/1982]  1759   198  10.1%
  bin  7:  2.3608 -  2.2430 [1955/1983]  1762   193   9.9%
  bin  8:  2.2430 -  2.1456 [1967/2003]  1772   195   9.9%
  bin  9:  2.1456 -  2.0633 [1942/1984]  1748   194  10.0%
  bin 10:  2.0633 -  1.9922 [1613/1986]  1450   163  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_776/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:
        1.81 -     2.42: 10
        2.42 -     3.04: 2187
        3.04 -     3.66: 4651
        3.66 -     4.28: 9048
        4.28 -     4.90: 12299
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " NH1BARG A 275 " - " O  BHOH Z 338 "  2.341 3.120
  " O   HOH Z  42 " - " O   HOH Z 183 "  2.363 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 341 " - " O   HOH Z 207 "  2.365 3.040 -x+1/2,-y+1,z-1/2
  ... (remaining 28190 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_776/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_776/model_refine_001.geo

CPU time processing inputs: 8.04


============================ 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 = 70.60125 46.69535 86.82195 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: 1.99 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2319   r_free= 0.2276   ksol= 0.00   Bsol= 0.00   scale= 1.002    |
|                                                                             |
| 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:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.728547                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0694 -  4.7544 0.99   1380  153 0.2533 0.2366      6.2522      6.1731|
|  2:  4.7544 -  3.7935 0.99   1325  149 0.1788 0.1694      6.0976      6.0591|
|  3:  3.7935 -  3.3199 0.99   1298  142 0.1854 0.1972      5.9606      6.1012|
|  4:  3.3199 -  3.0190 0.99   1289  145 0.2000 0.2040      5.8735      5.8776|
|  5:  3.0190 -  2.8041 0.99   1280  143 0.2327 0.2035      5.7821       5.697|
|  6:  2.8041 -  2.6397 0.99   1295  140 0.2229 0.2282      5.6746      5.6096|
|  7:  2.6397 -  2.5081 0.99   1272  144 0.2374 0.2376      5.6718      5.7107|
|  8:  2.5081 -  2.3994 0.98   1258  137 0.2415 0.2222      5.6464      5.6189|
|  9:  2.3994 -  2.3074 0.98   1263  144 0.2394 0.2480      5.5727      5.5729|
| 10:  2.3074 -  2.2280 1.00   1260  141 0.2502 0.2471      5.6021      5.5158|
| 11:  2.2280 -  2.1585 0.97   1266  137 0.2564 0.2649      5.5523      5.5607|
| 12:  2.1585 -  2.0970 0.98   1236  139 0.2535 0.2530      5.4936      5.5544|
| 13:  2.0970 -  2.0419 0.99   1286  142 0.2648 0.2695      5.4187      5.4107|
| 14:  2.0419 -  1.9922 0.73    922  103 0.2768 0.2607      5.4523      5.3179|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0694 -  4.7544  1380   153  0.83  22.27   0.87     0.84      31587.08|
|  2:  4.7544 -  3.7935  1325   149  0.90  16.04   0.99     0.95      25390.38|
|  3:  3.7935 -  3.3199  1298   142  0.89  17.02   1.02     1.00      20731.34|
|  4:  3.3199 -  3.0190  1289   145  0.89  17.30   1.02     1.00      16530.96|
|  5:  3.0190 -  2.8041  1280   143  0.86  20.54   1.04     1.00      13444.27|
|  6:  2.8041 -  2.6397  1295   140  0.87  19.83   1.03     1.00      10963.54|
|  7:  2.6397 -  2.5081  1272   144  0.86  21.12   1.05     1.00      10542.17|
|  8:  2.5081 -  2.3994  1258   137  0.86  21.36   1.06     1.02      10064.00|
|  9:  2.3994 -  2.3074  1263   144  0.86  21.41   1.08     1.03       9737.20|
| 10:  2.3074 -  2.2280  1260   141  0.84  22.47   1.10     1.04       9199.12|
| 11:  2.2280 -  2.1585  1266   137  0.83  23.68   1.09     1.05       9103.62|
| 12:  2.1585 -  2.0970  1236   139  0.84  23.05   1.10     1.06       8575.27|
| 13:  2.0970 -  2.0419  1286   142  0.82  24.51   1.10     1.06       7401.83|
| 14:  2.0419 -  1.9922   922   103  0.85  22.33   1.09     1.03       5577.88|
|alpha:            min =        0.84 max =            1.06 mean =         1.00|
|beta:             min =     5577.88 max =        31587.08 mean =     13817.44|
|figures of merit: min =        0.00 max =            1.00 mean =         0.86|
|phase err.(work): min =        0.00 max =           89.98 mean =        20.88|
|phase err.(test): min =        0.00 max =           89.95 mean =        20.63|
|-----------------------------------------------------------------------------|

============================== 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 = 2.760398              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.643   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.340090              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.639   (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 |  1.806 -  2.115:        1 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:        9 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      197 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1990 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1840 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2811 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4636 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4412 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5612 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6687 |
|-----------------------------------------------------------------------------|
|-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 |        0.160 |
| 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  1.806 |       0.136 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.972)------------------------------------------|
|    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: 1.99 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2319   r_free= 0.2276   ksol= 0.00   Bsol= 0.00   scale= 1.002    |
|                                                                             |
| 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:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.728547                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2142   r_free= 0.2122   ksol= 0.33   Bsol= 53.72   scale= 0.982   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.61,-2.11,-1.02,-0.00,-0.00,-0.00); trace/3= -1.91                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.690669                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.478857              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.747   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.181022              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.498   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2142      final r-factor (work) = 0.1340          |
| start r-factor (free) = 0.2122      final r-factor (free) = 0.1541          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.2727 = 2.48 * 0.50 * 5.7387 + 1.00 * 0.1600                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7341 = 2.48 * 0.50 * 5.3854 + 1.00 * 0.0592                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1340      final r-factor (work) = 0.1235          |
| start r-factor (free) = 0.1541      final r-factor (free) = 0.1572          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9810 = 0.18 * 1.00 * 5.3854 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9583 = 0.18 * 1.00 * 5.1817 + 1.00 * 0.0203                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 6      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.972)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    62.92   16.46    None  None   None       |
|    all(noH): 2823   0      0.00    62.92   16.46    None  None   None       |
|    Sol.    : 438    0      6.96    62.92   37.03    None  None   None       |
|    Mac.    : 2385   0      0.00    53.45   12.68    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 -   6.292:  147   |   5:    31.459 -  37.751:   93        |
|      1:     6.292 -  12.584: 1340   |   6:    37.751 -  44.043:  103        |
|      2:    12.584 -  18.875:  666   |   7:    44.043 -  50.334:   74        |
|      3:    18.875 -  25.167:  208   |   8:    50.334 -  56.626:   56        |
|      4:    25.167 -  31.459:  116   |   9:    56.626 -  62.918:   20        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1235 r_free = 0.1572             target_work(ml) = 5.191         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1230 r_free = 0.1568             target_work(ml) = 5.189         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1230   r_free= 0.1568   ksol= 0.33   Bsol= 53.72   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.61,-2.11,-1.02,-0.00,-0.00,-0.00); trace/3= -1.91                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.188723                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1233   r_free= 0.1563   ksol= 0.33   Bsol= 53.72   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.86,-2.65,-1.35,-0.00,-0.00,-0.00); trace/3= -2.29                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.191021                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.860773              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 119.725  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.150873              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.537   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1233      final r-factor (work) = 0.1114          |
| start r-factor (free) = 0.1563      final r-factor (free) = 0.1520          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.4752 = 2.86 * 0.50 * 5.1846 + 1.00 * 0.0592                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.4238 = 2.86 * 0.50 * 5.1407 + 1.00 * 0.0706                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1114      final r-factor (work) = 0.1090          |
| start r-factor (free) = 0.1520      final r-factor (free) = 0.1505          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8094 = 0.15 * 1.00 * 5.1407 + 1.00 * 0.0338                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7778 = 0.15 * 1.00 * 5.1122 + 1.00 * 0.0065                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.972)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.18    66.27   16.49    None  None   None       |
|    all(noH): 2823   0      2.18    66.27   16.49    None  None   None       |
|    Sol.    : 438    0      5.68    66.27   36.55    None  None   None       |
|    Mac.    : 2385   0      2.18    65.44   12.80    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.176 -   8.586:  586   |   5:    34.225 -  40.635:  115        |
|      1:     8.586 -  14.995: 1285   |   6:    40.635 -  47.044:   86        |
|      2:    14.995 -  21.405:  384   |   7:    47.044 -  53.454:   85        |
|      3:    21.405 -  27.815:  141   |   8:    53.454 -  59.864:   30        |
|      4:    27.815 -  34.225:  104   |   9:    59.864 -  66.274:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1090 r_free = 0.1505             target_work(ml) = 5.109         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1089 r_free = 0.1506             target_work(ml) = 5.109         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1089   r_free= 0.1506   ksol= 0.33   Bsol= 53.72   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.86,-2.65,-1.35,-0.00,-0.00,-0.00); trace/3= -2.29                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.108756                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1088   r_free= 0.1506   ksol= 0.33   Bsol= 53.72   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.67,-2.55,-1.22,-0.00,-0.00,-0.00); trace/3= -2.15                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.108751                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.864139              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 155.365  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.275167              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 151.704  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1088      final r-factor (work) = 0.1100          |
| start r-factor (free) = 0.1506      final r-factor (free) = 0.1521          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8357 = 1.86 * 0.50 * 5.1126 + 1.00 * 0.0704                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8255 = 1.86 * 0.50 * 5.1137 + 1.00 * 0.0592                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1100      final r-factor (work) = 0.1089          |
| start r-factor (free) = 0.1521      final r-factor (free) = 0.1521          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4137 = 0.28 * 1.00 * 5.1137 + 1.00 * 0.0065                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4146 = 0.28 * 1.00 * 5.1138 + 1.00 * 0.0074                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.972)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.48    71.20   16.61    None  None   None       |
|    all(noH): 2823   0      1.48    71.20   16.61    None  None   None       |
|    Sol.    : 438    0      6.71    67.84   37.50    None  None   None       |
|    Mac.    : 2385   0      1.48    71.20   12.77    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:     1.481 -   8.453:  615   |   5:    36.342 -  43.314:  117        |
|      1:     8.453 -  15.425: 1298   |   6:    43.314 -  50.287:   96        |
|      2:    15.425 -  22.397:  367   |   7:    50.287 -  57.259:   62        |
|      3:    22.397 -  29.370:  132   |   8:    57.259 -  64.231:   30        |
|      4:    29.370 -  36.342:  101   |   9:    64.231 -  71.203:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1089 r_free = 0.1521             target_work(ml) = 5.116         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1089 r_free = 0.1522             target_work(ml) = 5.117         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1089   r_free= 0.1522   ksol= 0.33   Bsol= 53.72   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.67,-2.55,-1.22,-0.00,-0.00,-0.00); trace/3= -2.15                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.116756                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1088   r_free= 0.1521   ksol= 0.33   Bsol= 53.72   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.51,-2.44,-1.08,-0.00,-0.00,-0.00); trace/3= -2.01                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.116570                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.175306              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 168.180  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.268342              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 140.025  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1088      final r-factor (work) = 0.1057          |
| start r-factor (free) = 0.1521      final r-factor (free) = 0.1529          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.1787 = 3.18 * 0.50 * 5.1141 + 1.00 * 0.0592                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.1754 = 3.18 * 0.50 * 5.1028 + 1.00 * 0.0739                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1057      final r-factor (work) = 0.1055          |
| start r-factor (free) = 0.1529      final r-factor (free) = 0.1530          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3767 = 0.27 * 1.00 * 5.1028 + 1.00 * 0.0074                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3765 = 0.27 * 1.00 * 5.1014 + 1.00 * 0.0076                               |
|-----------------------------------------------------------------------------|
| number of iterations = 9       |    number of function evaluations = 11     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.972)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.36    71.63   16.46    None  None   None       |
|    all(noH): 2823   0      1.36    71.63   16.46    None  None   None       |
|    Sol.    : 438    0      6.46    67.99   37.42    None  None   None       |
|    Mac.    : 2385   0      1.36    71.63   12.61    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:     1.360 -   8.386:  635   |   5:    36.494 -  43.521:  114        |
|      1:     8.386 -  15.413: 1288   |   6:    43.521 -  50.548:   95        |
|      2:    15.413 -  22.440:  364   |   7:    50.548 -  57.575:   62        |
|      3:    22.440 -  29.467:  124   |   8:    57.575 -  64.601:   30        |
|      4:    29.467 -  36.494:  106   |   9:    64.601 -  71.628:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1055 r_free = 0.1530             target_work(ml) = 5.102         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1055 r_free = 0.1530             target_work(ml) = 5.102         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1055   r_free= 0.1530   ksol= 0.33   Bsol= 53.72   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.51,-2.44,-1.08,-0.00,-0.00,-0.00); trace/3= -2.01                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.101982                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1054   r_free= 0.1530   ksol= 0.33   Bsol= 53.72   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.30,-2.25,-0.89,-0.00,-0.00,-0.00); trace/3= -1.81                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.102081                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.588735              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 166.234  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.452569              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.772  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1054      final r-factor (work) = 0.1065          |
| start r-factor (free) = 0.1530      final r-factor (free) = 0.1538          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6784 = 2.59 * 0.50 * 5.1025 + 1.00 * 0.0739                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6761 = 2.59 * 0.50 * 5.1065 + 1.00 * 0.0664                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1065      final r-factor (work) = 0.1063          |
| start r-factor (free) = 0.1538      final r-factor (free) = 0.1543          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3186 = 0.45 * 1.00 * 5.1065 + 1.00 * 0.0076                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3196 = 0.45 * 1.00 * 5.1077 + 1.00 * 0.0080                               |
|-----------------------------------------------------------------------------|
| number of iterations = 19      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.972)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.90    72.52   16.34    None  None   None       |
|    all(noH): 2823   0      0.90    72.52   16.34    None  None   None       |
|    Sol.    : 438    0      6.11    68.21   37.55    None  None   None       |
|    Mac.    : 2385   0      0.90    72.52   12.45    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:     0.899 -   8.061:  606   |   5:    36.709 -  43.871:  112        |
|      1:     8.061 -  15.223: 1304   |   6:    43.871 -  51.033:   95        |
|      2:    15.223 -  22.385:  373   |   7:    51.033 -  58.195:   62        |
|      3:    22.385 -  29.547:  130   |   8:    58.195 -  65.357:   29        |
|      4:    29.547 -  36.709:  107   |   9:    65.357 -  72.519:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1063 r_free = 0.1543             target_work(ml) = 5.111         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1063 r_free = 0.1543             target_work(ml) = 5.111         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1063   r_free= 0.1543   ksol= 0.33   Bsol= 53.72   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.30,-2.25,-0.89,-0.00,-0.00,-0.00); trace/3= -1.81                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.110804                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0694 -  4.7544 0.99   1380  153 0.0991 0.1308      5.3953      5.5495|
|  2:  4.7544 -  3.7935 0.99   1325  149 0.0848 0.1142      5.4408       5.642|
|  3:  3.7935 -  3.3199 0.99   1298  142 0.1024 0.1479       5.457      5.8501|
|  4:  3.3199 -  3.0190 0.99   1289  145 0.1166 0.1546      5.4271      5.5583|
|  5:  3.0190 -  2.8041 0.99   1280  143 0.1266 0.1676       5.305        5.56|
|  6:  2.8041 -  2.6397 0.99   1295  140 0.1126 0.1920      5.1811      5.4512|
|  7:  2.6397 -  2.5081 0.99   1272  144 0.1214 0.1502       5.133      5.3136|
|  8:  2.5081 -  2.3994 0.98   1258  137 0.1073 0.1663      5.0116      5.3146|
|  9:  2.3994 -  2.3074 0.98   1263  144 0.1077 0.1623      4.9813      5.2194|
| 10:  2.3074 -  2.2280 1.00   1260  141 0.1044 0.1702      4.9156      5.2367|
| 11:  2.2280 -  2.1585 0.97   1266  137 0.1054 0.1693      4.8937      5.2005|
| 12:  2.1585 -  2.0970 0.98   1236  139 0.1031 0.1646       4.836      5.1778|
| 13:  2.0970 -  2.0419 0.99   1286  142 0.1037 0.1743      4.7495      5.0551|
| 14:  2.0419 -  1.9922 0.73    922  103 0.0972 0.1680      4.6322      4.9099|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0694 -  4.7544  1380   153  0.94   9.33   0.98     0.95       7446.10|
|  2:  4.7544 -  3.7935  1325   149  0.95   7.96   1.01     1.00       9288.12|
|  3:  3.7935 -  3.3199  1298   142  0.94  10.93   1.02     1.01      10105.48|
|  4:  3.3199 -  3.0190  1289   145  0.92  13.37   1.00     0.98       9948.52|
|  5:  3.0190 -  2.8041  1280   143  0.90  15.41   0.99     0.96       8099.89|
|  6:  2.8041 -  2.6397  1295   140  0.90  15.51   0.98     0.96       6872.01|
|  7:  2.6397 -  2.5081  1272   144  0.91  15.26   0.98     0.96       5901.84|
|  8:  2.5081 -  2.3994  1258   137  0.92  14.10   0.99     0.97       4760.45|
|  9:  2.3994 -  2.3074  1263   144  0.92  14.32   1.00     0.96       4570.63|
| 10:  2.3074 -  2.2280  1260   141  0.91  14.66   0.99     0.96       4060.92|
| 11:  2.2280 -  2.1585  1266   137  0.90  15.77   0.99     0.95       4081.72|
| 12:  2.1585 -  2.0970  1236   139  0.92  14.43   1.00     0.99       3695.51|
| 13:  2.0970 -  2.0419  1286   142  0.91  15.40   0.99     0.97       3166.62|
| 14:  2.0419 -  1.9922   922   103  0.92  13.75   0.97     0.93       2461.53|
|alpha:            min =        0.93 max =            1.01 mean =         0.97|
|beta:             min =     2461.53 max =        10105.48 mean =      6140.23|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.92 mean =        13.54|
|phase err.(test): min =        0.00 max =           89.95 mean =        13.07|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1063   r_free= 0.1542   ksol= 0.33   Bsol= 53.69   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.07,-2.03,-0.67,-0.00,-0.00,-0.00); trace/3= -1.59                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.110907                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1063   r_free= 0.1542   ksol= 0.33   Bsol= 53.69   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.07,-2.03,-0.67,-0.00,-0.00,-0.00); trace/3= -1.59                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.110907                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0694 -  4.7544 0.99   1380  153 0.0991 0.1309      5.3959      5.5506|
|  2:  4.7544 -  3.7935 0.99   1325  149 0.0848 0.1142      5.4411      5.6418|
|  3:  3.7935 -  3.3199 0.99   1298  142 0.1024 0.1479       5.457      5.8503|
|  4:  3.3199 -  3.0190 0.99   1289  145 0.1166 0.1546      5.4271      5.5583|
|  5:  3.0190 -  2.8041 0.99   1280  143 0.1266 0.1676       5.305      5.5598|
|  6:  2.8041 -  2.6397 0.99   1295  140 0.1126 0.1921      5.1811      5.4514|
|  7:  2.6397 -  2.5081 0.99   1272  144 0.1214 0.1502      5.1331      5.3139|
|  8:  2.5081 -  2.3994 0.98   1258  137 0.1073 0.1663      5.0117      5.3145|
|  9:  2.3994 -  2.3074 0.98   1263  144 0.1077 0.1623      4.9814      5.2195|
| 10:  2.3074 -  2.2280 1.00   1260  141 0.1044 0.1702      4.9157      5.2366|
| 11:  2.2280 -  2.1585 0.97   1266  137 0.1054 0.1693      4.8938      5.2005|
| 12:  2.1585 -  2.0970 0.98   1236  139 0.1031 0.1646      4.8359      5.1778|
| 13:  2.0970 -  2.0419 0.99   1286  142 0.1037 0.1742      4.7495      5.0549|
| 14:  2.0419 -  1.9922 0.73    922  103 0.0972 0.1680      4.6324      4.9101|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0694 -  4.7544  1380   153  0.94   9.34   0.98     0.95       7459.87|
|  2:  4.7544 -  3.7935  1325   149  0.95   7.97   1.01     1.00       9296.85|
|  3:  3.7935 -  3.3199  1298   142  0.94  10.93   1.02     1.01      10105.16|
|  4:  3.3199 -  3.0190  1289   145  0.92  13.37   1.00     0.98       9947.85|
|  5:  3.0190 -  2.8041  1280   143  0.90  15.41   1.00     0.97       8099.26|
|  6:  2.8041 -  2.6397  1295   140  0.90  15.51   0.99     0.96       6871.18|
|  7:  2.6397 -  2.5081  1272   144  0.91  15.27   0.99     0.96       5902.29|
|  8:  2.5081 -  2.3994  1258   137  0.92  14.10   0.99     0.97       4760.76|
|  9:  2.3994 -  2.3074  1263   144  0.92  14.32   1.00     0.97       4571.19|
| 10:  2.3074 -  2.2280  1260   141  0.91  14.66   1.00     0.97       4061.30|
| 11:  2.2280 -  2.1585  1266   137  0.90  15.77   1.00     0.96       4081.31|
| 12:  2.1585 -  2.0970  1236   139  0.92  14.43   1.01     1.00       3695.06|
| 13:  2.0970 -  2.0419  1286   142  0.91  15.40   1.00     0.98       3166.38|
| 14:  2.0419 -  1.9922   922   103  0.92  13.75   0.98     0.94       2462.11|
|alpha:            min =        0.94 max =            1.01 mean =         0.97|
|beta:             min =     2462.11 max =        10105.16 mean =      6141.86|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.92 mean =        13.54|
|phase err.(test): min =        0.00 max =           89.95 mean =        13.07|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.972)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.87    72.49   16.31    None  None   None       |
|    all(noH): 2823   0      0.87    72.49   16.31    None  None   None       |
|    Sol.    : 438    0      6.08    68.18   37.52    None  None   None       |
|    Mac.    : 2385   0      0.87    72.49   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:     0.868 -   8.030:  606   |   5:    36.678 -  43.840:  112        |
|      1:     8.030 -  15.192: 1304   |   6:    43.840 -  51.002:   95        |
|      2:    15.192 -  22.354:  373   |   7:    51.002 -  58.164:   62        |
|      3:    22.354 -  29.516:  130   |   8:    58.164 -  65.326:   29        |
|      4:    29.516 -  36.678:  107   |   9:    65.326 -  72.488:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 282         
Filter by distance & map next to the model:
   mapped sites are within: 0.494 - 4.780
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 275 from: 282
   mapped sites are within: 0.731 - 4.780

peak=    5.911 closest distance to " NH2 ARG A  56 " =    2.213
peak=    5.593 closest distance to " CG  PRO A  54 " =    1.305
peak=    5.307 closest distance to " O   HOH Z 126 " =    1.944
peak=    5.186 closest distance to " O   HOH Z 232 " =    2.363
peak=    5.024 closest distance to " CB  ARG A 275 " =    0.911
peak=    4.949 closest distance to " NE2 GLN A  11 " =    1.119
peak=    4.949 closest distance to " CB  GLN A 223 " =    1.427
peak=    4.926 closest distance to " CB  SER A  63 " =    1.195
peak=    4.718 closest distance to " CB  ARG A  79 " =    1.324
peak=    4.710 closest distance to " O   HOH Z 144 " =    1.716
peak=    4.683 closest distance to " CB  GLN A 183 " =    1.208
peak=    4.587 closest distance to " O   HOH Z  15 " =    2.245
peak=    4.584 closest distance to " O   HOH Z 236 " =    2.038
peak=    4.510 closest distance to " C   PRO A 198 " =    1.455
peak=    4.492 closest distance to " CB  GLU A 152 " =    1.209
peak=    4.472 closest distance to " CB  PRO A  54 " =    0.949
peak=    4.453 closest distance to " O   HOH Z  78 " =    1.727
peak=    4.427 closest distance to " CA  TYR A  30 " =    0.952
peak=    4.387 closest distance to " CB  ARG A 190 " =    1.669
peak=    4.385 closest distance to " O   HOH Z 298 " =    1.885
peak=    4.379 closest distance to " O   HOH Z 250 " =    1.552
peak=    4.346 closest distance to " CB  ASN A 148 " =    1.501
peak=    4.340 closest distance to " O   HOH Z 427 " =    2.906
peak=    4.307 closest distance to " O   HOH Z 209 " =    2.277
peak=    4.277 closest distance to " O   HOH Z 303 " =    2.097
peak=    4.273 closest distance to " O   HOH Z 234 " =    3.705
peak=    4.245 closest distance to " O   HOH Z 158 " =    3.034
peak=    4.244 closest distance to " CB  LEU A 228 " =    1.086
peak=    4.241 closest distance to " CG2 VAL A 257 " =    0.921
peak=    4.234 closest distance to " O   HOH Z 189 " =    2.487
peak=    4.201 closest distance to " O   HOH Z 369 " =    2.085
peak=    4.200 closest distance to " ND2 ASN A 187 " =    1.463
peak=    4.190 closest distance to " CG  PRO A 198 " =    1.274
peak=    4.183 closest distance to " CA  ASN A 215 " =    1.211
peak=    4.173 closest distance to " OD1 ASN A  69 " =    2.579
peak=    4.151 closest distance to " O   HOH Z 272 " =    1.861
peak=    4.116 closest distance to " CB  TYR A 169 " =    0.733
peak=    4.113 closest distance to " O   HOH Z 346 " =    1.639
peak=    4.113 closest distance to " O   HOH Z 193 " =    1.895
peak=    4.058 closest distance to " OG ASER A 258 " =    3.125
peak=    4.037 closest distance to " CZ  PHE A 218 " =    1.047
peak=    4.003 closest distance to " O   HOH Z  61 " =    1.582
peak=    3.975 closest distance to " CB  TRP A 266 " =    0.990
peak=    3.975 closest distance to " O   HOH Z 392 " =    3.200
peak=    3.964 closest distance to " NZ  LYS A 117 " =    3.267
peak=    3.956 closest distance to " CD  ARG A 159 " =    0.731
peak=    3.930 closest distance to " CB  VAL A 265 " =    1.261
peak=    3.916 closest distance to " O   HOH Z  10 " =    1.838
peak=    3.914 closest distance to " CD2 TRP A 179 " =    1.312
peak=    3.906 closest distance to " CG  PRO A 243 " =    1.026
peak=    3.892 closest distance to " CB  ASP A 140 " =    0.973
peak=    3.880 closest distance to " CE  LYS A  76 " =    0.875
peak=    3.874 closest distance to " CB  ASN A 187 " =    1.051
peak=    3.865 closest distance to " CB  GLU A 128 " =    1.010
peak=    3.853 closest distance to " O   SER A  87 " =    2.275
peak=    3.852 closest distance to " NH1AARG A 145 " =    1.244
peak=    3.831 closest distance to " O   HOH Z 261 " =    2.163
peak=    3.821 closest distance to " O   HOH Z 389 " =    1.913
peak=    3.821 closest distance to " O   HOH Z  40 " =    1.694
peak=    3.813 closest distance to " CB  SER A 212 " =    1.145
peak=    3.808 closest distance to " O   HOH Z 368 " =    2.032
peak=    3.800 closest distance to " CB  SER A   3 " =    1.320
peak=    3.795 closest distance to " O   HOH Z 423 " =    1.834
peak=    3.793 closest distance to " O   HOH Z   9 " =    2.037
peak=    3.787 closest distance to " O   HOH Z 291 " =    1.591
peak=    3.784 closest distance to " O   HOH Z  78 " =    2.146
peak=    3.767 closest distance to " O   HOH Z   1 " =    1.869
peak=    3.760 closest distance to " O   HOH Z 203 " =    1.743
peak=    3.751 closest distance to " OD2 ASP A 286 " =    2.835
peak=    3.739 closest distance to " O   HOH Z 419 " =    2.008
peak=    3.733 closest distance to " O   HOH Z 248 " =    1.616
peak=    3.730 closest distance to " O   HOH Z 245 " =    1.296
peak=    3.711 closest distance to " N   ARG A 156 " =    1.323
peak=    3.708 closest distance to " O   HOH Z 214 " =    2.084
peak=    3.699 closest distance to " O   HOH Z 426 " =    1.857
peak=    3.697 closest distance to " O   HOH Z 344 " =    3.112
peak=    3.697 closest distance to " O   HOH Z  66 " =    2.176
peak=    3.697 closest distance to " CD  ARG A  66 " =    2.462
peak=    3.686 closest distance to " CB  VAL A 202 " =    1.575
peak=    3.684 closest distance to " O   HOH Z 213 " =    1.868
peak=    3.668 closest distance to " O   HOH Z  21 " =    1.746
peak=    3.662 closest distance to " CA  ARG A 195 " =    1.216
peak=    3.661 closest distance to " O   HOH Z 172 " =    3.174
peak=    3.660 closest distance to " O   HOH Z 180 " =    2.156
peak=    3.654 closest distance to " CB  ASN A 142 " =    1.037
peak=    3.652 closest distance to " O   HOH Z 280 " =    2.990
peak=    3.648 closest distance to " O   HOH Z  43 " =    1.847
peak=    3.643 closest distance to " O   HOH Z 193 " =    1.684
peak=    3.638 closest distance to " O   HOH Z 368 " =    3.578
peak=    3.629 closest distance to " O   HOH Z  53 " =    2.567
peak=    3.627 closest distance to " CA  ALA A  51 " =    0.894
peak=    3.621 closest distance to " O   HOH Z 313 " =    1.985
peak=    3.617 closest distance to " CA  THR A 264 " =    0.888
peak=    3.617 closest distance to " O   HOH Z 219 " =    1.974
peak=    3.605 closest distance to " CD2 LEU A 255 " =    1.466
peak=    3.600 closest distance to " CD1 LEU A 300 " =    1.226
peak=    3.590 closest distance to " CB  TRP A 179 " =    1.386
peak=    3.575 closest distance to " CB  ASN A  39 " =    0.887
peak=    3.569 closest distance to " CB  ALA A 291 " =    1.341
peak=    3.568 closest distance to " CG2 ILE A 120 " =    1.137
peak=    3.568 closest distance to " CB  GLU A  46 " =    0.999
peak=    3.566 closest distance to " O   HOH Z 371 " =    3.016
peak=    3.557 closest distance to " CG1BVAL A  72 " =    1.651
peak=    3.550 closest distance to " O   HOH Z 403 " =    1.651
peak=    3.550 closest distance to " CB  GLU A 277 " =    3.588
peak=    3.549 closest distance to " CG1 ILE A  33 " =    1.221
peak=    3.545 closest distance to " O   HOH Z 147 " =    1.821
peak=    3.541 closest distance to " CB  SER A 216 " =    0.820
peak=    3.539 closest distance to " O   HOH Z  61 " =    1.486
peak=    3.534 closest distance to " CB  ASN A 110 " =    1.088
peak=    3.530 closest distance to " O   HOH Z 305 " =    3.547
peak=    3.522 closest distance to " O   HOH Z 425 " =    2.034
peak=    3.519 closest distance to " CB  TYR A 116 " =    0.798
peak=    3.510 closest distance to " CA  SER A  87 " =    1.023
peak=    3.508 closest distance to " O   HOH Z 417 " =    3.247
peak=    3.505 closest distance to " CB  ALA A  34 " =    0.994
peak=    3.503 closest distance to " O  BHOH Z 338 " =    2.329
peak=    3.500 closest distance to " O   HOH Z 133 " =    2.478
peak=    3.496 closest distance to " O   HOH Z 132 " =    2.488
peak=    3.494 closest distance to " CA  ARG A  36 " =    1.041
peak=    3.493 closest distance to " O   HOH Z  96 " =    2.154
peak=    3.491 closest distance to " CG  LEU A 167 " =    1.266
peak=    3.491 closest distance to " CB  GLN A  88 " =    1.214
peak=    3.486 closest distance to " O   HOH Z 175 " =    2.222
peak=    3.474 closest distance to " CB  ARG A 139 " =    0.970
peak=    3.472 closest distance to " O   HOH Z 371 " =    1.856
peak=    3.470 closest distance to " CB  ASN A 224 " =    0.999
peak=    3.466 closest distance to " O   HOH Z 188 " =    2.084
peak=    3.466 closest distance to " CA  ALA A  21 " =    1.178
peak=    3.457 closest distance to " O   HOH Z 234 " =    1.849
peak=    3.455 closest distance to " NH2BARG A 145 " =    2.123
peak=    3.453 closest distance to " O   HOH Z 402 " =    1.348
peak=    3.450 closest distance to " O   HOH Z 128 " =    2.324
peak=    3.448 closest distance to " NE2 GLN A  73 " =    3.853
peak=    3.448 closest distance to " CA  ALA A 233 " =    1.248
peak=    3.435 closest distance to " CD BLYS A 290 " =    1.103
peak=    3.429 closest distance to " CD2 LEU A 297 " =    0.832
peak=    3.427 closest distance to " CB  ILE A 120 " =    1.256
peak=    3.426 closest distance to " O   HOH Z 359 " =    1.506
peak=    3.423 closest distance to " ND1 HIS A  86 " =    1.787
peak=    3.422 closest distance to " CB  MET A  47 " =    1.007
peak=    3.421 closest distance to " CG2 THR A 221 " =    1.074
peak=    3.417 closest distance to " CB  HIS A 108 " =    0.776
peak=    3.408 closest distance to " CD1 ILE A 106 " =    0.745
peak=    3.403 closest distance to " CA  THR A 221 " =    1.042
peak=    3.390 closest distance to " OE1 GLU A   2 " =    2.170
peak=    3.389 closest distance to " O   HOH Z 273 " =    2.836
peak=    3.388 closest distance to " O   HOH Z  44 " =    3.007
peak=    3.387 closest distance to " O   HOH Z 265 " =    2.432
peak=    3.386 closest distance to " CG1 VAL A 153 " =    0.919
peak=    3.386 closest distance to " O   HOH Z 148 " =    3.355
peak=    3.384 closest distance to " CD  LYS A 166 " =    1.236
peak=    3.379 closest distance to " O   HOH Z  97 " =    2.744
peak=    3.377 closest distance to " O   MET A 105 " =    1.831
peak=    3.374 closest distance to " NH2AARG A 275 " =    3.699
peak=    3.371 closest distance to " CB  MET A  40 " =    0.811
peak=    3.371 closest distance to " OG1 THR A 294 " =    2.422
peak=    3.371 closest distance to " CB  THR A 157 " =    1.110
peak=    3.370 closest distance to " O   HOH Z 435 " =    1.936
peak=    3.360 closest distance to " ND2 ASN A 110 " =    1.705
peak=    3.358 closest distance to " O   HOH Z 353 " =    2.685
peak=    3.355 closest distance to " CA  ALA A  84 " =    1.319
peak=    3.348 closest distance to " CB  ALA A 248 " =    0.890
peak=    3.345 closest distance to " CG  LYS A  76 " =    0.956
peak=    3.345 closest distance to " CG  MET A 185 " =    1.126
peak=    3.344 closest distance to " O   HOH Z 409 " =    2.840
peak=    3.342 closest distance to " O   HOH Z 406 " =    1.539
peak=    3.338 closest distance to " O   HOH Z  88 " =    3.103
peak=    3.336 closest distance to " O   HOH Z 128 " =    2.165
peak=    3.334 closest distance to " N   ASN A 127 " =    1.270
peak=    3.334 closest distance to " O   ASN A  74 " =    1.565
peak=    3.331 closest distance to " N   ASN A  39 " =    1.259
peak=    3.331 closest distance to " CZ2 TRP A 179 " =    1.765
peak=    3.322 closest distance to " OG BSER A 164 " =    2.338
peak=    3.322 closest distance to " NH2 ARG A 156 " =    1.202
peak=    3.322 closest distance to " CA  MET A  40 " =    1.133
peak=    3.319 closest distance to " OG  SER A  22 " =    2.694
peak=    3.311 closest distance to " O   HOH Z 287 " =    2.283
peak=    3.309 closest distance to " O   HOH Z 227 " =    1.690
peak=    3.309 closest distance to " CB  SER A 141 " =    1.045
peak=    3.307 closest distance to " CB  ALA A   9 " =    1.541
peak=    3.304 closest distance to " O   HOH Z 285 " =    2.750
peak=    3.302 closest distance to " N   PHE A 130 " =    1.250
peak=    3.300 closest distance to " O   HOH Z 411 " =    1.715
peak=    3.297 closest distance to " CA  MET A 105 " =    0.959
peak=    3.292 closest distance to " CA  ALA A  43 " =    1.259
peak=    3.286 closest distance to " O   HOH Z 391 " =    2.881
peak=    3.283 closest distance to " CE1 TYR A 186 " =    1.339
peak=    3.281 closest distance to " O   HOH Z 193 " =    2.033
peak=    3.276 closest distance to " CG  GLN A  11 " =    1.643
peak=    3.273 closest distance to " O   HOH Z 133 " =    1.590
peak=    3.271 closest distance to " O   HOH Z 185 " =    1.810
peak=    3.266 closest distance to " NE2 HIS A 207 " =    1.352
peak=    3.265 closest distance to " O   HOH Z 411 " =    3.906
peak=    3.264 closest distance to " O   HOH Z  59 " =    1.860
peak=    3.261 closest distance to " CD1 LEU A  96 " =    0.776
peak=    3.261 closest distance to " CB  GLN A  89 " =    1.284
peak=    3.260 closest distance to " CB  PRO A  90 " =    1.220
peak=    3.259 closest distance to " CA  ALA A 158 " =    1.261
peak=    3.259 closest distance to " CB  ARG A 138 " =    0.988
peak=    3.259 closest distance to " O   HOH Z 294 " =    1.478
peak=    3.259 closest distance to " CB  THR A  31 " =    1.647
peak=    3.259 closest distance to " O   THR A 251 " =    1.304
peak=    3.255 closest distance to " CA  TYR A 116 " =    1.325
peak=    3.246 closest distance to " O   HOH Z 135 " =    1.655
peak=    3.242 closest distance to " O   HOH Z 261 " =    2.316
peak=    3.239 closest distance to " CG2 ILE A  20 " =    1.474
peak=    3.236 closest distance to " CB  ALA A 242 " =    0.880
peak=    3.236 closest distance to " O   HOH Z 345 " =    3.488
peak=    3.232 closest distance to " OD1BASN A 224 " =    2.369
peak=    3.231 closest distance to " O   HOH Z 407 " =    2.340
peak=    3.230 closest distance to " CA  LYS A 117 " =    1.212
peak=    3.221 closest distance to " O   HOH Z 329 " =    3.917
peak=    3.219 closest distance to " CD  ARG A 269 " =    0.897
peak=    3.215 closest distance to " CB  THR A 235 " =    1.083
peak=    3.211 closest distance to " CG  PRO A 213 " =    0.953
peak=    3.209 closest distance to " O   HOH Z 302 " =    1.953
peak=    3.208 closest distance to " O   HOH Z 345 " =    1.650
peak=    3.206 closest distance to " CD2 HIS A  81 " =    1.103
peak=    3.204 closest distance to " CB  LYS A 117 " =    1.209
peak=    3.203 closest distance to " O   HOH Z 423 " =    2.907
peak=    3.202 closest distance to " CG1 VAL A 189 " =    1.977
peak=    3.200 closest distance to " O   HOH Z 383 " =    1.804
peak=    3.200 closest distance to " O   HOH Z  49 " =    2.943
peak=    3.197 closest distance to " ND2 ASN A 249 " =    0.875
peak=    3.197 closest distance to " CB  ASN A 215 " =    1.102
peak=    3.196 closest distance to " O   HOH Z  44 " =    1.673
peak=    3.195 closest distance to " CA  ALA A 291 " =    0.846
peak=    3.193 closest distance to " O   HOH Z  40 " =    1.941
peak=    3.192 closest distance to " O   HOH Z 271 " =    2.386
peak=    3.190 closest distance to " O   ALA A   1 " =    1.676
peak=    3.188 closest distance to " CD1 ILE A 263 " =    1.320
peak=    3.187 closest distance to " N   VAL A 126 " =    1.317
peak=    3.185 closest distance to " O   HOH Z 173 " =    1.794
peak=    3.184 closest distance to " CD  ARG A 219 " =    1.145
peak=    3.184 closest distance to " O   THR A 220 " =    1.287
peak=    3.180 closest distance to " O   HOH Z 403 " =    1.355
peak=    3.180 closest distance to " CB  LYS A 290 " =    1.050
peak=    3.179 closest distance to " CB  ALA A   1 " =    4.780
peak=    3.176 closest distance to " CG1 ILE A  49 " =    1.442
peak=    3.171 closest distance to " O   HOH Z 298 " =    2.497
peak=    3.171 closest distance to " O   HOH Z 171 " =    2.017
peak=    3.169 closest distance to " CA  ILE A 234 " =    0.921
peak=    3.168 closest distance to " CA  GLU A  46 " =    0.755
peak=    3.168 closest distance to " CA  ASN A 217 " =    1.216
peak=    3.162 closest distance to " O   TYR A 116 " =    1.333
peak=    3.161 closest distance to " NH1BARG A 145 " =    1.188
peak=    3.157 closest distance to " O   HOH Z 189 " =    3.630
peak=    3.155 closest distance to " CB  ALA A 248 " =    1.314
peak=    3.147 closest distance to " O   HOH Z  88 " =    1.978
peak=    3.145 closest distance to " CG  ARG A 159 " =    0.836
peak=    3.142 closest distance to " CA  ALA A 154 " =    0.968
peak=    3.140 closest distance to " CD  LYS A 119 " =    1.372
peak=    3.134 closest distance to " N   GLN A 278 " =    1.263
peak=    3.131 closest distance to " OG  SER A 206 " =    1.279
peak=    3.129 closest distance to " O   HOH Z 421 " =    1.795
peak=    3.127 closest distance to " O   TRP A 274 " =    1.838
peak=    3.125 closest distance to " CB  TRP A 150 " =    1.294
peak=    3.124 closest distance to " OG BSER A  99 " =    2.191
peak=    3.117 closest distance to " O   HOH Z 116 " =    1.769
peak=    3.107 closest distance to " O   HOH Z 327 " =    1.767
peak=    3.105 closest distance to " CB  GLN A 278 " =    0.841
peak=    3.103 closest distance to " O   HOH Z 325 " =    3.914
peak=    3.092 closest distance to " O   SER A 164 " =    1.293
peak=    3.090 closest distance to " CG  GLN A  77 " =    2.200
peak=    3.085 closest distance to " CA  ALA A 248 " =    1.165
peak=    3.084 closest distance to " NZ  LYS A  48 " =    1.281
peak=    3.067 closest distance to " CG  GLN A  89 " =    1.503
peak=    3.066 closest distance to " O   HOH Z 171 " =    4.035
peak=    3.061 closest distance to " CA  SER A 146 " =    1.647
peak=    3.044 closest distance to " O   HOH Z 433 " =    1.769
peak=    3.043 closest distance to " CB  SER A  62 " =    1.146
peak=    3.031 closest distance to " O   HOH Z 438 " =    2.861
peak=    3.025 closest distance to " CA  THR A 221 " =    1.429
peak=    3.007 closest distance to " CA  ALA A 299 " =    0.917

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 189         
Filter by distance & map next to the model:
   mapped sites are within: 0.563 - 5.608
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 186 from: 189
   mapped sites are within: 0.700 - 5.608

peak=   -4.687 closest distance to " CB  PRO A 243 " =    2.630
peak=   -4.545 closest distance to " O   HOH Z 266 " =    5.141
peak=   -4.440 closest distance to " CG1 VAL A 112 " =    2.634
peak=   -4.436 closest distance to " CD  GLN A  58 " =    0.936
peak=   -4.429 closest distance to " CD  ARG A 156 " =    2.038
peak=   -4.428 closest distance to " CG  GLN A 223 " =    1.941
peak=   -4.421 closest distance to " O   VAL A  67 " =    2.731
peak=   -4.373 closest distance to " SG  CYS A 254 " =    3.567
peak=   -4.294 closest distance to " O   HOH Z 389 " =    1.982
peak=   -4.292 closest distance to " CZ3 TRP A 179 " =    1.157
peak=   -4.213 closest distance to " O   HOH Z 377 " =    2.091
peak=   -4.135 closest distance to " C   HIS A 108 " =    1.112
peak=   -4.115 closest distance to " O   HOH Z 435 " =    2.843
peak=   -4.079 closest distance to " ND2 ASN A  45 " =    1.797
peak=   -4.030 closest distance to " OG BSER A 134 " =    1.247
peak=   -3.974 closest distance to " CG1 VAL A 112 " =    2.833
peak=   -3.959 closest distance to " O   HOH Z 231 " =    2.239
peak=   -3.937 closest distance to " N   ALA A  43 " =    2.623
peak=   -3.932 closest distance to " O   HOH Z 313 " =    1.937
peak=   -3.895 closest distance to " O   HOH Z 198 " =    2.053
peak=   -3.881 closest distance to " CE  MET A 105 " =    2.367
peak=   -3.880 closest distance to " CD2 PHE A 192 " =    2.044
peak=   -3.877 closest distance to " CA  VAL A  67 " =    2.902
peak=   -3.863 closest distance to " CD1 PHE A  59 " =    1.898
peak=   -3.853 closest distance to " O   HOH Z 372 " =    2.339
peak=   -3.845 closest distance to " OD1 ASP A 171 " =    1.643
peak=   -3.839 closest distance to " CG2 ILE A 263 " =    2.325
peak=   -3.825 closest distance to " O   HOH Z  73 " =    2.216
peak=   -3.825 closest distance to " O   HOH Z  10 " =    1.523
peak=   -3.808 closest distance to " CB  ALA A 291 " =    2.408
peak=   -3.808 closest distance to " O   HOH Z 290 " =    1.239
peak=   -3.792 closest distance to " CD  ARG A 139 " =    1.524
peak=   -3.791 closest distance to " O   HOH Z 114 " =    3.066
peak=   -3.772 closest distance to " CG  PHE A 283 " =    2.666
peak=   -3.766 closest distance to " CB  ALA A 291 " =    2.240
peak=   -3.757 closest distance to " O   HOH Z 198 " =    1.319
peak=   -3.735 closest distance to " O   HOH Z 351 " =    1.482
peak=   -3.733 closest distance to " CB  ALA A 161 " =    2.585
peak=   -3.727 closest distance to " CB  ALA A  43 " =    2.587
peak=   -3.712 closest distance to " OG  SER A  97 " =    2.235
peak=   -3.712 closest distance to " CE2 TYR A  30 " =    2.760
peak=   -3.709 closest distance to " O   HOH Z 407 " =    3.130
peak=   -3.706 closest distance to " O   PRO A 198 " =    1.294
peak=   -3.689 closest distance to " O   HOH Z 211 " =    1.668
peak=   -3.682 closest distance to " O   HOH Z 185 " =    2.258
peak=   -3.667 closest distance to " O   HOH Z  43 " =    1.655
peak=   -3.657 closest distance to " CB  ASN A  39 " =    2.299
peak=   -3.653 closest distance to " NH2AARG A 275 " =    5.348
peak=   -3.649 closest distance to " O   HOH Z 353 " =    2.179
peak=   -3.648 closest distance to " ND2 ASN A 249 " =    2.097
peak=   -3.646 closest distance to " CZ  PHE A  59 " =    1.533
peak=   -3.634 closest distance to " NE2 GLN A 278 " =    1.690
peak=   -3.630 closest distance to " NE2 GLN A 194 " =    1.737
peak=   -3.619 closest distance to " CB  PRO A 163 " =    2.485
peak=   -3.618 closest distance to " OXT GLY A 302 " =    2.825
peak=   -3.617 closest distance to " O   HOH Z 196 " =    2.059
peak=   -3.613 closest distance to " N   MET A 188 " =    1.936
peak=   -3.611 closest distance to " O   VAL A 189 " =    2.597
peak=   -3.577 closest distance to " O   PRO A 163 " =    2.044
peak=   -3.573 closest distance to " O   HOH Z  60 " =    2.322
peak=   -3.570 closest distance to " CZ  TYR A 169 " =    1.721
peak=   -3.566 closest distance to " CD1 LEU A 297 " =    2.457
peak=   -3.555 closest distance to " CG2 THR A 178 " =    2.290
peak=   -3.543 closest distance to " CA  GLY A 203 " =    2.377
peak=   -3.536 closest distance to " CE2 PHE A 218 " =    2.420
peak=   -3.533 closest distance to " CD1 LEU A 101 " =    2.301
peak=   -3.524 closest distance to " N   ASP A 286 " =    2.423
peak=   -3.523 closest distance to " CG1 VAL A 197 " =    2.291
peak=   -3.508 closest distance to " CB  ASP A 132 " =    2.285
peak=   -3.502 closest distance to " NH2 ARG A  79 " =    1.578
peak=   -3.498 closest distance to " O   HOH Z 359 " =    3.218
peak=   -3.497 closest distance to " O   ALA A 161 " =    1.709
peak=   -3.494 closest distance to " CA  GLY A 241 " =    3.078
peak=   -3.493 closest distance to " CG  ARG A 269 " =    2.352
peak=   -3.487 closest distance to " O   HOH Z  51 " =    1.532
peak=   -3.484 closest distance to " O   HOH Z 311 " =    3.730
peak=   -3.476 closest distance to " CD2 PHE A  61 " =    2.560
peak=   -3.475 closest distance to " O   HOH Z  38 " =    1.491
peak=   -3.473 closest distance to " NH2BARG A 275 " =    1.844
peak=   -3.471 closest distance to " C   MET A 188 " =    1.333
peak=   -3.467 closest distance to " N   ALA A 248 " =    1.728
peak=   -3.463 closest distance to " C   ALA A 158 " =    1.333
peak=   -3.462 closest distance to " CG1 VAL A 250 " =    2.680
peak=   -3.456 closest distance to " OD2 ASP A 171 " =    2.427
peak=   -3.428 closest distance to " O   HOH Z 295 " =    1.641
peak=   -3.424 closest distance to " CD1 LEU A 228 " =    2.286
peak=   -3.424 closest distance to " CA  GLY A  98 " =    1.934
peak=   -3.419 closest distance to " CB  ALA A 248 " =    2.121
peak=   -3.418 closest distance to " OD1 ASN A 148 " =    1.529
peak=   -3.413 closest distance to " O   HOH Z  52 " =    1.290
peak=   -3.404 closest distance to " N   GLN A  58 " =    1.723
peak=   -3.400 closest distance to " O   HOH Z 253 " =    3.905
peak=   -3.393 closest distance to " CG  ASP A 231 " =    0.780
peak=   -3.390 closest distance to " O   HOH Z 298 " =    1.285
peak=   -3.375 closest distance to " CB  ASP A 286 " =    2.134
peak=   -3.374 closest distance to " O   HOH Z 394 " =    1.411
peak=   -3.374 closest distance to " CD2 LEU A 237 " =    2.728
peak=   -3.373 closest distance to " CB  ALA A 248 " =    2.436
peak=   -3.369 closest distance to " CG  GLU A 277 " =    1.188
peak=   -3.369 closest distance to " C   LEU A 143 " =    1.135
peak=   -3.363 closest distance to " CB  PHE A 208 " =    2.232
peak=   -3.357 closest distance to " O   GLY A 211 " =    1.399
peak=   -3.357 closest distance to " OD1 ASN A 187 " =    1.574
peak=   -3.347 closest distance to " N   SER A 212 " =    2.015
peak=   -3.347 closest distance to " O   GLN A 240 " =    2.085
peak=   -3.346 closest distance to " O   PHE A 218 " =    1.603
peak=   -3.345 closest distance to " O   HOH Z 371 " =    1.501
peak=   -3.343 closest distance to " O   HOH Z  11 " =    1.712
peak=   -3.341 closest distance to " CB  TYR A  15 " =    2.155
peak=   -3.334 closest distance to " OG BSER A 134 " =    1.715
peak=   -3.332 closest distance to " O   SER A  95 " =    1.543
peak=   -3.328 closest distance to " CD  ARG A 195 " =    5.179
peak=   -3.326 closest distance to " CA  GLY A 133 " =    2.060
peak=   -3.320 closest distance to " OD2 ASP A 191 " =    1.471
peak=   -3.311 closest distance to " N   THR A 157 " =    1.535
peak=   -3.307 closest distance to " OE1 GLN A  88 " =    1.119
peak=   -3.301 closest distance to " O   PRO A 198 " =    1.304
peak=   -3.292 closest distance to " N   ASP A 171 " =    2.306
peak=   -3.286 closest distance to " O   HOH Z  13 " =    1.550
peak=   -3.283 closest distance to " CD1 ILE A 239 " =    2.414
peak=   -3.281 closest distance to " NH1 ARG A 195 " =    2.569
peak=   -3.278 closest distance to " CA  GLY A 241 " =    2.270
peak=   -3.276 closest distance to " O   HOH Z 114 " =    1.547
peak=   -3.270 closest distance to " O   ARG A 145 " =    1.572
peak=   -3.268 closest distance to " CA  GLY A 241 " =    2.824
peak=   -3.263 closest distance to " O   HOH Z 317 " =    1.535
peak=   -3.261 closest distance to " CZ  PHE A 155 " =    1.268
peak=   -3.259 closest distance to " O   HOH Z 244 " =    2.055
peak=   -3.258 closest distance to " O   SER A 135 " =    1.458
peak=   -3.255 closest distance to " O   ALA A  10 " =    1.640
peak=   -3.253 closest distance to " SG ACYS A 201 " =    1.925
peak=   -3.247 closest distance to " O   ALA A 292 " =    2.073
peak=   -3.242 closest distance to " O   HOH Z   6 " =    1.436
peak=   -3.242 closest distance to " CB  TRP A  85 " =    2.395
peak=   -3.235 closest distance to " OG  SER A  62 " =    1.618
peak=   -3.233 closest distance to " O   HOH Z 426 " =    1.567
peak=   -3.231 closest distance to " CA  ASP A 298 " =    1.090
peak=   -3.229 closest distance to " OD1AASN A 224 " =    1.752
peak=   -3.222 closest distance to " O   VAL A 189 " =    1.585
peak=   -3.216 closest distance to " O   ALA A  34 " =    2.595
peak=   -3.214 closest distance to " O   HOH Z 166 " =    2.015
peak=   -3.202 closest distance to " CA  TRP A 274 " =    1.452
peak=   -3.202 closest distance to " O   HOH Z 310 " =    1.797
peak=   -3.200 closest distance to " OD2 ASP A 171 " =    1.827
peak=   -3.197 closest distance to " O   MET A  40 " =    2.784
peak=   -3.188 closest distance to " CD2 TYR A 293 " =    2.041
peak=   -3.181 closest distance to " O   HOH Z 377 " =    0.838
peak=   -3.168 closest distance to " CG  MET A 105 " =    0.957
peak=   -3.167 closest distance to " CB  LEU A  83 " =    2.383
peak=   -3.165 closest distance to " O   HOH Z  37 " =    1.861
peak=   -3.163 closest distance to " CE BMET A  47 " =    1.822
peak=   -3.163 closest distance to " CD2 PHE A  61 " =    2.043
peak=   -3.160 closest distance to " CD  GLN A 223 " =    0.700
peak=   -3.159 closest distance to " O   VAL A 174 " =    2.085
peak=   -3.153 closest distance to " CG2 VAL A 189 " =    2.014
peak=   -3.151 closest distance to " OD2 ASP A  50 " =    1.730
peak=   -3.150 closest distance to " O   HOH Z 191 " =    5.608
peak=   -3.148 closest distance to " CE3 TRP A 150 " =    2.175
peak=   -3.144 closest distance to " OD1 ASP A 191 " =    1.692
peak=   -3.141 closest distance to " O   HOH Z 123 " =    2.382
peak=   -3.139 closest distance to " CG2 THR A 221 " =    2.170
peak=   -3.135 closest distance to " O   HOH Z 111 " =    1.802
peak=   -3.133 closest distance to " CE3 TRP A 274 " =    2.416
peak=   -3.132 closest distance to " O   HOH Z 298 " =    2.528
peak=   -3.130 closest distance to " SD  MET A 188 " =    2.233
peak=   -3.128 closest distance to " O   LEU A 101 " =    2.740
peak=   -3.125 closest distance to " NH2 ARG A  24 " =    1.841
peak=   -3.124 closest distance to " O   ALA A 180 " =    1.257
peak=   -3.123 closest distance to " O   HOH Z 357 " =    2.033
peak=   -3.122 closest distance to " CD1 ILE A 151 " =    2.439
peak=   -3.121 closest distance to " O   TRP A  70 " =    1.459
peak=   -3.115 closest distance to " O   HOH Z 175 " =    4.230
peak=   -3.115 closest distance to " O   HOH Z 134 " =    3.089
peak=   -3.115 closest distance to " CG1 VAL A 125 " =    1.969
peak=   -3.100 closest distance to " NE2 GLN A  88 " =    1.797
peak=   -3.099 closest distance to " O   ALA A  51 " =    1.365
peak=   -3.089 closest distance to " OXT GLY A 302 " =    3.431
peak=   -3.085 closest distance to " CG  ARG A 269 " =    2.040
peak=   -3.084 closest distance to " CG  TRP A 266 " =    1.887
peak=   -3.084 closest distance to " NH2 ARG A  79 " =    2.007
peak=   -3.081 closest distance to " O   HOH Z 393 " =    5.600
peak=   -3.073 closest distance to " CB  ASP A 132 " =    2.368
peak=   -3.070 closest distance to " CE  LYS A  76 " =    2.750
peak=   -3.057 closest distance to " O   HOH Z  41 " =    2.580
peak=   -3.057 closest distance to " O   HOH Z 262 " =    2.933
peak=   -3.046 closest distance to " CG2 ILE A  20 " =    2.949

================= 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    :  0.2319 0.2276   5.728547e+00   5.711201e+00
   1_bss:  0.2142 0.2122   5.690669e+00   5.668701e+00
   1_xyz:  0.1340 0.1541   5.240260e+00   5.361330e+00
   1_adp:  0.1235 0.1572   5.191100e+00   5.382680e+00
   1_occ:  0.1230 0.1568   5.188723e+00   5.381576e+00
   2_bss:  0.1233 0.1563   5.191021e+00   5.381463e+00
   2_xyz:  0.1114 0.1520   5.123132e+00   5.353723e+00
   2_adp:  0.1090 0.1505   5.108604e+00   5.346118e+00
   2_occ:  0.1089 0.1506   5.108756e+00   5.346725e+00
   3_bss:  0.1088 0.1506   5.108751e+00   5.346779e+00
   3_xyz:  0.1100 0.1521   5.119697e+00   5.358386e+00
   3_adp:  0.1089 0.1521   5.116392e+00   5.360492e+00
   3_occ:  0.1089 0.1522   5.116756e+00   5.361146e+00
   4_bss:  0.1088 0.1521   5.116570e+00   5.360979e+00
   4_xyz:  0.1057 0.1529   5.103118e+00   5.362741e+00
   4_adp:  0.1055 0.1530   5.101931e+00   5.362281e+00
   4_occ:  0.1055 0.1530   5.101982e+00   5.362385e+00
   5_bss:  0.1054 0.1530   5.102081e+00   5.362483e+00
   5_xyz:  0.1065 0.1538   5.110062e+00   5.368931e+00
   5_adp:  0.1063 0.1543   5.110754e+00   5.371828e+00
   5_occ:  0.1063 0.1543   5.110804e+00   5.371920e+00
   5_bss:  0.1063 0.1542   5.110907e+00   5.372008e+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:  0.334  53.719  -2.611  -2.110  -1.022  -0.000  -0.000  -0.000
   1_xyz:  0.334  53.719  -2.611  -2.110  -1.022  -0.000  -0.000  -0.000
   1_adp:  0.334  53.719  -2.611  -2.110  -1.022  -0.000  -0.000  -0.000
   1_occ:  0.334  53.719  -2.611  -2.110  -1.022  -0.000  -0.000  -0.000
   2_bss:  0.331  53.719  -2.862  -2.654  -1.353  -0.000  -0.000  -0.000
   2_xyz:  0.331  53.719  -2.862  -2.654  -1.353  -0.000  -0.000  -0.000
   2_adp:  0.331  53.719  -2.862  -2.654  -1.353  -0.000  -0.000  -0.000
   2_occ:  0.331  53.719  -2.862  -2.654  -1.353  -0.000  -0.000  -0.000
   3_bss:  0.331  53.719  -2.674  -2.553  -1.221  -0.000  -0.000  -0.000
   3_xyz:  0.331  53.719  -2.674  -2.553  -1.221  -0.000  -0.000  -0.000
   3_adp:  0.331  53.719  -2.674  -2.553  -1.221  -0.000  -0.000  -0.000
   3_occ:  0.331  53.719  -2.674  -2.553  -1.221  -0.000  -0.000  -0.000
   4_bss:  0.326  53.719  -2.512  -2.439  -1.082  -0.000  -0.000  -0.000
   4_xyz:  0.326  53.719  -2.512  -2.439  -1.082  -0.000  -0.000  -0.000
   4_adp:  0.326  53.719  -2.512  -2.439  -1.082  -0.000  -0.000  -0.000
   4_occ:  0.326  53.719  -2.512  -2.439  -1.082  -0.000  -0.000  -0.000
   5_bss:  0.326  53.719  -2.302  -2.252  -0.886  -0.000  -0.000  -0.000
   5_xyz:  0.326  53.719  -2.302  -2.252  -0.886  -0.000  -0.000  -0.000
   5_adp:  0.326  53.719  -2.302  -2.252  -0.886  -0.000  -0.000  -0.000
   5_occ:  0.326  53.719  -2.302  -2.252  -0.886  -0.000  -0.000  -0.000
   5_bss:  0.326  53.688  -2.074  -2.032  -0.672  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  20.851 0.8577  1.0040    13817.781
   1_bss:  19.497 0.8691  0.9530    11215.536
   1_xyz:  13.388 0.9202  0.9868     6086.772
   1_adp:  13.872 0.9161  0.9863     6300.669
   1_occ:  13.824 0.9165  0.9861     6264.597
   2_bss:  13.818 0.9166  0.9727     6263.075
   2_xyz:  13.166 0.9218  0.9742     5918.661
   2_adp:  13.025 0.9228  0.9705     5803.044
   2_occ:  13.045 0.9226  0.9703     5808.765
   3_bss:  13.046 0.9226  0.9753     5810.087
   3_xyz:  13.227 0.9214  0.9745     5983.011
   3_adp:  13.288 0.9209  0.9690     5986.391
   3_occ:  13.302 0.9208  0.9688     5994.449
   4_bss:  13.298 0.9209  0.9737     5989.727
   4_xyz:  13.332 0.9205  0.9740     6038.471
   4_adp:  13.318 0.9207  0.9681     6025.459
   4_occ:  13.322 0.9206  0.9680     6026.745
   5_bss:  13.324 0.9206  0.9750     6028.638
   5_xyz:  13.424 0.9199  0.9744     6115.365
   5_adp:  13.488 0.9194  0.9674     6139.393
   5_occ:  13.491 0.9194  0.9673     6140.290
   5_bss:  13.493 0.9194  0.9739     6141.919
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.113   1.6005e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.113   1.6005e-01
   1_xyz:   0.980  0.007  0.074 15.293  0.004  4.115   5.9241e-02
   1_adp:   0.980  0.007  0.074 15.293  0.004  4.115   5.9241e-02
   1_occ:   0.980  0.007  0.074 15.293  0.004  4.115   5.9241e-02
   2_bss:   0.980  0.007  0.074 15.293  0.004  4.115   5.9241e-02
   2_xyz:   1.059  0.009  0.083 15.306  0.004  4.118   7.0615e-02
   2_adp:   1.059  0.009  0.083 15.306  0.004  4.118   7.0615e-02
   2_occ:   1.059  0.009  0.083 15.306  0.004  4.118   7.0615e-02
   3_bss:   1.059  0.009  0.083 15.306  0.004  4.118   7.0615e-02
   3_xyz:   0.967  0.007  0.076 15.115  0.004  4.120   5.9245e-02
   3_adp:   0.967  0.007  0.076 15.115  0.004  4.120   5.9245e-02
   3_occ:   0.967  0.007  0.076 15.115  0.004  4.120   5.9245e-02
   4_bss:   0.967  0.007  0.076 15.115  0.004  4.120   5.9245e-02
   4_xyz:   1.082  0.010  0.084 15.343  0.004  4.122   7.3859e-02
   4_adp:   1.082  0.010  0.084 15.343  0.004  4.122   7.3859e-02
   4_occ:   1.082  0.010  0.084 15.343  0.004  4.122   7.3859e-02
   5_bss:   1.082  0.010  0.084 15.343  0.004  4.122   7.3859e-02
   5_xyz:   1.023  0.009  0.080 15.175  0.004  4.122   6.6447e-02
   5_adp:   1.023  0.009  0.080 15.175  0.004  4.122   6.6447e-02
   5_occ:   1.023  0.009  0.080 15.175  0.004  4.122   6.6447e-02
   5_bss:   1.023  0.009  0.080 15.175  0.004  4.122   6.6447e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4154e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4154e-01
   1_xyz:   7.491  0.039  0.231 84.170  0.039  2.380   4.8787e-02
   1_adp:   7.491  0.039  0.231 84.170  0.039  2.380   4.8787e-02
   1_occ:   7.491  0.039  0.231 84.170  0.039  2.380   4.8787e-02
   2_bss:   7.491  0.039  0.231 84.170  0.039  2.380   4.8787e-02
   2_xyz:   7.047  0.043  0.282 83.913  0.039  2.247   5.7062e-02
   2_adp:   7.047  0.043  0.282 83.913  0.039  2.247   5.7062e-02
   2_occ:   7.047  0.043  0.282 83.913  0.039  2.247   5.7062e-02
   3_bss:   7.047  0.043  0.282 83.913  0.039  2.247   5.7062e-02
   3_xyz:   6.962  0.042  0.241 83.923  0.036  2.351   3.9473e-02
   3_adp:   6.962  0.042  0.241 83.923  0.036  2.351   3.9473e-02
   3_occ:   6.962  0.042  0.241 83.923  0.036  2.351   3.9473e-02
   4_bss:   6.962  0.042  0.241 83.923  0.036  2.351   3.9473e-02
   4_xyz:   6.855  0.051  0.282 83.600  0.038  2.244   5.9115e-02
   4_adp:   6.855  0.051  0.282 83.600  0.038  2.244   5.9115e-02
   4_occ:   6.855  0.051  0.282 83.600  0.038  2.244   5.9115e-02
   5_bss:   6.855  0.051  0.282 83.600  0.038  2.244   5.9115e-02
   5_xyz:   6.664  0.048  0.258 83.676  0.037  2.318   5.1034e-02
   5_adp:   6.664  0.048  0.258 83.676  0.037  2.318   5.1034e-02
   5_occ:   6.664  0.048  0.258 83.676  0.037  2.318   5.1034e-02
   5_bss:   6.664  0.048  0.258 83.676  0.037  2.318   5.1034e-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:  62.92   0.00  16.46  53.45   0.00  12.68  62.92   6.96  37.03
   1_occ:  62.92   0.00  16.46  53.45   0.00  12.68  62.92   6.96  37.03
   2_bss:  62.92   0.00  16.46  53.45   0.00  12.68  62.92   6.96  37.03
   2_xyz:  62.92   0.00  16.46  53.45   0.00  12.68  62.92   6.96  37.03
   2_adp:  66.27   2.18  16.49  65.44   2.18  12.80  66.27   5.68  36.55
   2_occ:  66.27   2.18  16.49  65.44   2.18  12.80  66.27   5.68  36.55
   3_bss:  66.27   2.18  16.49  65.44   2.18  12.80  66.27   5.68  36.55
   3_xyz:  66.27   2.18  16.49  65.44   2.18  12.80  66.27   5.68  36.55
   3_adp:  71.20   1.48  16.61  71.20   1.48  12.77  67.84   6.71  37.50
   3_occ:  71.20   1.48  16.61  71.20   1.48  12.77  67.84   6.71  37.50
   4_bss:  71.20   1.48  16.61  71.20   1.48  12.77  67.84   6.71  37.50
   4_xyz:  71.20   1.48  16.61  71.20   1.48  12.77  67.84   6.71  37.50
   4_adp:  71.63   1.36  16.46  71.63   1.36  12.61  67.99   6.46  37.42
   4_occ:  71.63   1.36  16.46  71.63   1.36  12.61  67.99   6.46  37.42
   5_bss:  71.63   1.36  16.46  71.63   1.36  12.61  67.99   6.46  37.42
   5_xyz:  71.63   1.36  16.46  71.63   1.36  12.61  67.99   6.46  37.42
   5_adp:  72.52   0.90  16.34  72.52   0.90  12.45  68.21   6.11  37.55
   5_occ:  72.52   0.90  16.34  72.52   0.90  12.45  68.21   6.11  37.55
   5_bss:  72.49   0.87  16.31  72.49   0.87  12.42  68.18   6.08  37.52
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    0.528    0.009    0.193
   1_adp:    0.528    0.009    0.193
   1_occ:    0.528    0.009    0.193
   2_bss:    0.528    0.009    0.193
   2_xyz:    0.761    0.020    0.221
   2_adp:    0.761    0.020    0.221
   2_occ:    0.761    0.020    0.221
   3_bss:    0.761    0.020    0.221
   3_xyz:    0.937    0.022    0.225
   3_adp:    0.937    0.022    0.225
   3_occ:    0.937    0.022    0.225
   4_bss:    0.937    0.022    0.225
   4_xyz:    1.011    0.032    0.232
   4_adp:    1.011    0.032    0.232
   4_occ:    1.011    0.032    0.232
   5_bss:    1.011    0.032    0.232
   5_xyz:    1.113    0.017    0.234
   5_adp:    1.113    0.017    0.234
   5_occ:    1.113    0.017    0.234
   5_bss:    1.113    0.017    0.234
------------------------------------------------------------------------

CPU time actual refinement: 267.92


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_776/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_776/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_776/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_776/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_776/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 267.79 
  Macro-tasks:
    bulk solvent and scale       = 31.14  
    individual site refinement   = 112.15 
    weights calculation          = 24.36  
    collect and process          = 5.39   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 173.13 
  Micro-tasks:
    mask                            = 0.50   
    f_calc                          = 84.91  
    alpha_beta                      = 6.46   
    target                          = 0.92   
    gradients_wrt_atomic_parameters = 93.70  
    fmodel                         = 5.33   
    r_factors                      = 0.22   
    phase_errors                   = 9.27   
    foms                           = 0.24   
    TOTAL for micro-tasks          = 201.55 
NUMBER OF MASK CALCS=  2
Time per interpreted Python bytecode instruction: 3.771 micro seconds
Total CPU time: 4.66 minutes
from_scatterers_fft:    654 calls, 84.62 s
gradients_fft:          599 calls, 81.57 s

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

# Date 2008-01-16 Time 05:36:50 PST -0800 (1200490610.95 s)
Start R-work = 0.2319, R-free = 0.2276 (no bulk solvent and anisotropic scale)
Final R-work = 0.1301, R-free = 0.1731 (no bulk solvent and anisotropic scale)

Start R-work = 0.2142, R-free = 0.2122
Final R-work = 0.1063, R-free = 0.1542